Starting phenix.real_space_refine on Sat Apr 13 05:49:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p48_13191/04_2024/7p48_13191_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p48_13191/04_2024/7p48_13191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p48_13191/04_2024/7p48_13191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p48_13191/04_2024/7p48_13191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p48_13191/04_2024/7p48_13191_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p48_13191/04_2024/7p48_13191_trim_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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 4335 5.49 5 Mg 2 5.21 5 S 124 5.16 5 C 70222 2.51 5 N 25659 2.21 5 O 38481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 20": "NH1" <-> "NH2" Residue "2 ARG 22": "NH1" <-> "NH2" Residue "2 ARG 37": "NH1" <-> "NH2" Residue "2 ARG 40": "NH1" <-> "NH2" Residue "3 ARG 24": "NH1" <-> "NH2" Residue "3 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 42": "NH1" <-> "NH2" Residue "4 ARG 19": "NH1" <-> "NH2" Residue "6 PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 20": "NH1" <-> "NH2" Residue "6 PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 148": "OD1" <-> "OD2" Residue "6 ARG 178": "NH1" <-> "NH2" Residue "6 PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 187": "NH1" <-> "NH2" Residue "6 GLU 192": "OE1" <-> "OE2" Residue "6 ASP 203": "OD1" <-> "OD2" Residue "6 ARG 207": "NH1" <-> "NH2" Residue "6 TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 214": "OD1" <-> "OD2" Residue "6 GLU 224": "OE1" <-> "OE2" Residue "6 GLU 242": "OE1" <-> "OE2" Residue "6 TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 275": "NH1" <-> "NH2" Residue "6 PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 285": "NH1" <-> "NH2" Residue "6 TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 316": "NH1" <-> "NH2" Residue "6 TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 339": "NH1" <-> "NH2" Residue "6 GLU 346": "OE1" <-> "OE2" Residue "6 ASP 401": "OD1" <-> "OD2" Residue "6 GLU 403": "OE1" <-> "OE2" Residue "6 ASP 420": "OD1" <-> "OD2" Residue "6 ARG 429": "NH1" <-> "NH2" Residue "6 PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 494": "NH1" <-> "NH2" Residue "6 ASP 517": "OD1" <-> "OD2" Residue "6 ARG 535": "NH1" <-> "NH2" Residue "6 GLU 538": "OE1" <-> "OE2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ASP 20": "OD1" <-> "OD2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C ASP 84": "OD1" <-> "OD2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "D PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 62": "OD1" <-> "OD2" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D ASP 117": "OD1" <-> "OD2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 212": "NH1" <-> "NH2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 106": "NH1" <-> "NH2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "E GLU 138": "OE1" <-> "OE2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 160": "OD1" <-> "OD2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "E ASP 190": "OD1" <-> "OD2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "G ARG 171": "NH1" <-> "NH2" Residue "H ARG 2": "NH1" <-> "NH2" Residue "H ARG 14": "NH1" <-> "NH2" Residue "H ASP 20": "OD1" <-> "OD2" Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 94": "NH1" <-> "NH2" Residue "H ARG 95": "NH1" <-> "NH2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "H PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 88": "NH1" <-> "NH2" Residue "I ARG 107": "NH1" <-> "NH2" Residue "J ARG 16": "NH1" <-> "NH2" Residue "J ARG 21": "NH1" <-> "NH2" Residue "J GLU 51": "OE1" <-> "OE2" Residue "J PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 10": "NH1" <-> "NH2" Residue "K ARG 20": "NH1" <-> "NH2" Residue "K PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 45": "NH1" <-> "NH2" Residue "K ARG 51": "NH1" <-> "NH2" Residue "K ARG 56": "NH1" <-> "NH2" Residue "K PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "K GLU 135": "OE1" <-> "OE2" Residue "L ARG 8": "NH1" <-> "NH2" Residue "L GLU 45": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 74": "OE1" <-> "OE2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "L ARG 102": "NH1" <-> "NH2" Residue "L ARG 110": "NH1" <-> "NH2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M ARG 14": "NH1" <-> "NH2" Residue "M TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 35": "NH1" <-> "NH2" Residue "M TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 46": "OD1" <-> "OD2" Residue "M ASP 47": "OD1" <-> "OD2" Residue "M GLU 91": "OE1" <-> "OE2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 104": "NH1" <-> "NH2" Residue "N ARG 16": "NH1" <-> "NH2" Residue "N ARG 23": "NH1" <-> "NH2" Residue "N ARG 33": "NH1" <-> "NH2" Residue "N PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 91": "NH1" <-> "NH2" Residue "N TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 55": "NH1" <-> "NH2" Residue "O GLU 97": "OE1" <-> "OE2" Residue "O GLU 103": "OE1" <-> "OE2" Residue "O PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 115": "OD1" <-> "OD2" Residue "P GLU 15": "OE1" <-> "OE2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P ARG 67": "NH1" <-> "NH2" Residue "P ARG 79": "NH1" <-> "NH2" Residue "P TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 8": "NH1" <-> "NH2" Residue "Q ARG 11": "NH1" <-> "NH2" Residue "Q ARG 15": "NH1" <-> "NH2" Residue "Q ARG 18": "NH1" <-> "NH2" Residue "Q ASP 63": "OD1" <-> "OD2" Residue "Q ASP 67": "OD1" <-> "OD2" Residue "Q PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 28": "OD1" <-> "OD2" Residue "R ASP 30": "OD1" <-> "OD2" Residue "R GLU 44": "OE1" <-> "OE2" Residue "R PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 64": "NH1" <-> "NH2" Residue "R TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 76": "NH1" <-> "NH2" Residue "R PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 32": "NH1" <-> "NH2" Residue "S ASP 87": "OD1" <-> "OD2" Residue "T ARG 9": "NH1" <-> "NH2" Residue "T ARG 22": "NH1" <-> "NH2" Residue "T TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 53": "NH1" <-> "NH2" Residue "T GLU 54": "OE1" <-> "OE2" Residue "T ARG 57": "NH1" <-> "NH2" Residue "T ASP 76": "OD1" <-> "OD2" Residue "T ASP 90": "OD1" <-> "OD2" Residue "T PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 22": "NH1" <-> "NH2" Residue "U ASP 23": "OD1" <-> "OD2" Residue "U ARG 33": "NH1" <-> "NH2" Residue "U TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 47": "NH1" <-> "NH2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "W GLU 13": "OE1" <-> "OE2" Residue "W GLU 15": "OE1" <-> "OE2" Residue "W ARG 44": "NH1" <-> "NH2" Residue "W ARG 47": "NH1" <-> "NH2" Residue "W ARG 52": "NH1" <-> "NH2" Residue "W ARG 58": "NH1" <-> "NH2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "X ASP 39": "OD1" <-> "OD2" Residue "Z ARG 6": "NH1" <-> "NH2" Residue "Z GLU 29": "OE1" <-> "OE2" Residue "Z TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 21": "NH1" <-> "NH2" Residue "b ARG 22": "NH1" <-> "NH2" Residue "b ARG 35": "NH1" <-> "NH2" Residue "b TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 86": "NH1" <-> "NH2" Residue "b ARG 95": "NH1" <-> "NH2" Residue "b TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 110": "NH1" <-> "NH2" Residue "b ARG 113": "NH1" <-> "NH2" Residue "b GLU 140": "OE1" <-> "OE2" Residue "b ARG 143": "NH1" <-> "NH2" Residue "b ARG 152": "NH1" <-> "NH2" Residue "b ARG 167": "NH1" <-> "NH2" Residue "b GLU 169": "OE1" <-> "OE2" Residue "b ARG 170": "NH1" <-> "NH2" Residue "b ARG 177": "NH1" <-> "NH2" Residue "b ASP 194": "OD1" <-> "OD2" Residue "b TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 208": "NH1" <-> "NH2" Residue "c GLU 19": "OE1" <-> "OE2" Residue "c GLU 48": "OE1" <-> "OE2" Residue "c GLU 55": "OE1" <-> "OE2" Residue "c GLU 84": "OE1" <-> "OE2" Residue "c ASP 95": "OD1" <-> "OD2" Residue "c ASP 111": "OD1" <-> "OD2" Residue "c ARG 113": "NH1" <-> "NH2" Residue "c ARG 121": "NH1" <-> "NH2" Residue "c ARG 126": "NH1" <-> "NH2" Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 139": "NH1" <-> "NH2" Residue "c ARG 163": "NH1" <-> "NH2" Residue "c TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 27": "OE1" <-> "OE2" Residue "d ARG 52": "NH1" <-> "NH2" Residue "d ARG 58": "NH1" <-> "NH2" Residue "d ARG 69": "NH1" <-> "NH2" Residue "d ARG 93": "NH1" <-> "NH2" Residue "d ASP 127": "OD1" <-> "OD2" Residue "d TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 168": "OD1" <-> "OD2" Residue "d TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 29": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 32": "NH1" <-> "NH2" Residue "e PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 58": "OE1" <-> "OE2" Residue "e ASP 70": "OD1" <-> "OD2" Residue "e TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 142": "OD1" <-> "OD2" Residue "e ASP 152": "OD1" <-> "OD2" Residue "e ARG 157": "NH1" <-> "NH2" Residue "f TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 11": "NH1" <-> "NH2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "f TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 51": "OE1" <-> "OE2" Residue "f ASP 57": "OD1" <-> "OD2" Residue "f ARG 64": "NH1" <-> "NH2" Residue "f ASP 68": "OD1" <-> "OD2" Residue "f PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 78": "NH1" <-> "NH2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g ASP 15": "OD1" <-> "OD2" Residue "g ARG 36": "NH1" <-> "NH2" Residue "g ARG 41": "NH1" <-> "NH2" Residue "g ARG 53": "NH1" <-> "NH2" Residue "g ARG 56": "NH1" <-> "NH2" Residue "g ASP 57": "OD1" <-> "OD2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "g ARG 96": "NH1" <-> "NH2" Residue "g ARG 102": "NH1" <-> "NH2" Residue "g ARG 109": "NH1" <-> "NH2" Residue "g ARG 111": "NH1" <-> "NH2" Residue "g ARG 119": "NH1" <-> "NH2" Residue "g GLU 123": "OE1" <-> "OE2" Residue "g ARG 138": "NH1" <-> "NH2" Residue "g TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 155": "NH1" <-> "NH2" Residue "h GLU 35": "OE1" <-> "OE2" Residue "h ARG 61": "NH1" <-> "NH2" Residue "h PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 70": "OD1" <-> "OD2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h ARG 119": "NH1" <-> "NH2" Residue "i ARG 38": "NH1" <-> "NH2" Residue "i PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 49": "OD1" <-> "OD2" Residue "i ARG 82": "NH1" <-> "NH2" Residue "i GLU 91": "OE1" <-> "OE2" Residue "i ASP 93": "OD1" <-> "OD2" Residue "i ARG 108": "NH1" <-> "NH2" Residue "i PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 132": "NH1" <-> "NH2" Residue "j ARG 16": "NH1" <-> "NH2" Residue "j ARG 53": "NH1" <-> "NH2" Residue "j PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 66": "OE1" <-> "OE2" Residue "k GLU 17": "OE1" <-> "OE2" Residue "k ARG 24": "NH1" <-> "NH2" Residue "k ASP 36": "OD1" <-> "OD2" Residue "k ARG 111": "NH1" <-> "NH2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "l ARG 12": "NH1" <-> "NH2" Residue "l PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 63": "NH1" <-> "NH2" Residue "l ARG 69": "NH1" <-> "NH2" Residue "l ARG 127": "NH1" <-> "NH2" Residue "m ARG 14": "NH1" <-> "NH2" Residue "m TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 50": "OD1" <-> "OD2" Residue "m ASP 51": "OD1" <-> "OD2" Residue "m GLU 52": "OE1" <-> "OE2" Residue "m GLU 66": "OE1" <-> "OE2" Residue "m TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 87": "NH1" <-> "NH2" Residue "m ARG 90": "NH1" <-> "NH2" Residue "n TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 23": "NH1" <-> "NH2" Residue "n ARG 26": "NH1" <-> "NH2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "o GLU 6": "OE1" <-> "OE2" Residue "o ARG 7": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 54": "NH1" <-> "NH2" Residue "o ARG 63": "NH1" <-> "NH2" Residue "o ARG 71": "NH1" <-> "NH2" Residue "o ARG 88": "NH1" <-> "NH2" Residue "p ARG 6": "NH1" <-> "NH2" Residue "p ARG 19": "NH1" <-> "NH2" Residue "p ASP 24": "OD1" <-> "OD2" Residue "p ARG 29": "NH1" <-> "NH2" Residue "p ASP 53": "OD1" <-> "OD2" Residue "q ASP 17": "OD1" <-> "OD2" Residue "q ARG 67": "NH1" <-> "NH2" Residue "q PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 32": "OE1" <-> "OE2" Residue "r ARG 47": "NH1" <-> "NH2" Residue "r TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 3": "NH1" <-> "NH2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "s PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 10": "NH1" <-> "NH2" Residue "t ARG 73": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 138826 Number of models: 1 Model: "" Number of chains: 57 Chain: "1" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 394 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "2" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 367 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "3" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 521 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "4" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "5" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1560 Classifications: {'RNA': 73} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 31, 'rna3p_pyr': 29} Link IDs: {'rna2p': 13, 'rna3p': 59} Chain: "6" Number of atoms: 4190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4190 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 12, 'TRANS': 497} Chain breaks: 1 Chain: "7" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 57062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2661, 57062 Classifications: {'RNA': 2661} Modifications used: {'rna2p_pur': 270, 'rna2p_pyr': 174, 'rna3p_pur': 1261, 'rna3p_pyr': 956} Link IDs: {'rna2p': 444, 'rna3p': 2216} Chain breaks: 12 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' G%rna3p_pur:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 2408 Classifications: {'RNA': 113} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 54, 'rna3p_pyr': 46} Link IDs: {'rna2p': 13, 'rna3p': 99} Chain: "C" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2094 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 17, 'TRANS': 256} Chain: "D" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1628 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 8, 'TRANS': 206} Chain: "E" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1572 Classifications: {'peptide': 206} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 853 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 527 Unresolved non-hydrogen angles: 662 Unresolved non-hydrogen dihedrals: 426 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 4, 'ASN:plan1': 9, 'ASP:plan': 10, 'PHE:plan': 8, 'GLU:plan': 15, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 254 Chain: "G" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1180 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 7, 'TRANS': 165} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 86 Chain: "H" Number of atoms: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1150 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 918 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1097 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1096 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 7, 'TRANS': 129} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 950 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "N" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 921 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "O" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 943 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Chain: "P" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 797 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 2, 'TRANS': 99} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Q" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 861 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 724 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 739 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 94} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "T" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "U" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 590 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "V" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 458 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "W" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "X" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Y" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 390 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 5, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 117 Chain: "Z" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 385 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "a" Number of atoms: 31706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1479, 31706 Classifications: {'RNA': 1479} Modifications used: {'rna2p_pur': 126, 'rna2p_pyr': 87, 'rna3p_pur': 717, 'rna3p_pyr': 549} Link IDs: {'rna2p': 213, 'rna3p': 1265} Chain breaks: 8 Chain: "b" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1802 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "c" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1596 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 3, 'TRANS': 198} Chain: "d" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1616 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 8, 'TRANS': 190} Chain: "e" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1160 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 7, 'TRANS': 148} Chain: "f" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 789 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "g" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1242 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain: "h" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1031 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "i" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1007 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "j" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 773 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain: "k" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 844 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 7, 'TRANS': 106} Chain: "l" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1058 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "m" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 922 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "n" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 501 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "o" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 726 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "p" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "q" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 657 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "r" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 525 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "s" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 665 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "t" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 611 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} 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: "6" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1367 SG CYS 4 11 72.745 163.311 82.826 1.00 5.04 S ATOM 1391 SG CYS 4 14 76.007 163.710 81.653 1.00 3.86 S ATOM 1493 SG CYS 4 27 73.837 166.588 83.460 1.00 4.45 S ATOM 88692 SG CYS Z 30 176.689 210.375 101.206 1.00 7.06 S ATOM 88795 SG CYS Z 43 177.967 206.485 101.696 1.00 2.38 S ATOM A0QP6 SG CYS n 27 44.033 77.041 143.054 1.00 12.50 S ATOM A0QS9 SG CYS n 40 46.015 73.107 142.642 1.00 6.43 S ATOM A0QSY SG CYS n 43 44.401 73.548 145.666 1.00 7.85 S Time building chain proxies: 53.42, per 1000 atoms: 0.38 Number of scatterers: 138826 At special positions: 0 Unit cell: (253.59, 236.47, 240.75, 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 124 16.00 P 4335 15.00 Mg 2 11.99 O 38481 8.00 N 25659 7.00 C 70222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 1 9 " - pdb=" SG CYS 1 12 " distance=2.03 Simple disulfide: pdb=" SG CYS 1 12 " - pdb=" SG CYS 1 36 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 54.03 Conformation dependent library (CDL) restraints added in 8.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 4 100 " pdb="ZN ZN 4 100 " - pdb=" ND1 HIS 4 32 " pdb="ZN ZN 4 100 " - pdb=" SG CYS 4 11 " pdb="ZN ZN 4 100 " - pdb=" SG CYS 4 14 " pdb="ZN ZN 4 100 " - pdb=" SG CYS 4 27 " pdb=" ZN Z 100 " pdb="ZN ZN Z 100 " - pdb=" SG CYS Z 43 " pdb="ZN ZN Z 100 " - pdb=" SG CYS Z 30 " pdb=" ZN n 100 " pdb="ZN ZN n 100 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 100 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 100 " - pdb=" SG CYS n 43 " Number of angles added : 3 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10932 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: 174 helices and 76 sheets defined 37.4% alpha, 19.0% beta 1206 base pairs and 2507 stacking pairs defined. Time for finding SS restraints: 72.73 Creating SS restraints... Processing helix chain '1' and resid 22 through 27 Proline residue: 1 27 - end of helix Processing helix chain '2' and resid 9 through 17 Processing helix chain '2' and resid 18 through 26 removed outlier: 4.027A pdb=" N THR 2 25 " --> pdb=" O LYS 2 21 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS 2 26 " --> pdb=" O ARG 2 22 " (cutoff:3.500A) Processing helix chain '2' and resid 27 through 39 Processing helix chain '3' and resid 7 through 14 removed outlier: 3.895A pdb=" N LYS 3 12 " --> pdb=" O ARG 3 8 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG 3 13 " --> pdb=" O GLY 3 9 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL 3 14 " --> pdb=" O ALA 3 10 " (cutoff:3.500A) Processing helix chain '3' and resid 32 through 37 removed outlier: 4.156A pdb=" N LYS 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N SER 3 37 " --> pdb=" O PHE 3 33 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 32 through 37' Processing helix chain '3' and resid 38 through 46 removed outlier: 3.634A pdb=" N ARG 3 45 " --> pdb=" O LYS 3 41 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS 3 46 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 59 removed outlier: 4.324A pdb=" N ARG 3 57 " --> pdb=" O SER 3 53 " (cutoff:3.500A) Processing helix chain '6' and resid 40 through 51 removed outlier: 3.738A pdb=" N LEU 6 45 " --> pdb=" O LYS 6 41 " (cutoff:3.500A) Processing helix chain '6' and resid 70 through 77 removed outlier: 6.301A pdb=" N VAL 6 75 " --> pdb=" O VAL 6 71 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N MET 6 76 " --> pdb=" O MET 6 72 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER 6 77 " --> pdb=" O ASP 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 112 through 117 removed outlier: 4.903A pdb=" N LYS 6 116 " --> pdb=" O ILE 6 112 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU 6 117 " --> pdb=" O GLU 6 113 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 112 through 117' Processing helix chain '6' and resid 132 through 148 removed outlier: 3.645A pdb=" N GLN 6 136 " --> pdb=" O SER 6 132 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR 6 137 " --> pdb=" O GLY 6 133 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS 6 138 " --> pdb=" O GLY 6 134 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL 6 139 " --> pdb=" O GLU 6 135 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER 6 140 " --> pdb=" O GLN 6 136 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE 6 141 " --> pdb=" O THR 6 137 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU 6 142 " --> pdb=" O LYS 6 138 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS 6 143 " --> pdb=" O VAL 6 139 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER 6 147 " --> pdb=" O LYS 6 143 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASP 6 148 " --> pdb=" O VAL 6 144 " (cutoff:3.500A) Processing helix chain '6' and resid 162 through 176 removed outlier: 3.554A pdb=" N LYS 6 166 " --> pdb=" O ASP 6 162 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL 6 167 " --> pdb=" O LYS 6 163 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU 6 169 " --> pdb=" O MET 6 165 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE 6 170 " --> pdb=" O LYS 6 166 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS 6 171 " --> pdb=" O VAL 6 167 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS 6 174 " --> pdb=" O ILE 6 170 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER 6 175 " --> pdb=" O LYS 6 171 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU 6 176 " --> pdb=" O ALA 6 172 " (cutoff:3.500A) Processing helix chain '6' and resid 186 through 193 removed outlier: 4.784A pdb=" N ASN 6 191 " --> pdb=" O ARG 6 187 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU 6 192 " --> pdb=" O GLU 6 188 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR 6 193 " --> pdb=" O PHE 6 189 " (cutoff:3.500A) Processing helix chain '6' and resid 211 through 258 removed outlier: 3.523A pdb=" N GLN 6 218 " --> pdb=" O ASP 6 214 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE 6 223 " --> pdb=" O LYS 6 219 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR 6 225 " --> pdb=" O ILE 6 221 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU 6 226 " --> pdb=" O GLU 6 222 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS 6 227 " --> pdb=" O ILE 6 223 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS 6 235 " --> pdb=" O GLU 6 231 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU 6 236 " --> pdb=" O LYS 6 232 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA 6 239 " --> pdb=" O LYS 6 235 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE 6 240 " --> pdb=" O GLU 6 236 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG 6 253 " --> pdb=" O GLU 6 249 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN 6 256 " --> pdb=" O GLN 6 252 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS 6 257 " --> pdb=" O ARG 6 253 " (cutoff:3.500A) Processing helix chain '6' and resid 262 through 290 removed outlier: 3.711A pdb=" N PHE 6 276 " --> pdb=" O LEU 6 272 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS 6 279 " --> pdb=" O ARG 6 275 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS 6 281 " --> pdb=" O LYS 6 277 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN 6 282 " --> pdb=" O SER 6 278 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU 6 289 " --> pdb=" O ARG 6 285 " (cutoff:3.500A) Processing helix chain '6' and resid 352 through 362 removed outlier: 3.744A pdb=" N GLN 6 358 " --> pdb=" O SER 6 354 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU 6 361 " --> pdb=" O ILE 6 357 " (cutoff:3.500A) Processing helix chain '6' and resid 394 through 402 removed outlier: 3.538A pdb=" N MET 6 400 " --> pdb=" O LEU 6 396 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP 6 401 " --> pdb=" O GLU 6 397 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE 6 402 " --> pdb=" O GLU 6 398 " (cutoff:3.500A) Processing helix chain '6' and resid 406 through 418 removed outlier: 4.585A pdb=" N SER 6 416 " --> pdb=" O THR 6 412 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE 6 417 " --> pdb=" O ILE 6 413 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR 6 418 " --> pdb=" O LEU 6 414 " (cutoff:3.500A) Processing helix chain '6' and resid 432 through 448 removed outlier: 4.699A pdb=" N LYS 6 436 " --> pdb=" O SER 6 432 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS 6 437 " --> pdb=" O MET 6 433 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU 6 439 " --> pdb=" O GLU 6 435 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN 6 440 " --> pdb=" O LYS 6 436 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE 6 441 " --> pdb=" O CYS 6 437 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS 6 443 " --> pdb=" O LEU 6 439 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU 6 444 " --> pdb=" O GLN 6 440 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE 6 446 " --> pdb=" O VAL 6 442 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASN 6 448 " --> pdb=" O LEU 6 444 " (cutoff:3.500A) Processing helix chain '6' and resid 462 through 476 removed outlier: 4.387A pdb=" N GLU 6 467 " --> pdb=" O ILE 6 463 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS 6 468 " --> pdb=" O SER 6 464 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE 6 469 " --> pdb=" O MET 6 465 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE 6 470 " --> pdb=" O GLN 6 466 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU 6 472 " --> pdb=" O LYS 6 468 " (cutoff:3.500A) Processing helix chain '6' and resid 486 through 494 removed outlier: 3.724A pdb=" N LYS 6 490 " --> pdb=" O ASP 6 486 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLU 6 492 " --> pdb=" O ILE 6 488 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE 6 493 " --> pdb=" O PHE 6 489 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG 6 494 " --> pdb=" O LYS 6 490 " (cutoff:3.500A) Processing helix chain '6' and resid 519 through 529 removed outlier: 4.542A pdb=" N LEU 6 525 " --> pdb=" O MET 6 521 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS 6 526 " --> pdb=" O LYS 6 522 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE 6 527 " --> pdb=" O ASP 6 523 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU 6 528 " --> pdb=" O GLU 6 524 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU 6 529 " --> pdb=" O LEU 6 525 " (cutoff:3.500A) Processing helix chain '6' and resid 531 through 538 removed outlier: 3.961A pdb=" N ARG 6 535 " --> pdb=" O TYR 6 531 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN 6 536 " --> pdb=" O THR 6 532 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU 6 538 " --> pdb=" O GLU 6 534 " (cutoff:3.500A) Processing helix chain '6' and resid 420 through 426 removed outlier: 4.599A pdb=" N ARG 6 423 " --> pdb=" O ASP 6 420 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N MET 6 424 " --> pdb=" O LYS 6 421 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN 6 425 " --> pdb=" O SER 6 422 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP 6 426 " --> pdb=" O ARG 6 423 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 420 through 426' Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.928A pdb=" N ILE C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 removed outlier: 4.013A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.128A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 264 through 271 removed outlier: 4.770A pdb=" N LYS C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU C 269 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.724A pdb=" N GLU C 201 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 202 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 81 removed outlier: 3.526A pdb=" N HIS D 76 " --> pdb=" O PRO D 72 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS D 78 " --> pdb=" O GLU D 74 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA D 80 " --> pdb=" O HIS D 76 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 removed outlier: 4.773A pdb=" N TYR D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLU D 100 " --> pdb=" O VAL D 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 100' Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 106 through 111 removed outlier: 4.938A pdb=" N VAL D 111 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'E' and resid 20 through 25 removed outlier: 3.570A pdb=" N PHE E 24 " --> pdb=" O SER E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 45 removed outlier: 3.685A pdb=" N GLU E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU E 44 " --> pdb=" O GLN E 40 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 121 removed outlier: 3.641A pdb=" N LEU E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA E 109 " --> pdb=" O MET E 105 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 147 removed outlier: 3.585A pdb=" N ASN E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 146 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 168 removed outlier: 4.377A pdb=" N LEU E 165 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER E 166 " --> pdb=" O ASN E 162 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA E 167 " --> pdb=" O VAL E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.546A pdb=" N ILE E 186 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ASP E 190 " --> pdb=" O ILE E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.798A pdb=" N LYS E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU E 203 " --> pdb=" O ALA E 199 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU E 204 " --> pdb=" O LYS E 200 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU E 206 " --> pdb=" O VAL E 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 15 removed outlier: 3.614A pdb=" N ASN F 9 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL F 12 " --> pdb=" O PHE F 8 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 21 removed outlier: 3.950A pdb=" N ASN F 21 " --> pdb=" O MET F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 62 removed outlier: 4.008A pdb=" N ASP F 51 " --> pdb=" O SER F 47 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 3.555A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU F 100 " --> pdb=" O MET F 96 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 133 through 138 removed outlier: 7.070A pdb=" N ILE F 137 " --> pdb=" O LYS F 133 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N PHE F 138 " --> pdb=" O GLU F 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 133 through 138' Processing helix chain 'F' and resid 162 through 172 removed outlier: 3.530A pdb=" N ALA F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG F 167 " --> pdb=" O ASP F 163 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASN F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 8 removed outlier: 4.805A pdb=" N ILE G 8 " --> pdb=" O VAL G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 81 removed outlier: 3.673A pdb=" N THR G 63 " --> pdb=" O LYS G 59 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN G 64 " --> pdb=" O GLU G 60 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR G 67 " --> pdb=" O THR G 63 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR G 68 " --> pdb=" O ASN G 64 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG G 69 " --> pdb=" O HIS G 65 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL G 76 " --> pdb=" O LEU G 72 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N SER G 80 " --> pdb=" O VAL G 76 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN G 81 " --> pdb=" O GLN G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.552A pdb=" N GLY G 142 " --> pdb=" O LYS G 138 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN G 147 " --> pdb=" O ALA G 143 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE G 148 " --> pdb=" O LEU G 144 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL G 151 " --> pdb=" O ASN G 147 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) Proline residue: G 153 - end of helix Processing helix chain 'H' and resid 25 through 39 removed outlier: 3.835A pdb=" N SER H 31 " --> pdb=" O GLY H 27 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU H 32 " --> pdb=" O ARG H 28 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER H 35 " --> pdb=" O SER H 31 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG H 38 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 97 removed outlier: 3.564A pdb=" N ARG H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN H 97 " --> pdb=" O LEU H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 111 removed outlier: 3.947A pdb=" N ILE H 102 " --> pdb=" O PRO H 98 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N MET H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU H 110 " --> pdb=" O ILE H 106 " (cutoff:3.500A) Proline residue: H 111 - end of helix Processing helix chain 'H' and resid 113 through 123 removed outlier: 3.578A pdb=" N GLY H 120 " --> pdb=" O GLY H 116 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS H 121 " --> pdb=" O GLU H 117 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS H 122 " --> pdb=" O LYS H 118 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU H 123 " --> pdb=" O GLN H 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 110 removed outlier: 4.065A pdb=" N GLY I 109 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN I 110 " --> pdb=" O LEU I 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 105 through 110' Processing helix chain 'I' and resid 111 through 119 removed outlier: 3.587A pdb=" N ALA I 118 " --> pdb=" O ILE I 114 " (cutoff:3.500A) Proline residue: I 119 - end of helix Processing helix chain 'J' and resid 56 through 62 Proline residue: J 62 - end of helix Processing helix chain 'J' and resid 78 through 83 removed outlier: 3.703A pdb=" N LEU J 82 " --> pdb=" O ASN J 78 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN J 83 " --> pdb=" O LEU J 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 78 through 83' Processing helix chain 'J' and resid 92 through 100 removed outlier: 3.968A pdb=" N GLY J 100 " --> pdb=" O LEU J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 140 removed outlier: 3.505A pdb=" N ALA J 133 " --> pdb=" O SER J 129 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU J 134 " --> pdb=" O ALA J 130 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA J 135 " --> pdb=" O SER J 131 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE J 136 " --> pdb=" O ALA J 132 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP J 137 " --> pdb=" O ALA J 133 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS J 139 " --> pdb=" O ALA J 135 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY J 140 " --> pdb=" O ILE J 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 59 removed outlier: 6.088A pdb=" N ILE K 47 " --> pdb=" O THR K 43 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU K 48 " --> pdb=" O SER K 44 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER K 49 " --> pdb=" O ARG K 45 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA K 50 " --> pdb=" O GLN K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 126 removed outlier: 4.262A pdb=" N GLU K 116 " --> pdb=" O GLU K 112 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG K 119 " --> pdb=" O ARG K 115 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA K 121 " --> pdb=" O ALA K 117 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER K 122 " --> pdb=" O LEU K 118 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS K 123 " --> pdb=" O ARG K 119 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS K 124 " --> pdb=" O LEU K 120 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU K 125 " --> pdb=" O ALA K 121 " (cutoff:3.500A) Proline residue: K 126 - end of helix Processing helix chain 'L' and resid 9 through 27 removed outlier: 3.522A pdb=" N LEU L 17 " --> pdb=" O ARG L 13 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR L 22 " --> pdb=" O ARG L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 54 removed outlier: 3.607A pdb=" N LYS L 38 " --> pdb=" O GLU L 34 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU L 39 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER L 42 " --> pdb=" O LYS L 38 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL L 43 " --> pdb=" O GLU L 39 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU L 47 " --> pdb=" O VAL L 43 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU L 50 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 66 removed outlier: 3.660A pdb=" N ALA L 63 " --> pdb=" O ARG L 59 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS L 64 " --> pdb=" O ARG L 60 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR L 65 " --> pdb=" O ASN L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 94 removed outlier: 3.597A pdb=" N LEU L 85 " --> pdb=" O ALA L 81 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE L 89 " --> pdb=" O LEU L 85 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ALA L 90 " --> pdb=" O PHE L 86 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU L 91 " --> pdb=" O GLY L 87 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR L 93 " --> pdb=" O ILE L 89 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 23 removed outlier: 3.888A pdb=" N ARG M 11 " --> pdb=" O LYS M 7 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG M 14 " --> pdb=" O VAL M 10 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA M 16 " --> pdb=" O LEU M 12 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG M 17 " --> pdb=" O LYS M 13 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL M 18 " --> pdb=" O ARG M 14 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR M 20 " --> pdb=" O ALA M 16 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASN M 21 " --> pdb=" O ARG M 17 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU M 22 " --> pdb=" O VAL M 18 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER M 23 " --> pdb=" O ARG M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 88 removed outlier: 5.981A pdb=" N LEU M 72 " --> pdb=" O THR M 68 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR M 74 " --> pdb=" O VAL M 70 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS M 75 " --> pdb=" O GLU M 71 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL M 76 " --> pdb=" O LEU M 72 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU M 78 " --> pdb=" O THR M 74 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA M 79 " --> pdb=" O LYS M 75 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE M 80 " --> pdb=" O VAL M 76 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS M 82 " --> pdb=" O GLU M 78 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY M 88 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 116 removed outlier: 3.683A pdb=" N GLU M 114 " --> pdb=" O GLU M 110 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER M 115 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY M 116 " --> pdb=" O ALA M 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 12 removed outlier: 5.854A pdb=" N ALA N 9 " --> pdb=" O LYS N 5 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL N 10 " --> pdb=" O LEU N 6 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS N 12 " --> pdb=" O GLU N 8 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 106 removed outlier: 4.815A pdb=" N ARG N 103 " --> pdb=" O LEU N 99 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER N 104 " --> pdb=" O TYR N 100 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU N 105 " --> pdb=" O TYR N 101 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ARG N 106 " --> pdb=" O LEU N 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 99 through 106' Processing helix chain 'O' and resid 8 through 22 removed outlier: 3.783A pdb=" N ALA O 12 " --> pdb=" O THR O 8 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS O 16 " --> pdb=" O ALA O 12 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR O 17 " --> pdb=" O ARG O 13 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS O 22 " --> pdb=" O ILE O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 31 removed outlier: 4.110A pdb=" N THR O 30 " --> pdb=" O GLY O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 37 removed outlier: 3.615A pdb=" N GLN O 37 " --> pdb=" O LYS O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 39 through 56 removed outlier: 3.608A pdb=" N ARG O 48 " --> pdb=" O GLN O 44 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG O 51 " --> pdb=" O PHE O 47 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG O 55 " --> pdb=" O ARG O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 73 removed outlier: 3.528A pdb=" N THR O 63 " --> pdb=" O LYS O 59 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ARG O 64 " --> pdb=" O LEU O 60 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN O 71 " --> pdb=" O ALA O 67 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N HIS O 72 " --> pdb=" O ALA O 68 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU O 73 " --> pdb=" O ALA O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 87 removed outlier: 3.624A pdb=" N LYS O 84 " --> pdb=" O MET O 80 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS O 85 " --> pdb=" O ASN O 81 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY O 87 " --> pdb=" O LEU O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 102 removed outlier: 3.520A pdb=" N GLU O 97 " --> pdb=" O LYS O 93 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE O 100 " --> pdb=" O SER O 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 117 removed outlier: 3.602A pdb=" N THR O 111 " --> pdb=" O ALA O 107 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS O 112 " --> pdb=" O GLN O 108 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA O 116 " --> pdb=" O LYS O 112 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU O 117 " --> pdb=" O ALA O 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 25 removed outlier: 3.919A pdb=" N LEU Q 19 " --> pdb=" O ARG Q 15 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU Q 23 " --> pdb=" O LEU Q 19 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE Q 24 " --> pdb=" O VAL Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 39 removed outlier: 4.145A pdb=" N ALA Q 34 " --> pdb=" O ALA Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 61 removed outlier: 3.707A pdb=" N LYS Q 49 " --> pdb=" O PRO Q 45 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL Q 50 " --> pdb=" O VAL Q 46 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER Q 53 " --> pdb=" O LYS Q 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 8 removed outlier: 6.332A pdb=" N ILE R 6 " --> pdb=" O GLU R 2 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU R 7 " --> pdb=" O ALA R 3 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LYS R 8 " --> pdb=" O ARG R 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 2 through 8' Processing helix chain 'R' and resid 13 through 23 removed outlier: 3.537A pdb=" N ALA R 19 " --> pdb=" O LYS R 15 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU R 22 " --> pdb=" O GLU R 18 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP R 23 " --> pdb=" O ALA R 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 46 removed outlier: 3.617A pdb=" N VAL R 38 " --> pdb=" O ASN R 34 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 69 removed outlier: 4.503A pdb=" N VAL S 68 " --> pdb=" O HIS S 64 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLN S 69 " --> pdb=" O VAL S 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 64 through 69' Processing helix chain 'T' and resid 14 through 25 removed outlier: 3.688A pdb=" N LEU T 21 " --> pdb=" O ASP T 17 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG T 22 " --> pdb=" O LEU T 18 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS T 23 " --> pdb=" O LYS T 19 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER T 24 " --> pdb=" O GLN T 20 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY T 25 " --> pdb=" O LEU T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 56 removed outlier: 3.682A pdb=" N LYS T 50 " --> pdb=" O VAL T 46 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU T 54 " --> pdb=" O LYS T 50 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL T 55 " --> pdb=" O VAL T 51 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY T 56 " --> pdb=" O ILE T 52 " (cutoff:3.500A) Processing helix chain 'V' and resid 50 through 57 removed outlier: 5.148A pdb=" N SER V 56 " --> pdb=" O ARG V 52 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLY V 57 " --> pdb=" O ALA V 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 9 removed outlier: 3.540A pdb=" N ILE W 6 " --> pdb=" O LYS W 2 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG W 7 " --> pdb=" O ALA W 3 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASP W 8 " --> pdb=" O LYS W 4 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LEU W 9 " --> pdb=" O GLU W 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 2 through 9' Processing helix chain 'W' and resid 10 through 35 removed outlier: 6.323A pdb=" N ILE W 14 " --> pdb=" O THR W 10 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU W 15 " --> pdb=" O THR W 11 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU W 23 " --> pdb=" O LYS W 19 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU W 25 " --> pdb=" O SER W 21 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASN W 27 " --> pdb=" O GLU W 23 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR W 34 " --> pdb=" O PHE W 30 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N GLY W 35 " --> pdb=" O GLN W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 65 removed outlier: 4.347A pdb=" N ARG W 44 " --> pdb=" O THR W 40 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS W 48 " --> pdb=" O ARG W 44 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA W 51 " --> pdb=" O ARG W 47 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG W 58 " --> pdb=" O LYS W 54 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU W 59 " --> pdb=" O THR W 55 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG W 60 " --> pdb=" O VAL W 56 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU W 61 " --> pdb=" O ALA W 57 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU W 63 " --> pdb=" O GLU W 59 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN W 64 " --> pdb=" O ARG W 60 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER W 65 " --> pdb=" O GLU W 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 16 through 27 removed outlier: 3.514A pdb=" N THR X 22 " --> pdb=" O THR X 18 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY X 27 " --> pdb=" O VAL X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 51 removed outlier: 3.774A pdb=" N GLN X 46 " --> pdb=" O ALA X 42 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS X 49 " --> pdb=" O GLY X 45 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL X 50 " --> pdb=" O GLN X 46 " (cutoff:3.500A) Processing helix chain 'Y' and resid 70 through 79 Processing helix chain 'Z' and resid 9 through 19 removed outlier: 3.626A pdb=" N THR Z 18 " --> pdb=" O ASN Z 14 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N HIS Z 19 " --> pdb=" O LYS Z 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 13 removed outlier: 3.565A pdb=" N GLY b 13 " --> pdb=" O LEU b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 32 removed outlier: 4.377A pdb=" N LYS b 28 " --> pdb=" O ASN b 24 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LYS b 29 " --> pdb=" O PRO b 25 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TYR b 30 " --> pdb=" O LYS b 26 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE b 31 " --> pdb=" O MET b 27 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE b 32 " --> pdb=" O LYS b 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 24 through 32' Processing helix chain 'b' and resid 42 through 64 removed outlier: 3.669A pdb=" N THR b 46 " --> pdb=" O ASP b 42 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS b 48 " --> pdb=" O GLN b 44 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP b 51 " --> pdb=" O VAL b 47 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU b 52 " --> pdb=" O LYS b 48 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE b 56 " --> pdb=" O GLU b 52 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN b 59 " --> pdb=" O ASN b 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU b 62 " --> pdb=" O LYS b 58 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP b 63 " --> pdb=" O GLN b 59 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY b 64 " --> pdb=" O VAL b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 88 removed outlier: 4.617A pdb=" N GLU b 78 " --> pdb=" O LYS b 74 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER b 79 " --> pdb=" O GLN b 75 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS b 81 " --> pdb=" O GLN b 77 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU b 83 " --> pdb=" O SER b 79 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA b 87 " --> pdb=" O GLU b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 124 removed outlier: 3.625A pdb=" N ILE b 107 " --> pdb=" O ASN b 103 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS b 109 " --> pdb=" O LYS b 105 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG b 110 " --> pdb=" O THR b 106 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE b 114 " --> pdb=" O ARG b 110 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER b 115 " --> pdb=" O ILE b 111 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU b 116 " --> pdb=" O LYS b 112 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE b 117 " --> pdb=" O ARG b 113 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU b 118 " --> pdb=" O ILE b 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET b 120 " --> pdb=" O GLU b 116 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU b 122 " --> pdb=" O GLU b 118 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP b 123 " --> pdb=" O LYS b 119 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY b 124 " --> pdb=" O MET b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 125 through 130 removed outlier: 3.604A pdb=" N LEU b 129 " --> pdb=" O LEU b 125 " (cutoff:3.500A) Proline residue: b 130 - end of helix No H-bonds generated for 'chain 'b' and resid 125 through 130' Processing helix chain 'b' and resid 131 through 148 removed outlier: 5.200A pdb=" N GLU b 136 " --> pdb=" O LYS b 132 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU b 137 " --> pdb=" O GLU b 133 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS b 138 " --> pdb=" O VAL b 134 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS b 139 " --> pdb=" O VAL b 135 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR b 141 " --> pdb=" O LEU b 137 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP b 142 " --> pdb=" O LYS b 138 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG b 143 " --> pdb=" O LYS b 139 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU b 144 " --> pdb=" O GLU b 140 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE b 145 " --> pdb=" O TYR b 141 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 170 removed outlier: 4.958A pdb=" N ARG b 170 " --> pdb=" O PRO b 166 " (cutoff:3.500A) Processing helix chain 'b' and resid 171 through 180 removed outlier: 4.085A pdb=" N GLU b 175 " --> pdb=" O ASN b 171 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS b 178 " --> pdb=" O ALA b 174 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 225 removed outlier: 3.527A pdb=" N LEU b 213 " --> pdb=" O ALA b 209 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA b 218 " --> pdb=" O THR b 214 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE b 221 " --> pdb=" O MET b 217 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY b 224 " --> pdb=" O ALA b 220 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN b 225 " --> pdb=" O ILE b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.500A pdb=" N LEU c 10 " --> pdb=" O ASN c 6 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 46 removed outlier: 4.327A pdb=" N HIS c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP c 35 " --> pdb=" O LEU c 31 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS c 37 " --> pdb=" O HIS c 33 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE c 41 " --> pdb=" O LYS c 37 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP c 43 " --> pdb=" O ARG c 39 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASN c 44 " --> pdb=" O LYS c 40 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.981A pdb=" N VAL c 75 " --> pdb=" O LYS c 71 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE c 76 " --> pdb=" O PRO c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.680A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LYS c 85 " --> pdb=" O SER c 81 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU c 86 " --> pdb=" O GLU c 82 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG c 87 " --> pdb=" O ILE c 83 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS c 89 " --> pdb=" O LYS c 85 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ALA c 92 " --> pdb=" O ASN c 88 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR c 94 " --> pdb=" O LEU c 90 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP c 95 " --> pdb=" O ASN c 91 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.660A pdb=" N ALA c 116 " --> pdb=" O ALA c 112 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU c 117 " --> pdb=" O ARG c 113 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN c 122 " --> pdb=" O ASN c 118 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU c 123 " --> pdb=" O ILE c 119 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU c 124 " --> pdb=" O ALA c 120 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN c 125 " --> pdb=" O ARG c 121 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 4.471A pdb=" N GLN c 133 " --> pdb=" O PHE c 129 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS c 134 " --> pdb=" O ARG c 130 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA c 136 " --> pdb=" O VAL c 132 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR c 138 " --> pdb=" O LYS c 134 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA c 140 " --> pdb=" O ALA c 136 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET c 141 " --> pdb=" O ILE c 137 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS c 142 " --> pdb=" O THR c 138 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU c 143 " --> pdb=" O ARG c 139 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY c 144 " --> pdb=" O ALA c 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 3.669A pdb=" N LYS d 11 " --> pdb=" O SER d 7 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG d 14 " --> pdb=" O LYS d 10 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY d 16 " --> pdb=" O SER d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 62 removed outlier: 3.641A pdb=" N ARG d 52 " --> pdb=" O GLY d 48 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU d 53 " --> pdb=" O LEU d 49 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS d 54 " --> pdb=" O GLN d 50 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS d 56 " --> pdb=" O ARG d 52 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR d 61 " --> pdb=" O LEU d 57 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY d 62 " --> pdb=" O ARG d 58 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 78 removed outlier: 5.615A pdb=" N ARG d 69 " --> pdb=" O GLU d 65 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP d 73 " --> pdb=" O ARG d 69 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE d 74 " --> pdb=" O ASN d 70 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS d 77 " --> pdb=" O ASP d 73 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS d 78 " --> pdb=" O ILE d 74 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 93 removed outlier: 3.734A pdb=" N ASN d 85 " --> pdb=" O VAL d 81 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE d 86 " --> pdb=" O HIS d 82 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N MET d 87 " --> pdb=" O GLY d 83 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA d 91 " --> pdb=" O MET d 87 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG d 93 " --> pdb=" O LEU d 89 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 102 removed outlier: 3.959A pdb=" N TYR d 99 " --> pdb=" O ASP d 95 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER d 100 " --> pdb=" O ALA d 96 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLY d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 117 removed outlier: 3.702A pdb=" N ARG d 111 " --> pdb=" O ARG d 107 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN d 112 " --> pdb=" O ARG d 108 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL d 114 " --> pdb=" O ALA d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 159 removed outlier: 3.581A pdb=" N VAL d 152 " --> pdb=" O LEU d 148 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER d 154 " --> pdb=" O ILE d 150 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU d 156 " --> pdb=" O VAL d 152 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE d 157 " --> pdb=" O GLU d 153 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN d 158 " --> pdb=" O SER d 154 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASN d 159 " --> pdb=" O VAL d 155 " (cutoff:3.500A) Processing helix chain 'd' and resid 181 through 186 removed outlier: 4.529A pdb=" N LEU d 185 " --> pdb=" O GLU d 181 " (cutoff:3.500A) Proline residue: d 186 - end of helix No H-bonds generated for 'chain 'd' and resid 181 through 186' Processing helix chain 'd' and resid 190 through 200 removed outlier: 4.165A pdb=" N ILE d 194 " --> pdb=" O ASN d 190 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU d 196 " --> pdb=" O GLN d 192 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR d 197 " --> pdb=" O LEU d 193 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER d 199 " --> pdb=" O VAL d 195 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ARG d 200 " --> pdb=" O GLU d 196 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 71 removed outlier: 3.534A pdb=" N ILE e 60 " --> pdb=" O VAL e 56 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS e 61 " --> pdb=" O PRO e 57 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA e 66 " --> pdb=" O LYS e 62 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA e 67 " --> pdb=" O ALA e 63 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS e 68 " --> pdb=" O VAL e 64 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 119 removed outlier: 3.958A pdb=" N ALA e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL e 114 " --> pdb=" O PRO e 110 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA e 118 " --> pdb=" O VAL e 114 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY e 119 " --> pdb=" O LEU e 115 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 147 removed outlier: 3.729A pdb=" N ARG e 138 " --> pdb=" O ILE e 134 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA e 139 " --> pdb=" O ASN e 135 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE e 141 " --> pdb=" O VAL e 137 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN e 146 " --> pdb=" O ASP e 142 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU e 147 " --> pdb=" O GLY e 143 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 158 removed outlier: 3.831A pdb=" N ALA e 154 " --> pdb=" O ALA e 150 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS e 155 " --> pdb=" O GLU e 151 " (cutoff:3.500A) Processing helix chain 'e' and resid 160 through 165 removed outlier: 4.237A pdb=" N TYR e 165 " --> pdb=" O VAL e 161 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 32 removed outlier: 3.680A pdb=" N VAL f 23 " --> pdb=" O LYS f 19 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU f 24 " --> pdb=" O LYS f 20 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN f 27 " --> pdb=" O VAL f 23 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY f 28 " --> pdb=" O GLU f 24 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA f 31 " --> pdb=" O ASN f 27 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N THR f 32 " --> pdb=" O GLY f 28 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 84 removed outlier: 3.661A pdb=" N PHE f 76 " --> pdb=" O ALA f 72 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN f 77 " --> pdb=" O THR f 73 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU f 79 " --> pdb=" O GLU f 75 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE f 82 " --> pdb=" O ARG f 78 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP f 84 " --> pdb=" O ALA f 80 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 4.362A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS g 25 " --> pdb=" O LYS g 21 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU g 26 " --> pdb=" O LEU g 22 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE g 27 " --> pdb=" O VAL g 23 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN g 28 " --> pdb=" O THR g 24 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS g 29 " --> pdb=" O LYS g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 removed outlier: 4.003A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN g 40 " --> pdb=" O ARG g 36 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG g 41 " --> pdb=" O GLY g 37 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE g 42 " --> pdb=" O THR g 38 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR g 44 " --> pdb=" O GLN g 40 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA g 46 " --> pdb=" O ILE g 42 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE g 47 " --> pdb=" O LEU g 43 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP g 48 " --> pdb=" O TYR g 44 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU g 49 " --> pdb=" O SER g 45 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL g 50 " --> pdb=" O ALA g 46 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN g 52 " --> pdb=" O ASP g 48 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG g 53 " --> pdb=" O LEU g 49 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLY g 55 " --> pdb=" O GLU g 51 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.852A pdb=" N VAL g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE g 62 " --> pdb=" O ALA g 58 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU g 64 " --> pdb=" O GLU g 60 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA g 65 " --> pdb=" O VAL g 61 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN g 67 " --> pdb=" O GLU g 63 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN g 68 " --> pdb=" O GLU g 64 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ILE g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N MET g 70 " --> pdb=" O ILE g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 111 removed outlier: 4.056A pdb=" N ARG g 96 " --> pdb=" O ARG g 92 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N THR g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR g 98 " --> pdb=" O GLU g 94 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY g 100 " --> pdb=" O ARG g 96 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU g 101 " --> pdb=" O THR g 97 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG g 102 " --> pdb=" O THR g 98 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU g 104 " --> pdb=" O GLY g 100 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL g 105 " --> pdb=" O LEU g 101 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR g 107 " --> pdb=" O TRP g 103 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA g 108 " --> pdb=" O LEU g 104 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG g 109 " --> pdb=" O VAL g 105 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU g 110 " --> pdb=" O ASN g 106 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ARG g 111 " --> pdb=" O TYR g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.775A pdb=" N ARG g 119 " --> pdb=" O THR g 115 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU g 120 " --> pdb=" O MET g 116 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE g 124 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU g 125 " --> pdb=" O ALA g 121 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP g 126 " --> pdb=" O ASN g 122 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA g 128 " --> pdb=" O ILE g 124 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN g 130 " --> pdb=" O ASP g 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 133 through 149 removed outlier: 3.817A pdb=" N LYS g 137 " --> pdb=" O GLY g 133 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG g 138 " --> pdb=" O ALA g 134 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU g 139 " --> pdb=" O VAL g 135 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR g 141 " --> pdb=" O LYS g 137 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N HIS g 142 " --> pdb=" O ARG g 138 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS g 143 " --> pdb=" O GLU g 139 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET g 144 " --> pdb=" O ASP g 140 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA g 145 " --> pdb=" O THR g 141 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU g 146 " --> pdb=" O HIS g 142 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.605A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET h 10 " --> pdb=" O PRO h 6 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG h 13 " --> pdb=" O ASP h 9 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL h 14 " --> pdb=" O MET h 10 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET h 19 " --> pdb=" O ARG h 15 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL h 20 " --> pdb=" O ASN h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.767A pdb=" N ALA h 37 " --> pdb=" O LYS h 33 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU h 40 " --> pdb=" O ILE h 36 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS h 41 " --> pdb=" O ALA h 37 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER h 42 " --> pdb=" O GLU h 38 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY h 44 " --> pdb=" O LEU h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 122 removed outlier: 4.032A pdb=" N ALA h 118 " --> pdb=" O THR h 114 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS h 120 " --> pdb=" O LYS h 116 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG h 121 " --> pdb=" O GLU h 117 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN h 122 " --> pdb=" O ALA h 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 36 through 42 Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 43 through 58 removed outlier: 4.054A pdb=" N ILE i 47 " --> pdb=" O PHE i 43 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU i 48 " --> pdb=" O GLU i 44 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP i 49 " --> pdb=" O SER i 45 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASN i 51 " --> pdb=" O ILE i 47 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN i 52 " --> pdb=" O LEU i 48 " (cutoff:3.500A) Proline residue: i 53 - end of helix removed outlier: 3.835A pdb=" N GLU i 58 " --> pdb=" O PHE i 54 " (cutoff:3.500A) Processing helix chain 'i' and resid 73 through 94 removed outlier: 4.449A pdb=" N ARG i 82 " --> pdb=" O ALA i 78 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS i 83 " --> pdb=" O GLN i 79 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY i 84 " --> pdb=" O ALA i 80 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA i 86 " --> pdb=" O ARG i 82 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG i 87 " --> pdb=" O HIS i 83 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU i 89 " --> pdb=" O ILE i 85 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU i 90 " --> pdb=" O ALA i 86 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLU i 91 " --> pdb=" O ARG i 87 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA i 92 " --> pdb=" O ALA i 88 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP i 93 " --> pdb=" O LEU i 89 " (cutoff:3.500A) Proline residue: i 94 - end of helix Processing helix chain 'i' and resid 95 through 104 removed outlier: 6.124A pdb=" N SER i 99 " --> pdb=" O GLU i 95 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU i 100 " --> pdb=" O TYR i 96 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS i 101 " --> pdb=" O ARG i 97 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG i 102 " --> pdb=" O GLY i 98 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA i 103 " --> pdb=" O SER i 99 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY i 104 " --> pdb=" O LEU i 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 95 through 104' Processing helix chain 'j' and resid 14 through 33 removed outlier: 4.278A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER j 21 " --> pdb=" O VAL j 17 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA j 22 " --> pdb=" O ILE j 18 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS j 24 " --> pdb=" O GLN j 20 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLU j 27 " --> pdb=" O GLU j 23 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR j 28 " --> pdb=" O LYS j 24 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLY j 33 " --> pdb=" O ALA j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 88 removed outlier: 4.062A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP j 85 " --> pdb=" O PRO j 81 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU j 87 " --> pdb=" O THR j 83 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 80 through 88' Processing helix chain 'k' and resid 46 through 51 removed outlier: 3.546A pdb=" N LEU k 50 " --> pdb=" O SER k 46 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY k 51 " --> pdb=" O ALA k 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 46 through 51' Processing helix chain 'k' and resid 54 through 60 removed outlier: 6.658A pdb=" N SER k 58 " --> pdb=" O GLY k 54 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N THR k 59 " --> pdb=" O SER k 55 " (cutoff:3.500A) Proline residue: k 60 - end of helix No H-bonds generated for 'chain 'k' and resid 54 through 60' Processing helix chain 'k' and resid 61 through 76 removed outlier: 3.502A pdb=" N SER k 67 " --> pdb=" O ALA k 63 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU k 68 " --> pdb=" O GLN k 64 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER k 71 " --> pdb=" O SER k 67 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS k 72 " --> pdb=" O GLU k 68 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER k 73 " --> pdb=" O THR k 69 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU k 76 " --> pdb=" O LYS k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 104 removed outlier: 3.947A pdb=" N ALA k 96 " --> pdb=" O GLY k 92 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG k 98 " --> pdb=" O GLU k 94 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU k 100 " --> pdb=" O ALA k 96 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN k 101 " --> pdb=" O ILE k 97 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER k 102 " --> pdb=" O ARG k 98 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY k 104 " --> pdb=" O LEU k 100 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 removed outlier: 3.661A pdb=" N VAL l 8 " --> pdb=" O ILE l 4 " (cutoff:3.500A) Processing helix chain 'l' and resid 21 through 26 removed outlier: 4.333A pdb=" N ASN l 25 " --> pdb=" O SER l 21 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS l 26 " --> pdb=" O PRO l 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 21 through 26' Processing helix chain 'l' and resid 126 through 131 removed outlier: 5.128A pdb=" N TYR l 130 " --> pdb=" O GLY l 126 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY l 131 " --> pdb=" O ARG l 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 126 through 131' Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.974A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 4.589A pdb=" N ALA m 30 " --> pdb=" O GLY m 26 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN m 31 " --> pdb=" O THR m 27 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS m 32 " --> pdb=" O SER m 28 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU m 34 " --> pdb=" O ALA m 30 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLU m 35 " --> pdb=" O GLN m 31 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU m 36 " --> pdb=" O LYS m 32 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA m 37 " --> pdb=" O ILE m 33 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN m 38 " --> pdb=" O LEU m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 64 removed outlier: 3.662A pdb=" N LEU m 53 " --> pdb=" O THR m 49 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY m 54 " --> pdb=" O ASP m 50 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG m 55 " --> pdb=" O ASP m 51 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG m 57 " --> pdb=" O LEU m 53 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL m 59 " --> pdb=" O ARG m 55 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL m 60 " --> pdb=" O ILE m 56 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP m 61 " --> pdb=" O ARG m 57 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LYS m 64 " --> pdb=" O VAL m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 83 removed outlier: 6.076A pdb=" N ARG m 70 " --> pdb=" O GLU m 66 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG m 71 " --> pdb=" O GLY m 67 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU m 72 " --> pdb=" O ASP m 68 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN m 76 " --> pdb=" O GLU m 72 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE m 77 " --> pdb=" O THR m 73 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU m 80 " --> pdb=" O ASN m 76 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N MET m 81 " --> pdb=" O ILE m 77 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 removed outlier: 4.643A pdb=" N ILE m 89 " --> pdb=" O SER m 85 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG m 90 " --> pdb=" O TYR m 86 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N HIS m 91 " --> pdb=" O ARG m 87 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY m 94 " --> pdb=" O ARG m 90 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 13 removed outlier: 6.321A pdb=" N VAL n 7 " --> pdb=" O LYS n 3 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ALA n 8 " --> pdb=" O THR n 4 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS n 9 " --> pdb=" O SER n 5 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN n 10 " --> pdb=" O MET n 6 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LYS n 12 " --> pdb=" O ALA n 8 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS n 13 " --> pdb=" O LYS n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 51 removed outlier: 3.853A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS n 50 " --> pdb=" O GLU n 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 removed outlier: 3.770A pdb=" N ASN o 9 " --> pdb=" O GLN o 5 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU o 10 " --> pdb=" O GLU o 6 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE o 12 " --> pdb=" O LYS o 8 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR o 15 " --> pdb=" O ILE o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 47 removed outlier: 4.123A pdb=" N ILE o 29 " --> pdb=" O PRO o 25 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR o 33 " --> pdb=" O ILE o 29 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA o 34 " --> pdb=" O ALA o 30 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG o 44 " --> pdb=" O ASN o 40 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS o 47 " --> pdb=" O LEU o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.536A pdb=" N ARG o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS o 58 " --> pdb=" O ARG o 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET o 59 " --> pdb=" O GLY o 55 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY o 61 " --> pdb=" O LEU o 57 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS o 65 " --> pdb=" O GLY o 61 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU o 66 " --> pdb=" O ARG o 62 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR o 69 " --> pdb=" O HIS o 65 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS o 73 " --> pdb=" O TYR o 69 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 removed outlier: 3.596A pdb=" N GLU o 80 " --> pdb=" O GLN o 76 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU o 81 " --> pdb=" O ARG o 77 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS o 83 " --> pdb=" O ARG o 79 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER o 84 " --> pdb=" O GLU o 80 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY o 86 " --> pdb=" O ILE o 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.618A pdb=" N ALA p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU p 58 " --> pdb=" O GLU p 54 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS p 59 " --> pdb=" O ALA p 55 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP p 63 " --> pdb=" O LYS p 59 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY p 64 " --> pdb=" O TRP p 60 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 79 removed outlier: 4.298A pdb=" N ASN p 73 " --> pdb=" O ASP p 69 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE p 74 " --> pdb=" O THR p 70 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER p 76 " --> pdb=" O HIS p 72 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS p 77 " --> pdb=" O ASN p 73 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU p 78 " --> pdb=" O ILE p 74 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY p 79 " --> pdb=" O LEU p 75 " (cutoff:3.500A) Processing helix chain 'p' and resid 80 through 88 removed outlier: 4.235A pdb=" N ASP p 85 " --> pdb=" O MET p 81 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN p 87 " --> pdb=" O LYS p 83 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LYS p 88 " --> pdb=" O PHE p 84 " (cutoff:3.500A) Processing helix chain 'r' and resid 16 through 22 removed outlier: 6.231A pdb=" N ALA r 20 " --> pdb=" O CYS r 16 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN r 21 " --> pdb=" O TYR r 17 " (cutoff:3.500A) Processing helix chain 'r' and resid 30 through 39 removed outlier: 3.562A pdb=" N LEU r 34 " --> pdb=" O ASP r 30 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS r 35 " --> pdb=" O THR r 31 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ARG r 36 " --> pdb=" O GLU r 32 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE r 37 " --> pdb=" O LEU r 33 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE r 38 " --> pdb=" O LEU r 34 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N SER r 39 " --> pdb=" O LYS r 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 30 through 39' Processing helix chain 'r' and resid 46 through 51 removed outlier: 3.689A pdb=" N THR r 50 " --> pdb=" O PRO r 46 " (cutoff:3.500A) Processing helix chain 'r' and resid 53 through 71 removed outlier: 3.582A pdb=" N ARG r 58 " --> pdb=" O ALA r 54 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET r 59 " --> pdb=" O LYS r 55 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA r 63 " --> pdb=" O MET r 59 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG r 66 " --> pdb=" O THR r 62 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS r 69 " --> pdb=" O LYS r 65 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET r 70 " --> pdb=" O ARG r 66 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 24 removed outlier: 5.737A pdb=" N MET s 16 " --> pdb=" O ASP s 12 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS s 17 " --> pdb=" O GLU s 13 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL s 19 " --> pdb=" O LEU s 15 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLN s 22 " --> pdb=" O LYS s 18 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU s 23 " --> pdb=" O VAL s 19 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY s 24 " --> pdb=" O GLU s 20 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.737A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 42 removed outlier: 4.001A pdb=" N LYS t 12 " --> pdb=" O ILE t 8 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA t 17 " --> pdb=" O THR t 13 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU t 18 " --> pdb=" O THR t 14 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG t 20 " --> pdb=" O LYS t 16 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN t 21 " --> pdb=" O ALA t 17 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER t 23 " --> pdb=" O ALA t 19 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN t 24 " --> pdb=" O ARG t 20 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA t 31 " --> pdb=" O ALA t 27 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA t 35 " --> pdb=" O ALA t 31 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER t 40 " --> pdb=" O LYS t 36 " (cutoff:3.500A) Processing helix chain 't' and resid 45 through 64 removed outlier: 4.073A pdb=" N VAL t 50 " --> pdb=" O LYS t 46 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL t 54 " --> pdb=" O VAL t 50 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP t 58 " --> pdb=" O VAL t 54 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA t 61 " --> pdb=" O VAL t 57 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN t 62 " --> pdb=" O ASP t 58 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASN t 64 " --> pdb=" O ALA t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 82 removed outlier: 4.795A pdb=" N ASP t 72 " --> pdb=" O SER t 68 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG t 73 " --> pdb=" O ASN t 69 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR t 80 " --> pdb=" O SER t 76 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '1' and resid 3 through 7 Processing sheet with id= 2, first strand: chain '1' and resid 30 through 36 removed outlier: 5.669A pdb=" N ILE 1 30 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '3' and resid 22 through 25 removed outlier: 5.529A pdb=" N LEU 3 22 " --> pdb=" O VAL 3 50 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '4' and resid 1 through 4 removed outlier: 3.521A pdb=" N ARG 4 4 " --> pdb=" O ARG 4 35 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N HIS 4 32 " --> pdb=" O CYS 4 27 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N CYS 4 27 " --> pdb=" O HIS 4 32 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL 4 23 " --> pdb=" O GLN 4 36 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '6' and resid 2 through 6 Processing sheet with id= 6, first strand: chain '6' and resid 56 through 60 removed outlier: 5.767A pdb=" N LEU 6 153 " --> pdb=" O ALA 6 57 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA 6 196 " --> pdb=" O HIS 6 30 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP 6 195 " --> pdb=" O GLY 6 210 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY 6 210 " --> pdb=" O ASP 6 195 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N GLY 6 204 " --> pdb=" O THR 6 201 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '6' and resid 334 through 338 removed outlier: 4.359A pdb=" N PHE 6 335 " --> pdb=" O PHE 6 317 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL 6 315 " --> pdb=" O ILE 6 337 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N LEU 6 314 " --> pdb=" O HIS 6 374 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU 6 318 " --> pdb=" O ALA 6 370 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA 6 370 " --> pdb=" O GLU 6 318 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '6' and resid 342 through 347 removed outlier: 3.576A pdb=" N GLU 6 346 " --> pdb=" O TRP 6 498 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE 6 500 " --> pdb=" O GLU 6 346 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL 6 497 " --> pdb=" O GLU 6 508 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '6' and resid 378 through 383 removed outlier: 3.802A pdb=" N ILE 6 451 " --> pdb=" O ASP 6 378 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA 6 479 " --> pdb=" O HIS 6 450 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 2 through 5 removed outlier: 6.388A pdb=" N ALA C 2 " --> pdb=" O ASP C 20 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP C 20 " --> pdb=" O ALA C 2 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.592A pdb=" N SER C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU C 93 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLN C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY C 127 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 139 through 142 removed outlier: 4.540A pdb=" N THR C 139 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'C' and resid 91 through 96 removed outlier: 4.442A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 3 through 8 removed outlier: 7.255A pdb=" N LYS D 3 " --> pdb=" O THR D 213 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU D 208 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL D 121 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN D 176 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY D 124 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY D 174 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY D 126 " --> pdb=" O ARG D 172 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG D 172 " --> pdb=" O GLY D 126 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 11 through 17 removed outlier: 3.855A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY D 17 " --> pdb=" O GLU D 21 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN D 187 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'D' and resid 33 through 36 removed outlier: 6.677A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 51 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE D 87 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'D' and resid 114 through 117 removed outlier: 4.416A pdb=" N ASP D 114 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'E' and resid 2 through 7 removed outlier: 5.013A pdb=" N ALA E 2 " --> pdb=" O LEU E 19 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL E 6 " --> pdb=" O GLY E 15 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY E 15 " --> pdb=" O VAL E 6 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'E' and resid 122 through 125 removed outlier: 3.605A pdb=" N SER E 191 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'F' and resid 65 through 70 removed outlier: 6.727A pdb=" N LEU F 66 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA F 87 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR F 68 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA F 70 " --> pdb=" O MET F 83 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N MET F 83 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL F 40 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ALA F 87 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL F 89 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN F 37 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP F 153 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N MET F 152 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL F 132 " --> pdb=" O MET F 152 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE F 154 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE F 156 " --> pdb=" O TYR F 128 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR F 128 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLY F 126 " --> pdb=" O THR F 158 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'G' and resid 23 through 26 removed outlier: 3.761A pdb=" N LEU G 33 " --> pdb=" O VAL G 26 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 24, first strand: chain 'G' and resid 94 through 99 removed outlier: 3.766A pdb=" N ARG G 95 " --> pdb=" O ASN G 106 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN G 106 " --> pdb=" O ARG G 95 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP G 102 " --> pdb=" O GLN G 99 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU G 103 " --> pdb=" O ILE G 115 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'G' and resid 121 through 126 removed outlier: 6.716A pdb=" N VAL G 130 " --> pdb=" O GLU G 126 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'H' and resid 53 through 57 Processing sheet with id= 27, first strand: chain 'H' and resid 75 through 79 removed outlier: 7.586A pdb=" N GLY H 84 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'I' and resid 18 through 21 removed outlier: 4.739A pdb=" N THR I 6 " --> pdb=" O THR I 21 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASN I 82 " --> pdb=" O ARG I 7 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'I' and resid 38 through 41 Processing sheet with id= 30, first strand: chain 'I' and resid 68 through 71 removed outlier: 4.051A pdb=" N SER I 75 " --> pdb=" O ARG I 71 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'J' and resid 73 through 77 removed outlier: 4.944A pdb=" N GLY J 108 " --> pdb=" O GLU J 73 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'J' and resid 121 through 124 removed outlier: 3.724A pdb=" N ALA J 142 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU J 144 " --> pdb=" O VAL J 123 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'K' and resid 100 through 103 removed outlier: 4.039A pdb=" N ARG K 101 " --> pdb=" O ALA K 36 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU K 34 " --> pdb=" O LEU K 103 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE K 104 " --> pdb=" O LEU K 34 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'K' and resid 31 through 37 removed outlier: 8.685A pdb=" N GLU K 31 " --> pdb=" O ARG K 134 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LYS K 128 " --> pdb=" O THR K 37 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'L' and resid 29 through 33 removed outlier: 6.040A pdb=" N ALA L 114 " --> pdb=" O PRO L 108 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER L 116 " --> pdb=" O GLN L 106 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'M' and resid 30 through 35 removed outlier: 6.525A pdb=" N ILE M 40 " --> pdb=" O SER M 58 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA M 56 " --> pdb=" O ALA M 42 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA M 54 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'N' and resid 40 through 47 Processing sheet with id= 38, first strand: chain 'N' and resid 51 through 55 removed outlier: 3.701A pdb=" N LYS N 51 " --> pdb=" O THR N 62 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLY N 55 " --> pdb=" O SER N 58 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER N 58 " --> pdb=" O GLY N 55 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'P' and resid 2 through 6 Processing sheet with id= 40, first strand: chain 'P' and resid 18 through 21 removed outlier: 4.674A pdb=" N GLN P 18 " --> pdb=" O ILE P 97 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR P 59 " --> pdb=" O ASP P 98 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'P' and resid 39 through 42 removed outlier: 6.545A pdb=" N LEU P 39 " --> pdb=" O GLY P 49 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'P' and resid 64 through 69 removed outlier: 4.657A pdb=" N LYS P 64 " --> pdb=" O LYS P 94 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS P 94 " --> pdb=" O LYS P 64 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLN P 90 " --> pdb=" O GLY P 68 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Q' and resid 2 through 8 removed outlier: 6.592A pdb=" N VAL Q 106 " --> pdb=" O LYS Q 72 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Q' and resid 79 through 88 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain 'R' and resid 24 through 28 removed outlier: 4.506A pdb=" N TYR R 68 " --> pdb=" O MET R 65 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N MET R 65 " --> pdb=" O TYR R 68 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY R 70 " --> pdb=" O LYS R 63 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS R 61 " --> pdb=" O THR R 72 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LYS R 74 " --> pdb=" O LYS R 59 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LYS R 59 " --> pdb=" O LYS R 74 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG R 76 " --> pdb=" O ASN R 57 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN R 57 " --> pdb=" O ARG R 76 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA R 78 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE R 55 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL R 80 " --> pdb=" O VAL R 53 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL R 53 " --> pdb=" O VAL R 80 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'S' and resid 7 through 11 removed outlier: 4.943A pdb=" N ASP S 7 " --> pdb=" O VAL S 23 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS S 19 " --> pdb=" O VAL S 11 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'S' and resid 39 through 45 removed outlier: 5.643A pdb=" N ASN S 39 " --> pdb=" O ALA S 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR S 59 " --> pdb=" O MET S 41 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS S 43 " --> pdb=" O LEU S 57 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY S 55 " --> pdb=" O GLN S 45 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'S' and resid 82 through 85 removed outlier: 3.546A pdb=" N VAL S 91 " --> pdb=" O LYS S 84 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'T' and resid 69 through 73 removed outlier: 4.987A pdb=" N ALA T 2 " --> pdb=" O VAL T 60 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU T 4 " --> pdb=" O GLU T 62 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER T 6 " --> pdb=" O GLY T 64 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS T 88 " --> pdb=" O GLN T 78 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP T 76 " --> pdb=" O ASP T 90 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'U' and resid 73 through 78 removed outlier: 3.611A pdb=" N LYS U 76 " --> pdb=" O SER U 88 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'V' and resid 11 through 19 No H-bonds generated for sheet with id= 51 Processing sheet with id= 52, first strand: chain 'X' and resid 32 through 38 removed outlier: 4.367A pdb=" N SER X 33 " --> pdb=" O LEU X 8 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LEU X 53 " --> pdb=" O THR X 9 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'b' and resid 15 through 18 removed outlier: 6.279A pdb=" N HIS b 15 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY b 17 " --> pdb=" O TYR b 39 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TYR b 39 " --> pdb=" O GLY b 17 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'b' and resid 90 through 93 removed outlier: 3.933A pdb=" N PHE b 90 " --> pdb=" O VAL b 67 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY b 71 " --> pdb=" O ILE b 92 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU b 161 " --> pdb=" O PRO b 182 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'c' and resid 53 through 58 removed outlier: 6.049A pdb=" N HIS c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU c 55 " --> pdb=" O ALA c 66 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA c 66 " --> pdb=" O GLU c 55 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N HIS c 99 " --> pdb=" O ILE c 63 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR c 69 " --> pdb=" O ILE c 103 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE c 105 " --> pdb=" O THR c 69 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'c' and resid 163 through 170 removed outlier: 5.094A pdb=" N ARG c 163 " --> pdb=" O GLY c 154 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL c 152 " --> pdb=" O GLU c 165 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR c 167 " --> pdb=" O THR c 150 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER c 153 " --> pdb=" O GLY c 196 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'd' and resid 165 through 168 removed outlier: 6.160A pdb=" N ASN d 166 " --> pdb=" O THR d 175 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR d 175 " --> pdb=" O ASN d 166 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR d 173 " --> pdb=" O ASP d 168 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'e' and resid 11 through 16 removed outlier: 6.825A pdb=" N LEU e 36 " --> pdb=" O VAL e 16 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'e' and resid 84 through 88 removed outlier: 3.824A pdb=" N ILE e 85 " --> pdb=" O MET e 96 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER e 93 " --> pdb=" O LEU e 128 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASP e 122 " --> pdb=" O ALA e 99 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'e' and resid 33 through 40 removed outlier: 3.860A pdb=" N GLY e 51 " --> pdb=" O ALA e 35 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'f' and resid 39 through 44 removed outlier: 3.543A pdb=" N GLU f 39 " --> pdb=" O ARG f 64 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS f 41 " --> pdb=" O ILE f 62 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TRP f 43 " --> pdb=" O TYR f 60 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP f 57 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR f 8 " --> pdb=" O ASN f 61 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL f 65 " --> pdb=" O TYR f 4 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR f 4 " --> pdb=" O VAL f 65 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR f 3 " --> pdb=" O GLU f 94 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET f 7 " --> pdb=" O MET f 90 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG f 88 " --> pdb=" O ILE f 9 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'g' and resid 72 through 79 removed outlier: 6.692A pdb=" N VAL g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR g 85 " --> pdb=" O ARG g 78 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'h' and resid 23 through 29 removed outlier: 5.965A pdb=" N GLU h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU h 64 " --> pdb=" O GLU h 23 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU h 27 " --> pdb=" O LEU h 60 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLY h 58 " --> pdb=" O ALA h 29 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL h 59 " --> pdb=" O VAL h 52 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG h 61 " --> pdb=" O GLU h 50 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'h' and resid 76 through 79 removed outlier: 4.655A pdb=" N GLY h 76 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA h 129 " --> pdb=" O LEU h 105 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU h 105 " --> pdb=" O ILE h 128 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU h 126 " --> pdb=" O SER h 107 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'i' and resid 7 through 11 removed outlier: 3.584A pdb=" N ARG i 22 " --> pdb=" O LEU i 66 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU i 66 " --> pdb=" O ARG i 22 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP i 64 " --> pdb=" O VAL i 24 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TYR i 63 " --> pdb=" O GLU i 27 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN i 29 " --> pdb=" O TYR i 63 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR i 31 " --> pdb=" O VAL i 65 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.554A pdb=" N LYS j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE j 74 " --> pdb=" O ILE j 8 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ARG j 7 " --> pdb=" O LYS j 101 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'j' and resid 44 through 52 removed outlier: 3.659A pdb=" N TYR j 49 " --> pdb=" O PHE j 65 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'k' and resid 19 through 25 removed outlier: 3.505A pdb=" N THR k 33 " --> pdb=" O HIS k 22 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE k 31 " --> pdb=" O ARG k 24 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'k' and resid 83 through 87 removed outlier: 4.091A pdb=" N VAL k 84 " --> pdb=" O ALA k 109 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'l' and resid 27 through 30 removed outlier: 3.535A pdb=" N LYS l 34 " --> pdb=" O ASN l 29 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'l' and resid 42 through 46 removed outlier: 3.629A pdb=" N VAL l 93 " --> pdb=" O GLY l 45 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LEU l 94 " --> pdb=" O VAL l 111 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'l' and resid 49 through 54 removed outlier: 3.540A pdb=" N ARG l 49 " --> pdb=" O ARG l 67 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG l 67 " --> pdb=" O ARG l 49 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR l 65 " --> pdb=" O GLY l 51 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LYS l 64 " --> pdb=" O ILE l 80 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'p' and resid 5 through 11 removed outlier: 4.067A pdb=" N ARG p 19 " --> pdb=" O THR p 8 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE p 17 " --> pdb=" O LEU p 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE p 20 " --> pdb=" O GLY p 38 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN p 41 " --> pdb=" O GLU p 49 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU p 49 " --> pdb=" O ASN p 41 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'q' and resid 9 through 13 removed outlier: 3.593A pdb=" N ILE q 63 " --> pdb=" O TYR q 10 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL q 61 " --> pdb=" O GLY q 12 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS q 62 " --> pdb=" O VAL q 78 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'q' and resid 21 through 33 No H-bonds generated for sheet with id= 75 Processing sheet with id= 76, first strand: chain 's' and resid 30 through 34 removed outlier: 4.122A pdb=" N TYR s 52 " --> pdb=" O THR s 33 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) 1274 hydrogen bonds defined for protein. 3762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2938 hydrogen bonds 4678 hydrogen bond angles 0 basepair planarities 1206 basepair parallelities 2507 stacking parallelities Total time for adding SS restraints: 224.99 Time building geometry restraints manager: 59.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 436 1.20 - 1.36: 41639 1.36 - 1.52: 86897 1.52 - 1.68: 21353 1.68 - 1.84: 223 Bond restraints: 150548 Sorted by residual: bond pdb=" CB LYS t 46 " pdb=" CG LYS t 46 " ideal model delta sigma weight residual 1.520 1.159 0.361 3.00e-02 1.11e+03 1.45e+02 bond pdb=" CB ASP l 102 " pdb=" CG ASP l 102 " ideal model delta sigma weight residual 1.516 1.223 0.293 2.50e-02 1.60e+03 1.37e+02 bond pdb=" CG ARG l 124 " pdb=" CD ARG l 124 " ideal model delta sigma weight residual 1.520 1.186 0.334 3.00e-02 1.11e+03 1.24e+02 bond pdb=" CB GLU d 65 " pdb=" CG GLU d 65 " ideal model delta sigma weight residual 1.520 1.194 0.326 3.00e-02 1.11e+03 1.18e+02 bond pdb=" CA HIS k 22 " pdb=" CB HIS k 22 " ideal model delta sigma weight residual 1.528 1.272 0.257 2.61e-02 1.47e+03 9.67e+01 ... (remaining 150543 not shown) Histogram of bond angle deviations from ideal: 64.65 - 82.41: 8 82.41 - 100.17: 493 100.17 - 117.94: 141764 117.94 - 135.70: 82303 135.70 - 153.46: 34 Bond angle restraints: 224602 Sorted by residual: angle pdb=" PB ATP 6 602 " pdb=" O3B ATP 6 602 " pdb=" PG ATP 6 602 " ideal model delta sigma weight residual 139.87 119.51 20.36 1.00e+00 1.00e+00 4.15e+02 angle pdb=" PB ATP 6 601 " pdb=" O3B ATP 6 601 " pdb=" PG ATP 6 601 " ideal model delta sigma weight residual 139.87 120.22 19.65 1.00e+00 1.00e+00 3.86e+02 angle pdb=" CB LYS t 46 " pdb=" CG LYS t 46 " pdb=" CD LYS t 46 " ideal model delta sigma weight residual 111.30 153.46 -42.16 2.30e+00 1.89e-01 3.36e+02 angle pdb=" OP1 G a1095 " pdb=" P G a1095 " pdb=" OP2 G a1095 " ideal model delta sigma weight residual 119.60 64.65 54.95 3.00e+00 1.11e-01 3.36e+02 angle pdb=" PA ATP 6 602 " pdb=" O3A ATP 6 602 " pdb=" PB ATP 6 602 " ideal model delta sigma weight residual 136.83 120.89 15.94 1.00e+00 1.00e+00 2.54e+02 ... (remaining 224597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 83997 35.99 - 71.97: 10845 71.97 - 107.96: 1047 107.96 - 143.94: 32 143.94 - 179.93: 77 Dihedral angle restraints: 95998 sinusoidal: 79036 harmonic: 16962 Sorted by residual: dihedral pdb=" CA GLY d 21 " pdb=" C GLY d 21 " pdb=" N THR d 22 " pdb=" CA THR d 22 " ideal model delta harmonic sigma weight residual -180.00 -122.09 -57.91 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA GLN 6 156 " pdb=" C GLN 6 156 " pdb=" N PRO 6 157 " pdb=" CA PRO 6 157 " ideal model delta harmonic sigma weight residual -180.00 -125.71 -54.29 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA ALA t 2 " pdb=" C ALA t 2 " pdb=" N ASN t 3 " pdb=" CA ASN t 3 " ideal model delta harmonic sigma weight residual -180.00 -127.67 -52.33 0 5.00e+00 4.00e-02 1.10e+02 ... (remaining 95995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 27511 0.145 - 0.290: 977 0.290 - 0.435: 150 0.435 - 0.580: 34 0.580 - 0.725: 5 Chirality restraints: 28677 Sorted by residual: chirality pdb=" CB VAL l 111 " pdb=" CA VAL l 111 " pdb=" CG1 VAL l 111 " pdb=" CG2 VAL l 111 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA ASN k 119 " pdb=" N ASN k 119 " pdb=" C ASN k 119 " pdb=" CB ASN k 119 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" P C a1120 " pdb=" OP1 C a1120 " pdb=" OP2 C a1120 " pdb=" O5' C a1120 " both_signs ideal model delta sigma weight residual True 2.41 -1.76 0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 28674 not shown) Planarity restraints: 12394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A a 983 " -0.149 2.00e-02 2.50e+03 6.44e-02 1.14e+02 pdb=" N9 A a 983 " 0.125 2.00e-02 2.50e+03 pdb=" C8 A a 983 " 0.057 2.00e-02 2.50e+03 pdb=" N7 A a 983 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A a 983 " -0.011 2.00e-02 2.50e+03 pdb=" C6 A a 983 " -0.029 2.00e-02 2.50e+03 pdb=" N6 A a 983 " -0.052 2.00e-02 2.50e+03 pdb=" N1 A a 983 " 0.017 2.00e-02 2.50e+03 pdb=" C2 A a 983 " 0.014 2.00e-02 2.50e+03 pdb=" N3 A a 983 " 0.010 2.00e-02 2.50e+03 pdb=" C4 A a 983 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS n 31 " -0.091 2.00e-02 2.50e+03 7.26e-02 7.90e+01 pdb=" CG HIS n 31 " 0.119 2.00e-02 2.50e+03 pdb=" ND1 HIS n 31 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 HIS n 31 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS n 31 " -0.078 2.00e-02 2.50e+03 pdb=" NE2 HIS n 31 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U a1400 " -0.062 2.00e-02 2.50e+03 5.25e-02 6.21e+01 pdb=" N1 U a1400 " 0.072 2.00e-02 2.50e+03 pdb=" C2 U a1400 " 0.037 2.00e-02 2.50e+03 pdb=" O2 U a1400 " 0.024 2.00e-02 2.50e+03 pdb=" N3 U a1400 " -0.093 2.00e-02 2.50e+03 pdb=" C4 U a1400 " -0.014 2.00e-02 2.50e+03 pdb=" O4 U a1400 " 0.040 2.00e-02 2.50e+03 pdb=" C5 U a1400 " -0.043 2.00e-02 2.50e+03 pdb=" C6 U a1400 " 0.039 2.00e-02 2.50e+03 ... (remaining 12391 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 619 2.44 - 3.05: 79500 3.05 - 3.67: 234464 3.67 - 4.28: 398554 4.28 - 4.90: 538914 Nonbonded interactions: 1252051 Sorted by model distance: nonbonded pdb=" O ARG t 10 " pdb=" OG1 THR t 14 " model vdw 1.822 2.440 nonbonded pdb=" O SER h 109 " pdb=" OG SER h 109 " model vdw 1.958 2.440 nonbonded pdb=" O SER k 67 " pdb=" OG SER k 67 " model vdw 1.958 2.440 nonbonded pdb=" O2B ATP 6 602 " pdb="MG MG 6 604 " model vdw 1.967 2.170 nonbonded pdb=" O SER q 84 " pdb=" OG SER q 84 " model vdw 1.973 2.440 ... (remaining 1252046 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 19.560 Check model and map are aligned: 1.480 Set scattering table: 1.020 Process input model: 532.200 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 574.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.020 0.381 150548 Z= 1.234 Angle : 1.478 54.953 224602 Z= 0.744 Chirality : 0.070 0.725 28677 Planarity : 0.010 0.151 12394 Dihedral : 24.241 179.927 85060 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 13.46 % Favored : 86.16 % Rotamer: Outliers : 0.92 % Allowed : 12.03 % Favored : 87.05 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.50 % Twisted General : 0.63 % 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: -5.47 (0.08), residues: 5825 helix: -4.69 (0.06), residues: 1628 sheet: -2.79 (0.14), residues: 1096 loop : -3.38 (0.09), residues: 3101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.006 TRP c 200 HIS 0.045 0.005 HIS n 31 PHE 0.075 0.005 PHE e 48 TYR 0.089 0.006 TYR l 130 ARG 0.059 0.002 ARG e 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 994 time to evaluate : 6.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU K 136 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 15 ARG cc_start: 0.7623 (mpt-90) cc_final: 0.7393 (mpt-90) REVERT: 1 18 ILE cc_start: 0.8168 (mm) cc_final: 0.7759 (pt) REVERT: C 274 ARG cc_start: 0.7292 (ttm170) cc_final: 0.6847 (tpp-160) REVERT: D 103 GLN cc_start: 0.8234 (mt0) cc_final: 0.7996 (mt0) REVERT: D 189 ASP cc_start: 0.6835 (t0) cc_final: 0.6371 (t70) REVERT: J 63 LYS cc_start: 0.5752 (mppt) cc_final: 0.4535 (pttp) REVERT: K 91 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7233 (mm-30) REVERT: P 69 LYS cc_start: 0.8128 (tmmt) cc_final: 0.7924 (tttt) REVERT: V 8 THR cc_start: 0.8349 (t) cc_final: 0.7938 (m) REVERT: Z 44 LYS cc_start: 0.8054 (mmmm) cc_final: 0.7578 (mmtm) REVERT: l 28 PHE cc_start: 0.7223 (t80) cc_final: 0.7007 (t80) REVERT: m 112 PRO cc_start: 0.8028 (Cg_endo) cc_final: 0.7805 (Cg_exo) outliers start: 44 outliers final: 9 residues processed: 1028 average time/residue: 2.3019 time to fit residues: 3271.6681 Evaluate side-chains 681 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 672 time to evaluate : 5.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 13 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain e residue 101 PRO Chi-restraints excluded: chain g residue 50 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 846 optimal weight: 5.9990 chunk 759 optimal weight: 0.9990 chunk 421 optimal weight: 50.0000 chunk 259 optimal weight: 4.9990 chunk 512 optimal weight: 4.9990 chunk 405 optimal weight: 1.9990 chunk 785 optimal weight: 8.9990 chunk 303 optimal weight: 0.6980 chunk 477 optimal weight: 6.9990 chunk 584 optimal weight: 6.9990 chunk 909 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 25 ASN 1 40 ASN 2 17 HIS 3 7 HIS 3 21 GLN 3 43 GLN 6 24 HIS 6 156 GLN 6 282 GLN 6 340 ASN 6 358 GLN 6 450 HIS 6 471 GLN 6 485 HIS 6 507 HIS C 61 GLN C 75 ASN C 134 ASN C 163 GLN C 230 HIS C 232 HIS ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 HIS D 93 ASN E 158 ASN E 179 GLN E 182 ASN G 120 ASN H 8 ASN H 24 GLN H 41 ASN H 48 HIS H 119 GLN H 137 GLN I 3 GLN I 4 GLN ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 83 ASN ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 ASN M 37 ASN ** M 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 GLN O 37 GLN Q 28 ASN R 73 ASN S 44 HIS T 38 ASN T 78 GLN ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 64 GLN X 40 ASN Z 14 ASN b 8 GLN b 77 GLN ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 33 HIS c 133 GLN d 8 ASN d 115 ASN d 118 HIS d 149 ASN d 166 ASN e 83 HIS e 146 ASN g 67 ASN g 130 ASN g 148 ASN i 16 ASN i 52 GLN ** i 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 39 ASN l 59 ASN l 77 ASN l 90 HIS m 76 ASN o 37 ASN o 68 ASN q 33 HIS r 57 GLN s 43 ASN Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 150548 Z= 0.240 Angle : 0.711 13.325 224602 Z= 0.371 Chirality : 0.042 0.411 28677 Planarity : 0.006 0.147 12394 Dihedral : 24.093 179.848 73592 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.73 % Favored : 92.17 % Rotamer: Outliers : 3.63 % Allowed : 18.63 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.09), residues: 5825 helix: -3.40 (0.09), residues: 1731 sheet: -1.92 (0.15), residues: 1080 loop : -2.88 (0.09), residues: 3014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP b 23 HIS 0.010 0.001 HIS o 42 PHE 0.022 0.002 PHE 6 276 TYR 0.024 0.002 TYR o 78 ARG 0.009 0.001 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 747 time to evaluate : 6.261 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU K 136 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 15 ARG cc_start: 0.7476 (mpt-90) cc_final: 0.7193 (mpt180) REVERT: 1 18 ILE cc_start: 0.7963 (mm) cc_final: 0.7686 (pt) REVERT: 3 21 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7659 (mp-120) REVERT: 6 201 THR cc_start: 0.7415 (OUTLIER) cc_final: 0.6974 (m) REVERT: C 130 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8199 (pp) REVERT: C 274 ARG cc_start: 0.7303 (ttm170) cc_final: 0.6888 (tpp-160) REVERT: D 103 GLN cc_start: 0.8216 (mt0) cc_final: 0.7976 (mt0) REVERT: J 63 LYS cc_start: 0.5426 (mppt) cc_final: 0.4291 (pttp) REVERT: K 91 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7355 (mm-30) REVERT: K 137 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6692 (tp) REVERT: P 69 LYS cc_start: 0.8154 (tmmt) cc_final: 0.7851 (tttt) REVERT: R 56 MET cc_start: 0.8593 (mtm) cc_final: 0.8068 (mtm) REVERT: S 20 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6980 (mm-30) REVERT: U 82 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.6059 (ttm-80) REVERT: V 8 THR cc_start: 0.8197 (t) cc_final: 0.7789 (m) REVERT: W 5 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.6215 (tt0) REVERT: W 38 GLU cc_start: 0.7001 (tm-30) cc_final: 0.6666 (tm-30) REVERT: g 78 ARG cc_start: 0.6616 (ttt180) cc_final: 0.6121 (mmm160) REVERT: i 35 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.6954 (mtm-85) REVERT: k 27 PHE cc_start: 0.7716 (m-80) cc_final: 0.7393 (m-10) REVERT: n 31 HIS cc_start: 0.6893 (OUTLIER) cc_final: 0.6450 (t-90) outliers start: 174 outliers final: 58 residues processed: 858 average time/residue: 2.0443 time to fit residues: 2513.7830 Evaluate side-chains 688 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 621 time to evaluate : 5.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 21 GLN Chi-restraints excluded: chain 4 residue 17 ILE Chi-restraints excluded: chain 6 residue 144 VAL Chi-restraints excluded: chain 6 residue 161 MET Chi-restraints excluded: chain 6 residue 201 THR Chi-restraints excluded: chain 6 residue 290 SER Chi-restraints excluded: chain 6 residue 365 LEU Chi-restraints excluded: chain 6 residue 442 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain P residue 21 PHE Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 48 GLU Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain Q residue 73 GLU Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain U residue 82 ARG Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 20 SER Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain b residue 67 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 35 ARG Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 99 ARG Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain t residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 505 optimal weight: 8.9990 chunk 282 optimal weight: 10.0000 chunk 757 optimal weight: 20.0000 chunk 619 optimal weight: 0.9990 chunk 251 optimal weight: 8.9990 chunk 911 optimal weight: 9.9990 chunk 984 optimal weight: 9.9990 chunk 811 optimal weight: 20.0000 chunk 903 optimal weight: 20.0000 chunk 310 optimal weight: 5.9990 chunk 731 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 40 ASN 3 43 GLN 6 30 HIS ** 6 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 281 HIS 6 507 HIS D 33 ASN E 179 GLN G 106 ASN G 147 ASN H 24 GLN J 54 GLN L 73 ASN ** M 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 81 ASN P 88 HIS Q 28 ASN T 13 GLN W 27 ASN c 33 HIS c 44 ASN c 133 GLN d 50 GLN e 43 ASN ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 122 ASN h 18 ASN h 99 ASN i 16 ASN i 34 ASN ** i 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 GLN l 125 GLN o 18 HIS o 40 ASN p 87 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 150548 Z= 0.479 Angle : 0.899 14.896 224602 Z= 0.452 Chirality : 0.051 0.575 28677 Planarity : 0.007 0.151 12394 Dihedral : 24.068 179.512 73583 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.82 % Favored : 91.07 % Rotamer: Outliers : 5.60 % Allowed : 20.35 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.50 % Twisted General : 0.12 % 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: -3.69 (0.09), residues: 5825 helix: -2.70 (0.10), residues: 1787 sheet: -1.54 (0.15), residues: 1090 loop : -2.64 (0.10), residues: 2948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP c 18 HIS 0.011 0.002 HIS D 148 PHE 0.028 0.002 PHE 6 276 TYR 0.024 0.002 TYR O 32 ARG 0.015 0.001 ARG O 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 655 time to evaluate : 6.171 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU K 136 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 18 ILE cc_start: 0.7983 (mm) cc_final: 0.7647 (pt) REVERT: 3 21 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7803 (mp10) REVERT: 6 201 THR cc_start: 0.7516 (OUTLIER) cc_final: 0.7313 (m) REVERT: 6 298 GLU cc_start: 0.5214 (OUTLIER) cc_final: 0.4543 (pt0) REVERT: 6 388 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7462 (m-40) REVERT: C 183 MET cc_start: 0.7723 (mtm) cc_final: 0.7332 (mpp) REVERT: C 274 ARG cc_start: 0.7305 (ttm170) cc_final: 0.6825 (tpp-160) REVERT: D 103 GLN cc_start: 0.8227 (mt0) cc_final: 0.7988 (mt0) REVERT: H 19 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8423 (mt) REVERT: J 63 LYS cc_start: 0.5812 (OUTLIER) cc_final: 0.4565 (pttp) REVERT: K 91 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7262 (mm-30) REVERT: K 137 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7213 (tp) REVERT: L 24 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8541 (tt) REVERT: L 29 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7241 (ttp80) REVERT: L 85 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8698 (tp) REVERT: M 17 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.6952 (mtm180) REVERT: P 69 LYS cc_start: 0.8180 (tmmt) cc_final: 0.7898 (tttt) REVERT: T 80 ASP cc_start: 0.7418 (t0) cc_final: 0.7086 (t0) REVERT: U 25 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6173 (mp0) REVERT: U 47 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8181 (mtt-85) REVERT: U 64 ASP cc_start: 0.8306 (p0) cc_final: 0.8096 (p0) REVERT: U 82 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.5989 (ttm-80) REVERT: V 8 THR cc_start: 0.8488 (t) cc_final: 0.7980 (m) REVERT: V 33 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9053 (mp) REVERT: W 30 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.8077 (t80) REVERT: W 44 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7518 (ttp80) REVERT: c 17 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.6977 (t0) REVERT: c 203 ARG cc_start: 0.6759 (OUTLIER) cc_final: 0.5883 (ppt-90) REVERT: e 128 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7396 (mt) REVERT: i 35 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.6987 (mtm-85) REVERT: k 27 PHE cc_start: 0.8123 (m-80) cc_final: 0.7753 (m-10) REVERT: l 124 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6925 (ttt180) REVERT: o 40 ASN cc_start: 0.7615 (OUTLIER) cc_final: 0.7367 (m110) outliers start: 268 outliers final: 114 residues processed: 833 average time/residue: 2.0065 time to fit residues: 2405.9203 Evaluate side-chains 742 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 605 time to evaluate : 5.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 5 VAL Chi-restraints excluded: chain 1 residue 12 CYS Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 21 GLN Chi-restraints excluded: chain 6 residue 53 LEU Chi-restraints excluded: chain 6 residue 55 ASP Chi-restraints excluded: chain 6 residue 144 VAL Chi-restraints excluded: chain 6 residue 161 MET Chi-restraints excluded: chain 6 residue 201 THR Chi-restraints excluded: chain 6 residue 290 SER Chi-restraints excluded: chain 6 residue 298 GLU Chi-restraints excluded: chain 6 residue 315 VAL Chi-restraints excluded: chain 6 residue 388 ASN Chi-restraints excluded: chain 6 residue 405 MET Chi-restraints excluded: chain 6 residue 433 MET Chi-restraints excluded: chain 6 residue 442 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain J residue 63 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 29 ARG Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain M residue 17 ARG Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 19 LYS Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain P residue 21 PHE Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 48 GLU Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 49 ILE Chi-restraints excluded: chain U residue 19 LYS Chi-restraints excluded: chain U residue 25 GLU Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 82 ARG Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 44 ARG Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain b residue 67 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 203 ARG Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain g residue 69 ILE Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 35 ARG Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 124 ARG Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain o residue 40 ASN Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain p residue 8 THR Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain t residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 900 optimal weight: 3.9990 chunk 685 optimal weight: 20.0000 chunk 473 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 435 optimal weight: 50.0000 chunk 612 optimal weight: 4.9990 chunk 914 optimal weight: 5.9990 chunk 968 optimal weight: 10.0000 chunk 477 optimal weight: 10.0000 chunk 867 optimal weight: 0.0370 chunk 261 optimal weight: 2.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 21 GLN 3 43 GLN ** 6 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 496 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 ASN G 147 ASN H 24 GLN H 136 GLN M 43 GLN N 14 GLN Q 28 ASN T 13 GLN ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 122 GLN ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 67 ASN h 18 ASN i 33 ASN ** i 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 150548 Z= 0.246 Angle : 0.678 13.087 224602 Z= 0.352 Chirality : 0.041 0.443 28677 Planarity : 0.005 0.147 12394 Dihedral : 23.803 179.785 73583 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.48 % Favored : 92.43 % Rotamer: Outliers : 4.74 % Allowed : 22.25 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.05 % 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: -3.11 (0.10), residues: 5825 helix: -2.05 (0.11), residues: 1774 sheet: -1.22 (0.15), residues: 1097 loop : -2.40 (0.10), residues: 2954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 93 HIS 0.008 0.001 HIS O 29 PHE 0.023 0.002 PHE V 6 TYR 0.019 0.001 TYR T 32 ARG 0.018 0.001 ARG M 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 653 time to evaluate : 6.265 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU K 136 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 18 ILE cc_start: 0.7921 (mm) cc_final: 0.7679 (pt) REVERT: 3 21 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7641 (mp-120) REVERT: 6 365 LEU cc_start: 0.5525 (OUTLIER) cc_final: 0.5274 (mt) REVERT: C 81 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8425 (mp) REVERT: C 167 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7527 (tptt) REVERT: C 183 MET cc_start: 0.7671 (mtm) cc_final: 0.7435 (mpp) REVERT: C 274 ARG cc_start: 0.7290 (ttm170) cc_final: 0.6857 (tpp-160) REVERT: D 103 GLN cc_start: 0.8200 (mt0) cc_final: 0.7977 (mt0) REVERT: D 216 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6449 (mptt) REVERT: I 1 MET cc_start: 0.7802 (mtm) cc_final: 0.7556 (mtt) REVERT: I 73 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7196 (m-30) REVERT: J 63 LYS cc_start: 0.5564 (mppt) cc_final: 0.4405 (pttp) REVERT: K 91 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7366 (mm-30) REVERT: L 85 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8644 (tp) REVERT: N 73 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: R 34 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7841 (m-40) REVERT: T 17 ASP cc_start: 0.7675 (p0) cc_final: 0.7360 (p0) REVERT: U 25 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6359 (mt-10) REVERT: U 47 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8035 (mtt-85) REVERT: U 57 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: U 82 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.5865 (ttm-80) REVERT: V 8 THR cc_start: 0.8527 (t) cc_final: 0.7987 (m) REVERT: W 30 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8087 (t80) REVERT: W 44 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7454 (ttp80) REVERT: b 122 GLU cc_start: 0.5535 (OUTLIER) cc_final: 0.5176 (pt0) REVERT: c 203 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.5788 (ppt-90) REVERT: e 128 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7238 (mt) REVERT: k 27 PHE cc_start: 0.8082 (m-80) cc_final: 0.7700 (m-10) REVERT: l 102 ASP cc_start: 0.7948 (m-30) cc_final: 0.7706 (m-30) REVERT: l 124 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6605 (ttt180) outliers start: 227 outliers final: 100 residues processed: 799 average time/residue: 2.0511 time to fit residues: 2355.2686 Evaluate side-chains 738 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 619 time to evaluate : 6.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 CYS Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 21 GLN Chi-restraints excluded: chain 4 residue 17 ILE Chi-restraints excluded: chain 6 residue 144 VAL Chi-restraints excluded: chain 6 residue 161 MET Chi-restraints excluded: chain 6 residue 162 ASP Chi-restraints excluded: chain 6 residue 290 SER Chi-restraints excluded: chain 6 residue 315 VAL Chi-restraints excluded: chain 6 residue 365 LEU Chi-restraints excluded: chain 6 residue 482 ILE Chi-restraints excluded: chain 6 residue 513 ASN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 131 PHE Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 73 GLU Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain O residue 19 LYS Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain P residue 21 PHE Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 48 GLU Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain Q residue 73 GLU Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain T residue 49 ILE Chi-restraints excluded: chain U residue 19 LYS Chi-restraints excluded: chain U residue 25 GLU Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain U residue 57 GLU Chi-restraints excluded: chain U residue 82 ARG Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain W residue 24 GLU Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 29 ARG Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 44 ARG Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 67 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 122 GLU Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 203 ARG Chi-restraints excluded: chain d residue 134 LYS Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 9 ASP Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 124 ARG Chi-restraints excluded: chain l residue 129 LEU Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 806 optimal weight: 5.9990 chunk 549 optimal weight: 0.0470 chunk 14 optimal weight: 0.8980 chunk 721 optimal weight: 9.9990 chunk 399 optimal weight: 6.9990 chunk 826 optimal weight: 30.0000 chunk 669 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 494 optimal weight: 0.7980 chunk 869 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 43 GLN ** 6 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 266 GLN 6 496 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 ASN G 147 ASN H 137 GLN ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 ASN T 13 GLN ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 135 GLN e 131 ASN ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 77 GLN i 62 ASN ** j 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 125 GLN o 40 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.209 150548 Z= 0.139 Angle : 0.606 14.580 224602 Z= 0.320 Chirality : 0.038 0.375 28677 Planarity : 0.005 0.144 12394 Dihedral : 23.784 179.980 73583 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.06 % Favored : 92.86 % Rotamer: Outliers : 4.32 % Allowed : 23.21 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.10), residues: 5825 helix: -1.61 (0.12), residues: 1765 sheet: -1.01 (0.15), residues: 1091 loop : -2.23 (0.10), residues: 2969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP p 60 HIS 0.006 0.001 HIS O 29 PHE 0.020 0.001 PHE V 6 TYR 0.019 0.001 TYR c 23 ARG 0.010 0.000 ARG h 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 631 time to evaluate : 6.195 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU K 136 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 18 ILE cc_start: 0.7882 (mm) cc_final: 0.7656 (pt) REVERT: C 81 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8404 (mp) REVERT: C 167 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7503 (tptt) REVERT: C 183 MET cc_start: 0.7647 (mtm) cc_final: 0.7367 (mpp) REVERT: C 274 ARG cc_start: 0.7266 (ttm170) cc_final: 0.6849 (tpp-160) REVERT: D 103 GLN cc_start: 0.8174 (mt0) cc_final: 0.7937 (mt0) REVERT: H 24 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7701 (mp10) REVERT: I 81 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7354 (pp20) REVERT: J 63 LYS cc_start: 0.5391 (mppt) cc_final: 0.4319 (pttp) REVERT: K 91 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7325 (mm-30) REVERT: M 17 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.6847 (mtm180) REVERT: N 114 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6791 (mp0) REVERT: Q 2 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7026 (mt-10) REVERT: R 34 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7704 (m-40) REVERT: T 17 ASP cc_start: 0.7629 (p0) cc_final: 0.7340 (p0) REVERT: U 82 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6118 (ttm-80) REVERT: V 8 THR cc_start: 0.8509 (t) cc_final: 0.7967 (m) REVERT: W 30 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.8156 (t80) REVERT: W 44 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7448 (ttp80) REVERT: b 122 GLU cc_start: 0.5558 (OUTLIER) cc_final: 0.5303 (pt0) REVERT: c 203 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.5756 (ppt-90) REVERT: e 128 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7152 (mt) REVERT: i 35 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7057 (mtm-85) REVERT: k 27 PHE cc_start: 0.8047 (m-80) cc_final: 0.7658 (m-10) REVERT: l 102 ASP cc_start: 0.7926 (m-30) cc_final: 0.7701 (m-30) REVERT: l 124 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6594 (ttt180) REVERT: l 130 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.7021 (m-80) outliers start: 207 outliers final: 102 residues processed: 767 average time/residue: 2.0871 time to fit residues: 2313.4331 Evaluate side-chains 732 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 613 time to evaluate : 6.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 CYS Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 4 residue 17 ILE Chi-restraints excluded: chain 6 residue 53 LEU Chi-restraints excluded: chain 6 residue 131 LEU Chi-restraints excluded: chain 6 residue 144 VAL Chi-restraints excluded: chain 6 residue 161 MET Chi-restraints excluded: chain 6 residue 201 THR Chi-restraints excluded: chain 6 residue 290 SER Chi-restraints excluded: chain 6 residue 315 VAL Chi-restraints excluded: chain 6 residue 364 LEU Chi-restraints excluded: chain 6 residue 442 VAL Chi-restraints excluded: chain 6 residue 482 ILE Chi-restraints excluded: chain 6 residue 488 ILE Chi-restraints excluded: chain 6 residue 513 ASN Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 24 GLN Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 104 ASN Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 131 PHE Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain M residue 17 ARG Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 19 LYS Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain P residue 21 PHE Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 2 GLU Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain Q residue 73 GLU Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 18 LEU Chi-restraints excluded: chain T residue 49 ILE Chi-restraints excluded: chain U residue 19 LYS Chi-restraints excluded: chain U residue 82 ARG Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain W residue 24 GLU Chi-restraints excluded: chain W residue 29 ARG Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 44 ARG Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 67 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 122 GLU Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 203 ARG Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 134 LYS Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain g residue 69 ILE Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 35 ARG Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 57 LYS Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 124 ARG Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain n residue 41 ARG Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain t residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 325 optimal weight: 10.0000 chunk 872 optimal weight: 20.0000 chunk 191 optimal weight: 6.9990 chunk 568 optimal weight: 0.9980 chunk 239 optimal weight: 6.9990 chunk 969 optimal weight: 30.0000 chunk 804 optimal weight: 9.9990 chunk 448 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 320 optimal weight: 7.9990 chunk 508 optimal weight: 0.9980 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 43 GLN 6 388 ASN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 ASN G 147 ASN H 137 GLN Q 28 ASN T 13 GLN c 135 GLN e 131 ASN ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 77 GLN h 18 ASN h 99 ASN i 62 ASN j 56 HIS l 125 GLN o 40 ASN t 24 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 150548 Z= 0.313 Angle : 0.731 13.331 224602 Z= 0.374 Chirality : 0.043 0.497 28677 Planarity : 0.006 0.146 12394 Dihedral : 23.769 179.831 73583 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.88 % Favored : 92.03 % Rotamer: Outliers : 4.80 % Allowed : 22.96 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.10), residues: 5825 helix: -1.45 (0.12), residues: 1776 sheet: -0.92 (0.15), residues: 1128 loop : -2.15 (0.10), residues: 2921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 250 HIS 0.009 0.001 HIS O 29 PHE 0.026 0.002 PHE 6 276 TYR 0.019 0.002 TYR O 32 ARG 0.010 0.001 ARG 2 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 626 time to evaluate : 6.205 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU K 136 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 18 ILE cc_start: 0.7947 (mm) cc_final: 0.7697 (pt) REVERT: 3 59 LYS cc_start: 0.7750 (tptm) cc_final: 0.7515 (tptp) REVERT: 6 4 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8279 (tp) REVERT: C 81 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8455 (mp) REVERT: C 183 MET cc_start: 0.7693 (mtm) cc_final: 0.7407 (mpp) REVERT: C 274 ARG cc_start: 0.7305 (ttm170) cc_final: 0.6865 (tpp-160) REVERT: D 103 GLN cc_start: 0.8185 (mt0) cc_final: 0.7957 (mt0) REVERT: G 116 LYS cc_start: 0.6291 (OUTLIER) cc_final: 0.5930 (pttp) REVERT: H 19 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8421 (mt) REVERT: I 1 MET cc_start: 0.7871 (mtm) cc_final: 0.7637 (mtt) REVERT: J 63 LYS cc_start: 0.5671 (OUTLIER) cc_final: 0.4498 (pttp) REVERT: K 91 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7380 (mm-30) REVERT: K 137 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.7005 (tp) REVERT: M 17 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.6853 (mtm180) REVERT: N 73 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7477 (mp0) REVERT: N 114 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: P 94 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6090 (tptt) REVERT: Q 2 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: R 34 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.7848 (m-40) REVERT: T 80 ASP cc_start: 0.7384 (t0) cc_final: 0.7079 (t0) REVERT: U 25 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6450 (mt-10) REVERT: U 47 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8030 (mtt-85) REVERT: U 49 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8469 (mmt180) REVERT: U 82 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6056 (ttm-80) REVERT: V 8 THR cc_start: 0.8535 (t) cc_final: 0.7991 (m) REVERT: V 33 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9003 (mp) REVERT: W 44 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7489 (ttp80) REVERT: c 203 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.5770 (ppt-90) REVERT: e 128 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7382 (mt) REVERT: k 27 PHE cc_start: 0.8056 (m-80) cc_final: 0.7646 (m-10) REVERT: l 102 ASP cc_start: 0.8041 (m-30) cc_final: 0.7817 (m-30) REVERT: l 130 TYR cc_start: 0.7554 (OUTLIER) cc_final: 0.6958 (m-80) outliers start: 230 outliers final: 125 residues processed: 774 average time/residue: 2.0249 time to fit residues: 2252.5735 Evaluate side-chains 746 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 600 time to evaluate : 6.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 CYS Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 4 residue 17 ILE Chi-restraints excluded: chain 6 residue 4 LEU Chi-restraints excluded: chain 6 residue 131 LEU Chi-restraints excluded: chain 6 residue 144 VAL Chi-restraints excluded: chain 6 residue 161 MET Chi-restraints excluded: chain 6 residue 162 ASP Chi-restraints excluded: chain 6 residue 201 THR Chi-restraints excluded: chain 6 residue 290 SER Chi-restraints excluded: chain 6 residue 315 VAL Chi-restraints excluded: chain 6 residue 364 LEU Chi-restraints excluded: chain 6 residue 442 VAL Chi-restraints excluded: chain 6 residue 482 ILE Chi-restraints excluded: chain 6 residue 513 ASN Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 63 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 104 ASN Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 131 PHE Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain M residue 17 ARG Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain N residue 11 THR Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 73 GLU Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 19 LYS Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain P residue 21 PHE Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 94 LYS Chi-restraints excluded: chain Q residue 2 GLU Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain Q residue 73 GLU Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 49 ILE Chi-restraints excluded: chain U residue 19 LYS Chi-restraints excluded: chain U residue 25 GLU Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain U residue 49 ARG Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 76 LYS Chi-restraints excluded: chain U residue 82 ARG Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain W residue 24 GLU Chi-restraints excluded: chain W residue 29 ARG Chi-restraints excluded: chain W residue 44 ARG Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 67 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 203 ARG Chi-restraints excluded: chain d residue 134 LYS Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain g residue 69 ILE Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 19 SER Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 129 LEU Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 934 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 552 optimal weight: 10.0000 chunk 707 optimal weight: 20.0000 chunk 548 optimal weight: 1.9990 chunk 816 optimal weight: 7.9990 chunk 541 optimal weight: 0.9980 chunk 965 optimal weight: 10.0000 chunk 604 optimal weight: 7.9990 chunk 588 optimal weight: 9.9990 chunk 445 optimal weight: 20.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 43 GLN 6 388 ASN D 33 ASN E 141 ASN G 106 ASN G 140 GLN G 147 ASN N 14 GLN Q 28 ASN Q 65 ASN T 13 GLN c 135 GLN e 131 ASN ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 77 GLN g 122 ASN i 62 ASN j 15 HIS l 85 HIS l 125 GLN s 22 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 150548 Z= 0.403 Angle : 0.815 14.206 224602 Z= 0.412 Chirality : 0.048 0.543 28677 Planarity : 0.006 0.147 12394 Dihedral : 23.836 179.748 73583 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.98 % Favored : 91.95 % Rotamer: Outliers : 5.45 % Allowed : 23.02 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.50 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.10), residues: 5825 helix: -1.36 (0.12), residues: 1776 sheet: -0.89 (0.15), residues: 1079 loop : -2.11 (0.10), residues: 2970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 93 HIS 0.010 0.002 HIS O 29 PHE 0.028 0.002 PHE 6 276 TYR 0.022 0.002 TYR R 68 ARG 0.016 0.001 ARG H 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 634 time to evaluate : 5.631 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU K 136 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 18 ILE cc_start: 0.7921 (mm) cc_final: 0.7683 (pt) REVERT: 6 4 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8258 (tt) REVERT: C 81 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8519 (mp) REVERT: C 183 MET cc_start: 0.7706 (mtm) cc_final: 0.7418 (mpp) REVERT: C 274 ARG cc_start: 0.7297 (ttm170) cc_final: 0.6836 (tpp-160) REVERT: D 97 ASP cc_start: 0.6015 (OUTLIER) cc_final: 0.5603 (p0) REVERT: G 116 LYS cc_start: 0.6341 (OUTLIER) cc_final: 0.5968 (pttp) REVERT: H 19 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8421 (mt) REVERT: I 1 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7609 (mtt) REVERT: J 63 LYS cc_start: 0.5714 (OUTLIER) cc_final: 0.4548 (pttp) REVERT: K 91 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7349 (mm-30) REVERT: K 134 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6624 (ttp-170) REVERT: K 137 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7108 (tp) REVERT: L 29 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7235 (ttp80) REVERT: L 85 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8628 (tp) REVERT: M 17 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.6953 (mtm180) REVERT: N 33 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7246 (mtp180) REVERT: N 114 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: R 32 ARG cc_start: 0.8331 (mtp-110) cc_final: 0.8107 (mtm110) REVERT: R 34 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.7854 (m-40) REVERT: T 17 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7472 (p0) REVERT: T 80 ASP cc_start: 0.7363 (t0) cc_final: 0.7075 (t0) REVERT: U 25 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6100 (mp0) REVERT: U 47 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8087 (mtt-85) REVERT: U 49 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8568 (mmt180) REVERT: U 79 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6771 (ttm110) REVERT: U 82 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.6049 (ttm-80) REVERT: V 8 THR cc_start: 0.8591 (t) cc_final: 0.8035 (m) REVERT: V 33 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9013 (mp) REVERT: W 5 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.6188 (tt0) REVERT: W 44 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7501 (ttp80) REVERT: c 203 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.5949 (ppt-90) REVERT: e 128 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7474 (mt) REVERT: k 27 PHE cc_start: 0.8117 (m-80) cc_final: 0.7724 (m-10) REVERT: l 102 ASP cc_start: 0.8072 (m-30) cc_final: 0.7853 (m-30) REVERT: l 129 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6965 (mp) REVERT: l 130 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.6907 (m-80) outliers start: 261 outliers final: 143 residues processed: 805 average time/residue: 2.0150 time to fit residues: 2337.7837 Evaluate side-chains 789 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 618 time to evaluate : 6.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 CYS Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 4 residue 17 ILE Chi-restraints excluded: chain 6 residue 4 LEU Chi-restraints excluded: chain 6 residue 123 HIS Chi-restraints excluded: chain 6 residue 131 LEU Chi-restraints excluded: chain 6 residue 144 VAL Chi-restraints excluded: chain 6 residue 161 MET Chi-restraints excluded: chain 6 residue 201 THR Chi-restraints excluded: chain 6 residue 288 GLU Chi-restraints excluded: chain 6 residue 290 SER Chi-restraints excluded: chain 6 residue 315 VAL Chi-restraints excluded: chain 6 residue 442 VAL Chi-restraints excluded: chain 6 residue 482 ILE Chi-restraints excluded: chain 6 residue 513 ASN Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 63 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 131 PHE Chi-restraints excluded: chain K residue 134 ARG Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 29 ARG Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain M residue 17 ARG Chi-restraints excluded: chain M residue 49 LYS Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain N residue 11 THR Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 33 ARG Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 19 LYS Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain P residue 21 PHE Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 65 GLN Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain Q residue 73 GLU Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 49 ILE Chi-restraints excluded: chain U residue 19 LYS Chi-restraints excluded: chain U residue 25 GLU Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain U residue 49 ARG Chi-restraints excluded: chain U residue 76 LYS Chi-restraints excluded: chain U residue 79 ARG Chi-restraints excluded: chain U residue 82 ARG Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 24 GLU Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 29 ARG Chi-restraints excluded: chain W residue 34 THR Chi-restraints excluded: chain W residue 44 ARG Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 67 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain c residue 168 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 203 ARG Chi-restraints excluded: chain d residue 134 LYS Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain g residue 69 ILE Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 77 LEU Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 19 SER Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 99 ARG Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 129 LEU Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain m residue 82 GLU Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 597 optimal weight: 6.9990 chunk 385 optimal weight: 5.9990 chunk 576 optimal weight: 2.9990 chunk 290 optimal weight: 10.0000 chunk 189 optimal weight: 7.9990 chunk 187 optimal weight: 6.9990 chunk 613 optimal weight: 0.9990 chunk 657 optimal weight: 20.0000 chunk 477 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 759 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 43 GLN 6 388 ASN C 82 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 ASN E 141 ASN G 65 HIS G 106 ASN G 140 GLN G 147 ASN H 137 GLN J 104 ASN N 14 GLN Q 28 ASN T 13 GLN c 135 GLN ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 77 GLN h 18 ASN i 62 ASN l 85 HIS s 22 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 150548 Z= 0.327 Angle : 0.751 13.728 224602 Z= 0.384 Chirality : 0.045 0.854 28677 Planarity : 0.006 0.148 12394 Dihedral : 23.806 179.938 73583 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.97 % Favored : 91.97 % Rotamer: Outliers : 5.06 % Allowed : 23.61 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.10), residues: 5825 helix: -1.21 (0.12), residues: 1776 sheet: -0.83 (0.15), residues: 1100 loop : -2.10 (0.10), residues: 2949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 93 HIS 0.012 0.001 HIS G 65 PHE 0.025 0.002 PHE 6 276 TYR 0.018 0.002 TYR O 32 ARG 0.012 0.001 ARG H 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 616 time to evaluate : 6.245 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU K 136 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 18 ILE cc_start: 0.7911 (mm) cc_final: 0.7697 (pt) REVERT: 6 4 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8245 (tt) REVERT: 6 201 THR cc_start: 0.7441 (OUTLIER) cc_final: 0.7199 (m) REVERT: C 183 MET cc_start: 0.7705 (mtm) cc_final: 0.7456 (mpp) REVERT: C 274 ARG cc_start: 0.7377 (ttm170) cc_final: 0.6890 (tpp-160) REVERT: G 116 LYS cc_start: 0.6326 (OUTLIER) cc_final: 0.5957 (pttp) REVERT: H 19 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8404 (mt) REVERT: I 1 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7563 (mtt) REVERT: I 110 ASN cc_start: 0.8201 (OUTLIER) cc_final: 0.7986 (t0) REVERT: J 63 LYS cc_start: 0.5645 (OUTLIER) cc_final: 0.4522 (pttp) REVERT: J 104 ASN cc_start: 0.4819 (OUTLIER) cc_final: 0.4103 (t0) REVERT: K 42 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8205 (mm) REVERT: K 91 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7398 (mm-30) REVERT: K 134 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6615 (ttp-170) REVERT: K 137 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7086 (tp) REVERT: L 29 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7225 (ttp80) REVERT: N 33 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7220 (mtp180) REVERT: N 114 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: R 32 ARG cc_start: 0.8289 (mtp-110) cc_final: 0.8072 (mtm110) REVERT: R 34 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.7834 (m-40) REVERT: T 80 ASP cc_start: 0.7383 (t0) cc_final: 0.7083 (t0) REVERT: U 25 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6065 (mp0) REVERT: U 47 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8029 (mtt-85) REVERT: U 49 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8519 (mmt180) REVERT: U 79 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6814 (ttm110) REVERT: U 82 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6009 (ttm-80) REVERT: V 8 THR cc_start: 0.8575 (t) cc_final: 0.8029 (m) REVERT: V 33 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9024 (mp) REVERT: W 5 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.6135 (tt0) REVERT: W 44 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7497 (ttp80) REVERT: c 203 ARG cc_start: 0.6810 (OUTLIER) cc_final: 0.5936 (ppt-90) REVERT: e 128 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7455 (mt) REVERT: k 27 PHE cc_start: 0.8109 (m-80) cc_final: 0.7717 (m-10) REVERT: l 102 ASP cc_start: 0.8067 (m-30) cc_final: 0.7844 (m-30) REVERT: l 129 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6947 (mp) REVERT: l 130 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.6807 (m-80) REVERT: s 22 GLN cc_start: 0.5775 (OUTLIER) cc_final: 0.5362 (pt0) outliers start: 242 outliers final: 149 residues processed: 777 average time/residue: 2.0285 time to fit residues: 2262.9795 Evaluate side-chains 788 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 611 time to evaluate : 6.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 CYS Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 4 residue 17 ILE Chi-restraints excluded: chain 6 residue 4 LEU Chi-restraints excluded: chain 6 residue 123 HIS Chi-restraints excluded: chain 6 residue 131 LEU Chi-restraints excluded: chain 6 residue 144 VAL Chi-restraints excluded: chain 6 residue 161 MET Chi-restraints excluded: chain 6 residue 201 THR Chi-restraints excluded: chain 6 residue 290 SER Chi-restraints excluded: chain 6 residue 315 VAL Chi-restraints excluded: chain 6 residue 442 VAL Chi-restraints excluded: chain 6 residue 482 ILE Chi-restraints excluded: chain 6 residue 513 ASN Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 200 LYS Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 110 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 63 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 104 ASN Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 131 PHE Chi-restraints excluded: chain K residue 134 ARG Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 29 ARG Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain M residue 49 LYS Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain N residue 11 THR Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 33 ARG Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 19 LYS Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 21 PHE Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 65 GLN Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain Q residue 73 GLU Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 49 ILE Chi-restraints excluded: chain U residue 19 LYS Chi-restraints excluded: chain U residue 25 GLU Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain U residue 49 ARG Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 76 LYS Chi-restraints excluded: chain U residue 79 ARG Chi-restraints excluded: chain U residue 82 ARG Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 7 VAL Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 24 GLU Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 29 ARG Chi-restraints excluded: chain W residue 34 THR Chi-restraints excluded: chain W residue 44 ARG Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 67 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain c residue 168 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 203 ARG Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 134 LYS Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain g residue 69 ILE Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 99 ARG Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 129 LEU Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 41 ARG Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 28 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 878 optimal weight: 10.0000 chunk 925 optimal weight: 20.0000 chunk 844 optimal weight: 9.9990 chunk 899 optimal weight: 20.0000 chunk 924 optimal weight: 20.0000 chunk 541 optimal weight: 2.9990 chunk 392 optimal weight: 0.8980 chunk 706 optimal weight: 20.0000 chunk 276 optimal weight: 6.9990 chunk 813 optimal weight: 6.9990 chunk 851 optimal weight: 7.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 43 GLN 6 388 ASN 6 430 GLN C 82 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN G 97 GLN G 106 ASN G 147 ASN H 137 GLN c 135 GLN ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 77 GLN h 18 ASN i 33 ASN i 62 ASN l 85 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 150548 Z= 0.362 Angle : 0.771 13.669 224602 Z= 0.393 Chirality : 0.046 0.523 28677 Planarity : 0.006 0.148 12394 Dihedral : 23.768 179.939 73583 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.10 % Favored : 91.83 % Rotamer: Outliers : 4.41 % Allowed : 24.34 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.10), residues: 5825 helix: -1.11 (0.12), residues: 1771 sheet: -0.83 (0.15), residues: 1118 loop : -2.06 (0.10), residues: 2936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 93 HIS 0.009 0.001 HIS O 29 PHE 0.027 0.002 PHE 6 276 TYR 0.020 0.002 TYR O 32 ARG 0.013 0.001 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 617 time to evaluate : 6.237 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU K 136 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 18 ILE cc_start: 0.7913 (mm) cc_final: 0.7681 (pt) REVERT: 6 4 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8236 (tt) REVERT: C 183 MET cc_start: 0.7709 (mtm) cc_final: 0.7447 (mpp) REVERT: C 274 ARG cc_start: 0.7349 (ttm170) cc_final: 0.6904 (tpp-160) REVERT: G 116 LYS cc_start: 0.6323 (OUTLIER) cc_final: 0.5981 (pttp) REVERT: H 19 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8380 (mt) REVERT: I 1 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7596 (mtt) REVERT: I 110 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7944 (t0) REVERT: J 63 LYS cc_start: 0.5679 (OUTLIER) cc_final: 0.4532 (pttp) REVERT: J 104 ASN cc_start: 0.5047 (OUTLIER) cc_final: 0.4367 (t0) REVERT: K 91 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7408 (mm-30) REVERT: K 137 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7057 (tp) REVERT: L 29 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7256 (ttp80) REVERT: N 33 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7220 (mtp180) REVERT: N 114 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: R 34 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.7853 (m-40) REVERT: T 13 GLN cc_start: 0.7259 (mm-40) cc_final: 0.6977 (tp40) REVERT: T 80 ASP cc_start: 0.7380 (t0) cc_final: 0.7084 (t0) REVERT: U 25 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6043 (mp0) REVERT: U 47 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8037 (mtt-85) REVERT: U 49 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8511 (mmt180) REVERT: U 79 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6842 (ttm110) REVERT: U 82 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6015 (ttm-80) REVERT: V 8 THR cc_start: 0.8584 (t) cc_final: 0.8040 (m) REVERT: V 33 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9002 (mp) REVERT: W 5 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.6136 (tt0) REVERT: W 44 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7495 (ttp80) REVERT: b 221 ILE cc_start: 0.4891 (OUTLIER) cc_final: 0.4685 (tp) REVERT: c 203 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.5917 (ppt-90) REVERT: e 128 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7478 (mt) REVERT: k 27 PHE cc_start: 0.8095 (m-80) cc_final: 0.7723 (m-10) REVERT: l 99 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6456 (ptm160) REVERT: l 102 ASP cc_start: 0.8051 (m-30) cc_final: 0.7835 (m-30) REVERT: l 129 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6964 (mp) REVERT: l 130 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.6790 (m-80) outliers start: 211 outliers final: 151 residues processed: 756 average time/residue: 2.0550 time to fit residues: 2239.6191 Evaluate side-chains 790 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 613 time to evaluate : 6.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 CYS Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 4 residue 17 ILE Chi-restraints excluded: chain 6 residue 4 LEU Chi-restraints excluded: chain 6 residue 123 HIS Chi-restraints excluded: chain 6 residue 131 LEU Chi-restraints excluded: chain 6 residue 144 VAL Chi-restraints excluded: chain 6 residue 161 MET Chi-restraints excluded: chain 6 residue 201 THR Chi-restraints excluded: chain 6 residue 290 SER Chi-restraints excluded: chain 6 residue 315 VAL Chi-restraints excluded: chain 6 residue 430 GLN Chi-restraints excluded: chain 6 residue 442 VAL Chi-restraints excluded: chain 6 residue 482 ILE Chi-restraints excluded: chain 6 residue 513 ASN Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 110 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 63 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 104 ASN Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 131 PHE Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 29 ARG Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain M residue 49 LYS Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain N residue 11 THR Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 33 ARG Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 19 LYS Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain P residue 21 PHE Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 65 GLN Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 77 LYS Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain Q residue 73 GLU Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 49 ILE Chi-restraints excluded: chain U residue 19 LYS Chi-restraints excluded: chain U residue 25 GLU Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain U residue 49 ARG Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 76 LYS Chi-restraints excluded: chain U residue 79 ARG Chi-restraints excluded: chain U residue 82 ARG Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 7 VAL Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 24 GLU Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 29 ARG Chi-restraints excluded: chain W residue 34 THR Chi-restraints excluded: chain W residue 44 ARG Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 67 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain c residue 168 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 203 ARG Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 134 LYS Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain g residue 69 ILE Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 71 GLU Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 99 ARG Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 129 LEU Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 41 ARG Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 28 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 896 optimal weight: 20.0000 chunk 590 optimal weight: 6.9990 chunk 951 optimal weight: 7.9990 chunk 580 optimal weight: 3.9990 chunk 451 optimal weight: 5.9990 chunk 661 optimal weight: 10.0000 chunk 998 optimal weight: 9.9990 chunk 918 optimal weight: 8.9990 chunk 794 optimal weight: 0.3980 chunk 82 optimal weight: 10.0000 chunk 614 optimal weight: 7.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 43 GLN 6 388 ASN C 82 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN G 106 ASN G 140 GLN G 147 ASN H 137 GLN J 104 ASN Q 28 ASN c 135 GLN ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 77 GLN h 18 ASN i 62 ASN l 85 HIS s 22 GLN t 24 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 150548 Z= 0.355 Angle : 0.765 14.489 224602 Z= 0.389 Chirality : 0.045 0.516 28677 Planarity : 0.006 0.148 12394 Dihedral : 23.751 179.767 73583 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.90 % Favored : 92.03 % Rotamer: Outliers : 4.16 % Allowed : 24.55 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.10), residues: 5825 helix: -1.02 (0.12), residues: 1772 sheet: -0.81 (0.15), residues: 1107 loop : -2.03 (0.10), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP O 61 HIS 0.009 0.001 HIS O 29 PHE 0.033 0.002 PHE f 76 TYR 0.020 0.002 TYR O 32 ARG 0.016 0.001 ARG H 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11650 Ramachandran restraints generated. 5825 Oldfield, 0 Emsley, 5825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 624 time to evaluate : 6.245 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU K 136 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 18 ILE cc_start: 0.7915 (mm) cc_final: 0.7686 (pt) REVERT: C 183 MET cc_start: 0.7708 (mtm) cc_final: 0.7446 (mpp) REVERT: C 274 ARG cc_start: 0.7343 (ttm170) cc_final: 0.6903 (tpp-160) REVERT: G 116 LYS cc_start: 0.6316 (OUTLIER) cc_final: 0.5966 (pttp) REVERT: H 19 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8388 (mp) REVERT: I 1 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7587 (mtt) REVERT: I 110 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7960 (t0) REVERT: J 63 LYS cc_start: 0.5673 (OUTLIER) cc_final: 0.4526 (pttp) REVERT: K 42 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8287 (mm) REVERT: K 91 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7386 (mm-30) REVERT: K 137 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7054 (tp) REVERT: L 29 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7256 (ttp80) REVERT: L 85 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8586 (tp) REVERT: N 114 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: R 32 ARG cc_start: 0.8267 (mtm-85) cc_final: 0.7988 (mtm180) REVERT: R 34 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.7830 (m-40) REVERT: T 13 GLN cc_start: 0.7311 (mm-40) cc_final: 0.6951 (tp40) REVERT: T 17 ASP cc_start: 0.7724 (p0) cc_final: 0.7301 (p0) REVERT: T 80 ASP cc_start: 0.7375 (t0) cc_final: 0.7082 (t0) REVERT: U 25 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6027 (mp0) REVERT: U 47 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8040 (mtt-85) REVERT: U 49 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8506 (mmt180) REVERT: U 79 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6824 (ttm110) REVERT: U 82 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6010 (ttm-80) REVERT: V 8 THR cc_start: 0.8580 (t) cc_final: 0.8038 (m) REVERT: V 33 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8998 (mp) REVERT: W 5 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.6200 (tt0) REVERT: W 44 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7489 (ttp80) REVERT: c 203 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.5916 (ppt-90) REVERT: e 128 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7471 (mt) REVERT: k 27 PHE cc_start: 0.8118 (m-80) cc_final: 0.7736 (m-10) REVERT: l 99 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6486 (ptm160) REVERT: l 102 ASP cc_start: 0.7948 (m-30) cc_final: 0.7743 (m-30) REVERT: l 129 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6954 (mp) REVERT: l 130 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.6781 (m-80) outliers start: 199 outliers final: 147 residues processed: 754 average time/residue: 2.0854 time to fit residues: 2259.0147 Evaluate side-chains 786 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 615 time to evaluate : 6.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 CYS Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 4 residue 17 ILE Chi-restraints excluded: chain 6 residue 123 HIS Chi-restraints excluded: chain 6 residue 131 LEU Chi-restraints excluded: chain 6 residue 144 VAL Chi-restraints excluded: chain 6 residue 161 MET Chi-restraints excluded: chain 6 residue 201 THR Chi-restraints excluded: chain 6 residue 290 SER Chi-restraints excluded: chain 6 residue 315 VAL Chi-restraints excluded: chain 6 residue 442 VAL Chi-restraints excluded: chain 6 residue 482 ILE Chi-restraints excluded: chain 6 residue 513 ASN Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 110 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 63 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 131 PHE Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 29 ARG Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain M residue 49 LYS Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain N residue 11 THR Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 19 LYS Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain P residue 21 PHE Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 65 GLN Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 77 LYS Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain Q residue 73 GLU Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 49 ILE Chi-restraints excluded: chain U residue 19 LYS Chi-restraints excluded: chain U residue 25 GLU Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain U residue 49 ARG Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 76 LYS Chi-restraints excluded: chain U residue 79 ARG Chi-restraints excluded: chain U residue 82 ARG Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 7 VAL Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 24 GLU Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 29 ARG Chi-restraints excluded: chain W residue 34 THR Chi-restraints excluded: chain W residue 44 ARG Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 67 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain c residue 168 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 203 ARG Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain g residue 69 ILE Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 71 GLU Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 99 ARG Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 129 LEU Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 41 ARG Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 28 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 487 optimal weight: 4.9990 chunk 631 optimal weight: 0.8980 chunk 846 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 chunk 732 optimal weight: 30.0000 chunk 117 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 chunk 796 optimal weight: 20.0000 chunk 333 optimal weight: 5.9990 chunk 817 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 43 GLN 6 388 ASN 6 430 GLN C 82 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN G 147 ASN H 137 GLN J 104 ASN c 135 GLN e 131 ASN ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 77 GLN g 122 ASN h 18 ASN i 62 ASN l 85 HIS t 24 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.159971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.135857 restraints weight = 158045.683| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 0.98 r_work: 0.3348 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 150548 Z= 0.302 Angle : 0.731 13.472 224602 Z= 0.375 Chirality : 0.043 0.501 28677 Planarity : 0.006 0.148 12394 Dihedral : 23.745 179.745 73583 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.97 % Favored : 91.97 % Rotamer: Outliers : 4.14 % Allowed : 24.82 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.10), residues: 5825 helix: -0.96 (0.12), residues: 1772 sheet: -0.80 (0.15), residues: 1107 loop : -2.01 (0.10), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP O 61 HIS 0.009 0.001 HIS O 29 PHE 0.025 0.002 PHE 6 276 TYR 0.020 0.002 TYR c 23 ARG 0.019 0.001 ARG G 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34664.73 seconds wall clock time: 603 minutes 26.07 seconds (36206.07 seconds total)