Starting phenix.real_space_refine on Wed Feb 14 10:32:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mux_9259/02_2024/6mux_9259.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mux_9259/02_2024/6mux_9259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mux_9259/02_2024/6mux_9259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mux_9259/02_2024/6mux_9259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mux_9259/02_2024/6mux_9259.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mux_9259/02_2024/6mux_9259.pdb" } resolution = 3.9 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= -0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 288 5.16 5 C 38497 2.51 5 N 10031 2.21 5 O 11468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 19": "OD1" <-> "OD2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 161": "OD1" <-> "OD2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 140": "OD1" <-> "OD2" Residue "B TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 150": "OD1" <-> "OD2" Residue "B ASP 166": "OD1" <-> "OD2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B ASP 229": "OD1" <-> "OD2" Residue "C ASP 41": "OD1" <-> "OD2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D ASP 105": "OD1" <-> "OD2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D ASP 230": "OD1" <-> "OD2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E ASP 62": "OD1" <-> "OD2" Residue "E ASP 72": "OD1" <-> "OD2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 190": "OD1" <-> "OD2" Residue "E ASP 210": "OD1" <-> "OD2" Residue "F ASP 7": "OD1" <-> "OD2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F ASP 68": "OD1" <-> "OD2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "F TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 18": "OD1" <-> "OD2" Residue "G TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 97": "OE1" <-> "OE2" Residue "G GLU 178": "OE1" <-> "OE2" Residue "G TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 186": "OD1" <-> "OD2" Residue "G ASP 191": "OD1" <-> "OD2" Residue "G PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 234": "OE1" <-> "OE2" Residue "H PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 22": "OE1" <-> "OE2" Residue "I GLU 64": "OE1" <-> "OE2" Residue "I TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 157": "OE1" <-> "OE2" Residue "I GLU 218": "OE1" <-> "OE2" Residue "J ASP 26": "OD1" <-> "OD2" Residue "J PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 157": "OE1" <-> "OE2" Residue "J GLU 178": "OE1" <-> "OE2" Residue "J GLU 199": "OE1" <-> "OE2" Residue "K ASP 2": "OD1" <-> "OD2" Residue "K PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 125": "OD1" <-> "OD2" Residue "K TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 17": "OD1" <-> "OD2" Residue "L TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 189": "OE1" <-> "OE2" Residue "M ASP 35": "OD1" <-> "OD2" Residue "M ASP 54": "OD1" <-> "OD2" Residue "M ASP 76": "OD1" <-> "OD2" Residue "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 142": "OD1" <-> "OD2" Residue "M TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 180": "NH1" <-> "NH2" Residue "M ASP 213": "OD1" <-> "OD2" Residue "N GLU 57": "OE1" <-> "OE2" Residue "N ASP 84": "OD1" <-> "OD2" Residue "N ARG 97": "NH1" <-> "NH2" Residue "N PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 107": "OD1" <-> "OD2" Residue "N ASP 128": "OD1" <-> "OD2" Residue "N TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 199": "OE1" <-> "OE2" Residue "N TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 19": "OD1" <-> "OD2" Residue "O GLU 26": "OE1" <-> "OE2" Residue "O ASP 68": "OD1" <-> "OD2" Residue "O TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 80": "OD1" <-> "OD2" Residue "O TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 199": "OE1" <-> "OE2" Residue "O GLU 248": "OE1" <-> "OE2" Residue "P GLU 70": "OE1" <-> "OE2" Residue "P TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 109": "OE1" <-> "OE2" Residue "P GLU 120": "OE1" <-> "OE2" Residue "P ASP 140": "OD1" <-> "OD2" Residue "P ASP 150": "OD1" <-> "OD2" Residue "P ASP 186": "OD1" <-> "OD2" Residue "P ASP 215": "OD1" <-> "OD2" Residue "Q ASP 41": "OD1" <-> "OD2" Residue "Q ASP 82": "OD1" <-> "OD2" Residue "Q TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 182": "OD1" <-> "OD2" Residue "Q GLU 203": "OE1" <-> "OE2" Residue "R TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 5": "NH1" <-> "NH2" Residue "R GLU 20": "OE1" <-> "OE2" Residue "R ASP 66": "OD1" <-> "OD2" Residue "R PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 211": "OE1" <-> "OE2" Residue "R GLU 218": "OE1" <-> "OE2" Residue "S GLU 95": "OE1" <-> "OE2" Residue "S ASP 122": "OD1" <-> "OD2" Residue "S PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 149": "OD1" <-> "OD2" Residue "S GLU 177": "OE1" <-> "OE2" Residue "S ASP 226": "OD1" <-> "OD2" Residue "T ASP 7": "OD1" <-> "OD2" Residue "T TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "T PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 179": "OE1" <-> "OE2" Residue "T GLU 184": "OE1" <-> "OE2" Residue "U ASP 18": "OD1" <-> "OD2" Residue "U PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 97": "OE1" <-> "OE2" Residue "U PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 183": "OD1" <-> "OD2" Residue "U TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 17": "OD1" <-> "OD2" Residue "V TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 51": "OD1" <-> "OD2" Residue "W GLU 64": "OE1" <-> "OE2" Residue "W TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 104": "OD1" <-> "OD2" Residue "W TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 166": "OD1" <-> "OD2" Residue "W GLU 215": "OE1" <-> "OE2" Residue "X PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 138": "OD1" <-> "OD2" Residue "X ASP 148": "OD1" <-> "OD2" Residue "X ASP 170": "OD1" <-> "OD2" Residue "X GLU 199": "OE1" <-> "OE2" Residue "Y ASP 18": "OD1" <-> "OD2" Residue "Y PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 99": "OE1" <-> "OE2" Residue "Y ASP 108": "OD1" <-> "OD2" Residue "Y TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 17": "OD1" <-> "OD2" Residue "Z GLU 36": "OE1" <-> "OE2" Residue "Z GLU 67": "OE1" <-> "OE2" Residue "Z TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 54": "OD1" <-> "OD2" Residue "a ASP 76": "OD1" <-> "OD2" Residue "a PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 142": "OD1" <-> "OD2" Residue "a TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 160": "OE1" <-> "OE2" Residue "a ASP 178": "OD1" <-> "OD2" Residue "a ARG 180": "NH1" <-> "NH2" Residue "a ASP 213": "OD1" <-> "OD2" Residue "b PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 60": "OD1" <-> "OD2" Residue "b ASP 84": "OD1" <-> "OD2" Residue "b ARG 97": "NH1" <-> "NH2" Residue "b TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 57": "OE1" <-> "OE2" Residue "c ASP 68": "OD1" <-> "OD2" Residue "c GLU 182": "OE1" <-> "OE2" Residue "c GLU 183": "OE1" <-> "OE2" Residue "c GLU 187": "OE1" <-> "OE2" Residue "c GLU 193": "OE1" <-> "OE2" Residue "c GLU 208": "OE1" <-> "OE2" Residue "c ASP 233": "OD1" <-> "OD2" Residue "c GLU 263": "OE1" <-> "OE2" Residue "d ASP 200": "OD1" <-> "OD2" Residue "d GLU 208": "OE1" <-> "OE2" Residue "d GLU 227": "OE1" <-> "OE2" Residue "d GLU 263": "OE1" <-> "OE2" Residue "e ASP 66": "OD1" <-> "OD2" Residue "e ASP 68": "OD1" <-> "OD2" Residue "e ASP 172": "OD1" <-> "OD2" Residue "e GLU 187": "OE1" <-> "OE2" Residue "e GLU 192": "OE1" <-> "OE2" Residue "e ASP 200": "OD1" <-> "OD2" Residue "e GLU 208": "OE1" <-> "OE2" Residue "e ASP 233": "OD1" <-> "OD2" Residue "e GLU 234": "OE1" <-> "OE2" Residue "f GLU 20": "OE1" <-> "OE2" Residue "f GLU 35": "OE1" <-> "OE2" Residue "f GLU 57": "OE1" <-> "OE2" Residue "f GLU 143": "OE1" <-> "OE2" Residue "f GLU 171": "OE1" <-> "OE2" Residue "f ASP 172": "OD1" <-> "OD2" Residue "f GLU 183": "OE1" <-> "OE2" Residue "f GLU 192": "OE1" <-> "OE2" Residue "f GLU 193": "OE1" <-> "OE2" Residue "f PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 200": "OD1" <-> "OD2" Residue "f GLU 208": "OE1" <-> "OE2" Residue "f GLU 234": "OE1" <-> "OE2" Residue "f ASP 256": "OD1" <-> "OD2" Residue "g GLU 20": "OE1" <-> "OE2" Residue "g ASP 28": "OD1" <-> "OD2" Residue "g GLU 35": "OE1" <-> "OE2" Residue "g ASP 68": "OD1" <-> "OD2" Residue "g ASP 172": "OD1" <-> "OD2" Residue "g GLU 182": "OE1" <-> "OE2" Residue "g GLU 193": "OE1" <-> "OE2" Residue "g ASP 233": "OD1" <-> "OD2" Residue "g GLU 236": "OE1" <-> "OE2" Residue "g GLU 263": "OE1" <-> "OE2" Residue "h GLU 20": "OE1" <-> "OE2" Residue "h GLU 154": "OE1" <-> "OE2" Residue "h GLU 182": "OE1" <-> "OE2" Residue "h GLU 183": "OE1" <-> "OE2" Residue "h ASP 200": "OD1" <-> "OD2" Residue "h ASP 224": "OD1" <-> "OD2" Residue "h GLU 234": "OE1" <-> "OE2" Residue "h GLU 236": "OE1" <-> "OE2" Residue "i GLU 20": "OE1" <-> "OE2" Residue "i GLU 35": "OE1" <-> "OE2" Residue "i GLU 171": "OE1" <-> "OE2" Residue "i GLU 187": "OE1" <-> "OE2" Residue "i GLU 208": "OE1" <-> "OE2" Residue "i GLU 227": "OE1" <-> "OE2" Residue "i ASP 233": "OD1" <-> "OD2" Residue "i ASP 246": "OD1" <-> "OD2" Residue "i ASP 256": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 60284 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1928 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 4, 'TRANS': 239} Chain breaks: 1 Chain: "B" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1782 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1918 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "D" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1795 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain: "E" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1760 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 1 Chain: "F" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1870 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 5, 'TRANS': 229} Chain: "G" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1906 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain breaks: 1 Chain: "H" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1547 Classifications: {'peptide': 194} Link IDs: {'TRANS': 193} Chain breaks: 1 Chain: "I" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1676 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain: "J" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1595 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 198} Chain breaks: 1 Chain: "K" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1614 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain: "L" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1600 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 1, 'TRANS': 202} Chain: "M" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1676 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 205} Chain: "N" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1845 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 4, 'TRANS': 219} Chain breaks: 1 Chain: "O" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1928 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 4, 'TRANS': 239} Chain breaks: 1 Chain: "P" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1826 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 7, 'TRANS': 221} Chain: "Q" Number of atoms: 1965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1965 Classifications: {'peptide': 245} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 239} Chain: "R" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1845 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 7, 'TRANS': 225} Chain: "S" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 5, 'TRANS': 222} Chain breaks: 1 Chain: "T" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1858 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain: "U" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1906 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain breaks: 1 Chain: "V" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1547 Classifications: {'peptide': 194} Link IDs: {'TRANS': 193} Chain breaks: 1 Chain: "W" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1676 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain: "X" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1595 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 198} Chain breaks: 1 Chain: "Y" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1614 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain: "Z" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1600 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 1, 'TRANS': 202} Chain: "a" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1676 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 205} Chain: "b" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1845 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 4, 'TRANS': 219} Chain breaks: 1 Chain: "c" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1578 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "d" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1595 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 1 Chain: "e" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1571 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain breaks: 1 Chain: "f" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1595 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 1 Chain: "g" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1595 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 1 Chain: "h" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1595 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 1 Chain: "i" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1595 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 1 Time building chain proxies: 22.99, per 1000 atoms: 0.38 Number of scatterers: 60284 At special positions: 0 Unit cell: (133.62, 142.79, 243.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 288 16.00 O 11468 8.00 N 10031 7.00 C 38497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.45 Conformation dependent library (CDL) restraints added in 7.9 seconds 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14156 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 73 sheets defined 43.4% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.60 Creating SS restraints... Processing helix chain 'A' and resid 23 through 33 removed outlier: 3.559A pdb=" N VAL A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 112 removed outlier: 3.789A pdb=" N SER A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 134 removed outlier: 3.878A pdb=" N TYR A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 133 " --> pdb=" O GLN A 129 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.815A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 220 removed outlier: 4.114A pdb=" N THR A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 254 removed outlier: 3.645A pdb=" N THR A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'B' and resid 19 through 27 Processing helix chain 'B' and resid 28 through 32 removed outlier: 4.075A pdb=" N SER B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 101 removed outlier: 3.840A pdb=" N LEU B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS B 88 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 119 removed outlier: 3.872A pdb=" N ILE B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 removed outlier: 3.507A pdb=" N GLN B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 119 through 124' Processing helix chain 'B' and resid 168 through 176 removed outlier: 3.668A pdb=" N LYS B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.657A pdb=" N HIS B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 removed outlier: 3.727A pdb=" N LYS B 228 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP B 229 " --> pdb=" O ASN B 225 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 28 removed outlier: 3.734A pdb=" N GLU C 22 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 102 removed outlier: 3.781A pdb=" N ASN C 84 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU C 92 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR C 93 " --> pdb=" O GLN C 89 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 109 Processing helix chain 'C' and resid 110 through 124 removed outlier: 4.025A pdb=" N ILE C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 178 removed outlier: 3.584A pdb=" N ALA C 171 " --> pdb=" O ASN C 167 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 199 removed outlier: 3.683A pdb=" N ALA C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 199 " --> pdb=" O THR C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 241 removed outlier: 3.935A pdb=" N GLU C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU C 234 " --> pdb=" O LYS C 230 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 238 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 23 removed outlier: 3.532A pdb=" N LEU D 23 " --> pdb=" O VAL D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.524A pdb=" N LYS D 27 " --> pdb=" O GLU D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 86 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.934A pdb=" N TYR D 95 " --> pdb=" O CYS D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 121 removed outlier: 3.569A pdb=" N HIS D 120 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 175 removed outlier: 3.525A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN D 175 " --> pdb=" O PHE D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 removed outlier: 3.554A pdb=" N ALA D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 200 removed outlier: 3.818A pdb=" N LEU D 199 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N SER D 200 " --> pdb=" O VAL D 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 200' Processing helix chain 'D' and resid 218 through 231 removed outlier: 3.573A pdb=" N ILE D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE D 229 " --> pdb=" O MET D 225 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP D 230 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 28 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 84 through 103 removed outlier: 4.104A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE E 89 " --> pdb=" O ALA E 85 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 94 " --> pdb=" O ASP E 90 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 117 removed outlier: 4.548A pdb=" N LEU E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 120 No H-bonds generated for 'chain 'E' and resid 118 through 120' Processing helix chain 'E' and resid 175 through 185 removed outlier: 4.457A pdb=" N LEU E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E 182 " --> pdb=" O GLY E 178 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU E 183 " --> pdb=" O ALA E 179 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN E 184 " --> pdb=" O GLU E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 207 removed outlier: 3.590A pdb=" N LEU E 199 " --> pdb=" O GLN E 195 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL E 203 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU E 204 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN E 206 " --> pdb=" O THR E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 242 removed outlier: 3.615A pdb=" N ASP E 242 " --> pdb=" O SER E 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 27 removed outlier: 3.913A pdb=" N ALA F 25 " --> pdb=" O GLN F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.634A pdb=" N GLN F 31 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY F 32 " --> pdb=" O ILE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 81 through 94 removed outlier: 3.511A pdb=" N MET F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLU F 91 " --> pdb=" O PHE F 87 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER F 94 " --> pdb=" O ASN F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 99 Processing helix chain 'F' and resid 104 through 118 removed outlier: 3.720A pdb=" N ARG F 110 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER F 111 " --> pdb=" O SER F 107 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP F 114 " --> pdb=" O ARG F 110 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS F 115 " --> pdb=" O SER F 111 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR F 116 " --> pdb=" O VAL F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 173 removed outlier: 3.648A pdb=" N SER F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR F 170 " --> pdb=" O ALA F 166 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS F 173 " --> pdb=" O THR F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 196 removed outlier: 3.658A pdb=" N ILE F 187 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU F 194 " --> pdb=" O CYS F 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 32 Processing helix chain 'G' and resid 54 through 59 removed outlier: 4.287A pdb=" N ASN G 58 " --> pdb=" O ASN G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 106 removed outlier: 3.502A pdb=" N ARG G 88 " --> pdb=" O ASP G 84 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE G 90 " --> pdb=" O ASP G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 123 removed outlier: 4.637A pdb=" N ASN G 116 " --> pdb=" O HIS G 112 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR G 121 " --> pdb=" O ARG G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 127 removed outlier: 3.874A pdb=" N LEU G 127 " --> pdb=" O ALA G 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 124 through 127' Processing helix chain 'G' and resid 175 through 180 removed outlier: 3.744A pdb=" N GLU G 180 " --> pdb=" O LYS G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 203 removed outlier: 3.851A pdb=" N ILE G 193 " --> pdb=" O VAL G 189 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE G 199 " --> pdb=" O ASP G 195 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU G 201 " --> pdb=" O TYR G 197 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR G 202 " --> pdb=" O LYS G 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 65 Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.539A pdb=" N ILE H 82 " --> pdb=" O GLU H 78 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR H 83 " --> pdb=" O GLY H 79 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP H 84 " --> pdb=" O GLU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 188 No H-bonds generated for 'chain 'H' and resid 186 through 188' Processing helix chain 'H' and resid 189 through 197 Processing helix chain 'H' and resid 202 through 217 removed outlier: 3.544A pdb=" N ASN H 208 " --> pdb=" O LYS H 204 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS H 215 " --> pdb=" O LEU H 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 52 Processing helix chain 'I' and resid 56 through 68 removed outlier: 3.567A pdb=" N HIS I 66 " --> pdb=" O ASN I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.568A pdb=" N CYS I 79 " --> pdb=" O ARG I 75 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG I 82 " --> pdb=" O MET I 78 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN I 85 " --> pdb=" O SER I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 141 removed outlier: 3.764A pdb=" N ALA I 134 " --> pdb=" O GLY I 130 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL I 137 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS I 141 " --> pdb=" O VAL I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 164 removed outlier: 4.377A pdb=" N LEU I 154 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY I 162 " --> pdb=" O ALA I 158 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE I 164 " --> pdb=" O CYS I 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 77 removed outlier: 3.943A pdb=" N THR J 64 " --> pdb=" O THR J 60 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU J 75 " --> pdb=" O TYR J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 100 removed outlier: 3.526A pdb=" N ASN J 91 " --> pdb=" O GLU J 87 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET J 92 " --> pdb=" O CYS J 88 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER J 94 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER J 95 " --> pdb=" O ASN J 91 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR J 98 " --> pdb=" O SER J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 161 removed outlier: 3.953A pdb=" N GLY J 161 " --> pdb=" O GLU J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 165 removed outlier: 3.763A pdb=" N SER J 165 " --> pdb=" O MET J 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 162 through 165' Processing helix chain 'J' and resid 172 through 190 removed outlier: 3.625A pdb=" N GLN J 182 " --> pdb=" O GLU J 178 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N CYS J 183 " --> pdb=" O THR J 179 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER J 186 " --> pdb=" O GLN J 182 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA J 187 " --> pdb=" O CYS J 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 72 removed outlier: 3.582A pdb=" N GLY K 58 " --> pdb=" O ARG K 54 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE K 61 " --> pdb=" O PHE K 57 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG K 62 " --> pdb=" O GLY K 58 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN K 64 " --> pdb=" O PHE K 60 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL K 65 " --> pdb=" O ILE K 61 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN K 72 " --> pdb=" O TYR K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 92 removed outlier: 4.154A pdb=" N PHE K 84 " --> pdb=" O SER K 80 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS K 87 " --> pdb=" O PHE K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 140 Processing helix chain 'K' and resid 141 through 146 removed outlier: 3.674A pdb=" N LYS K 145 " --> pdb=" O ALA K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 171 removed outlier: 3.549A pdb=" N LEU K 157 " --> pdb=" O VAL K 153 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP K 158 " --> pdb=" O ASP K 154 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU K 165 " --> pdb=" O LYS K 161 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU K 166 " --> pdb=" O LEU K 162 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS K 169 " --> pdb=" O GLU K 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 70 removed outlier: 3.502A pdb=" N GLY L 60 " --> pdb=" O GLU L 56 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS L 61 " --> pdb=" O LYS L 57 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU L 68 " --> pdb=" O LYS L 64 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN L 70 " --> pdb=" O TYR L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 89 removed outlier: 3.682A pdb=" N ILE L 82 " --> pdb=" O ALA L 78 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU L 83 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 94 removed outlier: 3.821A pdb=" N TYR L 93 " --> pdb=" O TYR L 90 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY L 94 " --> pdb=" O LYS L 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 90 through 94' Processing helix chain 'L' and resid 129 through 133 removed outlier: 3.862A pdb=" N SER L 132 " --> pdb=" O GLY L 129 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR L 133 " --> pdb=" O SER L 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 129 through 133' Processing helix chain 'L' and resid 134 through 139 removed outlier: 3.592A pdb=" N ILE L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU L 139 " --> pdb=" O ALA L 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 134 through 139' Processing helix chain 'L' and resid 140 through 142 No H-bonds generated for 'chain 'L' and resid 140 through 142' Processing helix chain 'L' and resid 148 through 167 removed outlier: 3.656A pdb=" N VAL L 153 " --> pdb=" O LEU L 149 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU L 154 " --> pdb=" O ASP L 150 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE L 160 " --> pdb=" O ALA L 156 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP L 167 " --> pdb=" O ALA L 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 108 removed outlier: 4.346A pdb=" N LEU M 92 " --> pdb=" O ASP M 88 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE M 103 " --> pdb=" O LYS M 99 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU M 105 " --> pdb=" O GLN M 101 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU M 106 " --> pdb=" O LEU M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 126 removed outlier: 4.592A pdb=" N ARG M 118 " --> pdb=" O HIS M 114 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL M 122 " --> pdb=" O ARG M 118 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR M 125 " --> pdb=" O CYS M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 178 Processing helix chain 'M' and resid 194 through 206 removed outlier: 3.830A pdb=" N ASN M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 213 removed outlier: 3.619A pdb=" N THR M 210 " --> pdb=" O ILE M 206 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU M 211 " --> pdb=" O THR M 207 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG M 212 " --> pdb=" O SER M 208 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 77 removed outlier: 3.925A pdb=" N TYR N 63 " --> pdb=" O ALA N 59 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS N 71 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN N 72 " --> pdb=" O LEU N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.505A pdb=" N MET N 85 " --> pdb=" O LYS N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 105 Processing helix chain 'N' and resid 179 through 183 removed outlier: 3.689A pdb=" N ARG N 182 " --> pdb=" O GLY N 179 " (cutoff:3.500A) Processing helix chain 'N' and resid 184 through 193 removed outlier: 3.568A pdb=" N LEU N 188 " --> pdb=" O PHE N 184 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP N 191 " --> pdb=" O THR N 187 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS N 192 " --> pdb=" O LEU N 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 210 Processing helix chain 'N' and resid 210 through 217 Processing helix chain 'O' and resid 24 through 34 Processing helix chain 'O' and resid 91 through 110 removed outlier: 3.845A pdb=" N GLU O 103 " --> pdb=" O LYS O 99 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU O 106 " --> pdb=" O SER O 102 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 134 removed outlier: 3.644A pdb=" N VAL O 130 " --> pdb=" O ASP O 126 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR O 131 " --> pdb=" O LYS O 127 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR O 132 " --> pdb=" O ILE O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 183 through 194 removed outlier: 3.689A pdb=" N LYS O 191 " --> pdb=" O ARG O 187 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG O 192 " --> pdb=" O LEU O 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 203 through 220 removed outlier: 3.701A pdb=" N THR O 209 " --> pdb=" O ILE O 205 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU O 211 " --> pdb=" O ASN O 207 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA O 215 " --> pdb=" O LEU O 211 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE O 219 " --> pdb=" O ALA O 215 " (cutoff:3.500A) Processing helix chain 'O' and resid 245 through 254 removed outlier: 3.594A pdb=" N ASN O 251 " --> pdb=" O LYS O 247 " (cutoff:3.500A) Processing helix chain 'O' and resid 255 through 257 No H-bonds generated for 'chain 'O' and resid 255 through 257' Processing helix chain 'P' and resid 19 through 31 removed outlier: 3.728A pdb=" N GLU P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL P 29 " --> pdb=" O ALA P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 83 Processing helix chain 'P' and resid 84 through 101 removed outlier: 4.066A pdb=" N ALA P 90 " --> pdb=" O LEU P 86 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER P 98 " --> pdb=" O ALA P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 124 removed outlier: 3.860A pdb=" N ILE P 113 " --> pdb=" O GLU P 109 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER P 116 " --> pdb=" O LYS P 112 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN P 119 " --> pdb=" O ALA P 115 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU P 120 " --> pdb=" O SER P 116 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE P 121 " --> pdb=" O ILE P 117 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR P 122 " --> pdb=" O VAL P 118 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN P 123 " --> pdb=" O GLN P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 171 removed outlier: 3.797A pdb=" N MET P 171 " --> pdb=" O TYR P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 171 through 176 removed outlier: 3.759A pdb=" N LYS P 176 " --> pdb=" O SER P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 199 removed outlier: 3.598A pdb=" N ILE P 188 " --> pdb=" O ILE P 184 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N HIS P 189 " --> pdb=" O GLU P 185 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR P 194 " --> pdb=" O THR P 190 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER P 198 " --> pdb=" O THR P 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 223 through 231 removed outlier: 4.072A pdb=" N ASP P 229 " --> pdb=" O ASN P 225 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR P 230 " --> pdb=" O GLU P 226 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 28 Processing helix chain 'Q' and resid 79 through 102 removed outlier: 3.746A pdb=" N ASN Q 84 " --> pdb=" O ASN Q 80 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU Q 86 " --> pdb=" O ASP Q 82 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN Q 88 " --> pdb=" O ASN Q 84 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR Q 97 " --> pdb=" O TYR Q 93 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU Q 98 " --> pdb=" O ALA Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 111 Processing helix chain 'Q' and resid 111 through 120 removed outlier: 3.679A pdb=" N ASP Q 116 " --> pdb=" O VAL Q 112 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE Q 117 " --> pdb=" O GLN Q 113 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS Q 118 " --> pdb=" O ILE Q 114 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 179 removed outlier: 3.940A pdb=" N LEU Q 175 " --> pdb=" O ALA Q 171 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS Q 176 " --> pdb=" O SER Q 172 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN Q 177 " --> pdb=" O SER Q 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 184 through 199 removed outlier: 3.501A pdb=" N LEU Q 190 " --> pdb=" O GLU Q 186 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU Q 191 " --> pdb=" O GLU Q 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 231 through 241 removed outlier: 3.835A pdb=" N GLN Q 241 " --> pdb=" O LYS Q 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 23 Processing helix chain 'R' and resid 78 through 86 removed outlier: 4.257A pdb=" N VAL R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU R 83 " --> pdb=" O ASP R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 98 removed outlier: 3.596A pdb=" N TYR R 94 " --> pdb=" O GLU R 90 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR R 95 " --> pdb=" O CYS R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 119 removed outlier: 3.576A pdb=" N THR R 119 " --> pdb=" O GLN R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 173 removed outlier: 3.819A pdb=" N PHE R 171 " --> pdb=" O ILE R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 190 Processing helix chain 'R' and resid 218 through 231 removed outlier: 3.710A pdb=" N LEU R 228 " --> pdb=" O SER R 224 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE R 229 " --> pdb=" O MET R 225 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP R 230 " --> pdb=" O VAL R 226 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN R 231 " --> pdb=" O GLU R 227 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 29 removed outlier: 3.538A pdb=" N ALA S 27 " --> pdb=" O GLN S 23 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 103 removed outlier: 3.590A pdb=" N ARG S 86 " --> pdb=" O MET S 82 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP S 90 " --> pdb=" O ARG S 86 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN S 97 " --> pdb=" O ARG S 93 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS S 100 " --> pdb=" O CYS S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 118 removed outlier: 3.848A pdb=" N GLU S 114 " --> pdb=" O LYS S 110 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE S 116 " --> pdb=" O CYS S 112 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU S 118 " --> pdb=" O GLU S 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 173 through 175 No H-bonds generated for 'chain 'S' and resid 173 through 175' Processing helix chain 'S' and resid 176 through 187 removed outlier: 3.718A pdb=" N GLU S 180 " --> pdb=" O GLN S 176 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU S 181 " --> pdb=" O GLU S 177 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU S 182 " --> pdb=" O GLY S 178 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU S 185 " --> pdb=" O LEU S 181 " (cutoff:3.500A) Processing helix chain 'S' and resid 192 through 207 removed outlier: 3.556A pdb=" N GLU S 197 " --> pdb=" O PHE S 193 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN S 206 " --> pdb=" O THR S 202 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL S 207 " --> pdb=" O VAL S 203 " (cutoff:3.500A) Processing helix chain 'S' and resid 233 through 238 removed outlier: 3.524A pdb=" N ILE S 237 " --> pdb=" O ASN S 233 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER S 238 " --> pdb=" O THR S 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 233 through 238' Processing helix chain 'T' and resid 19 through 27 removed outlier: 3.704A pdb=" N GLU T 23 " --> pdb=" O LEU T 19 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA T 25 " --> pdb=" O GLN T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 31 Processing helix chain 'T' and resid 77 through 80 Processing helix chain 'T' and resid 81 through 94 Processing helix chain 'T' and resid 94 through 99 removed outlier: 3.561A pdb=" N TYR T 99 " --> pdb=" O HIS T 95 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 118 removed outlier: 4.043A pdb=" N SER T 111 " --> pdb=" O SER T 107 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL T 112 " --> pdb=" O LEU T 108 " (cutoff:3.500A) Processing helix chain 'T' and resid 119 through 121 No H-bonds generated for 'chain 'T' and resid 119 through 121' Processing helix chain 'T' and resid 163 through 173 removed outlier: 4.248A pdb=" N THR T 169 " --> pdb=" O HIS T 165 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR T 170 " --> pdb=" O ALA T 166 " (cutoff:3.500A) Processing helix chain 'T' and resid 182 through 196 removed outlier: 4.137A pdb=" N LEU T 188 " --> pdb=" O GLU T 184 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU T 194 " --> pdb=" O CYS T 190 " (cutoff:3.500A) Processing helix chain 'T' and resid 198 through 202 Processing helix chain 'T' and resid 231 through 236 removed outlier: 3.644A pdb=" N VAL T 235 " --> pdb=" O TYR T 231 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS T 236 " --> pdb=" O LEU T 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 231 through 236' Processing helix chain 'U' and resid 26 through 30 Processing helix chain 'U' and resid 84 through 106 removed outlier: 3.936A pdb=" N ARG U 88 " --> pdb=" O ASP U 84 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASN U 89 " --> pdb=" O GLY U 85 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE U 90 " --> pdb=" O ASP U 86 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARG U 93 " --> pdb=" O ASN U 89 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER U 96 " --> pdb=" O ASP U 92 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR U 102 " --> pdb=" O ALA U 98 " (cutoff:3.500A) Processing helix chain 'U' and resid 110 through 124 removed outlier: 4.538A pdb=" N ASN U 116 " --> pdb=" O HIS U 112 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG U 117 " --> pdb=" O ILE U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 171 through 181 removed outlier: 3.562A pdb=" N LYS U 176 " --> pdb=" O LYS U 172 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR U 177 " --> pdb=" O GLU U 173 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS U 181 " --> pdb=" O THR U 177 " (cutoff:3.500A) Processing helix chain 'U' and resid 188 through 201 removed outlier: 3.612A pdb=" N ILE U 193 " --> pdb=" O VAL U 189 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLU U 194 " --> pdb=" O ARG U 190 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP U 195 " --> pdb=" O ASP U 191 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR U 197 " --> pdb=" O ILE U 193 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE U 199 " --> pdb=" O ASP U 195 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 68 removed outlier: 4.235A pdb=" N ILE V 55 " --> pdb=" O HIS V 51 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL V 64 " --> pdb=" O LYS V 60 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 87 removed outlier: 3.756A pdb=" N ILE V 82 " --> pdb=" O GLU V 78 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TYR V 83 " --> pdb=" O GLY V 79 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP V 84 " --> pdb=" O GLU V 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 186 through 188 No H-bonds generated for 'chain 'V' and resid 186 through 188' Processing helix chain 'V' and resid 189 through 197 removed outlier: 3.710A pdb=" N GLN V 194 " --> pdb=" O GLN V 190 " (cutoff:3.500A) Processing helix chain 'V' and resid 202 through 220 removed outlier: 3.632A pdb=" N ASN V 220 " --> pdb=" O TYR V 216 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 68 removed outlier: 3.670A pdb=" N GLN W 60 " --> pdb=" O THR W 56 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS W 66 " --> pdb=" O ASN W 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 89 removed outlier: 3.841A pdb=" N CYS W 79 " --> pdb=" O ARG W 75 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL W 80 " --> pdb=" O VAL W 76 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN W 85 " --> pdb=" O SER W 81 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS W 89 " --> pdb=" O GLN W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 140 removed outlier: 3.781A pdb=" N VAL W 137 " --> pdb=" O ASN W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 164 removed outlier: 3.852A pdb=" N ASN W 153 " --> pdb=" O GLU W 149 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL W 155 " --> pdb=" O GLY W 151 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY W 162 " --> pdb=" O ALA W 158 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 80 removed outlier: 3.682A pdb=" N GLN X 63 " --> pdb=" O ALA X 59 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR X 64 " --> pdb=" O THR X 60 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU X 75 " --> pdb=" O TYR X 71 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR X 76 " --> pdb=" O ARG X 72 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL X 78 " --> pdb=" O ASN X 74 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG X 79 " --> pdb=" O LEU X 75 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN X 80 " --> pdb=" O TYR X 76 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 100 removed outlier: 3.665A pdb=" N ASN X 91 " --> pdb=" O GLU X 87 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N MET X 92 " --> pdb=" O CYS X 88 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU X 93 " --> pdb=" O PHE X 89 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER X 94 " --> pdb=" O ALA X 90 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR X 98 " --> pdb=" O SER X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 156 through 161 removed outlier: 4.010A pdb=" N GLY X 161 " --> pdb=" O GLU X 157 " (cutoff:3.500A) Processing helix chain 'X' and resid 161 through 166 removed outlier: 3.895A pdb=" N SER X 165 " --> pdb=" O GLY X 161 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU X 166 " --> pdb=" O MET X 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 161 through 166' Processing helix chain 'X' and resid 172 through 189 removed outlier: 3.540A pdb=" N GLU X 178 " --> pdb=" O ASN X 174 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA X 187 " --> pdb=" O CYS X 183 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP X 189 " --> pdb=" O LEU X 185 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 67 removed outlier: 3.929A pdb=" N GLU Y 59 " --> pdb=" O LEU Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 72 removed outlier: 3.798A pdb=" N ASN Y 72 " --> pdb=" O TYR Y 68 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 92 removed outlier: 3.858A pdb=" N PHE Y 84 " --> pdb=" O SER Y 80 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS Y 87 " --> pdb=" O PHE Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 137 removed outlier: 3.694A pdb=" N TYR Y 137 " --> pdb=" O TYR Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 146 removed outlier: 3.674A pdb=" N LYS Y 145 " --> pdb=" O ALA Y 141 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 170 removed outlier: 3.601A pdb=" N ASP Y 158 " --> pdb=" O ASP Y 154 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU Y 166 " --> pdb=" O LEU Y 162 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 71 removed outlier: 3.638A pdb=" N LEU Z 53 " --> pdb=" O ALA Z 49 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N TRP Z 55 " --> pdb=" O ASP Z 51 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY Z 60 " --> pdb=" O GLU Z 56 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU Z 68 " --> pdb=" O LYS Z 64 " (cutoff:3.500A) Processing helix chain 'Z' and resid 75 through 86 removed outlier: 3.848A pdb=" N LEU Z 83 " --> pdb=" O ALA Z 79 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 143 removed outlier: 4.195A pdb=" N ALA Z 135 " --> pdb=" O GLY Z 131 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU Z 139 " --> pdb=" O ALA Z 135 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP Z 140 " --> pdb=" O TYR Z 136 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER Z 141 " --> pdb=" O SER Z 137 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA Z 142 " --> pdb=" O ILE Z 138 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 166 removed outlier: 3.929A pdb=" N GLU Z 154 " --> pdb=" O ASP Z 150 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU Z 155 " --> pdb=" O GLN Z 151 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA Z 163 " --> pdb=" O ALA Z 159 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG Z 166 " --> pdb=" O HIS Z 162 " (cutoff:3.500A) Processing helix chain 'a' and resid 86 through 91 removed outlier: 3.696A pdb=" N LYS a 90 " --> pdb=" O GLN a 86 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR a 91 " --> pdb=" O SER a 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 86 through 91' Processing helix chain 'a' and resid 91 through 105 removed outlier: 3.906A pdb=" N PHE a 103 " --> pdb=" O LYS a 99 " (cutoff:3.500A) Processing helix chain 'a' and resid 112 through 126 removed outlier: 4.408A pdb=" N ARG a 118 " --> pdb=" O HIS a 114 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 178 Proline residue: a 175 - end of helix Processing helix chain 'a' and resid 194 through 213 removed outlier: 4.000A pdb=" N ASN a 200 " --> pdb=" O GLY a 196 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP a 204 " --> pdb=" O ASN a 200 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR a 207 " --> pdb=" O LYS a 203 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA a 209 " --> pdb=" O ALA a 205 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU a 211 " --> pdb=" O THR a 207 " (cutoff:3.500A) Processing helix chain 'b' and resid 58 through 76 removed outlier: 4.332A pdb=" N TYR b 63 " --> pdb=" O ALA b 59 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU b 64 " --> pdb=" O ASP b 60 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS b 71 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN b 72 " --> pdb=" O LEU b 68 " (cutoff:3.500A) Processing helix chain 'b' and resid 81 through 85 removed outlier: 3.966A pdb=" N MET b 85 " --> pdb=" O LYS b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 87 through 104 removed outlier: 3.540A pdb=" N ASN b 104 " --> pdb=" O TYR b 100 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 183 removed outlier: 3.756A pdb=" N ARG b 182 " --> pdb=" O GLY b 179 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR b 183 " --> pdb=" O TYR b 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 179 through 183' Processing helix chain 'b' and resid 184 through 189 removed outlier: 3.586A pdb=" N LEU b 188 " --> pdb=" O PHE b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 198 through 217 removed outlier: 3.865A pdb=" N LEU b 205 " --> pdb=" O GLU b 201 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE b 212 " --> pdb=" O GLU b 208 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE b 215 " --> pdb=" O ARG b 211 " (cutoff:3.500A) Processing helix chain 'c' and resid 17 through 39 Processing helix chain 'c' and resid 39 through 52 removed outlier: 3.559A pdb=" N LEU c 51 " --> pdb=" O PHE c 47 " (cutoff:3.500A) Processing helix chain 'c' and resid 135 through 166 removed outlier: 3.717A pdb=" N LEU c 140 " --> pdb=" O LYS c 136 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN c 158 " --> pdb=" O GLU c 154 " (cutoff:3.500A) Processing helix chain 'c' and resid 175 through 219 removed outlier: 3.929A pdb=" N GLY c 179 " --> pdb=" O ASN c 175 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU c 198 " --> pdb=" O SER c 194 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR c 199 " --> pdb=" O ALA c 195 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP c 200 " --> pdb=" O PHE c 196 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL c 203 " --> pdb=" O TYR c 199 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR c 206 " --> pdb=" O ILE c 202 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU c 217 " --> pdb=" O SER c 213 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS c 218 " --> pdb=" O THR c 214 " (cutoff:3.500A) Processing helix chain 'c' and resid 223 through 261 Processing helix chain 'c' and resid 261 through 267 Processing helix chain 'd' and resid 17 through 39 removed outlier: 3.544A pdb=" N GLU d 21 " --> pdb=" O LYS d 17 " (cutoff:3.500A) Processing helix chain 'd' and resid 39 through 52 removed outlier: 3.645A pdb=" N ARG d 44 " --> pdb=" O ARG d 40 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU d 51 " --> pdb=" O PHE d 47 " (cutoff:3.500A) Processing helix chain 'd' and resid 135 through 166 Processing helix chain 'd' and resid 175 through 219 removed outlier: 3.905A pdb=" N GLY d 179 " --> pdb=" O ASN d 175 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR d 199 " --> pdb=" O ALA d 195 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP d 200 " --> pdb=" O PHE d 196 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL d 203 " --> pdb=" O TYR d 199 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU d 217 " --> pdb=" O SER d 213 " (cutoff:3.500A) Processing helix chain 'd' and resid 222 through 261 removed outlier: 4.135A pdb=" N GLN d 226 " --> pdb=" O VAL d 222 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP d 233 " --> pdb=" O VAL d 229 " (cutoff:3.500A) Processing helix chain 'd' and resid 261 through 267 removed outlier: 3.585A pdb=" N VAL d 266 " --> pdb=" O TRP d 262 " (cutoff:3.500A) Processing helix chain 'e' and resid 17 through 39 removed outlier: 3.754A pdb=" N THR e 30 " --> pdb=" O LYS e 26 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS e 31 " --> pdb=" O TYR e 27 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN e 32 " --> pdb=" O ASP e 28 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 52 removed outlier: 3.692A pdb=" N LEU e 51 " --> pdb=" O PHE e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 135 through 165 removed outlier: 3.543A pdb=" N LYS e 144 " --> pdb=" O LEU e 140 " (cutoff:3.500A) Processing helix chain 'e' and resid 175 through 219 removed outlier: 3.905A pdb=" N GLY e 179 " --> pdb=" O ASN e 175 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU e 198 " --> pdb=" O SER e 194 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR e 199 " --> pdb=" O ALA e 195 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP e 200 " --> pdb=" O PHE e 196 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL e 203 " --> pdb=" O TYR e 199 " (cutoff:3.500A) Processing helix chain 'e' and resid 222 through 261 removed outlier: 4.321A pdb=" N GLN e 226 " --> pdb=" O VAL e 222 " (cutoff:3.500A) Processing helix chain 'e' and resid 261 through 267 Processing helix chain 'f' and resid 17 through 39 Processing helix chain 'f' and resid 39 through 50 removed outlier: 3.622A pdb=" N ARG f 44 " --> pdb=" O ARG f 40 " (cutoff:3.500A) Processing helix chain 'f' and resid 135 through 166 removed outlier: 3.657A pdb=" N LEU f 140 " --> pdb=" O LYS f 136 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU f 141 " --> pdb=" O GLN f 137 " (cutoff:3.500A) Processing helix chain 'f' and resid 175 through 197 Processing helix chain 'f' and resid 197 through 219 removed outlier: 3.694A pdb=" N VAL f 203 " --> pdb=" O TYR f 199 " (cutoff:3.500A) Processing helix chain 'f' and resid 222 through 261 removed outlier: 4.045A pdb=" N GLN f 226 " --> pdb=" O VAL f 222 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG f 230 " --> pdb=" O GLN f 226 " (cutoff:3.500A) Processing helix chain 'f' and resid 261 through 267 removed outlier: 3.537A pdb=" N VAL f 266 " --> pdb=" O TRP f 262 " (cutoff:3.500A) Processing helix chain 'g' and resid 17 through 39 Processing helix chain 'g' and resid 39 through 52 Processing helix chain 'g' and resid 135 through 166 Processing helix chain 'g' and resid 175 through 197 Processing helix chain 'g' and resid 197 through 219 removed outlier: 3.736A pdb=" N VAL g 203 " --> pdb=" O TYR g 199 " (cutoff:3.500A) Processing helix chain 'g' and resid 222 through 261 removed outlier: 4.199A pdb=" N GLN g 226 " --> pdb=" O VAL g 222 " (cutoff:3.500A) Processing helix chain 'g' and resid 261 through 267 Processing helix chain 'h' and resid 17 through 39 Processing helix chain 'h' and resid 39 through 52 Processing helix chain 'h' and resid 135 through 166 removed outlier: 3.603A pdb=" N LYS h 144 " --> pdb=" O LEU h 140 " (cutoff:3.500A) Processing helix chain 'h' and resid 175 through 197 Processing helix chain 'h' and resid 197 through 219 removed outlier: 3.649A pdb=" N VAL h 203 " --> pdb=" O TYR h 199 " (cutoff:3.500A) Processing helix chain 'h' and resid 222 through 261 removed outlier: 4.054A pdb=" N GLN h 226 " --> pdb=" O VAL h 222 " (cutoff:3.500A) Processing helix chain 'h' and resid 261 through 267 Processing helix chain 'i' and resid 17 through 39 removed outlier: 3.546A pdb=" N ASN i 23 " --> pdb=" O LYS i 19 " (cutoff:3.500A) Processing helix chain 'i' and resid 39 through 52 removed outlier: 3.528A pdb=" N LEU i 51 " --> pdb=" O PHE i 47 " (cutoff:3.500A) Processing helix chain 'i' and resid 135 through 166 removed outlier: 3.538A pdb=" N TYR i 139 " --> pdb=" O HIS i 135 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU i 140 " --> pdb=" O LYS i 136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU i 141 " --> pdb=" O GLN i 137 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN i 158 " --> pdb=" O GLU i 154 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 219 removed outlier: 3.763A pdb=" N GLY i 179 " --> pdb=" O ASN i 175 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU i 198 " --> pdb=" O SER i 194 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR i 199 " --> pdb=" O ALA i 195 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP i 200 " --> pdb=" O PHE i 196 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL i 203 " --> pdb=" O TYR i 199 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS i 215 " --> pdb=" O LYS i 211 " (cutoff:3.500A) Processing helix chain 'i' and resid 223 through 261 removed outlier: 3.639A pdb=" N GLU i 227 " --> pdb=" O SER i 223 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS i 241 " --> pdb=" O TRP i 237 " (cutoff:3.500A) Processing helix chain 'i' and resid 261 through 267 Processing sheet with id=AA1, first strand: chain 'A' and resid 171 through 174 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 77 Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 77 removed outlier: 3.995A pdb=" N GLY A 148 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 160 through 162 removed outlier: 4.222A pdb=" N GLY B 43 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 69 removed outlier: 6.643A pdb=" N ILE B 72 " --> pdb=" O ILE B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 149 Processing sheet with id=AA7, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.546A pdb=" N GLY C 46 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA C 213 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 72 through 78 Processing sheet with id=AA9, first strand: chain 'D' and resid 158 through 161 removed outlier: 3.629A pdb=" N THR D 210 " --> pdb=" O ASP D 213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 63 through 64 removed outlier: 3.541A pdb=" N CYS D 70 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 132 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY D 135 " --> pdb=" O CYS D 143 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS D 143 " --> pdb=" O GLY D 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 169 through 172 removed outlier: 3.503A pdb=" N ALA E 221 " --> pdb=" O TYR E 230 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 68 through 69 removed outlier: 3.565A pdb=" N THR E 165 " --> pdb=" O TYR E 157 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 35 through 39 removed outlier: 5.016A pdb=" N GLY F 215 " --> pdb=" O PRO F 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 70 through 71 Processing sheet with id=AB6, first strand: chain 'G' and resid 46 through 51 removed outlier: 3.719A pdb=" N LEU G 38 " --> pdb=" O CYS G 49 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR G 36 " --> pdb=" O ILE G 51 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 70 through 71 removed outlier: 3.574A pdb=" N ILE G 139 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER G 142 " --> pdb=" O ASP G 150 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP G 150 " --> pdb=" O SER G 142 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE G 151 " --> pdb=" O TYR G 163 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR G 161 " --> pdb=" O CYS G 153 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 182 through 183 Processing sheet with id=AB9, first strand: chain 'H' and resid 34 through 36 removed outlier: 4.085A pdb=" N ALA H 150 " --> pdb=" O SER H 46 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 124 through 127 removed outlier: 3.577A pdb=" N ILE I 3 " --> pdb=" O LEU I 127 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU I 6 " --> pdb=" O ILE I 13 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE I 13 " --> pdb=" O LEU I 6 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 20 through 21 removed outlier: 7.129A pdb=" N ALA I 20 " --> pdb=" O ALA I 27 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 35 through 38 removed outlier: 3.632A pdb=" N ILE I 37 " --> pdb=" O ILE I 41 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA I 97 " --> pdb=" O ALA I 46 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS I 120 " --> pdb=" O GLY I 112 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 215 through 216 removed outlier: 6.424A pdb=" N CYS J 11 " --> pdb=" O ASP J 26 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 215 through 216 removed outlier: 4.315A pdb=" N ALA J 198 " --> pdb=" O LEU J 213 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 44 through 46 removed outlier: 3.852A pdb=" N LEU J 134 " --> pdb=" O THR J 146 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 129 through 130 removed outlier: 4.667A pdb=" N VAL K 13 " --> pdb=" O MET K 183 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 129 through 130 removed outlier: 4.667A pdb=" N VAL K 13 " --> pdb=" O MET K 183 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 20 through 22 removed outlier: 3.930A pdb=" N ASN K 30 " --> pdb=" O SER K 21 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 36 through 38 Processing sheet with id=AD2, first strand: chain 'L' and resid 13 through 16 removed outlier: 3.547A pdb=" N HIS L 178 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 20 through 21 removed outlier: 3.726A pdb=" N SER L 28 " --> pdb=" O ALA L 20 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 41 through 42 removed outlier: 3.696A pdb=" N SER L 102 " --> pdb=" O LEU L 42 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 164 through 167 removed outlier: 3.677A pdb=" N ALA M 53 " --> pdb=" O LEU M 221 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU M 221 " --> pdb=" O ALA M 53 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN M 233 " --> pdb=" O ILE M 222 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL M 224 " --> pdb=" O ASN M 231 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 57 through 58 removed outlier: 7.055A pdb=" N LEU M 57 " --> pdb=" O TYR M 64 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 71 through 75 removed outlier: 6.602A pdb=" N CYS M 78 " --> pdb=" O LEU M 74 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN M 136 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR M 152 " --> pdb=" O ASN M 136 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU M 149 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 175 through 177 removed outlier: 3.682A pdb=" N ILE N 15 " --> pdb=" O MET N 22 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY N 233 " --> pdb=" O THR N 230 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 29 through 30 Processing sheet with id=AE1, first strand: chain 'N' and resid 50 through 53 removed outlier: 3.767A pdb=" N ILE N 115 " --> pdb=" O GLY N 162 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE N 171 " --> pdb=" O PHE N 163 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 47 through 48 removed outlier: 3.837A pdb=" N CYS O 47 " --> pdb=" O GLY O 44 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 75 through 77 removed outlier: 3.522A pdb=" N GLY O 148 " --> pdb=" O GLU O 156 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 160 through 162 Processing sheet with id=AE5, first strand: chain 'P' and resid 65 through 67 Processing sheet with id=AE6, first strand: chain 'Q' and resid 34 through 37 Processing sheet with id=AE7, first strand: chain 'Q' and resid 72 through 78 removed outlier: 3.609A pdb=" N SER Q 133 " --> pdb=" O ALA Q 77 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 158 through 162 removed outlier: 3.648A pdb=" N CYS R 31 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU R 209 " --> pdb=" O ALA R 41 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR R 215 " --> pdb=" O LEU R 208 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 63 through 64 removed outlier: 3.619A pdb=" N LEU R 132 " --> pdb=" O ALA R 72 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR R 131 " --> pdb=" O THR R 147 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE R 144 " --> pdb=" O TRP R 156 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 169 through 172 removed outlier: 3.524A pdb=" N ILE S 172 " --> pdb=" O ALA S 37 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY S 45 " --> pdb=" O VAL S 42 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 67 through 69 removed outlier: 4.214A pdb=" N LEU S 155 " --> pdb=" O PHE S 167 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 35 through 39 Processing sheet with id=AF4, first strand: chain 'T' and resid 35 through 39 removed outlier: 3.596A pdb=" N ALA T 212 " --> pdb=" O VAL T 46 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL T 213 " --> pdb=" O GLN T 221 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'T' and resid 70 through 71 removed outlier: 3.541A pdb=" N LEU T 132 " --> pdb=" O THR T 146 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 165 through 166 removed outlier: 3.628A pdb=" N ILE U 47 " --> pdb=" O LEU U 40 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS U 50 " --> pdb=" O ASN U 217 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 69 through 71 removed outlier: 3.555A pdb=" N ILE U 139 " --> pdb=" O THR U 79 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER U 142 " --> pdb=" O ASP U 150 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP U 150 " --> pdb=" O SER U 142 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 182 through 183 Processing sheet with id=AF9, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.867A pdb=" N LEU V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 46 through 47 removed outlier: 3.931A pdb=" N ALA V 150 " --> pdb=" O SER V 46 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 124 through 127 Processing sheet with id=AG3, first strand: chain 'W' and resid 35 through 38 removed outlier: 6.659A pdb=" N ILE W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP W 42 " --> pdb=" O GLY W 101 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU W 100 " --> pdb=" O TYR W 111 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 215 through 216 removed outlier: 6.528A pdb=" N CYS X 11 " --> pdb=" O ASP X 26 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 44 through 46 removed outlier: 3.678A pdb=" N LEU X 134 " --> pdb=" O THR X 146 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS X 144 " --> pdb=" O ALA X 136 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 129 through 130 removed outlier: 4.347A pdb=" N VAL Y 13 " --> pdb=" O MET Y 183 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 129 through 130 removed outlier: 4.347A pdb=" N VAL Y 13 " --> pdb=" O MET Y 183 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 20 through 22 removed outlier: 4.073A pdb=" N ASN Y 30 " --> pdb=" O SER Y 21 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Y' and resid 36 through 38 Processing sheet with id=AH1, first strand: chain 'Z' and resid 13 through 17 Processing sheet with id=AH2, first strand: chain 'Z' and resid 20 through 22 removed outlier: 7.353A pdb=" N ALA Z 20 " --> pdb=" O SER Z 27 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 34 through 36 removed outlier: 3.600A pdb=" N ILE Z 35 " --> pdb=" O GLY Z 43 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Z' and resid 99 through 102 Processing sheet with id=AH5, first strand: chain 'a' and resid 164 through 167 removed outlier: 3.536A pdb=" N VAL a 166 " --> pdb=" O VAL a 40 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL a 49 " --> pdb=" O ILE a 225 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA a 53 " --> pdb=" O LEU a 221 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'a' and resid 57 through 58 Processing sheet with id=AH7, first strand: chain 'a' and resid 71 through 73 removed outlier: 3.606A pdb=" N ASN a 136 " --> pdb=" O TYR a 152 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY a 140 " --> pdb=" O VAL a 148 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN a 151 " --> pdb=" O CYS a 159 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS a 159 " --> pdb=" O ASN a 151 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'b' and resid 175 through 177 removed outlier: 4.037A pdb=" N GLY b 233 " --> pdb=" O THR b 230 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'b' and resid 29 through 30 Processing sheet with id=AI1, first strand: chain 'b' and resid 43 through 44 removed outlier: 3.516A pdb=" N ILE b 115 " --> pdb=" O GLY b 162 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE b 171 " --> pdb=" O PHE b 163 " (cutoff:3.500A) 2581 hydrogen bonds defined for protein. 7419 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.77 Time building geometry restraints manager: 20.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 15178 1.33 - 1.45: 12489 1.45 - 1.57: 33285 1.57 - 1.69: 0 1.69 - 1.82: 418 Bond restraints: 61370 Sorted by residual: bond pdb=" C LEU I 199 " pdb=" N PRO I 200 " ideal model delta sigma weight residual 1.334 1.446 -0.112 2.34e-02 1.83e+03 2.31e+01 bond pdb=" C LEU W 199 " pdb=" N PRO W 200 " ideal model delta sigma weight residual 1.334 1.441 -0.107 2.34e-02 1.83e+03 2.11e+01 bond pdb=" C GLU I 191 " pdb=" O GLU I 191 " ideal model delta sigma weight residual 1.235 1.218 0.017 4.70e-03 4.53e+04 1.25e+01 bond pdb=" CB PHE Z 8 " pdb=" CG PHE Z 8 " ideal model delta sigma weight residual 1.502 1.421 0.081 2.30e-02 1.89e+03 1.23e+01 bond pdb=" CD1 TYR T 152 " pdb=" CE1 TYR T 152 " ideal model delta sigma weight residual 1.382 1.298 0.084 3.00e-02 1.11e+03 7.80e+00 ... (remaining 61365 not shown) Histogram of bond angle deviations from ideal: 97.82 - 105.76: 885 105.76 - 113.71: 34234 113.71 - 121.65: 34023 121.65 - 129.60: 13401 129.60 - 137.55: 303 Bond angle restraints: 82846 Sorted by residual: angle pdb=" N ILE L 188 " pdb=" CA ILE L 188 " pdb=" C ILE L 188 " ideal model delta sigma weight residual 110.30 122.75 -12.45 9.70e-01 1.06e+00 1.65e+02 angle pdb=" C PRO W 200 " pdb=" N HIS W 201 " pdb=" CA HIS W 201 " ideal model delta sigma weight residual 121.61 134.40 -12.79 1.39e+00 5.18e-01 8.47e+01 angle pdb=" N ILE U 90 " pdb=" CA ILE U 90 " pdb=" C ILE U 90 " ideal model delta sigma weight residual 112.96 104.35 8.61 1.00e+00 1.00e+00 7.41e+01 angle pdb=" N GLY T 161 " pdb=" CA GLY T 161 " pdb=" C GLY T 161 " ideal model delta sigma weight residual 113.18 130.10 -16.92 2.37e+00 1.78e-01 5.10e+01 angle pdb=" C ILE G 232 " pdb=" N HIS G 233 " pdb=" CA HIS G 233 " ideal model delta sigma weight residual 121.54 135.08 -13.54 1.91e+00 2.74e-01 5.03e+01 ... (remaining 82841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 32535 17.92 - 35.84: 3698 35.84 - 53.76: 646 53.76 - 71.68: 120 71.68 - 89.60: 47 Dihedral angle restraints: 37046 sinusoidal: 14971 harmonic: 22075 Sorted by residual: dihedral pdb=" C THR C 216 " pdb=" N THR C 216 " pdb=" CA THR C 216 " pdb=" CB THR C 216 " ideal model delta harmonic sigma weight residual -122.00 -131.68 9.68 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" N ASN c 174 " pdb=" C ASN c 174 " pdb=" CA ASN c 174 " pdb=" CB ASN c 174 " ideal model delta harmonic sigma weight residual 122.80 131.45 -8.65 0 2.50e+00 1.60e-01 1.20e+01 dihedral pdb=" CA ASP L 17 " pdb=" CB ASP L 17 " pdb=" CG ASP L 17 " pdb=" OD1 ASP L 17 " ideal model delta sinusoidal sigma weight residual -30.00 -89.85 59.85 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 37043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 7863 0.089 - 0.177: 1256 0.177 - 0.266: 134 0.266 - 0.355: 22 0.355 - 0.444: 4 Chirality restraints: 9279 Sorted by residual: chirality pdb=" CB ILE F 206 " pdb=" CA ILE F 206 " pdb=" CG1 ILE F 206 " pdb=" CG2 ILE F 206 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" CB ILE O 72 " pdb=" CA ILE O 72 " pdb=" CG1 ILE O 72 " pdb=" CG2 ILE O 72 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CB VAL i 178 " pdb=" CA VAL i 178 " pdb=" CG1 VAL i 178 " pdb=" CG2 VAL i 178 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 9276 not shown) Planarity restraints: 10541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 165 " 0.050 2.00e-02 2.50e+03 2.89e-02 1.67e+01 pdb=" CG TYR H 165 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR H 165 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR H 165 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR H 165 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR H 165 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR H 165 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 165 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 150 " -0.061 5.00e-02 4.00e+02 9.26e-02 1.37e+01 pdb=" N PRO B 151 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO B 151 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 151 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY W 23 " -0.061 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO W 24 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO W 24 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO W 24 " -0.050 5.00e-02 4.00e+02 ... (remaining 10538 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 3040 2.70 - 3.25: 57239 3.25 - 3.80: 95979 3.80 - 4.35: 119056 4.35 - 4.90: 202185 Nonbonded interactions: 477499 Sorted by model distance: nonbonded pdb=" O VAL T 109 " pdb=" OH TYR T 152 " model vdw 2.149 2.440 nonbonded pdb=" O VAL F 109 " pdb=" OH TYR F 152 " model vdw 2.239 2.440 nonbonded pdb=" O ARG K 8 " pdb=" OH TYR K 147 " model vdw 2.248 2.440 nonbonded pdb=" OH TYR G 22 " pdb=" OE2 GLU h 171 " model vdw 2.258 2.440 nonbonded pdb=" O LYS g 211 " pdb=" OG1 THR g 214 " model vdw 2.260 2.440 ... (remaining 477494 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = (chain 'P' and resid 10 through 233) } ncs_group { reference = chain 'C' selection = (chain 'Q' and resid 7 through 246) } ncs_group { reference = chain 'D' selection = (chain 'R' and resid 8 through 234) } ncs_group { reference = (chain 'E' and resid 8 through 245) selection = (chain 'S' and (resid 8 through 123 or resid 136 through 245)) } ncs_group { reference = (chain 'F' and resid 3 through 236) selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } ncs_group { reference = (chain 'c' and resid 16 through 267) selection = (chain 'd' and resid 16 through 267) selection = chain 'e' selection = (chain 'f' and resid 16 through 267) selection = (chain 'g' and resid 16 through 267) selection = (chain 'h' and resid 16 through 267) selection = (chain 'i' and resid 16 through 267) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 10.810 Check model and map are aligned: 0.680 Set scattering table: 0.450 Process input model: 119.480 Find NCS groups from input model: 4.900 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 0.009 0.112 61370 Z= 0.554 Angle : 1.220 21.245 82846 Z= 0.686 Chirality : 0.066 0.444 9279 Planarity : 0.006 0.093 10541 Dihedral : 15.133 89.598 22890 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.96 % Favored : 88.87 % Rotamer: Outliers : 0.80 % Allowed : 11.06 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.08), residues: 7393 helix: -2.90 (0.07), residues: 2960 sheet: -3.39 (0.12), residues: 1297 loop : -3.02 (0.09), residues: 3136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP c 162 HIS 0.021 0.002 HIS O 12 PHE 0.053 0.003 PHE f 196 TYR 0.059 0.003 TYR H 165 ARG 0.011 0.001 ARG G 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1640 residues out of total 6648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1587 time to evaluate : 5.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASN cc_start: 0.9076 (m-40) cc_final: 0.8875 (m-40) REVERT: A 96 MET cc_start: 0.8861 (mmm) cc_final: 0.8586 (tpp) REVERT: A 150 ASP cc_start: 0.7494 (p0) cc_final: 0.6611 (p0) REVERT: A 154 LYS cc_start: 0.8168 (mtmt) cc_final: 0.7434 (pttm) REVERT: A 156 GLU cc_start: 0.7759 (mp0) cc_final: 0.7379 (mp0) REVERT: A 170 ARG cc_start: 0.8367 (ptp-170) cc_final: 0.8101 (ttp80) REVERT: B 49 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7308 (tm-30) REVERT: B 50 LYS cc_start: 0.6379 (tttt) cc_final: 0.6020 (ttpt) REVERT: B 119 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8419 (tm-30) REVERT: B 157 ASN cc_start: 0.8745 (t0) cc_final: 0.8431 (t0) REVERT: B 206 LYS cc_start: 0.7467 (mttm) cc_final: 0.6527 (mttm) REVERT: C 41 ASP cc_start: 0.7639 (t0) cc_final: 0.6843 (t0) REVERT: C 54 LYS cc_start: 0.7883 (mttp) cc_final: 0.7544 (tptt) REVERT: C 57 ASP cc_start: 0.8042 (t0) cc_final: 0.7054 (t0) REVERT: C 61 ASN cc_start: 0.7734 (t0) cc_final: 0.7494 (t0) REVERT: C 68 ILE cc_start: 0.9130 (mm) cc_final: 0.8926 (mm) REVERT: C 111 VAL cc_start: 0.9241 (m) cc_final: 0.8928 (t) REVERT: D 121 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7857 (ttm170) REVERT: D 212 LYS cc_start: 0.8094 (mttt) cc_final: 0.7456 (mtmt) REVERT: E 99 TYR cc_start: 0.8902 (t80) cc_final: 0.8529 (t80) REVERT: E 144 LEU cc_start: 0.8509 (tp) cc_final: 0.8296 (tp) REVERT: E 242 ASP cc_start: 0.7941 (p0) cc_final: 0.7724 (p0) REVERT: F 66 ILE cc_start: 0.9061 (mm) cc_final: 0.8627 (mm) REVERT: F 88 MET cc_start: 0.8963 (ttm) cc_final: 0.8543 (ttm) REVERT: F 106 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7911 (tm-30) REVERT: F 133 MET cc_start: 0.8490 (ttp) cc_final: 0.8174 (ttm) REVERT: F 158 LEU cc_start: 0.9455 (mt) cc_final: 0.8872 (mt) REVERT: F 190 CYS cc_start: 0.9033 (t) cc_final: 0.8603 (t) REVERT: G 46 ILE cc_start: 0.9142 (mm) cc_final: 0.8915 (mm) REVERT: G 151 ILE cc_start: 0.9422 (mt) cc_final: 0.9203 (mt) REVERT: G 232 ILE cc_start: 0.8411 (mp) cc_final: 0.7789 (mp) REVERT: H 17 ASP cc_start: 0.8183 (p0) cc_final: 0.7879 (p0) REVERT: H 80 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8413 (tm-30) REVERT: H 222 ASN cc_start: 0.8711 (m110) cc_final: 0.8208 (m-40) REVERT: I 17 ASP cc_start: 0.8712 (p0) cc_final: 0.8244 (p0) REVERT: I 51 ASP cc_start: 0.7863 (t0) cc_final: 0.7652 (t0) REVERT: I 66 HIS cc_start: 0.8538 (t-90) cc_final: 0.8249 (t-90) REVERT: J 84 MET cc_start: 0.8621 (ttt) cc_final: 0.8337 (ttt) REVERT: K 95 ARG cc_start: 0.7410 (mpp-170) cc_final: 0.7123 (mpt180) REVERT: K 162 LEU cc_start: 0.9307 (tp) cc_final: 0.9071 (tt) REVERT: K 166 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8826 (tm-30) REVERT: K 170 ARG cc_start: 0.8419 (mmt180) cc_final: 0.7532 (mmt180) REVERT: K 192 TYR cc_start: 0.7821 (p90) cc_final: 0.7271 (p90) REVERT: L 40 ASN cc_start: 0.8020 (t0) cc_final: 0.7740 (t0) REVERT: L 67 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7751 (mm-30) REVERT: L 69 ARG cc_start: 0.8708 (mtt180) cc_final: 0.8484 (mtt90) REVERT: M 30 TRP cc_start: 0.7434 (t-100) cc_final: 0.6575 (t-100) REVERT: M 114 HIS cc_start: 0.7782 (m-70) cc_final: 0.7518 (m-70) REVERT: N 113 ILE cc_start: 0.9571 (mm) cc_final: 0.9249 (mm) REVERT: N 166 MET cc_start: 0.8800 (ptp) cc_final: 0.8416 (ptp) REVERT: N 199 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7763 (tp30) REVERT: O 26 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8121 (mp0) REVERT: O 37 ILE cc_start: 0.9352 (mt) cc_final: 0.9058 (mm) REVERT: O 106 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8510 (tm-30) REVERT: O 170 ARG cc_start: 0.8665 (ptp-170) cc_final: 0.8252 (ttm110) REVERT: O 214 GLU cc_start: 0.8254 (pt0) cc_final: 0.7827 (pt0) REVERT: O 225 LYS cc_start: 0.8037 (mppt) cc_final: 0.7502 (mmmt) REVERT: P 21 GLN cc_start: 0.9081 (mm110) cc_final: 0.8552 (mm-40) REVERT: P 96 ARG cc_start: 0.7937 (ttm-80) cc_final: 0.7697 (ttp80) REVERT: P 109 GLU cc_start: 0.8779 (tm-30) cc_final: 0.7675 (tm-30) REVERT: P 119 GLN cc_start: 0.8786 (tp-100) cc_final: 0.8218 (tm-30) REVERT: Q 3 ARG cc_start: 0.7050 (pmt-80) cc_final: 0.6182 (ptm160) REVERT: Q 26 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7260 (tm-30) REVERT: Q 98 LEU cc_start: 0.9464 (tp) cc_final: 0.9258 (tt) REVERT: Q 187 GLU cc_start: 0.8561 (tt0) cc_final: 0.8333 (tp30) REVERT: Q 225 LYS cc_start: 0.7694 (mttp) cc_final: 0.7448 (mttm) REVERT: R 79 ASP cc_start: 0.8309 (m-30) cc_final: 0.7853 (m-30) REVERT: R 90 GLU cc_start: 0.8245 (tp30) cc_final: 0.8016 (tp30) REVERT: R 109 LYS cc_start: 0.8909 (ttmm) cc_final: 0.8519 (tmmt) REVERT: R 167 ILE cc_start: 0.9268 (tt) cc_final: 0.8975 (tt) REVERT: R 180 MET cc_start: 0.8336 (mpp) cc_final: 0.7840 (mpp) REVERT: S 71 ASP cc_start: 0.8335 (t70) cc_final: 0.7886 (t0) REVERT: S 176 GLN cc_start: 0.8160 (pp30) cc_final: 0.7794 (pp30) REVERT: S 205 ARG cc_start: 0.8506 (ttp80) cc_final: 0.8261 (ttm110) REVERT: T 7 ASP cc_start: 0.7545 (p0) cc_final: 0.7275 (p0) REVERT: T 42 ASP cc_start: 0.8611 (p0) cc_final: 0.8391 (p0) REVERT: T 74 MET cc_start: 0.8243 (ppp) cc_final: 0.8025 (ppp) REVERT: T 86 LYS cc_start: 0.8833 (ttmt) cc_final: 0.8562 (ttpt) REVERT: T 154 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7151 (tm-30) REVERT: T 190 CYS cc_start: 0.9256 (t) cc_final: 0.8903 (t) REVERT: U 71 HIS cc_start: 0.7933 (p-80) cc_final: 0.7526 (p-80) REVERT: U 86 ASP cc_start: 0.8146 (m-30) cc_final: 0.7786 (m-30) REVERT: U 131 MET cc_start: 0.8411 (mtt) cc_final: 0.8089 (mtp) REVERT: U 174 MET cc_start: 0.8076 (tpt) cc_final: 0.7875 (tpp) REVERT: V 13 MET cc_start: 0.8064 (mtp) cc_final: 0.7787 (mtp) REVERT: V 17 ASP cc_start: 0.8493 (p0) cc_final: 0.8131 (p0) REVERT: V 39 GLU cc_start: 0.7423 (tt0) cc_final: 0.7183 (tt0) REVERT: V 69 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7785 (mt-10) REVERT: V 80 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8545 (tm-30) REVERT: V 146 PHE cc_start: 0.5642 (m-80) cc_final: 0.5397 (t80) REVERT: V 156 TYR cc_start: 0.8551 (t80) cc_final: 0.8244 (t80) REVERT: V 221 ASP cc_start: 0.8334 (t0) cc_final: 0.7586 (t70) REVERT: V 248 MET cc_start: 0.6972 (mmm) cc_final: 0.6589 (mmm) REVERT: W 111 TYR cc_start: 0.8872 (m-80) cc_final: 0.8491 (m-80) REVERT: W 166 ASP cc_start: 0.8946 (t70) cc_final: 0.8689 (t0) REVERT: W 184 GLN cc_start: 0.7814 (mp10) cc_final: 0.7461 (mp10) REVERT: Y 29 LYS cc_start: 0.7615 (mmpt) cc_final: 0.7377 (mmmt) REVERT: Y 132 HIS cc_start: 0.8792 (m170) cc_final: 0.8563 (m170) REVERT: Y 134 TYR cc_start: 0.8985 (m-10) cc_final: 0.8504 (m-80) REVERT: Y 153 VAL cc_start: 0.9382 (t) cc_final: 0.9163 (t) REVERT: Y 192 TYR cc_start: 0.7690 (p90) cc_final: 0.7408 (p90) REVERT: Z 35 ILE cc_start: 0.9323 (mp) cc_final: 0.9056 (mt) REVERT: Z 115 ASP cc_start: 0.8596 (m-30) cc_final: 0.8321 (m-30) REVERT: a 30 TRP cc_start: 0.8528 (t-100) cc_final: 0.8133 (t-100) REVERT: a 143 GLU cc_start: 0.8750 (pp20) cc_final: 0.8309 (pm20) REVERT: a 182 GLU cc_start: 0.5803 (tt0) cc_final: 0.5102 (tm-30) REVERT: b 108 PRO cc_start: 0.9543 (Cg_endo) cc_final: 0.9255 (Cg_exo) REVERT: b 184 PHE cc_start: 0.8182 (m-80) cc_final: 0.7906 (m-80) REVERT: c 182 GLU cc_start: 0.8592 (mm-30) cc_final: 0.7877 (pt0) REVERT: c 192 GLU cc_start: 0.7167 (pp20) cc_final: 0.6917 (pp20) REVERT: c 207 MET cc_start: 0.8073 (mmm) cc_final: 0.7311 (tmm) REVERT: c 226 GLN cc_start: 0.7927 (mt0) cc_final: 0.7523 (mp10) REVERT: c 233 ASP cc_start: 0.9261 (m-30) cc_final: 0.8996 (m-30) REVERT: c 247 MET cc_start: 0.8162 (mmm) cc_final: 0.7796 (mmm) REVERT: c 262 TRP cc_start: 0.7695 (t-100) cc_final: 0.6698 (t60) REVERT: d 38 ARG cc_start: 0.6351 (mtt90) cc_final: 0.5211 (ptm-80) REVERT: d 162 TRP cc_start: 0.8683 (t60) cc_final: 0.8155 (t-100) REVERT: d 226 GLN cc_start: 0.7383 (tm-30) cc_final: 0.6946 (tm-30) REVERT: d 262 TRP cc_start: 0.7072 (t-100) cc_final: 0.6564 (t60) REVERT: e 142 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7267 (tt) REVERT: e 162 TRP cc_start: 0.8663 (t60) cc_final: 0.8317 (t60) REVERT: f 182 GLU cc_start: 0.6785 (mt-10) cc_final: 0.6466 (mt-10) REVERT: g 144 LYS cc_start: 0.7706 (mttt) cc_final: 0.7259 (ptpt) REVERT: g 182 GLU cc_start: 0.8328 (mm-30) cc_final: 0.6938 (tm-30) REVERT: g 250 ASN cc_start: 0.8661 (m110) cc_final: 0.8162 (m-40) REVERT: g 262 TRP cc_start: 0.8074 (t-100) cc_final: 0.7809 (t-100) REVERT: h 135 HIS cc_start: 0.6916 (t-90) cc_final: 0.6531 (t-90) REVERT: h 166 ASN cc_start: 0.7972 (OUTLIER) cc_final: 0.6533 (t0) REVERT: h 253 MET cc_start: 0.6915 (mtt) cc_final: 0.6695 (mtt) REVERT: i 164 GLN cc_start: 0.8109 (mt0) cc_final: 0.7820 (pt0) REVERT: i 207 MET cc_start: 0.8613 (tpp) cc_final: 0.8247 (mmm) REVERT: i 237 TRP cc_start: 0.8461 (t-100) cc_final: 0.7899 (t-100) REVERT: i 253 MET cc_start: 0.8676 (ttp) cc_final: 0.8399 (ttp) outliers start: 53 outliers final: 28 residues processed: 1629 average time/residue: 0.5847 time to fit residues: 1573.5388 Evaluate side-chains 1155 residues out of total 6648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1125 time to evaluate : 5.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain O residue 15 ILE Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain a residue 91 THR Chi-restraints excluded: chain a residue 235 LEU Chi-restraints excluded: chain c residue 64 VAL Chi-restraints excluded: chain e residue 142 LEU Chi-restraints excluded: chain h residue 166 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 736 random chunks: chunk 621 optimal weight: 1.9990 chunk 557 optimal weight: 1.9990 chunk 309 optimal weight: 0.9980 chunk 190 optimal weight: 0.9980 chunk 376 optimal weight: 0.9980 chunk 298 optimal weight: 0.8980 chunk 576 optimal weight: 0.5980 chunk 223 optimal weight: 0.9990 chunk 350 optimal weight: 3.9990 chunk 429 optimal weight: 2.9990 chunk 668 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS A 24 GLN A 71 ASN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN A 238 ASN B 21 GLN B 145 HIS C 29 ASN C 168 ASN D 120 HIS ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 GLN D 223 ASN E 23 GLN E 186 ASN E 195 GLN F 4 ASN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 HIS ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN G 171 ASN H 61 HIS ** H 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN I 133 ASN J 158 GLN J 171 GLN J 182 GLN K 69 GLN L 89 GLN L 162 HIS ** M 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 183 GLN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 ASN N 92 HIS N 125 ASN N 126 ASN N 167 HIS O 24 GLN ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 21 GLN P 67 GLN P 100 GLN P 123 GLN P 216 ASN ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 146 GLN R 77 ASN S 23 GLN S 97 ASN ** S 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 195 GLN T 60 GLN T 95 HIS T 100 ASN ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 165 HIS T 217 ASN U 64 ASN U 89 ASN ** U 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 231 ASN U 233 HIS ** V 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 168 ASN V 208 ASN ** V 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 232 ASN V 245 ASN W 71 ASN ** W 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 106 ASN X 6 ASN Y 40 HIS Y 69 GLN Y 73 ASN Y 123 ASN Z 29 GLN Z 85 ASN Z 158 ASN Z 162 HIS Z 178 HIS b 75 ASN b 92 HIS b 111 ASN c 158 ASN c 164 GLN c 197 ASN ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 55 ASN d 135 HIS d 158 ASN ** d 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 261 ASN e 239 HIS ** e 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 16 GLN f 65 ASN f 239 HIS g 49 ASN ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 158 ASN g 181 GLN g 221 ASN ** g 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 166 ASN h 181 GLN h 221 ASN ** i 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 50 ASN i 135 HIS i 164 GLN Total number of N/Q/H flips: 94 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 61370 Z= 0.203 Angle : 0.663 14.460 82846 Z= 0.352 Chirality : 0.044 0.254 9279 Planarity : 0.005 0.096 10541 Dihedral : 4.930 77.301 8240 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.17 % Favored : 93.82 % Rotamer: Outliers : 3.07 % Allowed : 17.82 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.09), residues: 7393 helix: -0.94 (0.09), residues: 3035 sheet: -2.84 (0.13), residues: 1277 loop : -2.81 (0.10), residues: 3081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP U 129 HIS 0.012 0.001 HIS D 120 PHE 0.029 0.002 PHE S 15 TYR 0.024 0.001 TYR U 80 ARG 0.006 0.001 ARG g 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1550 residues out of total 6648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1346 time to evaluate : 5.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7835 (tp30) cc_final: 0.7622 (tp30) REVERT: A 74 ASN cc_start: 0.9028 (m-40) cc_final: 0.8787 (m-40) REVERT: A 108 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8267 (tt) REVERT: A 150 ASP cc_start: 0.7570 (p0) cc_final: 0.7240 (p0) REVERT: A 154 LYS cc_start: 0.7703 (mtmt) cc_final: 0.7411 (pttp) REVERT: A 166 CYS cc_start: 0.7626 (p) cc_final: 0.7180 (p) REVERT: A 170 ARG cc_start: 0.8368 (ptp-170) cc_final: 0.8028 (ttp80) REVERT: B 49 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7188 (tm-30) REVERT: B 50 LYS cc_start: 0.6647 (tttt) cc_final: 0.6286 (ttpt) REVERT: B 79 MET cc_start: 0.8694 (mtm) cc_final: 0.8475 (mtp) REVERT: B 119 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8483 (tm-30) REVERT: B 157 ASN cc_start: 0.8299 (t0) cc_final: 0.7958 (t0) REVERT: C 41 ASP cc_start: 0.7759 (t0) cc_final: 0.7180 (t0) REVERT: C 54 LYS cc_start: 0.7788 (mttp) cc_final: 0.7445 (tptt) REVERT: C 61 ASN cc_start: 0.7673 (t0) cc_final: 0.7441 (t0) REVERT: C 186 GLU cc_start: 0.8587 (tp30) cc_final: 0.8181 (tp30) REVERT: D 93 ARG cc_start: 0.7776 (tmt170) cc_final: 0.7522 (tmt170) REVERT: D 117 LYS cc_start: 0.6211 (mttt) cc_final: 0.5677 (ttmt) REVERT: D 121 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7900 (ttm170) REVERT: D 180 MET cc_start: 0.8505 (mpp) cc_final: 0.7985 (mmm) REVERT: D 212 LYS cc_start: 0.8168 (mttt) cc_final: 0.7426 (mtmt) REVERT: E 193 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7979 (t80) REVERT: F 88 MET cc_start: 0.8868 (ttm) cc_final: 0.8414 (ttm) REVERT: F 106 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7578 (tm-30) REVERT: F 112 VAL cc_start: 0.9525 (OUTLIER) cc_final: 0.9253 (p) REVERT: F 133 MET cc_start: 0.8384 (ttp) cc_final: 0.8180 (ttp) REVERT: F 190 CYS cc_start: 0.9224 (t) cc_final: 0.8830 (t) REVERT: G 46 ILE cc_start: 0.9091 (mm) cc_final: 0.8867 (mm) REVERT: G 232 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7511 (mp) REVERT: H 165 TYR cc_start: 0.7432 (OUTLIER) cc_final: 0.6666 (p90) REVERT: H 222 ASN cc_start: 0.8694 (m110) cc_final: 0.7966 (m110) REVERT: I 17 ASP cc_start: 0.8608 (p0) cc_final: 0.8122 (p0) REVERT: I 51 ASP cc_start: 0.8058 (t0) cc_final: 0.7732 (t0) REVERT: I 59 LEU cc_start: 0.8772 (tp) cc_final: 0.8520 (tp) REVERT: I 66 HIS cc_start: 0.8502 (t-90) cc_final: 0.8226 (t-90) REVERT: I 174 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7939 (p0) REVERT: J 47 MET cc_start: 0.8690 (tpp) cc_final: 0.8034 (tpp) REVERT: J 84 MET cc_start: 0.8696 (ttt) cc_final: 0.8292 (ttt) REVERT: J 189 ASP cc_start: 0.8149 (t0) cc_final: 0.7783 (t0) REVERT: K 166 GLU cc_start: 0.9125 (tm-30) cc_final: 0.8760 (tm-30) REVERT: K 178 TYR cc_start: 0.8477 (m-80) cc_final: 0.8220 (m-80) REVERT: K 192 TYR cc_start: 0.7700 (p90) cc_final: 0.7282 (p90) REVERT: L 40 ASN cc_start: 0.7923 (t0) cc_final: 0.7660 (t0) REVERT: L 93 TYR cc_start: 0.7710 (m-80) cc_final: 0.7337 (m-80) REVERT: M 30 TRP cc_start: 0.7489 (t-100) cc_final: 0.6727 (t-100) REVERT: M 33 TYR cc_start: 0.8617 (m-10) cc_final: 0.8372 (m-10) REVERT: M 47 ASP cc_start: 0.8077 (p0) cc_final: 0.7802 (p0) REVERT: M 198 ASP cc_start: 0.8239 (m-30) cc_final: 0.7980 (m-30) REVERT: M 222 ILE cc_start: 0.9311 (mm) cc_final: 0.9047 (tp) REVERT: N 166 MET cc_start: 0.8716 (ptp) cc_final: 0.8346 (ptp) REVERT: O 37 ILE cc_start: 0.9234 (mt) cc_final: 0.9002 (mm) REVERT: O 106 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8111 (tm-30) REVERT: O 214 GLU cc_start: 0.8013 (pt0) cc_final: 0.7366 (pt0) REVERT: O 225 LYS cc_start: 0.7981 (mppt) cc_final: 0.7778 (mtmt) REVERT: P 96 ARG cc_start: 0.7808 (ttm-80) cc_final: 0.7524 (ttp80) REVERT: P 109 GLU cc_start: 0.8632 (tm-30) cc_final: 0.7557 (tm-30) REVERT: P 134 LEU cc_start: 0.8799 (mt) cc_final: 0.8559 (mt) REVERT: Q 3 ARG cc_start: 0.7084 (pmt-80) cc_final: 0.6034 (ptp-170) REVERT: Q 17 ARG cc_start: 0.7419 (ttp-110) cc_final: 0.7093 (ttp-110) REVERT: Q 26 GLU cc_start: 0.7307 (tm-30) cc_final: 0.7036 (tm-30) REVERT: Q 187 GLU cc_start: 0.8587 (tt0) cc_final: 0.8330 (tp30) REVERT: R 5 ARG cc_start: 0.8807 (ttp-110) cc_final: 0.8219 (ttp-170) REVERT: R 90 GLU cc_start: 0.8208 (tp30) cc_final: 0.7881 (tp30) REVERT: R 109 LYS cc_start: 0.8816 (ttmm) cc_final: 0.8330 (tmmt) REVERT: S 97 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8427 (t0) REVERT: S 206 GLN cc_start: 0.8443 (mm110) cc_final: 0.8228 (mp10) REVERT: T 7 ASP cc_start: 0.7595 (p0) cc_final: 0.7295 (p0) REVERT: T 20 TYR cc_start: 0.8764 (m-10) cc_final: 0.8183 (m-80) REVERT: T 24 TYR cc_start: 0.8884 (m-10) cc_final: 0.8619 (m-80) REVERT: T 86 LYS cc_start: 0.8650 (ttmt) cc_final: 0.8419 (ttpt) REVERT: T 116 TYR cc_start: 0.8971 (m-10) cc_final: 0.8425 (m-10) REVERT: T 154 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6753 (tm-30) REVERT: T 190 CYS cc_start: 0.9214 (t) cc_final: 0.8834 (t) REVERT: T 217 ASN cc_start: 0.8796 (m-40) cc_final: 0.8583 (m-40) REVERT: T 227 GLN cc_start: 0.8560 (tm-30) cc_final: 0.7915 (tm-30) REVERT: U 48 CYS cc_start: 0.8655 (m) cc_final: 0.8142 (m) REVERT: U 71 HIS cc_start: 0.7795 (p-80) cc_final: 0.7403 (p-80) REVERT: U 73 ASN cc_start: 0.7669 (p0) cc_final: 0.7419 (p0) REVERT: U 74 ASN cc_start: 0.7714 (p0) cc_final: 0.7475 (p0) REVERT: U 131 MET cc_start: 0.8319 (mtt) cc_final: 0.8101 (mtp) REVERT: V 13 MET cc_start: 0.7474 (mtp) cc_final: 0.7260 (mtp) REVERT: V 69 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7839 (mt-10) REVERT: V 80 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8306 (tm-30) REVERT: V 222 ASN cc_start: 0.8743 (m-40) cc_final: 0.8225 (m110) REVERT: V 247 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6996 (mm-40) REVERT: W 111 TYR cc_start: 0.8951 (m-80) cc_final: 0.8659 (m-80) REVERT: W 184 GLN cc_start: 0.7644 (mp10) cc_final: 0.7340 (mp10) REVERT: X 80 GLN cc_start: 0.8894 (mm110) cc_final: 0.8486 (mm110) REVERT: X 157 GLU cc_start: 0.8225 (tt0) cc_final: 0.8019 (tt0) REVERT: X 173 GLU cc_start: 0.8226 (tt0) cc_final: 0.8005 (tt0) REVERT: X 191 ASP cc_start: 0.7593 (m-30) cc_final: 0.7117 (m-30) REVERT: X 196 TRP cc_start: 0.6301 (t60) cc_final: 0.5712 (t60) REVERT: Y 134 TYR cc_start: 0.8899 (m-10) cc_final: 0.8327 (m-80) REVERT: Z 115 ASP cc_start: 0.8340 (m-30) cc_final: 0.8024 (m-30) REVERT: Z 125 LEU cc_start: 0.9202 (tp) cc_final: 0.8783 (tp) REVERT: Z 194 PHE cc_start: 0.5655 (OUTLIER) cc_final: 0.5375 (m-10) REVERT: a 30 TRP cc_start: 0.8378 (t-100) cc_final: 0.8143 (t-100) REVERT: a 143 GLU cc_start: 0.8712 (pp20) cc_final: 0.8350 (pm20) REVERT: a 182 GLU cc_start: 0.5982 (tt0) cc_final: 0.4859 (tm-30) REVERT: a 237 LEU cc_start: 0.8974 (mt) cc_final: 0.8654 (mt) REVERT: b 108 PRO cc_start: 0.9493 (Cg_endo) cc_final: 0.9249 (Cg_exo) REVERT: b 224 ILE cc_start: 0.9116 (mm) cc_final: 0.8790 (pt) REVERT: c 233 ASP cc_start: 0.9165 (m-30) cc_final: 0.8814 (m-30) REVERT: c 247 MET cc_start: 0.8168 (mmm) cc_final: 0.7483 (mmm) REVERT: c 253 MET cc_start: 0.8278 (tpp) cc_final: 0.7946 (mmt) REVERT: d 38 ARG cc_start: 0.6071 (mtt90) cc_final: 0.5151 (ptm-80) REVERT: d 44 ARG cc_start: 0.7964 (tpp80) cc_final: 0.7172 (mmm-85) REVERT: d 152 LEU cc_start: 0.7758 (tp) cc_final: 0.7069 (tp) REVERT: d 162 TRP cc_start: 0.8465 (t60) cc_final: 0.7991 (t60) REVERT: d 193 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7870 (tm-30) REVERT: d 247 MET cc_start: 0.7676 (mmp) cc_final: 0.7160 (mmm) REVERT: d 251 TYR cc_start: 0.7489 (m-80) cc_final: 0.7120 (m-80) REVERT: d 262 TRP cc_start: 0.6983 (t-100) cc_final: 0.6639 (t60) REVERT: e 162 TRP cc_start: 0.8590 (t60) cc_final: 0.8264 (t60) REVERT: e 204 LYS cc_start: 0.7789 (tptt) cc_final: 0.6713 (mmtt) REVERT: e 247 MET cc_start: 0.8138 (mmm) cc_final: 0.7842 (mmm) REVERT: f 48 PHE cc_start: 0.7538 (m-80) cc_final: 0.6986 (m-80) REVERT: g 182 GLU cc_start: 0.8282 (mm-30) cc_final: 0.6824 (tm-30) REVERT: g 250 ASN cc_start: 0.8821 (m110) cc_final: 0.8273 (m110) REVERT: g 253 MET cc_start: 0.8632 (ptp) cc_final: 0.8182 (ptp) REVERT: h 44 ARG cc_start: 0.5709 (OUTLIER) cc_final: 0.5409 (mtm-85) REVERT: h 47 PHE cc_start: 0.8570 (t80) cc_final: 0.8311 (t80) REVERT: h 135 HIS cc_start: 0.7272 (t-90) cc_final: 0.6566 (t-90) REVERT: h 230 ARG cc_start: 0.6195 (ttp80) cc_final: 0.5406 (ttm170) REVERT: h 246 ASP cc_start: 0.8345 (t70) cc_final: 0.7976 (t0) REVERT: h 250 ASN cc_start: 0.8442 (m110) cc_final: 0.7742 (m110) REVERT: i 164 GLN cc_start: 0.7978 (mt0) cc_final: 0.7570 (mt0) REVERT: i 237 TRP cc_start: 0.8511 (t-100) cc_final: 0.7445 (t-100) outliers start: 204 outliers final: 110 residues processed: 1472 average time/residue: 0.5588 time to fit residues: 1386.7649 Evaluate side-chains 1251 residues out of total 6648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1132 time to evaluate : 5.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain D residue 10 PHE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain E residue 154 CYS Chi-restraints excluded: chain E residue 193 PHE Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 77 HIS Chi-restraints excluded: chain H residue 165 TYR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 4 CYS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 148 HIS Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 166 VAL Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain O residue 77 ASN Chi-restraints excluded: chain O residue 136 TYR Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain P residue 181 ASP Chi-restraints excluded: chain Q residue 8 ARG Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain R residue 31 CYS Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain S residue 97 ASN Chi-restraints excluded: chain S residue 151 ASN Chi-restraints excluded: chain T residue 92 CYS Chi-restraints excluded: chain T residue 187 ILE Chi-restraints excluded: chain T residue 214 VAL Chi-restraints excluded: chain U residue 80 TYR Chi-restraints excluded: chain V residue 149 CYS Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 165 ASN Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 74 THR Chi-restraints excluded: chain Y residue 148 HIS Chi-restraints excluded: chain Y residue 157 LEU Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 193 VAL Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 91 THR Chi-restraints excluded: chain a residue 214 ILE Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 33 SER Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain c residue 64 VAL Chi-restraints excluded: chain c residue 160 LYS Chi-restraints excluded: chain c residue 180 ILE Chi-restraints excluded: chain c residue 229 VAL Chi-restraints excluded: chain d residue 135 HIS Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 172 ASP Chi-restraints excluded: chain e residue 165 LEU Chi-restraints excluded: chain g residue 66 ASP Chi-restraints excluded: chain g residue 239 HIS Chi-restraints excluded: chain h residue 44 ARG Chi-restraints excluded: chain h residue 53 ASN Chi-restraints excluded: chain h residue 188 LEU Chi-restraints excluded: chain i residue 180 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 736 random chunks: chunk 371 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 556 optimal weight: 0.6980 chunk 455 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 669 optimal weight: 20.0000 chunk 723 optimal weight: 5.9990 chunk 596 optimal weight: 2.9990 chunk 663 optimal weight: 6.9990 chunk 228 optimal weight: 0.9990 chunk 537 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 ASN C 168 ASN D 120 HIS ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN F 21 GLN F 117 GLN ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 GLN J 158 GLN K 69 GLN K 177 ASN L 89 GLN L 180 HIS M 93 HIS ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 67 GLN P 100 GLN P 123 GLN ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 80 ASN Q 89 GLN Q 113 GLN S 97 ASN T 100 ASN ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 165 HIS ** U 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 231 ASN U 233 HIS ** V 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 168 ASN ** V 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 245 ASN ** W 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 150 ASN Z 158 ASN ** b 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 197 ASN c 239 HIS ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 135 HIS d 158 ASN ** d 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 239 HIS e 261 ASN f 16 GLN ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 164 GLN ** i 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 270 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 61370 Z= 0.252 Angle : 0.632 13.853 82846 Z= 0.333 Chirality : 0.044 0.214 9279 Planarity : 0.004 0.087 10541 Dihedral : 4.858 80.101 8228 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.39 % Favored : 92.60 % Rotamer: Outliers : 4.23 % Allowed : 19.98 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.09), residues: 7393 helix: -0.20 (0.09), residues: 3016 sheet: -2.53 (0.13), residues: 1268 loop : -2.60 (0.10), residues: 3109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 58 HIS 0.016 0.001 HIS d 135 PHE 0.026 0.002 PHE E 123 TYR 0.039 0.001 TYR e 148 ARG 0.008 0.000 ARG U 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1491 residues out of total 6648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1210 time to evaluate : 5.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8265 (tt) REVERT: A 122 ARG cc_start: 0.7667 (mtt-85) cc_final: 0.7010 (mtt90) REVERT: A 150 ASP cc_start: 0.8111 (p0) cc_final: 0.7049 (p0) REVERT: A 154 LYS cc_start: 0.8245 (mtmt) cc_final: 0.7322 (pttm) REVERT: A 166 CYS cc_start: 0.7716 (p) cc_final: 0.7271 (p) REVERT: A 170 ARG cc_start: 0.8368 (ptp-170) cc_final: 0.8060 (ttp80) REVERT: B 49 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7249 (tm-30) REVERT: B 50 LYS cc_start: 0.6705 (tttt) cc_final: 0.6290 (ttpt) REVERT: B 79 MET cc_start: 0.8721 (mtm) cc_final: 0.8474 (mtp) REVERT: B 109 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8149 (mm-30) REVERT: B 119 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8510 (tm-30) REVERT: B 157 ASN cc_start: 0.8441 (t0) cc_final: 0.8036 (t0) REVERT: B 224 GLN cc_start: 0.7576 (mm-40) cc_final: 0.7375 (tp-100) REVERT: C 41 ASP cc_start: 0.7922 (t0) cc_final: 0.7595 (t0) REVERT: C 54 LYS cc_start: 0.7800 (mttp) cc_final: 0.7418 (tptt) REVERT: C 61 ASN cc_start: 0.7683 (t0) cc_final: 0.7474 (t0) REVERT: C 186 GLU cc_start: 0.8546 (tp30) cc_final: 0.8279 (tp30) REVERT: D 66 ASP cc_start: 0.7466 (t0) cc_final: 0.7230 (t0) REVERT: D 117 LYS cc_start: 0.6317 (mttt) cc_final: 0.5864 (ttmt) REVERT: D 121 ARG cc_start: 0.8276 (ttm170) cc_final: 0.7983 (ttm170) REVERT: D 212 LYS cc_start: 0.8154 (mttt) cc_final: 0.7434 (mtmt) REVERT: D 225 MET cc_start: 0.8744 (tpt) cc_final: 0.8347 (tpt) REVERT: E 176 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8059 (pp30) REVERT: E 193 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8011 (t80) REVERT: E 239 ARG cc_start: 0.8688 (tmt170) cc_final: 0.8351 (tmt170) REVERT: F 88 MET cc_start: 0.8843 (ttm) cc_final: 0.8336 (ttm) REVERT: F 106 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7485 (tm-30) REVERT: F 112 VAL cc_start: 0.9573 (OUTLIER) cc_final: 0.9285 (p) REVERT: F 118 LYS cc_start: 0.9061 (mttt) cc_final: 0.8031 (ttpt) REVERT: F 190 CYS cc_start: 0.9203 (t) cc_final: 0.8829 (t) REVERT: G 232 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7634 (mp) REVERT: H 219 HIS cc_start: 0.8178 (t70) cc_final: 0.7942 (t-170) REVERT: H 222 ASN cc_start: 0.8712 (m110) cc_final: 0.8038 (m110) REVERT: I 17 ASP cc_start: 0.8739 (p0) cc_final: 0.8321 (p0) REVERT: I 51 ASP cc_start: 0.8010 (t0) cc_final: 0.7571 (t70) REVERT: I 174 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8021 (p0) REVERT: I 181 ASP cc_start: 0.8270 (p0) cc_final: 0.8022 (p0) REVERT: J 44 ILE cc_start: 0.9078 (pt) cc_final: 0.8815 (pt) REVERT: J 47 MET cc_start: 0.8762 (tpp) cc_final: 0.8099 (tpp) REVERT: J 84 MET cc_start: 0.8755 (ttt) cc_final: 0.8272 (ttt) REVERT: J 182 GLN cc_start: 0.8049 (mm110) cc_final: 0.7763 (mm110) REVERT: J 189 ASP cc_start: 0.8196 (t0) cc_final: 0.7838 (t0) REVERT: K 76 MET cc_start: 0.8175 (ttt) cc_final: 0.7962 (ttt) REVERT: K 80 SER cc_start: 0.9037 (OUTLIER) cc_final: 0.8406 (t) REVERT: K 166 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8921 (tm-30) REVERT: K 192 TYR cc_start: 0.7762 (p90) cc_final: 0.7300 (p90) REVERT: L 40 ASN cc_start: 0.8055 (t0) cc_final: 0.7719 (t0) REVERT: L 93 TYR cc_start: 0.7736 (m-80) cc_final: 0.7328 (m-80) REVERT: M 30 TRP cc_start: 0.7397 (t-100) cc_final: 0.6601 (t-100) REVERT: M 33 TYR cc_start: 0.8736 (m-10) cc_final: 0.8435 (m-10) REVERT: M 47 ASP cc_start: 0.8171 (p0) cc_final: 0.7857 (p0) REVERT: M 152 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.7442 (p90) REVERT: M 171 GLN cc_start: 0.8492 (mt0) cc_final: 0.7292 (mt0) REVERT: M 198 ASP cc_start: 0.8283 (m-30) cc_final: 0.8030 (m-30) REVERT: N 31 TYR cc_start: 0.8645 (t80) cc_final: 0.8363 (t80) REVERT: N 166 MET cc_start: 0.8697 (ptp) cc_final: 0.8303 (ptp) REVERT: O 37 ILE cc_start: 0.9228 (mt) cc_final: 0.9016 (mm) REVERT: O 106 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8124 (tm-30) REVERT: O 170 ARG cc_start: 0.8594 (ptp-170) cc_final: 0.8371 (mtm180) REVERT: O 214 GLU cc_start: 0.7977 (pt0) cc_final: 0.7330 (pt0) REVERT: P 96 ARG cc_start: 0.7798 (ttm-80) cc_final: 0.7498 (ttp80) REVERT: P 109 GLU cc_start: 0.8680 (tm-30) cc_final: 0.7700 (tm-30) REVERT: P 134 LEU cc_start: 0.8823 (mt) cc_final: 0.8554 (mt) REVERT: P 159 MET cc_start: 0.7737 (mtt) cc_final: 0.7091 (mtt) REVERT: Q 3 ARG cc_start: 0.7275 (pmt-80) cc_final: 0.6145 (ptp-170) REVERT: Q 17 ARG cc_start: 0.7597 (ttp-110) cc_final: 0.7252 (ttp-110) REVERT: Q 26 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7032 (tm-30) REVERT: R 90 GLU cc_start: 0.8422 (tp30) cc_final: 0.8091 (tp30) REVERT: R 109 LYS cc_start: 0.8863 (ttmm) cc_final: 0.8371 (tmmt) REVERT: R 186 ILE cc_start: 0.9062 (mt) cc_final: 0.8859 (mt) REVERT: R 212 LYS cc_start: 0.8583 (mttt) cc_final: 0.8330 (mttp) REVERT: S 15 PHE cc_start: 0.9210 (m-10) cc_final: 0.8938 (m-10) REVERT: S 44 ASP cc_start: 0.8294 (p0) cc_final: 0.7179 (p0) REVERT: S 67 LEU cc_start: 0.8297 (mt) cc_final: 0.7870 (tp) REVERT: S 164 ASN cc_start: 0.7506 (p0) cc_final: 0.7245 (p0) REVERT: S 176 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7912 (tm-30) REVERT: S 206 GLN cc_start: 0.8553 (mm110) cc_final: 0.8284 (mp10) REVERT: T 20 TYR cc_start: 0.8777 (m-10) cc_final: 0.8326 (m-80) REVERT: T 24 TYR cc_start: 0.9069 (m-10) cc_final: 0.8646 (m-80) REVERT: T 86 LYS cc_start: 0.8737 (ttmt) cc_final: 0.8489 (ttpt) REVERT: T 88 MET cc_start: 0.8945 (ttp) cc_final: 0.8729 (ttp) REVERT: T 91 GLU cc_start: 0.5742 (mt-10) cc_final: 0.4620 (tp30) REVERT: T 100 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.7956 (t0) REVERT: T 116 TYR cc_start: 0.8908 (m-10) cc_final: 0.8550 (m-10) REVERT: T 117 GLN cc_start: 0.8641 (tp40) cc_final: 0.7865 (tp40) REVERT: T 154 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6745 (tm-30) REVERT: T 190 CYS cc_start: 0.9038 (t) cc_final: 0.8571 (t) REVERT: T 227 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8072 (tm-30) REVERT: U 48 CYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8225 (m) REVERT: U 125 TYR cc_start: 0.8931 (m-80) cc_final: 0.8436 (m-80) REVERT: V 13 MET cc_start: 0.7513 (mtp) cc_final: 0.6828 (mtp) REVERT: V 69 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7827 (mt-10) REVERT: V 80 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8415 (tm-30) REVERT: V 156 TYR cc_start: 0.8534 (t80) cc_final: 0.7648 (t80) REVERT: V 205 GLU cc_start: 0.7029 (tp30) cc_final: 0.6822 (tp30) REVERT: W 48 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.8087 (m) REVERT: W 64 GLU cc_start: 0.8220 (tp30) cc_final: 0.7927 (tp30) REVERT: W 111 TYR cc_start: 0.8995 (m-80) cc_final: 0.8757 (m-80) REVERT: W 184 GLN cc_start: 0.7640 (mp10) cc_final: 0.7287 (mp10) REVERT: X 158 GLN cc_start: 0.7798 (mp10) cc_final: 0.7340 (mt0) REVERT: X 166 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.7951 (tt) REVERT: X 173 GLU cc_start: 0.8273 (tt0) cc_final: 0.8007 (tt0) REVERT: Y 134 TYR cc_start: 0.8951 (m-10) cc_final: 0.8285 (m-80) REVERT: Y 166 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8536 (tm-30) REVERT: Y 183 MET cc_start: 0.8452 (mtm) cc_final: 0.7960 (mmm) REVERT: Z 115 ASP cc_start: 0.8331 (m-30) cc_final: 0.7959 (m-30) REVERT: Z 194 PHE cc_start: 0.5493 (OUTLIER) cc_final: 0.5053 (m-10) REVERT: Z 204 GLU cc_start: 0.8403 (mp0) cc_final: 0.8101 (mp0) REVERT: a 143 GLU cc_start: 0.8702 (pp20) cc_final: 0.8348 (pm20) REVERT: a 182 GLU cc_start: 0.6333 (tt0) cc_final: 0.4855 (tm-30) REVERT: b 108 PRO cc_start: 0.9468 (Cg_endo) cc_final: 0.9211 (Cg_exo) REVERT: b 224 ILE cc_start: 0.9235 (mm) cc_final: 0.8959 (pt) REVERT: c 68 ASP cc_start: 0.5427 (t0) cc_final: 0.5126 (t0) REVERT: c 193 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7290 (mm-30) REVERT: c 233 ASP cc_start: 0.8975 (m-30) cc_final: 0.8616 (m-30) REVERT: c 247 MET cc_start: 0.8292 (mmm) cc_final: 0.7973 (mmm) REVERT: d 38 ARG cc_start: 0.6052 (mtt90) cc_final: 0.5248 (ptm-80) REVERT: d 44 ARG cc_start: 0.7869 (tpp80) cc_final: 0.7031 (mmm-85) REVERT: d 52 VAL cc_start: 0.7229 (OUTLIER) cc_final: 0.6951 (m) REVERT: d 152 LEU cc_start: 0.7916 (tp) cc_final: 0.7098 (tp) REVERT: d 162 TRP cc_start: 0.8459 (t60) cc_final: 0.8235 (t-100) REVERT: d 193 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7923 (tm-30) REVERT: d 226 GLN cc_start: 0.7188 (tm-30) cc_final: 0.6590 (tm-30) REVERT: d 247 MET cc_start: 0.7974 (mmp) cc_final: 0.7350 (mmm) REVERT: d 251 TYR cc_start: 0.7441 (m-80) cc_final: 0.7002 (m-80) REVERT: d 262 TRP cc_start: 0.6940 (t-100) cc_final: 0.6602 (t60) REVERT: e 164 GLN cc_start: 0.8365 (mt0) cc_final: 0.7933 (tt0) REVERT: e 204 LYS cc_start: 0.7803 (tptt) cc_final: 0.6638 (mmtt) REVERT: e 207 MET cc_start: 0.7996 (mtm) cc_final: 0.7739 (mtt) REVERT: e 247 MET cc_start: 0.8096 (mmm) cc_final: 0.7740 (mmm) REVERT: f 48 PHE cc_start: 0.7532 (m-80) cc_final: 0.7006 (m-80) REVERT: g 32 GLN cc_start: 0.8330 (tp40) cc_final: 0.7926 (tp40) REVERT: g 253 MET cc_start: 0.8623 (ptp) cc_final: 0.8268 (ptp) REVERT: h 44 ARG cc_start: 0.5832 (OUTLIER) cc_final: 0.5480 (mtm-85) REVERT: h 135 HIS cc_start: 0.7320 (t-90) cc_final: 0.6606 (t-90) REVERT: h 193 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7581 (tm-30) REVERT: h 230 ARG cc_start: 0.6506 (ttp80) cc_final: 0.5478 (ttp-170) REVERT: h 246 ASP cc_start: 0.8333 (t70) cc_final: 0.8013 (t0) REVERT: h 250 ASN cc_start: 0.8328 (m110) cc_final: 0.7665 (m110) REVERT: i 237 TRP cc_start: 0.8547 (t-100) cc_final: 0.7433 (t-100) REVERT: i 247 MET cc_start: 0.8503 (mmp) cc_final: 0.8131 (mmm) outliers start: 281 outliers final: 169 residues processed: 1382 average time/residue: 0.5608 time to fit residues: 1306.8957 Evaluate side-chains 1285 residues out of total 6648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1101 time to evaluate : 5.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain D residue 10 PHE Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 193 PHE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 77 HIS Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 165 TYR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 4 CYS Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 148 HIS Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain M residue 76 ASP Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 152 TYR Chi-restraints excluded: chain M residue 166 VAL Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain O residue 136 TYR Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain P residue 181 ASP Chi-restraints excluded: chain Q residue 8 ARG Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 141 THR Chi-restraints excluded: chain Q residue 183 MET Chi-restraints excluded: chain Q residue 195 THR Chi-restraints excluded: chain R residue 31 CYS Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 78 MET Chi-restraints excluded: chain S residue 151 ASN Chi-restraints excluded: chain S residue 180 GLU Chi-restraints excluded: chain T residue 100 ASN Chi-restraints excluded: chain T residue 187 ILE Chi-restraints excluded: chain T residue 214 VAL Chi-restraints excluded: chain U residue 48 CYS Chi-restraints excluded: chain U residue 80 TYR Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 3 ILE Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 228 ILE Chi-restraints excluded: chain V residue 231 VAL Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 165 ASN Chi-restraints excluded: chain X residue 105 TYR Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 166 LEU Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 74 THR Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain Y residue 132 HIS Chi-restraints excluded: chain Y residue 148 HIS Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 160 ILE Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 188 ILE Chi-restraints excluded: chain Z residue 193 VAL Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 78 CYS Chi-restraints excluded: chain a residue 91 THR Chi-restraints excluded: chain a residue 110 TYR Chi-restraints excluded: chain a residue 214 ILE Chi-restraints excluded: chain a residue 235 LEU Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain c residue 64 VAL Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain c residue 180 ILE Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain c residue 222 VAL Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 135 HIS Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 222 VAL Chi-restraints excluded: chain e residue 28 ASP Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 165 LEU Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain f residue 213 SER Chi-restraints excluded: chain g residue 60 SER Chi-restraints excluded: chain g residue 66 ASP Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain g residue 239 HIS Chi-restraints excluded: chain g residue 266 VAL Chi-restraints excluded: chain h residue 44 ARG Chi-restraints excluded: chain h residue 53 ASN Chi-restraints excluded: chain i residue 137 GLN Chi-restraints excluded: chain i residue 147 THR Chi-restraints excluded: chain i residue 180 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 736 random chunks: chunk 661 optimal weight: 10.0000 chunk 503 optimal weight: 5.9990 chunk 347 optimal weight: 20.0000 chunk 74 optimal weight: 0.3980 chunk 319 optimal weight: 5.9990 chunk 449 optimal weight: 5.9990 chunk 671 optimal weight: 9.9990 chunk 711 optimal weight: 6.9990 chunk 351 optimal weight: 0.8980 chunk 636 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 HIS ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 GLN E 195 GLN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 HIS ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN L 180 HIS ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 67 GLN P 100 GLN ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 165 HIS U 89 ASN ** U 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 231 ASN U 233 HIS ** V 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 245 ASN ** W 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 114 HIS ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 158 ASN ** b 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 135 HIS ** d 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 239 HIS f 16 GLN f 197 ASN ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 181 GLN g 250 ASN h 164 GLN h 181 GLN h 250 ASN ** i 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 55 ASN i 164 GLN ** i 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 61370 Z= 0.334 Angle : 0.662 14.494 82846 Z= 0.347 Chirality : 0.045 0.337 9279 Planarity : 0.004 0.086 10541 Dihedral : 5.047 82.712 8224 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.68 % Favored : 92.30 % Rotamer: Outliers : 4.96 % Allowed : 21.03 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.09), residues: 7393 helix: 0.13 (0.09), residues: 3020 sheet: -2.50 (0.14), residues: 1224 loop : -2.56 (0.10), residues: 3149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP U 129 HIS 0.017 0.001 HIS d 135 PHE 0.023 0.002 PHE E 123 TYR 0.035 0.002 TYR e 148 ARG 0.008 0.001 ARG S 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1470 residues out of total 6648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 330 poor density : 1140 time to evaluate : 5.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8302 (tt) REVERT: A 150 ASP cc_start: 0.8001 (p0) cc_final: 0.7089 (p0) REVERT: A 154 LYS cc_start: 0.8084 (mtmt) cc_final: 0.7397 (pttm) REVERT: A 166 CYS cc_start: 0.7490 (p) cc_final: 0.7107 (p) REVERT: A 170 ARG cc_start: 0.8318 (ptp-170) cc_final: 0.8012 (ttp80) REVERT: B 49 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7294 (tm-30) REVERT: B 50 LYS cc_start: 0.6702 (tttt) cc_final: 0.6375 (ttpt) REVERT: B 109 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8058 (mm-30) REVERT: B 119 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8649 (tm-30) REVERT: B 157 ASN cc_start: 0.8456 (t0) cc_final: 0.8021 (t0) REVERT: C 41 ASP cc_start: 0.7981 (t0) cc_final: 0.7581 (t0) REVERT: C 54 LYS cc_start: 0.7816 (mttp) cc_final: 0.7258 (tptt) REVERT: D 117 LYS cc_start: 0.6221 (mttt) cc_final: 0.5589 (ttmt) REVERT: D 121 ARG cc_start: 0.8315 (ttm170) cc_final: 0.7966 (ttp-170) REVERT: D 212 LYS cc_start: 0.8047 (mttt) cc_final: 0.7342 (mtmt) REVERT: E 176 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8116 (pp30) REVERT: E 193 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8210 (t80) REVERT: F 9 ASP cc_start: 0.8228 (m-30) cc_final: 0.8027 (m-30) REVERT: F 66 ILE cc_start: 0.9010 (mm) cc_final: 0.8544 (mm) REVERT: F 88 MET cc_start: 0.8845 (ttm) cc_final: 0.8284 (ttm) REVERT: F 106 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7533 (tm-30) REVERT: F 112 VAL cc_start: 0.9533 (OUTLIER) cc_final: 0.9262 (p) REVERT: F 117 GLN cc_start: 0.8666 (tp40) cc_final: 0.8013 (tp40) REVERT: F 190 CYS cc_start: 0.9188 (t) cc_final: 0.8818 (t) REVERT: G 18 ASP cc_start: 0.8335 (p0) cc_final: 0.8039 (p0) REVERT: G 123 HIS cc_start: 0.9191 (OUTLIER) cc_final: 0.8456 (t70) REVERT: G 232 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7751 (mp) REVERT: H 219 HIS cc_start: 0.8278 (t70) cc_final: 0.8056 (t70) REVERT: H 222 ASN cc_start: 0.8732 (m110) cc_final: 0.8112 (m110) REVERT: I 17 ASP cc_start: 0.8658 (p0) cc_final: 0.8276 (p0) REVERT: I 51 ASP cc_start: 0.8039 (t0) cc_final: 0.7649 (t0) REVERT: I 174 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8175 (p0) REVERT: I 181 ASP cc_start: 0.8378 (p0) cc_final: 0.8123 (p0) REVERT: J 47 MET cc_start: 0.8818 (tpp) cc_final: 0.8223 (tpp) REVERT: J 84 MET cc_start: 0.8784 (ttt) cc_final: 0.8356 (ttt) REVERT: J 101 ARG cc_start: 0.7765 (ttp80) cc_final: 0.7353 (ttp80) REVERT: J 189 ASP cc_start: 0.8188 (t0) cc_final: 0.7850 (t0) REVERT: K 80 SER cc_start: 0.9088 (OUTLIER) cc_final: 0.8536 (t) REVERT: L 19 ARG cc_start: 0.8617 (ttm170) cc_final: 0.8159 (ttm170) REVERT: L 40 ASN cc_start: 0.8110 (t0) cc_final: 0.7738 (t0) REVERT: L 67 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8234 (mm-30) REVERT: L 93 TYR cc_start: 0.7798 (m-80) cc_final: 0.7388 (m-80) REVERT: M 30 TRP cc_start: 0.7315 (t-100) cc_final: 0.6494 (t-100) REVERT: M 152 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.7867 (p90) REVERT: M 194 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.8605 (p0) REVERT: M 198 ASP cc_start: 0.8309 (m-30) cc_final: 0.8061 (m-30) REVERT: M 222 ILE cc_start: 0.9261 (mm) cc_final: 0.9016 (tp) REVERT: N 31 TYR cc_start: 0.8717 (t80) cc_final: 0.8431 (t80) REVERT: N 166 MET cc_start: 0.8708 (ptp) cc_final: 0.8337 (ptp) REVERT: O 37 ILE cc_start: 0.9270 (mt) cc_final: 0.9060 (mm) REVERT: O 138 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8563 (ptt-90) REVERT: O 214 GLU cc_start: 0.8083 (pt0) cc_final: 0.7514 (pt0) REVERT: P 96 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7551 (ttp80) REVERT: P 109 GLU cc_start: 0.8741 (tm-30) cc_final: 0.7712 (tm-30) REVERT: P 157 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8395 (p0) REVERT: P 159 MET cc_start: 0.7831 (mtt) cc_final: 0.7236 (mtt) REVERT: Q 3 ARG cc_start: 0.7547 (pmt-80) cc_final: 0.6426 (ptp-170) REVERT: Q 17 ARG cc_start: 0.7578 (ttp-110) cc_final: 0.7194 (ttp-110) REVERT: Q 26 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7041 (tm-30) REVERT: R 90 GLU cc_start: 0.8477 (tp30) cc_final: 0.8184 (tp30) REVERT: R 109 LYS cc_start: 0.8901 (ttmm) cc_final: 0.8394 (tmmt) REVERT: R 212 LYS cc_start: 0.8551 (mttt) cc_final: 0.8229 (mtmm) REVERT: R 228 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7839 (tt) REVERT: S 15 PHE cc_start: 0.9237 (m-10) cc_final: 0.8935 (m-10) REVERT: S 44 ASP cc_start: 0.8361 (p0) cc_final: 0.7137 (p0) REVERT: S 71 ASP cc_start: 0.8246 (t70) cc_final: 0.7792 (t0) REVERT: S 206 GLN cc_start: 0.8546 (mm110) cc_final: 0.8314 (mp10) REVERT: T 20 TYR cc_start: 0.8902 (m-10) cc_final: 0.8433 (m-80) REVERT: T 24 TYR cc_start: 0.9056 (m-10) cc_final: 0.8616 (m-80) REVERT: T 86 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8460 (ttpt) REVERT: T 88 MET cc_start: 0.8947 (ttp) cc_final: 0.8717 (ttp) REVERT: T 91 GLU cc_start: 0.5845 (mt-10) cc_final: 0.4543 (tp30) REVERT: T 116 TYR cc_start: 0.8862 (m-80) cc_final: 0.8411 (m-10) REVERT: T 154 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6859 (tm-30) REVERT: T 227 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8089 (tm-30) REVERT: U 48 CYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8240 (m) REVERT: U 125 TYR cc_start: 0.8978 (m-80) cc_final: 0.8708 (m-80) REVERT: U 144 ASN cc_start: 0.8425 (t0) cc_final: 0.8003 (t0) REVERT: V 8 TYR cc_start: 0.7349 (m-10) cc_final: 0.6569 (m-80) REVERT: V 13 MET cc_start: 0.7736 (mtp) cc_final: 0.6990 (mtp) REVERT: V 69 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7985 (mt-10) REVERT: V 80 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8501 (tm-30) REVERT: V 156 TYR cc_start: 0.8530 (t80) cc_final: 0.7662 (t80) REVERT: W 89 LYS cc_start: 0.7987 (mtmm) cc_final: 0.7002 (mmtt) REVERT: W 90 TYR cc_start: 0.7351 (m-80) cc_final: 0.7137 (m-10) REVERT: W 184 GLN cc_start: 0.7655 (mp10) cc_final: 0.7310 (mp10) REVERT: X 158 GLN cc_start: 0.7904 (mp10) cc_final: 0.7452 (mt0) REVERT: X 166 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8017 (tt) REVERT: X 196 TRP cc_start: 0.6520 (t60) cc_final: 0.5837 (t60) REVERT: Y 31 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.7082 (m-30) REVERT: Y 134 TYR cc_start: 0.9043 (m-10) cc_final: 0.8389 (m-80) REVERT: Y 166 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8573 (tm-30) REVERT: Y 183 MET cc_start: 0.8525 (mtm) cc_final: 0.8027 (mmm) REVERT: Z 115 ASP cc_start: 0.8381 (m-30) cc_final: 0.8165 (m-30) REVERT: Z 194 PHE cc_start: 0.5288 (OUTLIER) cc_final: 0.4679 (m-10) REVERT: Z 200 TYR cc_start: 0.7208 (t80) cc_final: 0.6990 (t80) REVERT: a 143 GLU cc_start: 0.8740 (pp20) cc_final: 0.8423 (pm20) REVERT: a 182 GLU cc_start: 0.6474 (tt0) cc_final: 0.4982 (tm-30) REVERT: b 108 PRO cc_start: 0.9443 (Cg_endo) cc_final: 0.9195 (Cg_exo) REVERT: b 224 ILE cc_start: 0.9248 (mm) cc_final: 0.8975 (pt) REVERT: c 135 HIS cc_start: 0.6102 (OUTLIER) cc_final: 0.5673 (t-90) REVERT: c 193 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7258 (mm-30) REVERT: c 224 ASP cc_start: 0.8151 (m-30) cc_final: 0.7907 (m-30) REVERT: c 233 ASP cc_start: 0.9094 (m-30) cc_final: 0.8554 (m-30) REVERT: c 247 MET cc_start: 0.8328 (mmm) cc_final: 0.7850 (mmm) REVERT: d 38 ARG cc_start: 0.5789 (mtt90) cc_final: 0.4812 (mtp-110) REVERT: d 44 ARG cc_start: 0.7862 (tpp80) cc_final: 0.6997 (mmm-85) REVERT: d 52 VAL cc_start: 0.7147 (OUTLIER) cc_final: 0.6897 (m) REVERT: d 162 TRP cc_start: 0.8526 (t60) cc_final: 0.8324 (t-100) REVERT: d 193 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7888 (tm-30) REVERT: d 247 MET cc_start: 0.7967 (mmp) cc_final: 0.7300 (mtp) REVERT: d 262 TRP cc_start: 0.6978 (t-100) cc_final: 0.6495 (t60) REVERT: e 164 GLN cc_start: 0.8292 (mt0) cc_final: 0.7884 (tt0) REVERT: e 207 MET cc_start: 0.8111 (mtm) cc_final: 0.7904 (mtt) REVERT: f 48 PHE cc_start: 0.7511 (m-80) cc_final: 0.7024 (m-80) REVERT: g 32 GLN cc_start: 0.8538 (tp40) cc_final: 0.8098 (tp40) REVERT: g 250 ASN cc_start: 0.8826 (m-40) cc_final: 0.8339 (m110) REVERT: g 253 MET cc_start: 0.8660 (ptp) cc_final: 0.8448 (ptp) REVERT: h 44 ARG cc_start: 0.5823 (OUTLIER) cc_final: 0.5480 (mtm-85) REVERT: h 208 GLU cc_start: 0.8502 (tm-30) cc_final: 0.7840 (tm-30) REVERT: h 230 ARG cc_start: 0.6587 (ttp80) cc_final: 0.5470 (ttp-170) REVERT: i 28 ASP cc_start: 0.7006 (t0) cc_final: 0.6738 (t0) REVERT: i 32 GLN cc_start: 0.7640 (pt0) cc_final: 0.6855 (pt0) REVERT: i 237 TRP cc_start: 0.8546 (t-100) cc_final: 0.8133 (t-100) REVERT: i 246 ASP cc_start: 0.8264 (m-30) cc_final: 0.8010 (m-30) outliers start: 330 outliers final: 225 residues processed: 1355 average time/residue: 0.6194 time to fit residues: 1437.3565 Evaluate side-chains 1320 residues out of total 6648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1075 time to evaluate : 5.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain D residue 10 PHE Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 193 PHE Chi-restraints excluded: chain E residue 227 GLN Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain E residue 233 ASN Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 123 HIS Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 77 HIS Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 165 TYR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 4 CYS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 148 HIS Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain M residue 76 ASP Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 83 SER Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 152 TYR Chi-restraints excluded: chain M residue 166 VAL Chi-restraints excluded: chain M residue 194 ASN Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 26 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 136 TYR Chi-restraints excluded: chain O residue 138 ARG Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain P residue 157 ASN Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain P residue 181 ASP Chi-restraints excluded: chain P residue 203 LEU Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 141 THR Chi-restraints excluded: chain Q residue 193 LEU Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 151 ASN Chi-restraints excluded: chain S residue 180 GLU Chi-restraints excluded: chain S residue 219 ILE Chi-restraints excluded: chain T residue 87 PHE Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 187 ILE Chi-restraints excluded: chain T residue 205 THR Chi-restraints excluded: chain T residue 214 VAL Chi-restraints excluded: chain U residue 48 CYS Chi-restraints excluded: chain U residue 80 TYR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 3 ILE Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 149 CYS Chi-restraints excluded: chain V residue 164 LEU Chi-restraints excluded: chain V residue 228 ILE Chi-restraints excluded: chain V residue 231 VAL Chi-restraints excluded: chain V residue 244 VAL Chi-restraints excluded: chain W residue 7 VAL Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 165 ASN Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 166 LEU Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 31 ASP Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 74 THR Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain Y residue 132 HIS Chi-restraints excluded: chain Y residue 148 HIS Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 160 ILE Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 188 ILE Chi-restraints excluded: chain Z residue 193 VAL Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 78 CYS Chi-restraints excluded: chain a residue 91 THR Chi-restraints excluded: chain a residue 214 ILE Chi-restraints excluded: chain a residue 235 LEU Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 15 ILE Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 177 THR Chi-restraints excluded: chain b residue 178 THR Chi-restraints excluded: chain b residue 230 THR Chi-restraints excluded: chain c residue 64 VAL Chi-restraints excluded: chain c residue 135 HIS Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain c residue 180 ILE Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain c residue 222 VAL Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 135 HIS Chi-restraints excluded: chain d residue 172 ASP Chi-restraints excluded: chain d residue 222 VAL Chi-restraints excluded: chain e residue 28 ASP Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 165 LEU Chi-restraints excluded: chain f residue 140 LEU Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain g residue 60 SER Chi-restraints excluded: chain g residue 66 ASP Chi-restraints excluded: chain g residue 142 LEU Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain g residue 182 GLU Chi-restraints excluded: chain g residue 239 HIS Chi-restraints excluded: chain g residue 266 VAL Chi-restraints excluded: chain h residue 44 ARG Chi-restraints excluded: chain h residue 53 ASN Chi-restraints excluded: chain i residue 137 GLN Chi-restraints excluded: chain i residue 180 ILE Chi-restraints excluded: chain i residue 230 ARG Chi-restraints excluded: chain i residue 256 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 736 random chunks: chunk 592 optimal weight: 0.7980 chunk 403 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 529 optimal weight: 0.9990 chunk 293 optimal weight: 4.9990 chunk 607 optimal weight: 3.9990 chunk 491 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 363 optimal weight: 0.9980 chunk 638 optimal weight: 10.0000 chunk 179 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN F 21 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 HIS L 180 HIS ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 100 GLN ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 165 HIS U 157 ASN U 231 ASN U 233 HIS ** V 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 247 GLN ** W 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 126 ASN d 135 HIS ** d 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 239 HIS f 197 ASN ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 239 HIS h 164 GLN h 226 GLN ** i 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 174 ASN ** i 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 61370 Z= 0.175 Angle : 0.576 12.687 82846 Z= 0.302 Chirality : 0.043 0.337 9279 Planarity : 0.003 0.076 10541 Dihedral : 4.834 80.332 8221 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.15 % Favored : 93.83 % Rotamer: Outliers : 4.11 % Allowed : 22.97 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.10), residues: 7393 helix: 0.45 (0.10), residues: 3039 sheet: -2.31 (0.14), residues: 1230 loop : -2.38 (0.10), residues: 3124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 58 HIS 0.019 0.001 HIS d 135 PHE 0.023 0.001 PHE c 196 TYR 0.030 0.001 TYR Q 223 ARG 0.010 0.000 ARG U 88 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1476 residues out of total 6648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1203 time to evaluate : 5.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7780 (mtt-85) cc_final: 0.7554 (mtt-85) REVERT: A 150 ASP cc_start: 0.7753 (p0) cc_final: 0.6919 (p0) REVERT: A 154 LYS cc_start: 0.8099 (mtmt) cc_final: 0.7427 (pttm) REVERT: A 156 GLU cc_start: 0.8117 (mp0) cc_final: 0.7871 (mp0) REVERT: A 166 CYS cc_start: 0.7530 (p) cc_final: 0.7034 (p) REVERT: A 170 ARG cc_start: 0.8226 (ptp-170) cc_final: 0.7857 (ttp80) REVERT: B 49 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7303 (tm-30) REVERT: B 50 LYS cc_start: 0.6402 (tttt) cc_final: 0.6125 (ttpt) REVERT: B 119 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8484 (tm-30) REVERT: B 157 ASN cc_start: 0.8382 (t0) cc_final: 0.7981 (t0) REVERT: C 41 ASP cc_start: 0.7836 (t0) cc_final: 0.7451 (t0) REVERT: C 54 LYS cc_start: 0.7754 (mttp) cc_final: 0.7227 (tptt) REVERT: C 98 LEU cc_start: 0.9581 (tp) cc_final: 0.9338 (tt) REVERT: C 186 GLU cc_start: 0.8345 (tp30) cc_final: 0.8064 (tp30) REVERT: C 222 VAL cc_start: 0.7272 (OUTLIER) cc_final: 0.6989 (t) REVERT: D 117 LYS cc_start: 0.6119 (mttt) cc_final: 0.5555 (ttmt) REVERT: D 121 ARG cc_start: 0.8264 (ttm170) cc_final: 0.7913 (ttp-170) REVERT: D 180 MET cc_start: 0.8625 (mmm) cc_final: 0.8408 (mmm) REVERT: D 212 LYS cc_start: 0.8082 (mttt) cc_final: 0.7434 (mtmt) REVERT: E 176 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7990 (pp30) REVERT: E 193 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.8201 (t80) REVERT: F 9 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: F 88 MET cc_start: 0.8876 (ttm) cc_final: 0.8351 (ttm) REVERT: F 106 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7533 (tm-30) REVERT: F 112 VAL cc_start: 0.9543 (OUTLIER) cc_final: 0.9273 (p) REVERT: F 117 GLN cc_start: 0.8626 (tp40) cc_final: 0.7950 (tp40) REVERT: F 190 CYS cc_start: 0.9153 (t) cc_final: 0.8794 (t) REVERT: G 91 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8501 (mt) REVERT: G 232 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7666 (mp) REVERT: H 219 HIS cc_start: 0.8217 (t70) cc_final: 0.7983 (t70) REVERT: H 222 ASN cc_start: 0.8617 (m110) cc_final: 0.7995 (m110) REVERT: I 17 ASP cc_start: 0.8742 (p0) cc_final: 0.8295 (p0) REVERT: I 51 ASP cc_start: 0.7968 (t0) cc_final: 0.7486 (t70) REVERT: I 166 ASP cc_start: 0.8971 (t70) cc_final: 0.8622 (t70) REVERT: I 174 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8043 (p0) REVERT: J 44 ILE cc_start: 0.9073 (pt) cc_final: 0.8814 (pt) REVERT: J 47 MET cc_start: 0.8688 (tpp) cc_final: 0.8196 (tpp) REVERT: J 61 ASP cc_start: 0.8720 (m-30) cc_final: 0.8502 (m-30) REVERT: J 84 MET cc_start: 0.8693 (ttt) cc_final: 0.8257 (ttt) REVERT: J 101 ARG cc_start: 0.7660 (ttp80) cc_final: 0.7297 (ttp80) REVERT: J 189 ASP cc_start: 0.8220 (t0) cc_final: 0.7913 (t0) REVERT: J 191 ASP cc_start: 0.7967 (t70) cc_final: 0.7670 (t70) REVERT: K 21 SER cc_start: 0.9089 (t) cc_final: 0.8163 (p) REVERT: K 139 VAL cc_start: 0.9224 (m) cc_final: 0.8920 (p) REVERT: L 19 ARG cc_start: 0.8682 (ttm170) cc_final: 0.8322 (ttm170) REVERT: L 40 ASN cc_start: 0.8065 (t0) cc_final: 0.7692 (t0) REVERT: L 67 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8189 (mm-30) REVERT: L 93 TYR cc_start: 0.7728 (m-80) cc_final: 0.7309 (m-80) REVERT: L 194 PHE cc_start: 0.6708 (OUTLIER) cc_final: 0.6106 (m-10) REVERT: M 30 TRP cc_start: 0.7383 (t-100) cc_final: 0.6602 (t-100) REVERT: M 33 TYR cc_start: 0.8656 (m-10) cc_final: 0.8332 (m-10) REVERT: M 56 ARG cc_start: 0.9059 (ttm170) cc_final: 0.8293 (ttm-80) REVERT: M 171 GLN cc_start: 0.8531 (mt0) cc_final: 0.7550 (mt0) REVERT: M 194 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8572 (p0) REVERT: M 198 ASP cc_start: 0.8243 (m-30) cc_final: 0.8016 (m-30) REVERT: N 166 MET cc_start: 0.8672 (ptp) cc_final: 0.8292 (ptp) REVERT: O 214 GLU cc_start: 0.7990 (pt0) cc_final: 0.7412 (pt0) REVERT: P 20 VAL cc_start: 0.8496 (m) cc_final: 0.8288 (p) REVERT: P 96 ARG cc_start: 0.7728 (ttm-80) cc_final: 0.7512 (ttp80) REVERT: P 109 GLU cc_start: 0.8660 (tm-30) cc_final: 0.7703 (tm-30) REVERT: P 159 MET cc_start: 0.7679 (mtt) cc_final: 0.6975 (mtt) REVERT: Q 3 ARG cc_start: 0.7486 (pmt-80) cc_final: 0.6388 (ptp-170) REVERT: Q 8 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7609 (ptp90) REVERT: Q 17 ARG cc_start: 0.7688 (ttp-110) cc_final: 0.7292 (ttp-110) REVERT: Q 26 GLU cc_start: 0.7403 (tm-30) cc_final: 0.6970 (tm-30) REVERT: Q 243 TYR cc_start: 0.6807 (OUTLIER) cc_final: 0.5588 (t80) REVERT: R 90 GLU cc_start: 0.8388 (tp30) cc_final: 0.8091 (tp30) REVERT: R 109 LYS cc_start: 0.8838 (ttmm) cc_final: 0.8351 (tmmt) REVERT: R 212 LYS cc_start: 0.8558 (mttt) cc_final: 0.8229 (mttm) REVERT: S 15 PHE cc_start: 0.9199 (m-80) cc_final: 0.8907 (m-10) REVERT: S 71 ASP cc_start: 0.8128 (t70) cc_final: 0.7758 (t0) REVERT: S 206 GLN cc_start: 0.8597 (mm110) cc_final: 0.8318 (mp10) REVERT: T 20 TYR cc_start: 0.8752 (m-10) cc_final: 0.8163 (m-80) REVERT: T 24 TYR cc_start: 0.8940 (m-10) cc_final: 0.8357 (m-80) REVERT: T 61 GLU cc_start: 0.7568 (pp20) cc_final: 0.7230 (pp20) REVERT: T 86 LYS cc_start: 0.8666 (ttmt) cc_final: 0.8426 (ttpt) REVERT: T 91 GLU cc_start: 0.5909 (mt-10) cc_final: 0.5085 (tp30) REVERT: T 116 TYR cc_start: 0.8832 (m-80) cc_final: 0.8392 (m-10) REVERT: T 117 GLN cc_start: 0.8527 (tp40) cc_final: 0.8121 (tp-100) REVERT: T 133 MET cc_start: 0.7671 (ttp) cc_final: 0.7468 (ttp) REVERT: T 145 GLU cc_start: 0.7959 (tt0) cc_final: 0.7624 (tt0) REVERT: T 154 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6762 (tm-30) REVERT: T 190 CYS cc_start: 0.8952 (t) cc_final: 0.8508 (t) REVERT: T 217 ASN cc_start: 0.8802 (m-40) cc_final: 0.8492 (m-40) REVERT: T 227 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8085 (tm-30) REVERT: U 48 CYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8208 (m) REVERT: U 60 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7177 (mpp) REVERT: U 144 ASN cc_start: 0.8401 (t0) cc_final: 0.8005 (t0) REVERT: V 8 TYR cc_start: 0.6831 (m-10) cc_final: 0.5946 (m-80) REVERT: V 13 MET cc_start: 0.7504 (mtp) cc_final: 0.6767 (mtp) REVERT: V 69 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8036 (mt-10) REVERT: V 80 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8397 (tm-30) REVERT: V 156 TYR cc_start: 0.8404 (t80) cc_final: 0.7510 (t80) REVERT: V 168 ASN cc_start: 0.8490 (t0) cc_final: 0.8277 (t0) REVERT: V 248 MET cc_start: 0.7192 (tpt) cc_final: 0.6583 (tpt) REVERT: V 250 PHE cc_start: 0.5798 (p90) cc_final: 0.5532 (p90) REVERT: W 184 GLN cc_start: 0.7574 (mp10) cc_final: 0.7265 (mp10) REVERT: W 213 LEU cc_start: 0.8547 (mt) cc_final: 0.8263 (mt) REVERT: X 157 GLU cc_start: 0.8162 (tt0) cc_final: 0.7841 (tt0) REVERT: X 158 GLN cc_start: 0.7687 (mp10) cc_final: 0.7260 (mt0) REVERT: X 196 TRP cc_start: 0.6499 (t60) cc_final: 0.5635 (t60) REVERT: X 201 LEU cc_start: 0.9324 (tp) cc_final: 0.9069 (tp) REVERT: Y 134 TYR cc_start: 0.8940 (m-10) cc_final: 0.8263 (m-80) REVERT: Y 166 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8631 (tm-30) REVERT: Y 183 MET cc_start: 0.8442 (mtm) cc_final: 0.7989 (mmm) REVERT: Z 115 ASP cc_start: 0.8227 (m-30) cc_final: 0.8019 (m-30) REVERT: Z 194 PHE cc_start: 0.5315 (OUTLIER) cc_final: 0.4872 (m-10) REVERT: a 143 GLU cc_start: 0.8672 (pp20) cc_final: 0.8372 (pm20) REVERT: a 182 GLU cc_start: 0.6225 (tt0) cc_final: 0.4915 (tm-30) REVERT: c 188 LEU cc_start: 0.8517 (mm) cc_final: 0.8272 (tp) REVERT: c 193 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6941 (mm-30) REVERT: c 224 ASP cc_start: 0.8162 (m-30) cc_final: 0.7343 (m-30) REVERT: c 233 ASP cc_start: 0.9160 (m-30) cc_final: 0.8822 (m-30) REVERT: c 247 MET cc_start: 0.8282 (mmm) cc_final: 0.7796 (mmm) REVERT: d 38 ARG cc_start: 0.5771 (mtt90) cc_final: 0.4809 (mtp-110) REVERT: d 44 ARG cc_start: 0.7679 (tpp80) cc_final: 0.6874 (mmm-85) REVERT: d 52 VAL cc_start: 0.6742 (OUTLIER) cc_final: 0.6436 (m) REVERT: d 135 HIS cc_start: 0.7146 (OUTLIER) cc_final: 0.6466 (m170) REVERT: d 162 TRP cc_start: 0.8522 (t60) cc_final: 0.8260 (t-100) REVERT: d 193 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7736 (tm-30) REVERT: d 262 TRP cc_start: 0.6920 (t-100) cc_final: 0.6501 (t60) REVERT: f 48 PHE cc_start: 0.7422 (m-80) cc_final: 0.6916 (m-80) REVERT: g 32 GLN cc_start: 0.8537 (tp40) cc_final: 0.8158 (tp40) REVERT: g 250 ASN cc_start: 0.8726 (m-40) cc_final: 0.8268 (m110) REVERT: g 253 MET cc_start: 0.8681 (ptp) cc_final: 0.8465 (ptp) REVERT: h 44 ARG cc_start: 0.5797 (OUTLIER) cc_final: 0.5446 (mpt180) REVERT: h 48 PHE cc_start: 0.8227 (m-80) cc_final: 0.7920 (m-80) REVERT: h 181 GLN cc_start: 0.8141 (mt0) cc_final: 0.7924 (mt0) REVERT: h 207 MET cc_start: 0.8081 (mmm) cc_final: 0.7789 (mmm) REVERT: h 208 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7542 (tm-30) REVERT: h 230 ARG cc_start: 0.6587 (ttp80) cc_final: 0.5488 (ttp-170) REVERT: h 248 ARG cc_start: 0.7835 (ttp-170) cc_final: 0.7628 (ttp-170) REVERT: i 32 GLN cc_start: 0.7577 (pt0) cc_final: 0.7088 (pt0) REVERT: i 164 GLN cc_start: 0.8157 (mt0) cc_final: 0.7749 (tt0) REVERT: i 237 TRP cc_start: 0.8494 (t-100) cc_final: 0.8046 (t-100) outliers start: 273 outliers final: 176 residues processed: 1387 average time/residue: 0.5588 time to fit residues: 1307.5647 Evaluate side-chains 1325 residues out of total 6648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1131 time to evaluate : 5.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 10 PHE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 193 PHE Chi-restraints excluded: chain E residue 227 GLN Chi-restraints excluded: chain E residue 233 ASN Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 49 CYS Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 51 HIS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 77 HIS Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 165 TYR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 4 CYS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 148 HIS Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain M residue 76 ASP Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 166 VAL Chi-restraints excluded: chain M residue 192 ASN Chi-restraints excluded: chain M residue 194 ASN Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 26 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain O residue 136 TYR Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain P residue 181 ASP Chi-restraints excluded: chain P residue 203 LEU Chi-restraints excluded: chain Q residue 8 ARG Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 141 THR Chi-restraints excluded: chain Q residue 243 TYR Chi-restraints excluded: chain R residue 10 PHE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 230 ASP Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 78 MET Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 151 ASN Chi-restraints excluded: chain S residue 180 GLU Chi-restraints excluded: chain T residue 87 PHE Chi-restraints excluded: chain T residue 205 THR Chi-restraints excluded: chain T residue 214 VAL Chi-restraints excluded: chain U residue 48 CYS Chi-restraints excluded: chain U residue 60 MET Chi-restraints excluded: chain U residue 80 TYR Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 164 LEU Chi-restraints excluded: chain V residue 201 MET Chi-restraints excluded: chain V residue 231 VAL Chi-restraints excluded: chain V residue 244 VAL Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 165 ASN Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 74 THR Chi-restraints excluded: chain Y residue 148 HIS Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 160 ILE Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 182 ASN Chi-restraints excluded: chain Z residue 188 ILE Chi-restraints excluded: chain Z residue 193 VAL Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 57 LEU Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 91 THR Chi-restraints excluded: chain a residue 185 ASN Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 177 THR Chi-restraints excluded: chain b residue 178 THR Chi-restraints excluded: chain c residue 64 VAL Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain c residue 222 VAL Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 135 HIS Chi-restraints excluded: chain d residue 152 LEU Chi-restraints excluded: chain d residue 172 ASP Chi-restraints excluded: chain d residue 222 VAL Chi-restraints excluded: chain e residue 28 ASP Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 165 LEU Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain f residue 193 GLU Chi-restraints excluded: chain f residue 197 ASN Chi-restraints excluded: chain g residue 66 ASP Chi-restraints excluded: chain g residue 142 LEU Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain g residue 239 HIS Chi-restraints excluded: chain h residue 44 ARG Chi-restraints excluded: chain h residue 53 ASN Chi-restraints excluded: chain i residue 180 ILE Chi-restraints excluded: chain i residue 256 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 736 random chunks: chunk 239 optimal weight: 0.7980 chunk 640 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 417 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 chunk 712 optimal weight: 10.0000 chunk 591 optimal weight: 7.9990 chunk 329 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 235 optimal weight: 0.8980 chunk 373 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 HIS ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN L 180 HIS ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 165 HIS U 89 ASN U 231 ASN U 233 HIS ** V 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 247 GLN ** W 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 55 ASN ** c 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 135 HIS ** d 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 137 GLN e 239 HIS f 197 ASN ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 181 GLN g 197 ASN ** h 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 164 GLN h 226 GLN ** i 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 61370 Z= 0.337 Angle : 0.651 12.639 82846 Z= 0.340 Chirality : 0.045 0.335 9279 Planarity : 0.004 0.086 10541 Dihedral : 5.003 83.251 8220 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.98 % Allowed : 23.42 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.10), residues: 7393 helix: 0.50 (0.10), residues: 3037 sheet: -2.32 (0.14), residues: 1230 loop : -2.41 (0.10), residues: 3126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP a 30 HIS 0.014 0.001 HIS K 40 PHE 0.026 0.002 PHE Q 73 TYR 0.033 0.002 TYR e 148 ARG 0.009 0.001 ARG Z 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1463 residues out of total 6648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 1132 time to evaluate : 5.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: A 53 GLN cc_start: 0.8503 (tt0) cc_final: 0.8177 (tp40) REVERT: A 150 ASP cc_start: 0.7986 (p0) cc_final: 0.7226 (p0) REVERT: A 154 LYS cc_start: 0.8228 (mtmt) cc_final: 0.7603 (pttm) REVERT: A 166 CYS cc_start: 0.7599 (p) cc_final: 0.7171 (p) REVERT: A 170 ARG cc_start: 0.8258 (ptp-170) cc_final: 0.7912 (ttp80) REVERT: B 49 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7383 (tm-30) REVERT: B 50 LYS cc_start: 0.6508 (tttt) cc_final: 0.6229 (ttpt) REVERT: B 109 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8221 (mm-30) REVERT: B 119 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8625 (tm-30) REVERT: C 41 ASP cc_start: 0.7932 (t0) cc_final: 0.7576 (t0) REVERT: C 54 LYS cc_start: 0.7764 (mttp) cc_final: 0.7310 (tptt) REVERT: C 186 GLU cc_start: 0.8282 (tp30) cc_final: 0.8055 (tp30) REVERT: C 222 VAL cc_start: 0.7708 (OUTLIER) cc_final: 0.7506 (t) REVERT: D 117 LYS cc_start: 0.6222 (mttt) cc_final: 0.5621 (ttmt) REVERT: D 121 ARG cc_start: 0.8308 (ttm170) cc_final: 0.7958 (ttp-170) REVERT: D 180 MET cc_start: 0.8775 (mmm) cc_final: 0.8515 (mmm) REVERT: D 212 LYS cc_start: 0.8036 (mttt) cc_final: 0.7329 (mtmt) REVERT: D 225 MET cc_start: 0.8639 (tpt) cc_final: 0.8305 (tpt) REVERT: E 176 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8113 (pp30) REVERT: F 9 ASP cc_start: 0.8309 (m-30) cc_final: 0.8060 (m-30) REVERT: F 88 MET cc_start: 0.8828 (ttm) cc_final: 0.8337 (ttm) REVERT: F 117 GLN cc_start: 0.8785 (tp40) cc_final: 0.8237 (tp40) REVERT: F 190 CYS cc_start: 0.9174 (t) cc_final: 0.8822 (t) REVERT: G 18 ASP cc_start: 0.8342 (p0) cc_final: 0.8051 (p0) REVERT: G 123 HIS cc_start: 0.9216 (OUTLIER) cc_final: 0.8464 (t70) REVERT: G 232 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7728 (mp) REVERT: H 222 ASN cc_start: 0.8714 (m110) cc_final: 0.8167 (m110) REVERT: I 17 ASP cc_start: 0.8673 (p0) cc_final: 0.8275 (p0) REVERT: I 51 ASP cc_start: 0.8042 (t0) cc_final: 0.7629 (t0) REVERT: I 174 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8207 (p0) REVERT: I 181 ASP cc_start: 0.8290 (p0) cc_final: 0.8074 (p0) REVERT: J 47 MET cc_start: 0.8816 (tpp) cc_final: 0.8231 (tpp) REVERT: J 84 MET cc_start: 0.8752 (ttt) cc_final: 0.8318 (ttt) REVERT: J 101 ARG cc_start: 0.7596 (ttp80) cc_final: 0.7151 (ttp80) REVERT: J 110 ILE cc_start: 0.9097 (mm) cc_final: 0.8704 (pt) REVERT: J 189 ASP cc_start: 0.8253 (t0) cc_final: 0.7944 (t0) REVERT: J 191 ASP cc_start: 0.8126 (t70) cc_final: 0.7818 (t70) REVERT: K 166 GLU cc_start: 0.9301 (tm-30) cc_final: 0.9065 (tm-30) REVERT: L 19 ARG cc_start: 0.8653 (ttm170) cc_final: 0.8280 (ttm170) REVERT: L 40 ASN cc_start: 0.8233 (t0) cc_final: 0.7873 (t0) REVERT: L 93 TYR cc_start: 0.7783 (m-80) cc_final: 0.7350 (m-80) REVERT: M 30 TRP cc_start: 0.7312 (t-100) cc_final: 0.6520 (t-100) REVERT: M 194 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8418 (p0) REVERT: M 198 ASP cc_start: 0.8291 (m-30) cc_final: 0.8048 (m-30) REVERT: N 166 MET cc_start: 0.8703 (ptp) cc_final: 0.8332 (ptp) REVERT: O 138 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8595 (tmm160) REVERT: O 214 GLU cc_start: 0.8007 (pt0) cc_final: 0.7486 (pt0) REVERT: O 234 VAL cc_start: 0.9386 (OUTLIER) cc_final: 0.9175 (t) REVERT: P 96 ARG cc_start: 0.7824 (ttm-80) cc_final: 0.7599 (ttp80) REVERT: P 109 GLU cc_start: 0.8762 (tm-30) cc_final: 0.7719 (tm-30) REVERT: Q 3 ARG cc_start: 0.7792 (pmt-80) cc_final: 0.6530 (ptp-170) REVERT: Q 17 ARG cc_start: 0.7644 (ttp-110) cc_final: 0.7200 (ttp-110) REVERT: Q 26 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7003 (tm-30) REVERT: Q 231 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8722 (pt0) REVERT: Q 243 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.5544 (t80) REVERT: R 90 GLU cc_start: 0.8529 (tp30) cc_final: 0.8236 (tp30) REVERT: R 212 LYS cc_start: 0.8469 (mttt) cc_final: 0.8174 (mttm) REVERT: S 15 PHE cc_start: 0.9213 (m-80) cc_final: 0.8859 (m-10) REVERT: S 44 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.7558 (p0) REVERT: S 71 ASP cc_start: 0.8225 (t70) cc_final: 0.7816 (t0) REVERT: S 206 GLN cc_start: 0.8702 (mm110) cc_final: 0.8422 (mp10) REVERT: T 61 GLU cc_start: 0.7767 (pp20) cc_final: 0.7540 (pp20) REVERT: T 86 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8454 (ttpt) REVERT: T 91 GLU cc_start: 0.5865 (mt-10) cc_final: 0.4667 (tp30) REVERT: T 116 TYR cc_start: 0.8883 (m-80) cc_final: 0.8320 (m-10) REVERT: T 117 GLN cc_start: 0.8637 (tp40) cc_final: 0.8414 (tp-100) REVERT: T 154 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6842 (tm-30) REVERT: T 158 LEU cc_start: 0.8957 (mp) cc_final: 0.8588 (mp) REVERT: U 48 CYS cc_start: 0.8742 (m) cc_final: 0.8260 (m) REVERT: U 60 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7533 (mtm) REVERT: U 89 ASN cc_start: 0.9548 (OUTLIER) cc_final: 0.9132 (t0) REVERT: U 144 ASN cc_start: 0.8430 (t0) cc_final: 0.8009 (t0) REVERT: V 13 MET cc_start: 0.7757 (mtp) cc_final: 0.7038 (mtp) REVERT: V 69 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8000 (mt-10) REVERT: V 80 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8495 (tm-30) REVERT: V 156 TYR cc_start: 0.8509 (t80) cc_final: 0.7711 (t80) REVERT: W 41 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8780 (mt) REVERT: W 139 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7316 (tm-30) REVERT: W 184 GLN cc_start: 0.7604 (mp10) cc_final: 0.7309 (mp10) REVERT: W 213 LEU cc_start: 0.8684 (mt) cc_final: 0.8402 (mt) REVERT: X 158 GLN cc_start: 0.7861 (mp10) cc_final: 0.7372 (mt0) REVERT: X 196 TRP cc_start: 0.6513 (t60) cc_final: 0.5796 (t60) REVERT: Y 31 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7135 (m-30) REVERT: Y 134 TYR cc_start: 0.9042 (m-10) cc_final: 0.8391 (m-80) REVERT: Y 166 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8636 (tm-30) REVERT: Y 183 MET cc_start: 0.8511 (mtm) cc_final: 0.8032 (mmm) REVERT: Z 189 GLU cc_start: 0.7106 (mp0) cc_final: 0.6779 (mp0) REVERT: Z 194 PHE cc_start: 0.5281 (OUTLIER) cc_final: 0.4706 (m-10) REVERT: Z 200 TYR cc_start: 0.7229 (t80) cc_final: 0.6984 (t80) REVERT: a 143 GLU cc_start: 0.8729 (pp20) cc_final: 0.8423 (pm20) REVERT: a 182 GLU cc_start: 0.6429 (tt0) cc_final: 0.5010 (tm-30) REVERT: c 135 HIS cc_start: 0.6071 (OUTLIER) cc_final: 0.5554 (t-90) REVERT: c 188 LEU cc_start: 0.8524 (mm) cc_final: 0.8258 (tp) REVERT: c 247 MET cc_start: 0.8438 (mmm) cc_final: 0.8034 (mmm) REVERT: d 38 ARG cc_start: 0.5804 (mtt90) cc_final: 0.4886 (mtp-110) REVERT: d 44 ARG cc_start: 0.7590 (tpp80) cc_final: 0.6683 (mmm-85) REVERT: d 52 VAL cc_start: 0.6831 (OUTLIER) cc_final: 0.6547 (m) REVERT: d 135 HIS cc_start: 0.7086 (OUTLIER) cc_final: 0.6607 (m170) REVERT: d 162 TRP cc_start: 0.8579 (t60) cc_final: 0.8328 (t-100) REVERT: d 193 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7723 (tm-30) REVERT: d 262 TRP cc_start: 0.6959 (t-100) cc_final: 0.6481 (t60) REVERT: f 48 PHE cc_start: 0.7440 (m-80) cc_final: 0.6958 (m-80) REVERT: g 250 ASN cc_start: 0.8666 (m-40) cc_final: 0.8272 (m110) REVERT: g 253 MET cc_start: 0.8686 (ptp) cc_final: 0.8485 (ptp) REVERT: h 24 LYS cc_start: 0.6762 (tptm) cc_final: 0.6492 (tmtt) REVERT: h 48 PHE cc_start: 0.8190 (m-80) cc_final: 0.7833 (m-80) REVERT: h 53 ASN cc_start: 0.6900 (OUTLIER) cc_final: 0.6632 (t0) REVERT: h 181 GLN cc_start: 0.8147 (mt0) cc_final: 0.7942 (mt0) REVERT: h 207 MET cc_start: 0.8106 (mmm) cc_final: 0.7799 (mmm) REVERT: h 208 GLU cc_start: 0.8570 (tm-30) cc_final: 0.7682 (tm-30) REVERT: h 230 ARG cc_start: 0.6571 (ttp80) cc_final: 0.5455 (ttp-170) REVERT: i 28 ASP cc_start: 0.6407 (t70) cc_final: 0.6158 (t70) REVERT: i 32 GLN cc_start: 0.7458 (pt0) cc_final: 0.7137 (pt0) REVERT: i 237 TRP cc_start: 0.8506 (t-100) cc_final: 0.8091 (t-100) REVERT: i 247 MET cc_start: 0.8491 (mmp) cc_final: 0.8170 (mmm) outliers start: 331 outliers final: 245 residues processed: 1350 average time/residue: 0.5546 time to fit residues: 1267.2905 Evaluate side-chains 1354 residues out of total 6648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1089 time to evaluate : 6.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 10 PHE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 227 GLN Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain E residue 233 ASN Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 49 CYS Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 123 HIS Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 51 HIS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 77 HIS Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 165 TYR Chi-restraints excluded: chain H residue 201 MET Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 4 CYS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 148 HIS Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain M residue 76 ASP Chi-restraints excluded: chain M residue 91 THR Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 166 VAL Chi-restraints excluded: chain M residue 192 ASN Chi-restraints excluded: chain M residue 194 ASN Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 26 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 71 ASN Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 136 TYR Chi-restraints excluded: chain O residue 138 ARG Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain P residue 156 PHE Chi-restraints excluded: chain P residue 181 ASP Chi-restraints excluded: chain P residue 203 LEU Chi-restraints excluded: chain Q residue 8 ARG Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 141 THR Chi-restraints excluded: chain Q residue 193 LEU Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 210 ILE Chi-restraints excluded: chain Q residue 224 GLN Chi-restraints excluded: chain Q residue 231 GLU Chi-restraints excluded: chain Q residue 243 TYR Chi-restraints excluded: chain R residue 10 PHE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 31 CYS Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 229 ILE Chi-restraints excluded: chain R residue 230 ASP Chi-restraints excluded: chain S residue 44 ASP Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 78 MET Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 151 ASN Chi-restraints excluded: chain S residue 180 GLU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 105 ILE Chi-restraints excluded: chain T residue 187 ILE Chi-restraints excluded: chain T residue 205 THR Chi-restraints excluded: chain T residue 214 VAL Chi-restraints excluded: chain U residue 60 MET Chi-restraints excluded: chain U residue 80 TYR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain U residue 131 MET Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 3 ILE Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 164 LEU Chi-restraints excluded: chain V residue 201 MET Chi-restraints excluded: chain V residue 231 VAL Chi-restraints excluded: chain V residue 244 VAL Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 156 CYS Chi-restraints excluded: chain W residue 165 ASN Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 31 ASP Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 74 THR Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain Y residue 132 HIS Chi-restraints excluded: chain Y residue 148 HIS Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 160 ILE Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 188 ILE Chi-restraints excluded: chain Z residue 193 VAL Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 57 LEU Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 78 CYS Chi-restraints excluded: chain a residue 91 THR Chi-restraints excluded: chain a residue 141 VAL Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 15 ILE Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 177 THR Chi-restraints excluded: chain b residue 178 THR Chi-restraints excluded: chain b residue 230 THR Chi-restraints excluded: chain c residue 64 VAL Chi-restraints excluded: chain c residue 135 HIS Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain c residue 222 VAL Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 135 HIS Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 172 ASP Chi-restraints excluded: chain d residue 222 VAL Chi-restraints excluded: chain e residue 28 ASP Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 165 LEU Chi-restraints excluded: chain f residue 66 ASP Chi-restraints excluded: chain f residue 140 LEU Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain f residue 213 SER Chi-restraints excluded: chain f residue 243 THR Chi-restraints excluded: chain g residue 60 SER Chi-restraints excluded: chain g residue 66 ASP Chi-restraints excluded: chain g residue 142 LEU Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain g residue 222 VAL Chi-restraints excluded: chain h residue 44 ARG Chi-restraints excluded: chain h residue 53 ASN Chi-restraints excluded: chain h residue 65 ASN Chi-restraints excluded: chain i residue 137 GLN Chi-restraints excluded: chain i residue 180 ILE Chi-restraints excluded: chain i residue 253 MET Chi-restraints excluded: chain i residue 256 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 736 random chunks: chunk 686 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 405 optimal weight: 0.8980 chunk 520 optimal weight: 0.4980 chunk 402 optimal weight: 0.7980 chunk 599 optimal weight: 0.4980 chunk 397 optimal weight: 3.9990 chunk 709 optimal weight: 9.9990 chunk 443 optimal weight: 0.0570 chunk 432 optimal weight: 0.6980 chunk 327 optimal weight: 0.8980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN C 177 GLN ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 180 HIS ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 71 ASN ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 109 GLN T 165 HIS U 89 ASN U 231 ASN U 233 HIS ** V 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 247 GLN W 91 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 261 ASN d 135 HIS ** d 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 239 HIS ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 164 GLN h 226 GLN ** i 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 174 ASN ** i 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 61370 Z= 0.163 Angle : 0.575 12.244 82846 Z= 0.299 Chirality : 0.042 0.328 9279 Planarity : 0.003 0.073 10541 Dihedral : 4.786 79.622 8218 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.70 % Allowed : 25.23 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.10), residues: 7393 helix: 0.68 (0.10), residues: 3051 sheet: -2.17 (0.14), residues: 1285 loop : -2.28 (0.11), residues: 3057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 196 HIS 0.013 0.001 HIS d 135 PHE 0.023 0.001 PHE g 47 TYR 0.036 0.001 TYR N 31 ARG 0.008 0.000 ARG g 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1444 residues out of total 6648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1198 time to evaluate : 5.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: A 122 ARG cc_start: 0.7672 (mtt-85) cc_final: 0.7466 (mmt90) REVERT: A 150 ASP cc_start: 0.7736 (p0) cc_final: 0.6914 (p0) REVERT: A 154 LYS cc_start: 0.8217 (mtmt) cc_final: 0.7637 (pttm) REVERT: A 156 GLU cc_start: 0.8078 (mp0) cc_final: 0.7793 (mp0) REVERT: A 170 ARG cc_start: 0.8024 (ptp-170) cc_final: 0.7683 (ttp80) REVERT: B 49 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7342 (tm-30) REVERT: B 50 LYS cc_start: 0.6388 (tttt) cc_final: 0.6106 (ttpt) REVERT: B 109 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8121 (mm-30) REVERT: B 119 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8430 (tm-30) REVERT: C 41 ASP cc_start: 0.7845 (t0) cc_final: 0.7457 (t0) REVERT: C 54 LYS cc_start: 0.7745 (mttp) cc_final: 0.7219 (tptt) REVERT: C 98 LEU cc_start: 0.9560 (tp) cc_final: 0.9335 (tt) REVERT: C 222 VAL cc_start: 0.7146 (OUTLIER) cc_final: 0.6772 (t) REVERT: D 117 LYS cc_start: 0.6072 (mttt) cc_final: 0.5498 (ttmt) REVERT: D 121 ARG cc_start: 0.8252 (ttm170) cc_final: 0.7896 (ttp-170) REVERT: D 180 MET cc_start: 0.8739 (mmm) cc_final: 0.8485 (mmm) REVERT: D 212 LYS cc_start: 0.8139 (mttt) cc_final: 0.7514 (mtmt) REVERT: E 176 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8071 (pp30) REVERT: F 9 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.8036 (m-30) REVERT: F 88 MET cc_start: 0.8809 (ttm) cc_final: 0.8438 (ttm) REVERT: F 106 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7496 (tm-30) REVERT: F 112 VAL cc_start: 0.9513 (OUTLIER) cc_final: 0.9303 (p) REVERT: F 117 GLN cc_start: 0.8772 (tp40) cc_final: 0.8250 (tp40) REVERT: F 190 CYS cc_start: 0.9163 (t) cc_final: 0.8878 (t) REVERT: G 48 CYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8509 (m) REVERT: G 151 ILE cc_start: 0.9470 (mp) cc_final: 0.8996 (mt) REVERT: G 232 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7654 (mp) REVERT: H 222 ASN cc_start: 0.8521 (m110) cc_final: 0.7939 (m110) REVERT: I 17 ASP cc_start: 0.8692 (p0) cc_final: 0.8264 (p0) REVERT: I 51 ASP cc_start: 0.7923 (t0) cc_final: 0.7516 (t70) REVERT: I 174 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.8014 (p0) REVERT: J 44 ILE cc_start: 0.9054 (pt) cc_final: 0.8834 (pt) REVERT: J 47 MET cc_start: 0.8620 (tpp) cc_final: 0.8275 (mmm) REVERT: J 84 MET cc_start: 0.8655 (ttt) cc_final: 0.8235 (ttt) REVERT: J 98 TYR cc_start: 0.8628 (t80) cc_final: 0.8277 (t80) REVERT: J 101 ARG cc_start: 0.7453 (ttp80) cc_final: 0.6942 (ttp80) REVERT: J 189 ASP cc_start: 0.8274 (t0) cc_final: 0.7970 (t0) REVERT: J 191 ASP cc_start: 0.8015 (t70) cc_final: 0.7750 (t70) REVERT: K 76 MET cc_start: 0.8705 (tpt) cc_final: 0.8215 (tpt) REVERT: K 139 VAL cc_start: 0.9140 (m) cc_final: 0.8771 (p) REVERT: K 166 GLU cc_start: 0.9331 (tm-30) cc_final: 0.9055 (tm-30) REVERT: L 19 ARG cc_start: 0.8637 (ttm170) cc_final: 0.8251 (ttm170) REVERT: L 40 ASN cc_start: 0.8116 (t0) cc_final: 0.7758 (t0) REVERT: L 67 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8156 (mm-30) REVERT: L 93 TYR cc_start: 0.7708 (m-80) cc_final: 0.7296 (m-80) REVERT: M 30 TRP cc_start: 0.7367 (t-100) cc_final: 0.6608 (t-100) REVERT: M 33 TYR cc_start: 0.8577 (m-10) cc_final: 0.8278 (m-10) REVERT: M 114 HIS cc_start: 0.7492 (m-70) cc_final: 0.7220 (m-70) REVERT: M 171 GLN cc_start: 0.8474 (mt0) cc_final: 0.8091 (mt0) REVERT: M 194 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8374 (p0) REVERT: M 232 VAL cc_start: 0.8945 (t) cc_final: 0.8516 (p) REVERT: N 166 MET cc_start: 0.8678 (ptp) cc_final: 0.8313 (ptp) REVERT: O 137 MET cc_start: 0.7439 (mpp) cc_final: 0.7188 (mpp) REVERT: O 138 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8567 (tmm160) REVERT: O 214 GLU cc_start: 0.7983 (pt0) cc_final: 0.7432 (pt0) REVERT: O 234 VAL cc_start: 0.9367 (OUTLIER) cc_final: 0.9127 (t) REVERT: P 20 VAL cc_start: 0.8412 (m) cc_final: 0.8105 (p) REVERT: P 109 GLU cc_start: 0.8726 (tm-30) cc_final: 0.7688 (tm-30) REVERT: Q 3 ARG cc_start: 0.7611 (pmt-80) cc_final: 0.6433 (ptp-170) REVERT: Q 8 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7820 (ptp90) REVERT: Q 17 ARG cc_start: 0.7638 (ttp-110) cc_final: 0.7230 (ttp-110) REVERT: Q 26 GLU cc_start: 0.7408 (tm-30) cc_final: 0.6937 (tm-30) REVERT: Q 231 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8547 (pt0) REVERT: Q 243 TYR cc_start: 0.6881 (OUTLIER) cc_final: 0.5871 (m-80) REVERT: R 90 GLU cc_start: 0.8242 (tp30) cc_final: 0.7888 (tp30) REVERT: R 212 LYS cc_start: 0.8432 (mttt) cc_final: 0.8134 (mttm) REVERT: S 15 PHE cc_start: 0.9189 (m-80) cc_final: 0.8820 (m-10) REVERT: S 44 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.7530 (p0) REVERT: S 62 ASP cc_start: 0.7203 (t70) cc_final: 0.6858 (t0) REVERT: S 71 ASP cc_start: 0.8122 (t70) cc_final: 0.7807 (t0) REVERT: S 206 GLN cc_start: 0.8655 (mm110) cc_final: 0.8361 (mp10) REVERT: T 20 TYR cc_start: 0.8753 (m-80) cc_final: 0.8161 (m-80) REVERT: T 24 TYR cc_start: 0.8914 (m-10) cc_final: 0.8372 (m-80) REVERT: T 86 LYS cc_start: 0.8630 (ttmt) cc_final: 0.8408 (ttpt) REVERT: T 88 MET cc_start: 0.8927 (ttp) cc_final: 0.8679 (ttp) REVERT: T 91 GLU cc_start: 0.5828 (mt-10) cc_final: 0.5332 (tp30) REVERT: T 116 TYR cc_start: 0.8830 (m-80) cc_final: 0.8528 (m-10) REVERT: T 117 GLN cc_start: 0.8580 (tp40) cc_final: 0.8212 (tp40) REVERT: T 145 GLU cc_start: 0.7958 (tt0) cc_final: 0.7714 (tt0) REVERT: T 154 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6734 (tm-30) REVERT: T 190 CYS cc_start: 0.8958 (t) cc_final: 0.8548 (t) REVERT: T 217 ASN cc_start: 0.8801 (m-40) cc_final: 0.8507 (m-40) REVERT: T 227 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8488 (tm-30) REVERT: U 48 CYS cc_start: 0.8670 (m) cc_final: 0.8155 (m) REVERT: U 60 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7514 (mtm) REVERT: U 89 ASN cc_start: 0.9390 (OUTLIER) cc_final: 0.8854 (t0) REVERT: U 144 ASN cc_start: 0.8395 (t0) cc_final: 0.8021 (t0) REVERT: V 8 TYR cc_start: 0.6817 (m-10) cc_final: 0.5941 (m-80) REVERT: V 13 MET cc_start: 0.7479 (mtp) cc_final: 0.6747 (mtp) REVERT: V 69 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8096 (mt-10) REVERT: V 80 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8462 (tm-30) REVERT: V 85 GLU cc_start: 0.8479 (tt0) cc_final: 0.8161 (tt0) REVERT: V 156 TYR cc_start: 0.8416 (t80) cc_final: 0.7595 (t80) REVERT: V 248 MET cc_start: 0.7248 (tpt) cc_final: 0.6968 (tpp) REVERT: W 184 GLN cc_start: 0.7539 (mp10) cc_final: 0.7041 (mp10) REVERT: W 213 LEU cc_start: 0.8459 (mt) cc_final: 0.8133 (mt) REVERT: X 80 GLN cc_start: 0.8847 (mm110) cc_final: 0.8466 (mm110) REVERT: X 158 GLN cc_start: 0.7575 (mp10) cc_final: 0.7247 (mt0) REVERT: X 201 LEU cc_start: 0.9295 (tp) cc_final: 0.9035 (tp) REVERT: Y 166 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8611 (tm-30) REVERT: Y 183 MET cc_start: 0.8399 (mtm) cc_final: 0.7968 (mmm) REVERT: Z 189 GLU cc_start: 0.6963 (mp0) cc_final: 0.6632 (mp0) REVERT: Z 194 PHE cc_start: 0.5224 (OUTLIER) cc_final: 0.4695 (m-10) REVERT: a 143 GLU cc_start: 0.8627 (pp20) cc_final: 0.8425 (pm20) REVERT: a 152 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7744 (p90) REVERT: a 182 GLU cc_start: 0.6070 (tt0) cc_final: 0.4867 (tm-30) REVERT: c 135 HIS cc_start: 0.6076 (OUTLIER) cc_final: 0.5598 (t-90) REVERT: c 188 LEU cc_start: 0.8470 (mm) cc_final: 0.8197 (tp) REVERT: c 233 ASP cc_start: 0.9034 (m-30) cc_final: 0.8624 (m-30) REVERT: c 251 TYR cc_start: 0.6697 (m-80) cc_final: 0.6413 (m-80) REVERT: d 38 ARG cc_start: 0.6075 (mtt90) cc_final: 0.5184 (mtp-110) REVERT: d 44 ARG cc_start: 0.7529 (tpp80) cc_final: 0.6658 (mmm-85) REVERT: d 52 VAL cc_start: 0.6583 (OUTLIER) cc_final: 0.6303 (m) REVERT: d 135 HIS cc_start: 0.7447 (OUTLIER) cc_final: 0.6851 (m170) REVERT: d 262 TRP cc_start: 0.6909 (t-100) cc_final: 0.6553 (t60) REVERT: e 139 TYR cc_start: 0.7101 (t80) cc_final: 0.6358 (t80) REVERT: f 40 ARG cc_start: 0.7367 (mtt90) cc_final: 0.7080 (mtt90) REVERT: f 48 PHE cc_start: 0.7548 (m-80) cc_final: 0.6902 (m-80) REVERT: f 182 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6526 (mt-10) REVERT: g 22 TYR cc_start: 0.7000 (t80) cc_final: 0.6764 (t80) REVERT: g 192 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8183 (tm-30) REVERT: g 207 MET cc_start: 0.8150 (ttp) cc_final: 0.7379 (mmt) REVERT: g 250 ASN cc_start: 0.8627 (m-40) cc_final: 0.8136 (m110) REVERT: g 253 MET cc_start: 0.8678 (ptp) cc_final: 0.8458 (ptp) REVERT: h 44 ARG cc_start: 0.5827 (OUTLIER) cc_final: 0.5555 (mpt180) REVERT: h 48 PHE cc_start: 0.8166 (m-80) cc_final: 0.7811 (m-80) REVERT: h 53 ASN cc_start: 0.6866 (OUTLIER) cc_final: 0.6592 (t0) REVERT: h 207 MET cc_start: 0.8057 (mmm) cc_final: 0.7758 (mmm) REVERT: h 208 GLU cc_start: 0.8441 (tm-30) cc_final: 0.7320 (tm-30) REVERT: h 230 ARG cc_start: 0.6583 (ttp80) cc_final: 0.5595 (ttp-170) REVERT: i 137 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.6923 (pt0) REVERT: i 160 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7432 (tttm) REVERT: i 204 LYS cc_start: 0.8506 (mmmt) cc_final: 0.8228 (mmmt) REVERT: i 237 TRP cc_start: 0.8438 (t-100) cc_final: 0.7980 (t-100) REVERT: i 246 ASP cc_start: 0.8049 (m-30) cc_final: 0.7840 (m-30) outliers start: 246 outliers final: 172 residues processed: 1364 average time/residue: 0.5513 time to fit residues: 1271.8948 Evaluate side-chains 1307 residues out of total 6648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1111 time to evaluate : 5.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 10 PHE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 227 GLN Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain E residue 233 ASN Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 49 CYS Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 51 HIS Chi-restraints excluded: chain H residue 77 HIS Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 165 TYR Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 148 HIS Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain M residue 76 ASP Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 166 VAL Chi-restraints excluded: chain M residue 192 ASN Chi-restraints excluded: chain M residue 194 ASN Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 26 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 136 TYR Chi-restraints excluded: chain O residue 138 ARG Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 156 PHE Chi-restraints excluded: chain P residue 181 ASP Chi-restraints excluded: chain P residue 203 LEU Chi-restraints excluded: chain Q residue 8 ARG Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 141 THR Chi-restraints excluded: chain Q residue 210 ILE Chi-restraints excluded: chain Q residue 231 GLU Chi-restraints excluded: chain Q residue 243 TYR Chi-restraints excluded: chain R residue 10 PHE Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain S residue 44 ASP Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 78 MET Chi-restraints excluded: chain S residue 151 ASN Chi-restraints excluded: chain S residue 180 GLU Chi-restraints excluded: chain T residue 205 THR Chi-restraints excluded: chain T residue 214 VAL Chi-restraints excluded: chain U residue 60 MET Chi-restraints excluded: chain U residue 80 TYR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 164 LEU Chi-restraints excluded: chain V residue 201 MET Chi-restraints excluded: chain V residue 244 VAL Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 165 ASN Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 72 ASN Chi-restraints excluded: chain Y residue 74 THR Chi-restraints excluded: chain Y residue 148 HIS Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 160 ILE Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 182 ASN Chi-restraints excluded: chain Z residue 188 ILE Chi-restraints excluded: chain Z residue 193 VAL Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 78 CYS Chi-restraints excluded: chain a residue 91 THR Chi-restraints excluded: chain a residue 152 TYR Chi-restraints excluded: chain a residue 185 ASN Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 178 THR Chi-restraints excluded: chain b residue 230 THR Chi-restraints excluded: chain c residue 64 VAL Chi-restraints excluded: chain c residue 135 HIS Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain c residue 222 VAL Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 135 HIS Chi-restraints excluded: chain d residue 172 ASP Chi-restraints excluded: chain d residue 222 VAL Chi-restraints excluded: chain e residue 28 ASP Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 165 LEU Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain e residue 242 ILE Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain g residue 66 ASP Chi-restraints excluded: chain g residue 142 LEU Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain g residue 222 VAL Chi-restraints excluded: chain g residue 239 HIS Chi-restraints excluded: chain h residue 44 ARG Chi-restraints excluded: chain h residue 53 ASN Chi-restraints excluded: chain h residue 65 ASN Chi-restraints excluded: chain h residue 188 LEU Chi-restraints excluded: chain h residue 252 ILE Chi-restraints excluded: chain i residue 137 GLN Chi-restraints excluded: chain i residue 180 ILE Chi-restraints excluded: chain i residue 253 MET Chi-restraints excluded: chain i residue 256 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 736 random chunks: chunk 438 optimal weight: 3.9990 chunk 283 optimal weight: 8.9990 chunk 423 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 139 optimal weight: 0.2980 chunk 137 optimal weight: 5.9990 chunk 451 optimal weight: 1.9990 chunk 483 optimal weight: 0.8980 chunk 350 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 557 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 180 HIS ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 98 HIS T 165 HIS U 89 ASN U 231 ASN U 233 HIS ** V 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 170 ASN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 181 GLN c 261 ASN d 135 HIS ** d 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 239 HIS f 197 ASN ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 164 GLN h 181 GLN ** i 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 61370 Z= 0.181 Angle : 0.580 12.241 82846 Z= 0.300 Chirality : 0.043 0.317 9279 Planarity : 0.003 0.112 10541 Dihedral : 4.726 79.793 8218 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.96 % Allowed : 25.54 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.10), residues: 7393 helix: 0.82 (0.10), residues: 3025 sheet: -2.06 (0.14), residues: 1276 loop : -2.22 (0.11), residues: 3092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP g 262 HIS 0.011 0.001 HIS d 135 PHE 0.025 0.001 PHE D 73 TYR 0.026 0.001 TYR e 148 ARG 0.009 0.000 ARG g 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1437 residues out of total 6648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1174 time to evaluate : 5.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7713 (p0) cc_final: 0.7137 (p0) REVERT: A 154 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7514 (pttm) REVERT: A 165 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7823 (t80) REVERT: A 170 ARG cc_start: 0.8133 (ptp-170) cc_final: 0.7709 (ttp80) REVERT: B 49 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7435 (tm-30) REVERT: B 50 LYS cc_start: 0.6422 (tttt) cc_final: 0.6145 (ttpt) REVERT: B 119 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8373 (tm-30) REVERT: C 41 ASP cc_start: 0.7948 (t0) cc_final: 0.7596 (t0) REVERT: C 54 LYS cc_start: 0.7710 (mttp) cc_final: 0.7363 (tptt) REVERT: C 98 LEU cc_start: 0.9582 (tp) cc_final: 0.9354 (tt) REVERT: C 222 VAL cc_start: 0.6980 (OUTLIER) cc_final: 0.6634 (t) REVERT: D 117 LYS cc_start: 0.6066 (mttt) cc_final: 0.5509 (ttmt) REVERT: D 121 ARG cc_start: 0.8267 (ttm170) cc_final: 0.7903 (ttp-170) REVERT: D 212 LYS cc_start: 0.8121 (mttt) cc_final: 0.7506 (mtmt) REVERT: F 6 TYR cc_start: 0.8706 (m-80) cc_final: 0.8066 (m-10) REVERT: F 9 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: F 88 MET cc_start: 0.8794 (ttm) cc_final: 0.8470 (ttm) REVERT: F 106 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7504 (tm-30) REVERT: F 112 VAL cc_start: 0.9537 (OUTLIER) cc_final: 0.9312 (p) REVERT: F 117 GLN cc_start: 0.8602 (tp40) cc_final: 0.8362 (tp-100) REVERT: F 190 CYS cc_start: 0.9108 (t) cc_final: 0.8758 (t) REVERT: G 151 ILE cc_start: 0.9460 (mp) cc_final: 0.8992 (mt) REVERT: G 232 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7657 (mp) REVERT: H 66 MET cc_start: 0.8243 (ttp) cc_final: 0.8039 (ttp) REVERT: H 222 ASN cc_start: 0.8514 (m110) cc_final: 0.7960 (m110) REVERT: I 17 ASP cc_start: 0.8756 (p0) cc_final: 0.8374 (p0) REVERT: I 51 ASP cc_start: 0.7934 (t0) cc_final: 0.7497 (t70) REVERT: I 145 ASN cc_start: 0.7748 (t0) cc_final: 0.7541 (t0) REVERT: I 174 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.8044 (p0) REVERT: J 44 ILE cc_start: 0.9056 (pt) cc_final: 0.8766 (pt) REVERT: J 47 MET cc_start: 0.8637 (tpp) cc_final: 0.8325 (mmm) REVERT: J 84 MET cc_start: 0.8668 (ttt) cc_final: 0.8263 (ttt) REVERT: J 98 TYR cc_start: 0.8676 (t80) cc_final: 0.8339 (t80) REVERT: J 101 ARG cc_start: 0.7442 (ttp80) cc_final: 0.7003 (ttp80) REVERT: J 162 MET cc_start: 0.8549 (tpp) cc_final: 0.7523 (tpt) REVERT: J 189 ASP cc_start: 0.8262 (t0) cc_final: 0.7957 (t0) REVERT: J 191 ASP cc_start: 0.8112 (t70) cc_final: 0.7841 (t70) REVERT: J 196 TRP cc_start: 0.6664 (t60) cc_final: 0.6231 (t60) REVERT: K 76 MET cc_start: 0.8746 (tpt) cc_final: 0.8257 (tpt) REVERT: K 86 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8822 (ttp80) REVERT: K 153 VAL cc_start: 0.8722 (t) cc_final: 0.8490 (t) REVERT: K 166 GLU cc_start: 0.9289 (tm-30) cc_final: 0.9063 (tm-30) REVERT: L 19 ARG cc_start: 0.8638 (ttm170) cc_final: 0.8250 (ttm170) REVERT: L 40 ASN cc_start: 0.8129 (t0) cc_final: 0.7703 (t0) REVERT: L 67 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8112 (mm-30) REVERT: L 93 TYR cc_start: 0.7705 (m-80) cc_final: 0.7281 (m-80) REVERT: M 30 TRP cc_start: 0.7362 (t-100) cc_final: 0.6585 (t-100) REVERT: M 33 TYR cc_start: 0.8590 (m-10) cc_final: 0.8258 (m-10) REVERT: M 114 HIS cc_start: 0.7485 (m-70) cc_final: 0.7211 (m-70) REVERT: M 194 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8355 (p0) REVERT: M 232 VAL cc_start: 0.8896 (t) cc_final: 0.8623 (p) REVERT: N 52 MET cc_start: 0.8974 (ppp) cc_final: 0.8538 (ppp) REVERT: N 113 ILE cc_start: 0.9212 (mm) cc_final: 0.9005 (mm) REVERT: N 166 MET cc_start: 0.8585 (ptp) cc_final: 0.8264 (ptp) REVERT: O 214 GLU cc_start: 0.7940 (pt0) cc_final: 0.7403 (pt0) REVERT: O 234 VAL cc_start: 0.9393 (OUTLIER) cc_final: 0.9148 (t) REVERT: P 20 VAL cc_start: 0.8402 (m) cc_final: 0.8089 (p) REVERT: P 109 GLU cc_start: 0.8734 (tm-30) cc_final: 0.7723 (tm-30) REVERT: Q 3 ARG cc_start: 0.7639 (pmt-80) cc_final: 0.6440 (ptp-170) REVERT: Q 17 ARG cc_start: 0.7646 (ttp-110) cc_final: 0.7247 (ttp-110) REVERT: Q 26 GLU cc_start: 0.7402 (tm-30) cc_final: 0.6951 (tm-30) REVERT: Q 243 TYR cc_start: 0.6875 (OUTLIER) cc_final: 0.5950 (m-80) REVERT: R 90 GLU cc_start: 0.8330 (tp30) cc_final: 0.7961 (tp30) REVERT: R 212 LYS cc_start: 0.8482 (mttt) cc_final: 0.8206 (mttm) REVERT: R 225 MET cc_start: 0.8701 (tpp) cc_final: 0.8461 (tpp) REVERT: S 15 PHE cc_start: 0.9159 (m-80) cc_final: 0.8805 (m-10) REVERT: S 44 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.7906 (p0) REVERT: S 62 ASP cc_start: 0.7178 (t70) cc_final: 0.6836 (t0) REVERT: S 71 ASP cc_start: 0.8131 (t70) cc_final: 0.7833 (t0) REVERT: S 206 GLN cc_start: 0.8682 (mm110) cc_final: 0.8393 (mp10) REVERT: T 20 TYR cc_start: 0.8749 (m-80) cc_final: 0.8118 (m-80) REVERT: T 24 TYR cc_start: 0.8934 (m-10) cc_final: 0.8371 (m-80) REVERT: T 88 MET cc_start: 0.8942 (ttp) cc_final: 0.8727 (ttp) REVERT: T 91 GLU cc_start: 0.5777 (mt-10) cc_final: 0.5444 (tp30) REVERT: T 116 TYR cc_start: 0.8847 (m-80) cc_final: 0.8493 (m-10) REVERT: T 117 GLN cc_start: 0.8601 (tp40) cc_final: 0.8204 (tp40) REVERT: T 145 GLU cc_start: 0.7867 (tt0) cc_final: 0.7596 (tt0) REVERT: T 190 CYS cc_start: 0.8918 (t) cc_final: 0.8465 (t) REVERT: T 217 ASN cc_start: 0.8761 (m-40) cc_final: 0.8482 (m-40) REVERT: T 227 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8533 (tm-30) REVERT: U 48 CYS cc_start: 0.8623 (m) cc_final: 0.8086 (m) REVERT: U 60 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7465 (mtm) REVERT: U 144 ASN cc_start: 0.8395 (t0) cc_final: 0.8042 (t0) REVERT: V 8 TYR cc_start: 0.6914 (m-10) cc_final: 0.5939 (m-80) REVERT: V 13 MET cc_start: 0.7454 (mtp) cc_final: 0.6712 (mtp) REVERT: V 69 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8085 (mt-10) REVERT: V 80 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8405 (tm-30) REVERT: V 156 TYR cc_start: 0.8403 (t80) cc_final: 0.8192 (t80) REVERT: W 36 TYR cc_start: 0.8511 (t80) cc_final: 0.8041 (t80) REVERT: W 213 LEU cc_start: 0.8372 (mt) cc_final: 0.8153 (mt) REVERT: X 80 GLN cc_start: 0.8832 (mm110) cc_final: 0.8471 (mm110) REVERT: X 158 GLN cc_start: 0.7555 (mp10) cc_final: 0.7274 (mp10) REVERT: Y 31 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.7009 (m-30) REVERT: Y 166 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8557 (tm-30) REVERT: Y 183 MET cc_start: 0.8315 (mtm) cc_final: 0.7908 (mmm) REVERT: Z 125 LEU cc_start: 0.9053 (tp) cc_final: 0.8552 (tp) REVERT: Z 189 GLU cc_start: 0.6905 (mp0) cc_final: 0.6619 (mp0) REVERT: Z 194 PHE cc_start: 0.5313 (OUTLIER) cc_final: 0.4713 (m-10) REVERT: a 133 TYR cc_start: 0.9061 (t80) cc_final: 0.8643 (t80) REVERT: a 152 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7736 (p90) REVERT: a 182 GLU cc_start: 0.5980 (tt0) cc_final: 0.4812 (tm-30) REVERT: c 135 HIS cc_start: 0.6061 (OUTLIER) cc_final: 0.5587 (t-90) REVERT: c 188 LEU cc_start: 0.8468 (mm) cc_final: 0.8198 (tp) REVERT: c 233 ASP cc_start: 0.9037 (m-30) cc_final: 0.8638 (m-30) REVERT: c 247 MET cc_start: 0.8078 (mmm) cc_final: 0.7251 (mmm) REVERT: d 38 ARG cc_start: 0.6030 (mtt90) cc_final: 0.5188 (mtp-110) REVERT: d 44 ARG cc_start: 0.7489 (tpp80) cc_final: 0.6697 (mmm-85) REVERT: d 135 HIS cc_start: 0.7345 (OUTLIER) cc_final: 0.6691 (m170) REVERT: d 162 TRP cc_start: 0.8670 (t60) cc_final: 0.8378 (t60) REVERT: d 262 TRP cc_start: 0.7010 (t-100) cc_final: 0.6555 (t60) REVERT: e 139 TYR cc_start: 0.7065 (t80) cc_final: 0.6309 (t80) REVERT: e 207 MET cc_start: 0.8021 (mtm) cc_final: 0.7683 (mpp) REVERT: f 48 PHE cc_start: 0.7540 (m-80) cc_final: 0.6895 (m-80) REVERT: f 182 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6553 (mt-10) REVERT: f 235 LYS cc_start: 0.7557 (tmtt) cc_final: 0.6666 (ttpt) REVERT: g 22 TYR cc_start: 0.7003 (t80) cc_final: 0.6735 (t80) REVERT: g 192 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8255 (tm-30) REVERT: g 207 MET cc_start: 0.8155 (ttp) cc_final: 0.7393 (mmt) REVERT: g 250 ASN cc_start: 0.8607 (m-40) cc_final: 0.8129 (m110) REVERT: g 253 MET cc_start: 0.8670 (ptp) cc_final: 0.8451 (ptp) REVERT: h 44 ARG cc_start: 0.5989 (OUTLIER) cc_final: 0.5639 (mpt180) REVERT: h 48 PHE cc_start: 0.7988 (m-80) cc_final: 0.7673 (m-80) REVERT: h 49 ASN cc_start: 0.8588 (t0) cc_final: 0.8240 (t0) REVERT: h 53 ASN cc_start: 0.6949 (OUTLIER) cc_final: 0.6492 (t0) REVERT: h 135 HIS cc_start: 0.7625 (OUTLIER) cc_final: 0.6533 (t-90) REVERT: h 207 MET cc_start: 0.8163 (mmm) cc_final: 0.7898 (mmm) REVERT: h 208 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8155 (tp30) REVERT: h 230 ARG cc_start: 0.6598 (ttp80) cc_final: 0.5619 (ttp-170) REVERT: i 137 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6915 (pt0) REVERT: i 160 LYS cc_start: 0.8478 (ttmt) cc_final: 0.7471 (tttm) REVERT: i 237 TRP cc_start: 0.8427 (t-100) cc_final: 0.7964 (t-100) outliers start: 263 outliers final: 196 residues processed: 1351 average time/residue: 0.5584 time to fit residues: 1275.4122 Evaluate side-chains 1337 residues out of total 6648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1120 time to evaluate : 5.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 10 PHE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 227 GLN Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain E residue 233 ASN Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 155 TYR Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 49 CYS Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 51 HIS Chi-restraints excluded: chain H residue 77 HIS Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 165 TYR Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 86 ARG Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 148 HIS Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain M residue 76 ASP Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 166 VAL Chi-restraints excluded: chain M residue 192 ASN Chi-restraints excluded: chain M residue 194 ASN Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 26 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 136 TYR Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain P residue 156 PHE Chi-restraints excluded: chain P residue 181 ASP Chi-restraints excluded: chain P residue 203 LEU Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 141 THR Chi-restraints excluded: chain Q residue 183 MET Chi-restraints excluded: chain Q residue 210 ILE Chi-restraints excluded: chain Q residue 243 TYR Chi-restraints excluded: chain R residue 10 PHE Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain S residue 44 ASP Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 78 MET Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 151 ASN Chi-restraints excluded: chain S residue 180 GLU Chi-restraints excluded: chain T residue 105 ILE Chi-restraints excluded: chain T residue 205 THR Chi-restraints excluded: chain T residue 214 VAL Chi-restraints excluded: chain U residue 60 MET Chi-restraints excluded: chain U residue 80 TYR Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 164 LEU Chi-restraints excluded: chain V residue 201 MET Chi-restraints excluded: chain V residue 244 VAL Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 165 ASN Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 31 ASP Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 72 ASN Chi-restraints excluded: chain Y residue 74 THR Chi-restraints excluded: chain Y residue 148 HIS Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 160 ILE Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 182 ASN Chi-restraints excluded: chain Z residue 188 ILE Chi-restraints excluded: chain Z residue 193 VAL Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 78 CYS Chi-restraints excluded: chain a residue 91 THR Chi-restraints excluded: chain a residue 141 VAL Chi-restraints excluded: chain a residue 152 TYR Chi-restraints excluded: chain a residue 185 ASN Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain b residue 15 ILE Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 178 THR Chi-restraints excluded: chain b residue 230 THR Chi-restraints excluded: chain c residue 29 ILE Chi-restraints excluded: chain c residue 64 VAL Chi-restraints excluded: chain c residue 135 HIS Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain c residue 222 VAL Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain d residue 135 HIS Chi-restraints excluded: chain d residue 172 ASP Chi-restraints excluded: chain d residue 222 VAL Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 165 LEU Chi-restraints excluded: chain e residue 242 ILE Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain f residue 197 ASN Chi-restraints excluded: chain f residue 253 MET Chi-restraints excluded: chain g residue 142 LEU Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain g residue 222 VAL Chi-restraints excluded: chain g residue 239 HIS Chi-restraints excluded: chain h residue 44 ARG Chi-restraints excluded: chain h residue 53 ASN Chi-restraints excluded: chain h residue 65 ASN Chi-restraints excluded: chain h residue 135 HIS Chi-restraints excluded: chain h residue 252 ILE Chi-restraints excluded: chain i residue 28 ASP Chi-restraints excluded: chain i residue 137 GLN Chi-restraints excluded: chain i residue 180 ILE Chi-restraints excluded: chain i residue 230 ARG Chi-restraints excluded: chain i residue 256 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 736 random chunks: chunk 645 optimal weight: 7.9990 chunk 679 optimal weight: 10.0000 chunk 620 optimal weight: 9.9990 chunk 661 optimal weight: 5.9990 chunk 397 optimal weight: 3.9990 chunk 287 optimal weight: 6.9990 chunk 519 optimal weight: 0.7980 chunk 202 optimal weight: 7.9990 chunk 597 optimal weight: 3.9990 chunk 625 optimal weight: 5.9990 chunk 658 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN D 21 HIS ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 GLN L 158 ASN L 180 HIS ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 98 HIS T 165 HIS ** T 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 ASN U 231 ASN U 233 HIS ** V 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 247 GLN ** W 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 40 HIS ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 261 ASN d 65 ASN d 135 HIS ** d 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 164 GLN e 239 HIS ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 181 GLN h 181 GLN ** i 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 61370 Z= 0.492 Angle : 0.769 12.806 82846 Z= 0.398 Chirality : 0.049 0.320 9279 Planarity : 0.005 0.120 10541 Dihedral : 5.249 85.001 8218 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 4.65 % Allowed : 25.38 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.10), residues: 7393 helix: 0.51 (0.09), residues: 3056 sheet: -2.32 (0.14), residues: 1235 loop : -2.41 (0.10), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP U 129 HIS 0.023 0.001 HIS d 135 PHE 0.049 0.002 PHE f 196 TYR 0.049 0.002 TYR h 225 ARG 0.012 0.001 ARG Z 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1380 residues out of total 6648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 309 poor density : 1071 time to evaluate : 5.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8121 (p0) cc_final: 0.7302 (p0) REVERT: A 154 LYS cc_start: 0.8341 (mtmt) cc_final: 0.7726 (pttm) REVERT: A 170 ARG cc_start: 0.8225 (ptp-170) cc_final: 0.7950 (ttp80) REVERT: B 49 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7399 (tm-30) REVERT: B 50 LYS cc_start: 0.6702 (tttt) cc_final: 0.6339 (ttpt) REVERT: C 41 ASP cc_start: 0.8081 (t0) cc_final: 0.7751 (t0) REVERT: C 54 LYS cc_start: 0.7876 (mttp) cc_final: 0.7421 (tptt) REVERT: C 222 VAL cc_start: 0.8083 (OUTLIER) cc_final: 0.7675 (p) REVERT: D 117 LYS cc_start: 0.6116 (mttt) cc_final: 0.5544 (ttmt) REVERT: D 121 ARG cc_start: 0.8399 (ttm170) cc_final: 0.8041 (ttp-170) REVERT: E 176 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8234 (pp30) REVERT: E 208 MET cc_start: 0.9035 (tpt) cc_final: 0.8832 (tpt) REVERT: F 9 ASP cc_start: 0.8401 (m-30) cc_final: 0.8144 (m-30) REVERT: F 68 ASP cc_start: 0.8027 (p0) cc_final: 0.7638 (p0) REVERT: F 88 MET cc_start: 0.8818 (ttm) cc_final: 0.8330 (ttm) REVERT: F 117 GLN cc_start: 0.8816 (tp40) cc_final: 0.8307 (tp40) REVERT: F 190 CYS cc_start: 0.9184 (t) cc_final: 0.8842 (t) REVERT: G 18 ASP cc_start: 0.8386 (p0) cc_final: 0.8090 (p0) REVERT: G 123 HIS cc_start: 0.9256 (OUTLIER) cc_final: 0.8398 (t70) REVERT: G 232 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7597 (mp) REVERT: H 222 ASN cc_start: 0.8877 (m110) cc_final: 0.8348 (m110) REVERT: I 17 ASP cc_start: 0.8676 (p0) cc_final: 0.8326 (p0) REVERT: I 51 ASP cc_start: 0.8105 (t0) cc_final: 0.7744 (t0) REVERT: I 174 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8254 (p0) REVERT: J 47 MET cc_start: 0.8957 (tpp) cc_final: 0.8301 (tpp) REVERT: J 84 MET cc_start: 0.8738 (ttt) cc_final: 0.8331 (ttt) REVERT: J 101 ARG cc_start: 0.7701 (ttp80) cc_final: 0.7271 (ttp80) REVERT: J 162 MET cc_start: 0.8674 (tpp) cc_final: 0.7696 (tpt) REVERT: J 189 ASP cc_start: 0.8310 (t0) cc_final: 0.8006 (t0) REVERT: K 76 MET cc_start: 0.8842 (tpt) cc_final: 0.8556 (tpt) REVERT: K 80 SER cc_start: 0.9305 (p) cc_final: 0.8745 (t) REVERT: L 19 ARG cc_start: 0.8648 (ttm170) cc_final: 0.8248 (ttm170) REVERT: L 40 ASN cc_start: 0.8339 (t0) cc_final: 0.7909 (t0) REVERT: L 93 TYR cc_start: 0.7868 (m-80) cc_final: 0.7402 (m-80) REVERT: M 152 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.7872 (p90) REVERT: M 194 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8335 (p0) REVERT: N 52 MET cc_start: 0.8854 (ppp) cc_final: 0.8396 (ppp) REVERT: N 113 ILE cc_start: 0.9453 (mm) cc_final: 0.9240 (mm) REVERT: N 166 MET cc_start: 0.8732 (ptp) cc_final: 0.8293 (ptp) REVERT: O 137 MET cc_start: 0.7653 (mpp) cc_final: 0.7279 (mpp) REVERT: O 214 GLU cc_start: 0.8020 (pt0) cc_final: 0.7491 (pt0) REVERT: P 13 PHE cc_start: 0.9159 (OUTLIER) cc_final: 0.8099 (m-10) REVERT: P 72 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.8996 (mm) REVERT: P 96 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7639 (ttp80) REVERT: P 109 GLU cc_start: 0.8777 (tm-30) cc_final: 0.7733 (tm-30) REVERT: Q 3 ARG cc_start: 0.8073 (pmt-80) cc_final: 0.6603 (ptp-170) REVERT: Q 17 ARG cc_start: 0.7514 (ttp-110) cc_final: 0.7100 (ttp-110) REVERT: Q 26 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7024 (tm-30) REVERT: Q 149 HIS cc_start: 0.8844 (OUTLIER) cc_final: 0.8209 (t70) REVERT: R 90 GLU cc_start: 0.8565 (tp30) cc_final: 0.8289 (tp30) REVERT: R 212 LYS cc_start: 0.8464 (mttt) cc_final: 0.8185 (mttm) REVERT: S 44 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.7910 (p0) REVERT: S 71 ASP cc_start: 0.8296 (t70) cc_final: 0.7896 (t0) REVERT: S 206 GLN cc_start: 0.8748 (mm110) cc_final: 0.8474 (mp10) REVERT: T 61 GLU cc_start: 0.7754 (pp20) cc_final: 0.7215 (pp20) REVERT: T 88 MET cc_start: 0.8989 (ttp) cc_final: 0.8757 (ttp) REVERT: T 91 GLU cc_start: 0.5960 (mt-10) cc_final: 0.4588 (tp30) REVERT: T 116 TYR cc_start: 0.8878 (m-80) cc_final: 0.8266 (m-10) REVERT: T 154 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6996 (tm-30) REVERT: T 227 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8625 (tm-30) REVERT: U 48 CYS cc_start: 0.8657 (m) cc_final: 0.8180 (m) REVERT: U 60 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7729 (mtm) REVERT: U 89 ASN cc_start: 0.9585 (OUTLIER) cc_final: 0.9297 (t0) REVERT: U 144 ASN cc_start: 0.8515 (t0) cc_final: 0.8114 (t0) REVERT: V 13 MET cc_start: 0.7894 (mtp) cc_final: 0.7179 (mtp) REVERT: V 80 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8552 (tm-30) REVERT: V 156 TYR cc_start: 0.8577 (t80) cc_final: 0.7818 (t80) REVERT: V 247 GLN cc_start: 0.7286 (mm110) cc_final: 0.7002 (mm110) REVERT: W 41 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8766 (mt) REVERT: W 139 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7455 (tm-30) REVERT: X 158 GLN cc_start: 0.7851 (mp10) cc_final: 0.7444 (mt0) REVERT: X 166 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8464 (tt) REVERT: X 196 TRP cc_start: 0.6824 (t60) cc_final: 0.5998 (t60) REVERT: Y 134 TYR cc_start: 0.9086 (m-10) cc_final: 0.8457 (m-80) REVERT: Y 166 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8614 (tm-30) REVERT: Z 189 GLU cc_start: 0.6926 (mp0) cc_final: 0.6619 (mp0) REVERT: Z 200 TYR cc_start: 0.7192 (t80) cc_final: 0.6948 (t80) REVERT: a 182 GLU cc_start: 0.6547 (tt0) cc_final: 0.5000 (tm-30) REVERT: a 211 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7504 (mm-30) REVERT: c 135 HIS cc_start: 0.6150 (OUTLIER) cc_final: 0.5631 (t-90) REVERT: c 188 LEU cc_start: 0.8591 (mm) cc_final: 0.8235 (tp) REVERT: c 233 ASP cc_start: 0.9003 (m-30) cc_final: 0.8609 (m-30) REVERT: c 247 MET cc_start: 0.8097 (mmm) cc_final: 0.7365 (mmm) REVERT: d 38 ARG cc_start: 0.5906 (mtt90) cc_final: 0.5019 (mtp-110) REVERT: d 44 ARG cc_start: 0.7779 (tpp80) cc_final: 0.7089 (mmm-85) REVERT: d 135 HIS cc_start: 0.7366 (OUTLIER) cc_final: 0.6788 (m170) REVERT: d 262 TRP cc_start: 0.6867 (t-100) cc_final: 0.6468 (t60) REVERT: e 139 TYR cc_start: 0.7183 (t80) cc_final: 0.6387 (t80) REVERT: e 207 MET cc_start: 0.7911 (mtm) cc_final: 0.7548 (mpp) REVERT: f 48 PHE cc_start: 0.7547 (m-80) cc_final: 0.6922 (m-80) REVERT: f 182 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6592 (mt-10) REVERT: g 22 TYR cc_start: 0.6978 (t80) cc_final: 0.6741 (t80) REVERT: g 192 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8321 (tm-30) REVERT: g 207 MET cc_start: 0.8094 (ttp) cc_final: 0.7382 (mmt) REVERT: h 44 ARG cc_start: 0.6073 (OUTLIER) cc_final: 0.5654 (mpt180) REVERT: h 48 PHE cc_start: 0.8208 (m-80) cc_final: 0.7849 (m-80) REVERT: h 49 ASN cc_start: 0.8645 (t0) cc_final: 0.8278 (t0) REVERT: h 53 ASN cc_start: 0.7023 (OUTLIER) cc_final: 0.6546 (t0) REVERT: h 135 HIS cc_start: 0.7453 (OUTLIER) cc_final: 0.6520 (t-90) REVERT: h 207 MET cc_start: 0.8206 (mmm) cc_final: 0.7933 (mmm) REVERT: h 225 TYR cc_start: 0.7510 (m-10) cc_final: 0.7303 (m-10) REVERT: h 230 ARG cc_start: 0.6656 (ttp80) cc_final: 0.5571 (ttp-170) REVERT: i 164 GLN cc_start: 0.8176 (tt0) cc_final: 0.7901 (tt0) REVERT: i 237 TRP cc_start: 0.8420 (t-100) cc_final: 0.7985 (t-100) outliers start: 309 outliers final: 231 residues processed: 1289 average time/residue: 0.5637 time to fit residues: 1229.8289 Evaluate side-chains 1290 residues out of total 6648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1039 time to evaluate : 5.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 10 PHE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain E residue 233 ASN Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 155 TYR Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 123 HIS Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 77 HIS Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 165 TYR Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain M residue 76 ASP Chi-restraints excluded: chain M residue 91 THR Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 152 TYR Chi-restraints excluded: chain M residue 166 VAL Chi-restraints excluded: chain M residue 194 ASN Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 26 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 136 TYR Chi-restraints excluded: chain O residue 184 VAL Chi-restraints excluded: chain P residue 13 PHE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 156 PHE Chi-restraints excluded: chain P residue 181 ASP Chi-restraints excluded: chain P residue 203 LEU Chi-restraints excluded: chain Q residue 8 ARG Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 183 MET Chi-restraints excluded: chain Q residue 193 LEU Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 243 TYR Chi-restraints excluded: chain R residue 10 PHE Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 230 ASP Chi-restraints excluded: chain S residue 44 ASP Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 78 MET Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 151 ASN Chi-restraints excluded: chain S residue 180 GLU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 105 ILE Chi-restraints excluded: chain T residue 107 SER Chi-restraints excluded: chain T residue 155 TYR Chi-restraints excluded: chain T residue 187 ILE Chi-restraints excluded: chain T residue 205 THR Chi-restraints excluded: chain T residue 214 VAL Chi-restraints excluded: chain U residue 60 MET Chi-restraints excluded: chain U residue 80 TYR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 164 LEU Chi-restraints excluded: chain V residue 231 VAL Chi-restraints excluded: chain V residue 244 VAL Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 156 CYS Chi-restraints excluded: chain W residue 165 ASN Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 166 LEU Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 72 ASN Chi-restraints excluded: chain Y residue 74 THR Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain Y residue 132 HIS Chi-restraints excluded: chain Y residue 148 HIS Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 160 ILE Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 188 ILE Chi-restraints excluded: chain Z residue 193 VAL Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 78 CYS Chi-restraints excluded: chain a residue 91 THR Chi-restraints excluded: chain a residue 141 VAL Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain b residue 15 ILE Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 177 THR Chi-restraints excluded: chain b residue 178 THR Chi-restraints excluded: chain b residue 230 THR Chi-restraints excluded: chain c residue 64 VAL Chi-restraints excluded: chain c residue 135 HIS Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain c residue 222 VAL Chi-restraints excluded: chain c residue 229 VAL Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain d residue 135 HIS Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 172 ASP Chi-restraints excluded: chain d residue 222 VAL Chi-restraints excluded: chain e residue 28 ASP Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 242 ILE Chi-restraints excluded: chain f residue 66 ASP Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain f residue 197 ASN Chi-restraints excluded: chain f residue 213 SER Chi-restraints excluded: chain g residue 142 LEU Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain g residue 182 GLU Chi-restraints excluded: chain g residue 222 VAL Chi-restraints excluded: chain g residue 239 HIS Chi-restraints excluded: chain h residue 44 ARG Chi-restraints excluded: chain h residue 53 ASN Chi-restraints excluded: chain h residue 65 ASN Chi-restraints excluded: chain h residue 135 HIS Chi-restraints excluded: chain h residue 252 ILE Chi-restraints excluded: chain i residue 28 ASP Chi-restraints excluded: chain i residue 137 GLN Chi-restraints excluded: chain i residue 180 ILE Chi-restraints excluded: chain i residue 230 ARG Chi-restraints excluded: chain i residue 247 MET Chi-restraints excluded: chain i residue 256 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 736 random chunks: chunk 434 optimal weight: 1.9990 chunk 699 optimal weight: 7.9990 chunk 426 optimal weight: 0.9990 chunk 331 optimal weight: 9.9990 chunk 485 optimal weight: 4.9990 chunk 733 optimal weight: 7.9990 chunk 674 optimal weight: 20.0000 chunk 583 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 451 optimal weight: 0.8980 chunk 358 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 ASN L 180 HIS ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 98 HIS S 227 GLN ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 60 GLN T 165 HIS ** T 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 ASN U 233 HIS ** V 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 239 HIS ** d 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 239 HIS ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.217 61370 Z= 0.369 Angle : 0.812 59.200 82846 Z= 0.430 Chirality : 0.047 0.311 9279 Planarity : 0.005 0.118 10541 Dihedral : 5.247 85.016 8218 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 4.26 % Allowed : 25.78 % Favored : 69.96 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.10), residues: 7393 helix: 0.53 (0.09), residues: 3054 sheet: -2.35 (0.14), residues: 1235 loop : -2.42 (0.10), residues: 3104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP d 262 HIS 0.099 0.002 HIS d 135 PHE 0.040 0.002 PHE b 54 TYR 0.040 0.002 TYR a 64 ARG 0.010 0.001 ARG g 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14786 Ramachandran restraints generated. 7393 Oldfield, 0 Emsley, 7393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1330 residues out of total 6648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 1047 time to evaluate : 5.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: A 150 ASP cc_start: 0.8085 (p0) cc_final: 0.7480 (p0) REVERT: A 154 LYS cc_start: 0.8304 (mtmt) cc_final: 0.7731 (pttm) REVERT: A 170 ARG cc_start: 0.8207 (ptp-170) cc_final: 0.7922 (ttp80) REVERT: B 49 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7391 (tm-30) REVERT: B 50 LYS cc_start: 0.6641 (tttt) cc_final: 0.6334 (ttpt) REVERT: C 41 ASP cc_start: 0.8067 (t0) cc_final: 0.7738 (t0) REVERT: C 54 LYS cc_start: 0.7859 (mttp) cc_final: 0.7406 (tptt) REVERT: C 222 VAL cc_start: 0.8046 (OUTLIER) cc_final: 0.7668 (p) REVERT: D 117 LYS cc_start: 0.6076 (mttt) cc_final: 0.5513 (ttmt) REVERT: D 121 ARG cc_start: 0.8400 (ttm170) cc_final: 0.8035 (ttp-170) REVERT: E 176 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8215 (pp30) REVERT: E 208 MET cc_start: 0.9036 (tpt) cc_final: 0.8814 (tpt) REVERT: F 9 ASP cc_start: 0.8394 (m-30) cc_final: 0.8130 (m-30) REVERT: F 88 MET cc_start: 0.8807 (ttm) cc_final: 0.8327 (ttm) REVERT: F 117 GLN cc_start: 0.8781 (tp40) cc_final: 0.8308 (tp40) REVERT: F 190 CYS cc_start: 0.9180 (t) cc_final: 0.8832 (t) REVERT: G 18 ASP cc_start: 0.8361 (p0) cc_final: 0.8062 (p0) REVERT: G 123 HIS cc_start: 0.9239 (OUTLIER) cc_final: 0.8378 (t70) REVERT: G 232 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7600 (mp) REVERT: H 222 ASN cc_start: 0.8873 (m110) cc_final: 0.8330 (m110) REVERT: I 17 ASP cc_start: 0.8657 (p0) cc_final: 0.8302 (p0) REVERT: I 51 ASP cc_start: 0.8096 (t0) cc_final: 0.7737 (t0) REVERT: I 174 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8240 (p0) REVERT: I 216 LYS cc_start: 0.8207 (tptt) cc_final: 0.7994 (tppt) REVERT: J 47 MET cc_start: 0.8934 (tpp) cc_final: 0.8296 (tpp) REVERT: J 84 MET cc_start: 0.8763 (ttt) cc_final: 0.8353 (ttt) REVERT: J 101 ARG cc_start: 0.7682 (ttp80) cc_final: 0.7252 (ttp80) REVERT: J 189 ASP cc_start: 0.8292 (t0) cc_final: 0.8009 (t0) REVERT: K 76 MET cc_start: 0.8864 (tpt) cc_final: 0.8573 (tpt) REVERT: L 19 ARG cc_start: 0.8641 (ttm170) cc_final: 0.8248 (ttm170) REVERT: L 40 ASN cc_start: 0.8326 (t0) cc_final: 0.7895 (t0) REVERT: L 93 TYR cc_start: 0.7853 (m-80) cc_final: 0.7398 (m-80) REVERT: M 152 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7839 (p90) REVERT: M 194 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8320 (p0) REVERT: N 52 MET cc_start: 0.8839 (ppp) cc_final: 0.8374 (ppp) REVERT: N 113 ILE cc_start: 0.9440 (mm) cc_final: 0.9226 (mm) REVERT: N 166 MET cc_start: 0.8711 (ptp) cc_final: 0.8276 (ptp) REVERT: O 214 GLU cc_start: 0.8004 (pt0) cc_final: 0.7475 (pt0) REVERT: P 72 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8989 (mm) REVERT: P 96 ARG cc_start: 0.7862 (ttm-80) cc_final: 0.7628 (ttp80) REVERT: P 109 GLU cc_start: 0.8773 (tm-30) cc_final: 0.7704 (tm-30) REVERT: Q 3 ARG cc_start: 0.8064 (pmt-80) cc_final: 0.6591 (ptp-170) REVERT: Q 17 ARG cc_start: 0.7582 (ttp-110) cc_final: 0.7135 (ttp-110) REVERT: Q 26 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7001 (tm-30) REVERT: Q 149 HIS cc_start: 0.8820 (OUTLIER) cc_final: 0.8503 (t-170) REVERT: R 90 GLU cc_start: 0.8538 (tp30) cc_final: 0.8264 (tp30) REVERT: R 212 LYS cc_start: 0.8449 (mttt) cc_final: 0.8164 (mttm) REVERT: S 44 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.7894 (p0) REVERT: S 71 ASP cc_start: 0.8286 (t70) cc_final: 0.7886 (t0) REVERT: S 206 GLN cc_start: 0.8724 (mm110) cc_final: 0.8467 (mp10) REVERT: T 61 GLU cc_start: 0.7752 (pp20) cc_final: 0.7201 (pp20) REVERT: T 116 TYR cc_start: 0.8877 (m-80) cc_final: 0.8349 (m-10) REVERT: T 154 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6982 (tm-30) REVERT: T 227 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8563 (tm-30) REVERT: U 48 CYS cc_start: 0.8701 (m) cc_final: 0.8193 (m) REVERT: U 60 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7703 (mtm) REVERT: U 144 ASN cc_start: 0.8509 (t0) cc_final: 0.8120 (t0) REVERT: V 80 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8535 (tm-30) REVERT: V 156 TYR cc_start: 0.8568 (t80) cc_final: 0.7792 (t80) REVERT: W 36 TYR cc_start: 0.8725 (t80) cc_final: 0.8201 (t80) REVERT: W 139 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7434 (tm-30) REVERT: W 213 LEU cc_start: 0.8745 (mt) cc_final: 0.8476 (mt) REVERT: X 158 GLN cc_start: 0.7849 (mp10) cc_final: 0.7419 (mt0) REVERT: X 166 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8446 (tt) REVERT: Y 134 TYR cc_start: 0.9093 (m-10) cc_final: 0.8438 (m-80) REVERT: Y 166 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8600 (tm-30) REVERT: Z 189 GLU cc_start: 0.6892 (mp0) cc_final: 0.6540 (mp0) REVERT: Z 200 TYR cc_start: 0.7249 (t80) cc_final: 0.6987 (t80) REVERT: a 182 GLU cc_start: 0.6339 (tt0) cc_final: 0.4965 (tm-30) REVERT: a 211 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7470 (mm-30) REVERT: c 188 LEU cc_start: 0.8584 (mm) cc_final: 0.8229 (tp) REVERT: c 233 ASP cc_start: 0.9000 (m-30) cc_final: 0.8615 (m-30) REVERT: d 38 ARG cc_start: 0.5905 (mtt90) cc_final: 0.5012 (mtp-110) REVERT: d 44 ARG cc_start: 0.7772 (tpp80) cc_final: 0.7083 (mmm-85) REVERT: d 135 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.6797 (m90) REVERT: d 262 TRP cc_start: 0.6765 (t-100) cc_final: 0.6426 (t60) REVERT: e 139 TYR cc_start: 0.7186 (t80) cc_final: 0.6384 (t80) REVERT: e 207 MET cc_start: 0.7904 (mtm) cc_final: 0.7542 (mpp) REVERT: f 48 PHE cc_start: 0.7540 (m-80) cc_final: 0.6919 (m-80) REVERT: f 182 GLU cc_start: 0.6836 (mt-10) cc_final: 0.6591 (mt-10) REVERT: g 22 TYR cc_start: 0.6975 (t80) cc_final: 0.6741 (t80) REVERT: g 192 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8319 (tm-30) REVERT: g 207 MET cc_start: 0.8049 (ttp) cc_final: 0.7357 (mmt) REVERT: g 253 MET cc_start: 0.8118 (ptp) cc_final: 0.7559 (ptp) REVERT: h 44 ARG cc_start: 0.6063 (OUTLIER) cc_final: 0.5653 (mpt180) REVERT: h 48 PHE cc_start: 0.8206 (m-80) cc_final: 0.7852 (m-80) REVERT: h 49 ASN cc_start: 0.8638 (t0) cc_final: 0.8272 (t0) REVERT: h 53 ASN cc_start: 0.7016 (OUTLIER) cc_final: 0.6542 (t0) REVERT: h 135 HIS cc_start: 0.7441 (OUTLIER) cc_final: 0.6521 (t-90) REVERT: h 207 MET cc_start: 0.8203 (mmm) cc_final: 0.7926 (mmm) REVERT: h 230 ARG cc_start: 0.6652 (ttp80) cc_final: 0.5567 (ttp-170) REVERT: i 164 GLN cc_start: 0.8137 (tt0) cc_final: 0.7925 (tt0) REVERT: i 237 TRP cc_start: 0.8416 (t-100) cc_final: 0.7980 (t-100) outliers start: 283 outliers final: 251 residues processed: 1237 average time/residue: 0.5566 time to fit residues: 1165.2900 Evaluate side-chains 1309 residues out of total 6648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1042 time to evaluate : 5.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 10 PHE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 155 TYR Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 123 HIS Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 51 HIS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 77 HIS Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 165 TYR Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 201 MET Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 148 HIS Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 128 CYS Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain M residue 76 ASP Chi-restraints excluded: chain M residue 83 SER Chi-restraints excluded: chain M residue 91 THR Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 152 TYR Chi-restraints excluded: chain M residue 166 VAL Chi-restraints excluded: chain M residue 192 ASN Chi-restraints excluded: chain M residue 194 ASN Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 26 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain O residue 8 MET Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 136 TYR Chi-restraints excluded: chain O residue 184 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 121 PHE Chi-restraints excluded: chain P residue 156 PHE Chi-restraints excluded: chain P residue 181 ASP Chi-restraints excluded: chain P residue 203 LEU Chi-restraints excluded: chain Q residue 8 ARG Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 183 MET Chi-restraints excluded: chain Q residue 193 LEU Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 243 TYR Chi-restraints excluded: chain R residue 10 PHE Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 230 ASP Chi-restraints excluded: chain S residue 44 ASP Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 78 MET Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 151 ASN Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 180 GLU Chi-restraints excluded: chain S residue 219 ILE Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 105 ILE Chi-restraints excluded: chain T residue 107 SER Chi-restraints excluded: chain T residue 155 TYR Chi-restraints excluded: chain T residue 187 ILE Chi-restraints excluded: chain T residue 205 THR Chi-restraints excluded: chain T residue 214 VAL Chi-restraints excluded: chain U residue 60 MET Chi-restraints excluded: chain U residue 80 TYR Chi-restraints excluded: chain U residue 131 MET Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 66 MET Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 164 LEU Chi-restraints excluded: chain V residue 231 VAL Chi-restraints excluded: chain V residue 244 VAL Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 165 ASN Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 140 ILE Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 166 LEU Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 22 ILE Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 72 ASN Chi-restraints excluded: chain Y residue 74 THR Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain Y residue 132 HIS Chi-restraints excluded: chain Y residue 148 HIS Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 160 ILE Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 188 ILE Chi-restraints excluded: chain Z residue 193 VAL Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 57 LEU Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 78 CYS Chi-restraints excluded: chain a residue 91 THR Chi-restraints excluded: chain a residue 141 VAL Chi-restraints excluded: chain b residue 15 ILE Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 177 THR Chi-restraints excluded: chain b residue 178 THR Chi-restraints excluded: chain b residue 230 THR Chi-restraints excluded: chain c residue 16 GLN Chi-restraints excluded: chain c residue 64 VAL Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain c residue 222 VAL Chi-restraints excluded: chain c residue 229 VAL Chi-restraints excluded: chain c residue 239 HIS Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain d residue 135 HIS Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 172 ASP Chi-restraints excluded: chain d residue 222 VAL Chi-restraints excluded: chain e residue 28 ASP Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 148 TYR Chi-restraints excluded: chain e residue 242 ILE Chi-restraints excluded: chain f residue 66 ASP Chi-restraints excluded: chain f residue 140 LEU Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain g residue 142 LEU Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain g residue 182 GLU Chi-restraints excluded: chain g residue 239 HIS Chi-restraints excluded: chain h residue 44 ARG Chi-restraints excluded: chain h residue 53 ASN Chi-restraints excluded: chain h residue 65 ASN Chi-restraints excluded: chain h residue 135 HIS Chi-restraints excluded: chain h residue 252 ILE Chi-restraints excluded: chain i residue 28 ASP Chi-restraints excluded: chain i residue 45 ILE Chi-restraints excluded: chain i residue 137 GLN Chi-restraints excluded: chain i residue 180 ILE Chi-restraints excluded: chain i residue 230 ARG Chi-restraints excluded: chain i residue 247 MET Chi-restraints excluded: chain i residue 256 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 736 random chunks: chunk 463 optimal weight: 0.8980 chunk 621 optimal weight: 4.9990 chunk 178 optimal weight: 0.7980 chunk 538 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 162 optimal weight: 0.0670 chunk 584 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 600 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 HIS C 177 GLN ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN F 121 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 180 HIS ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 98 HIS S 227 GLN ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 165 HIS U 233 HIS ** V 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 247 GLN W 91 GLN ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 128 ASN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 183 GLN ** b 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 239 HIS d 135 HIS ** d 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 137 GLN e 239 HIS f 197 ASN ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 250 ASN ** i 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.142474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.112454 restraints weight = 96574.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113967 restraints weight = 57694.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.115840 restraints weight = 43377.798| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 61370 Z= 0.182 Angle : 0.622 12.495 82846 Z= 0.322 Chirality : 0.043 0.315 9279 Planarity : 0.004 0.104 10541 Dihedral : 4.940 80.371 8218 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.02 % Allowed : 27.02 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.10), residues: 7393 helix: 0.75 (0.10), residues: 3067 sheet: -2.21 (0.14), residues: 1248 loop : -2.22 (0.11), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP d 162 HIS 0.025 0.001 HIS c 239 PHE 0.025 0.001 PHE R 194 TYR 0.046 0.001 TYR h 225 ARG 0.013 0.001 ARG U 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17549.49 seconds wall clock time: 308 minutes 2.01 seconds (18482.01 seconds total)