Starting phenix.real_space_refine on Tue Mar 12 05:31:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8e_10119/03_2024/6s8e_10119.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8e_10119/03_2024/6s8e_10119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8e_10119/03_2024/6s8e_10119.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8e_10119/03_2024/6s8e_10119.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8e_10119/03_2024/6s8e_10119.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8e_10119/03_2024/6s8e_10119.pdb" } resolution = 3.1 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= -0.015 sd= 0.622 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 90 5.49 5 S 103 5.16 5 C 39655 2.51 5 N 10248 2.21 5 O 12127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ASP 121": "OD1" <-> "OD2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B GLU 153": "OE1" <-> "OE2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "C GLU 39": "OE1" <-> "OE2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 124": "OD1" <-> "OD2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "D PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D ASP 66": "OD1" <-> "OD2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D ASP 102": "OD1" <-> "OD2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "E GLU 8": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E GLU 74": "OE1" <-> "OE2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E ASP 88": "OD1" <-> "OD2" Residue "E ASP 102": "OD1" <-> "OD2" Residue "E ASP 157": "OD1" <-> "OD2" Residue "E GLU 174": "OE1" <-> "OE2" Residue "E ASP 195": "OD1" <-> "OD2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "F ASP 168": "OD1" <-> "OD2" Residue "F ASP 195": "OD1" <-> "OD2" Residue "F GLU 200": "OE1" <-> "OE2" Residue "F ASP 217": "OD1" <-> "OD2" Residue "F GLU 222": "OE1" <-> "OE2" Residue "F PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 280": "NH1" <-> "NH2" Residue "G GLU 27": "OE1" <-> "OE2" Residue "G GLU 29": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G ASP 168": "OD1" <-> "OD2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H ARG 15": "NH1" <-> "NH2" Residue "H TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 114": "NH1" <-> "NH2" Residue "H GLU 115": "OE1" <-> "OE2" Residue "H GLU 120": "OE1" <-> "OE2" Residue "H PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 175": "OD1" <-> "OD2" Residue "H GLU 198": "OE1" <-> "OE2" Residue "H TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 70": "OE1" <-> "OE2" Residue "I GLU 71": "OE1" <-> "OE2" Residue "I GLU 117": "OE1" <-> "OE2" Residue "I GLU 175": "OE1" <-> "OE2" Residue "I ASP 199": "OD1" <-> "OD2" Residue "I TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 245": "OE1" <-> "OE2" Residue "I ASP 253": "OD1" <-> "OD2" Residue "J GLU 3": "OE1" <-> "OE2" Residue "J GLU 31": "OE1" <-> "OE2" Residue "J GLU 65": "OE1" <-> "OE2" Residue "J GLU 87": "OE1" <-> "OE2" Residue "J ARG 97": "NH1" <-> "NH2" Residue "J TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 106": "OD1" <-> "OD2" Residue "J ARG 113": "NH1" <-> "NH2" Residue "J ASP 122": "OD1" <-> "OD2" Residue "J PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 173": "OE1" <-> "OE2" Residue "J GLU 198": "OE1" <-> "OE2" Residue "J ARG 246": "NH1" <-> "NH2" Residue "J TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 335": "NH1" <-> "NH2" Residue "J GLU 353": "OE1" <-> "OE2" Residue "J ASP 383": "OD1" <-> "OD2" Residue "J ASP 420": "OD1" <-> "OD2" Residue "J ARG 433": "NH1" <-> "NH2" Residue "J TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 73": "OD1" <-> "OD2" Residue "K TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 95": "OE1" <-> "OE2" Residue "K ARG 97": "NH1" <-> "NH2" Residue "K ASP 169": "OD1" <-> "OD2" Residue "K ARG 171": "NH1" <-> "NH2" Residue "K PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 179": "OD1" <-> "OD2" Residue "K ASP 212": "OD1" <-> "OD2" Residue "K ARG 218": "NH1" <-> "NH2" Residue "K GLU 244": "OE1" <-> "OE2" Residue "K ASP 248": "OD1" <-> "OD2" Residue "K PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 272": "OE1" <-> "OE2" Residue "K ASP 294": "OD1" <-> "OD2" Residue "K ARG 311": "NH1" <-> "NH2" Residue "K TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 345": "OE1" <-> "OE2" Residue "K ARG 355": "NH1" <-> "NH2" Residue "K ARG 360": "NH1" <-> "NH2" Residue "K GLU 363": "OE1" <-> "OE2" Residue "K GLU 397": "OE1" <-> "OE2" Residue "K GLU 399": "OE1" <-> "OE2" Residue "K ARG 419": "NH1" <-> "NH2" Residue "K GLU 424": "OE1" <-> "OE2" Residue "K ASP 448": "OD1" <-> "OD2" Residue "K ARG 510": "NH1" <-> "NH2" Residue "K TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 549": "NH1" <-> "NH2" Residue "K ASP 550": "OD1" <-> "OD2" Residue "K GLU 568": "OE1" <-> "OE2" Residue "K PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 648": "NH1" <-> "NH2" Residue "K TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 680": "OE1" <-> "OE2" Residue "K GLU 691": "OE1" <-> "OE2" Residue "K TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 714": "OE1" <-> "OE2" Residue "K GLU 756": "OE1" <-> "OE2" Residue "K GLU 761": "OE1" <-> "OE2" Residue "K ARG 763": "NH1" <-> "NH2" Residue "K ASP 802": "OD1" <-> "OD2" Residue "K GLU 812": "OE1" <-> "OE2" Residue "K GLU 819": "OE1" <-> "OE2" Residue "K ARG 821": "NH1" <-> "NH2" Residue "K TYR 849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 886": "OE1" <-> "OE2" Residue "K ARG 891": "NH1" <-> "NH2" Residue "K TYR 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 904": "OD1" <-> "OD2" Residue "K ARG 923": "NH1" <-> "NH2" Residue "K GLU 934": "OE1" <-> "OE2" Residue "K TYR 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 1000": "OD1" <-> "OD2" Residue "K GLU 1001": "OE1" <-> "OE2" Residue "X PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 19": "OD1" <-> "OD2" Residue "X ASP 34": "OD1" <-> "OD2" Residue "X GLU 35": "OE1" <-> "OE2" Residue "X ASP 61": "OD1" <-> "OD2" Residue "X TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 116": "OD1" <-> "OD2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ASP 130": "OD1" <-> "OD2" Residue "X ASP 143": "OD1" <-> "OD2" Residue "X TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 165": "OE1" <-> "OE2" Residue "X PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 118": "NH1" <-> "NH2" Residue "x ASP 131": "OD1" <-> "OD2" Residue "x GLU 152": "OE1" <-> "OE2" Residue "x GLU 157": "OE1" <-> "OE2" Residue "T TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 118": "NH1" <-> "NH2" Residue "T ASP 130": "OD1" <-> "OD2" Residue "T TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 165": "OE1" <-> "OE2" Residue "T PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 35": "OE1" <-> "OE2" Residue "W ASP 61": "OD1" <-> "OD2" Residue "W ARG 118": "NH1" <-> "NH2" Residue "W ASP 130": "OD1" <-> "OD2" Residue "W TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 34": "OD1" <-> "OD2" Residue "t GLU 35": "OE1" <-> "OE2" Residue "t ASP 61": "OD1" <-> "OD2" Residue "t TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 116": "OD1" <-> "OD2" Residue "t ARG 118": "NH1" <-> "NH2" Residue "t ASP 130": "OD1" <-> "OD2" Residue "t GLU 140": "OE1" <-> "OE2" Residue "t ASP 143": "OD1" <-> "OD2" Residue "w GLU 6": "OE1" <-> "OE2" Residue "w ASP 28": "OD1" <-> "OD2" Residue "w ASP 34": "OD1" <-> "OD2" Residue "w GLU 51": "OE1" <-> "OE2" Residue "w ASP 82": "OD1" <-> "OD2" Residue "w ARG 118": "NH1" <-> "NH2" Residue "w ASP 131": "OD1" <-> "OD2" Residue "w TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 161": "OE1" <-> "OE2" Residue "w ASP 162": "OD1" <-> "OD2" Residue "L TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 50": "OD1" <-> "OD2" Residue "L TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 118": "NH1" <-> "NH2" Residue "L ASP 130": "OD1" <-> "OD2" Residue "L ASP 131": "OD1" <-> "OD2" Residue "L PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 6": "OE1" <-> "OE2" Residue "M ASP 34": "OD1" <-> "OD2" Residue "M TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 118": "NH1" <-> "NH2" Residue "M PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 165": "OE1" <-> "OE2" Residue "M GLU 173": "OE1" <-> "OE2" Residue "O PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 34": "OD1" <-> "OD2" Residue "O TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 118": "NH1" <-> "NH2" Residue "O ASP 130": "OD1" <-> "OD2" Residue "O ASP 131": "OD1" <-> "OD2" Residue "O GLU 165": "OE1" <-> "OE2" Residue "O PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 61": "OD1" <-> "OD2" Residue "P ASP 64": "OD1" <-> "OD2" Residue "P TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 105": "OD1" <-> "OD2" Residue "P TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 118": "NH1" <-> "NH2" Residue "P ASP 130": "OD1" <-> "OD2" Residue "P GLU 157": "OE1" <-> "OE2" Residue "l PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 34": "OD1" <-> "OD2" Residue "l ARG 118": "NH1" <-> "NH2" Residue "l ASP 130": "OD1" <-> "OD2" Residue "l TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 161": "OE1" <-> "OE2" Residue "m GLU 6": "OE1" <-> "OE2" Residue "m ASP 19": "OD1" <-> "OD2" Residue "m ASP 64": "OD1" <-> "OD2" Residue "m TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 118": "NH1" <-> "NH2" Residue "m ASP 130": "OD1" <-> "OD2" Residue "m PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 162": "OD1" <-> "OD2" Residue "o GLU 6": "OE1" <-> "OE2" Residue "o ASP 64": "OD1" <-> "OD2" Residue "o TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 118": "NH1" <-> "NH2" Residue "o PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 157": "OE1" <-> "OE2" Residue "o GLU 165": "OE1" <-> "OE2" Residue "p GLU 6": "OE1" <-> "OE2" Residue "p ASP 28": "OD1" <-> "OD2" Residue "p ASP 34": "OD1" <-> "OD2" Residue "p ARG 118": "NH1" <-> "NH2" Residue "p ASP 131": "OD1" <-> "OD2" Residue "p PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 157": "OE1" <-> "OE2" Residue "p GLU 161": "OE1" <-> "OE2" Residue "p PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 34": "OD1" <-> "OD2" Residue "N GLU 35": "OE1" <-> "OE2" Residue "N GLU 51": "OE1" <-> "OE2" Residue "N ASP 61": "OD1" <-> "OD2" Residue "N TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 116": "OD1" <-> "OD2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "N TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 6": "OE1" <-> "OE2" Residue "n TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 34": "OD1" <-> "OD2" Residue "n GLU 35": "OE1" <-> "OE2" Residue "n ASP 61": "OD1" <-> "OD2" Residue "n TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "n ASP 131": "OD1" <-> "OD2" Residue "n PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 152": "OE1" <-> "OE2" Residue "Q GLU 35": "OE1" <-> "OE2" Residue "Q ASP 104": "OD1" <-> "OD2" Residue "Q TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 118": "NH1" <-> "NH2" Residue "Q PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 6": "OE1" <-> "OE2" Residue "R PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 64": "OD1" <-> "OD2" Residue "R TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 118": "NH1" <-> "NH2" Residue "R PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 152": "OE1" <-> "OE2" Residue "R ASP 162": "OD1" <-> "OD2" Residue "R GLU 165": "OE1" <-> "OE2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "S GLU 35": "OE1" <-> "OE2" Residue "S GLU 51": "OE1" <-> "OE2" Residue "S ASP 104": "OD1" <-> "OD2" Residue "S ASP 105": "OD1" <-> "OD2" Residue "S TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 118": "NH1" <-> "NH2" Residue "S ASP 131": "OD1" <-> "OD2" Residue "S GLU 140": "OE1" <-> "OE2" Residue "S PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 143": "OD1" <-> "OD2" Residue "S GLU 173": "OE1" <-> "OE2" Residue "q TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 61": "OD1" <-> "OD2" Residue "q ASP 104": "OD1" <-> "OD2" Residue "q TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 118": "NH1" <-> "NH2" Residue "q ASP 130": "OD1" <-> "OD2" Residue "q PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 165": "OE1" <-> "OE2" Residue "q GLU 173": "OE1" <-> "OE2" Residue "r ASP 61": "OD1" <-> "OD2" Residue "r ASP 64": "OD1" <-> "OD2" Residue "r TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 118": "NH1" <-> "NH2" Residue "r ASP 130": "OD1" <-> "OD2" Residue "r PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 161": "OE1" <-> "OE2" Residue "r GLU 165": "OE1" <-> "OE2" Residue "r PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 19": "OD1" <-> "OD2" Residue "s GLU 35": "OE1" <-> "OE2" Residue "s ASP 50": "OD1" <-> "OD2" Residue "s GLU 51": "OE1" <-> "OE2" Residue "s TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 118": "NH1" <-> "NH2" Residue "s GLU 140": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 62224 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1261 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "B" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1261 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "C" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1261 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "D" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2274 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain: "E" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2274 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain: "F" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2274 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain: "G" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2274 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain: "H" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2528 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain: "I" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2282 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 12, 'TRANS': 271} Chain: "J" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3889 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 469} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "K" Number of atoms: 8403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8403 Classifications: {'peptide': 1023} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 987} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "U" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 923 Classifications: {'RNA': 44} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 14, 'rna3p_pyr': 23} Link IDs: {'rna2p': 7, 'rna3p': 36} Chain: "V" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1003 Classifications: {'RNA': 47} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 7, 'rna3p_pur': 16, 'rna3p_pyr': 12} Link IDs: {'rna2p': 19, 'rna3p': 27} Chain: "X" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "x" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "T" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "W" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "t" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "w" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "L" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "M" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "O" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "P" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "l" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "m" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "o" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "p" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "N" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "n" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "Q" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "R" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "S" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "q" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "r" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "s" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25333 SG CYS K 464 75.005 103.791 43.723 1.00 82.23 S ATOM 25700 SG CYS K 512 74.905 102.208 39.735 1.00 77.71 S ATOM 25727 SG CYS K 515 72.989 101.185 42.504 1.00 78.12 S Time building chain proxies: 23.69, per 1000 atoms: 0.38 Number of scatterers: 62224 At special positions: 0 Unit cell: (153, 171, 249, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 103 16.00 P 90 15.00 O 12127 8.00 N 10248 7.00 C 39655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS R 63 " distance=2.03 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS Q 63 " distance=2.03 Simple disulfide: pdb=" SG CYS C 115 " - pdb=" SG CYS S 63 " distance=2.03 Simple disulfide: pdb=" SG CYS D 256 " - pdb=" SG CYS O 63 " distance=2.04 Simple disulfide: pdb=" SG CYS E 256 " - pdb=" SG CYS l 63 " distance=2.03 Simple disulfide: pdb=" SG CYS F 256 " - pdb=" SG CYS m 63 " distance=2.03 Simple disulfide: pdb=" SG CYS G 256 " - pdb=" SG CYS N 63 " distance=2.03 Simple disulfide: pdb=" SG CYS H 304 " - pdb=" SG CYS x 63 " distance=2.03 Simple disulfide: pdb=" SG CYS I 252 " - pdb=" SG CYS p 63 " distance=2.03 Simple disulfide: pdb=" SG CYS J 111 " - pdb=" SG CYS t 63 " distance=2.03 Simple disulfide: pdb=" SG CYS J 262 " - pdb=" SG CYS J 268 " distance=2.03 Simple disulfide: pdb=" SG CYS J 356 " - pdb=" SG CYS J 474 " distance=2.03 Simple disulfide: pdb=" SG CYS J 466 " - pdb=" SG CYS w 63 " distance=2.03 Simple disulfide: pdb=" SG CYS K 578 " - pdb=" SG CYS K 587 " distance=2.03 Simple disulfide: pdb=" SG CYS K 711 " - pdb=" SG CYS K 721 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.79 Conformation dependent library (CDL) restraints added in 8.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K1101 " pdb="ZN ZN K1101 " - pdb=" SG CYS K 512 " pdb="ZN ZN K1101 " - pdb=" SG CYS K 464 " pdb="ZN ZN K1101 " - pdb=" SG CYS K 515 " 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14294 Finding SS restraints... Secondary structure from input PDB file: 202 helices and 0 sheets defined 29.8% alpha, 0.0% beta 31 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 14.34 Creating SS restraints... Processing helix chain 'A' and resid 4 through 18 removed outlier: 3.881A pdb=" N LYS A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 44 removed outlier: 3.541A pdb=" N LYS A 27 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.902A pdb=" N THR A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 73 removed outlier: 3.558A pdb=" N SER A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 101 Processing helix chain 'A' and resid 105 through 115 removed outlier: 3.552A pdb=" N CYS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 152 removed outlier: 3.990A pdb=" N ASP A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Proline residue: A 131 - end of helix removed outlier: 4.459A pdb=" N ARG A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N THR A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 21 removed outlier: 3.736A pdb=" N LEU B 11 " --> pdb=" O TYR B 7 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 21 " --> pdb=" O VAL B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 44 removed outlier: 4.236A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLU B 39 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 58 removed outlier: 3.616A pdb=" N THR B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 73 removed outlier: 3.600A pdb=" N SER B 72 " --> pdb=" O ILE B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 101 removed outlier: 4.817A pdb=" N TYR B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 113 Processing helix chain 'B' and resid 115 through 129 removed outlier: 3.650A pdb=" N LEU B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 123 " --> pdb=" O ARG B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.750A pdb=" N ALA B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 152 removed outlier: 4.677A pdb=" N TYR B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 19 removed outlier: 3.756A pdb=" N LYS C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 35 removed outlier: 3.629A pdb=" N LYS C 27 " --> pdb=" O HIS C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 45 Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.504A pdb=" N THR C 49 " --> pdb=" O GLY C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 73 removed outlier: 3.749A pdb=" N PHE C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 101 removed outlier: 4.681A pdb=" N TYR C 87 " --> pdb=" O GLU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 112 Processing helix chain 'C' and resid 116 through 135 removed outlier: 4.265A pdb=" N LEU C 120 " --> pdb=" O GLU C 116 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) Proline residue: C 131 - end of helix removed outlier: 3.671A pdb=" N ALA C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 152 removed outlier: 3.846A pdb=" N ALA C 143 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 144 " --> pdb=" O TYR C 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 61 Processing helix chain 'D' and resid 64 through 73 Processing helix chain 'D' and resid 115 through 131 Processing helix chain 'D' and resid 136 through 148 removed outlier: 3.654A pdb=" N ILE D 146 " --> pdb=" O LYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 204 Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 256 through 261 Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 281 through 286 Processing helix chain 'E' and resid 45 through 61 removed outlier: 3.967A pdb=" N LYS E 59 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 72 Processing helix chain 'E' and resid 115 through 133 removed outlier: 3.825A pdb=" N ASN E 133 " --> pdb=" O SER E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 148 removed outlier: 3.736A pdb=" N ILE E 146 " --> pdb=" O LYS E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 205 removed outlier: 4.460A pdb=" N GLU E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 257 removed outlier: 3.520A pdb=" N SER E 255 " --> pdb=" O ALA E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 285 No H-bonds generated for 'chain 'E' and resid 283 through 285' Processing helix chain 'F' and resid 45 through 61 removed outlier: 3.503A pdb=" N SER F 55 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 72 removed outlier: 3.735A pdb=" N TYR F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 132 removed outlier: 3.665A pdb=" N LEU F 118 " --> pdb=" O THR F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 148 removed outlier: 4.026A pdb=" N ILE F 146 " --> pdb=" O LYS F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 194 through 205 removed outlier: 4.518A pdb=" N GLU F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 256 Processing helix chain 'F' and resid 257 through 261 Processing helix chain 'F' and resid 282 through 286 Processing helix chain 'G' and resid 45 through 61 removed outlier: 3.891A pdb=" N LYS G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 72 Processing helix chain 'G' and resid 115 through 130 removed outlier: 3.527A pdb=" N TYR G 124 " --> pdb=" O LYS G 120 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN G 130 " --> pdb=" O ASP G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 147 Processing helix chain 'G' and resid 148 through 150 No H-bonds generated for 'chain 'G' and resid 148 through 150' Processing helix chain 'G' and resid 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'G' and resid 197 through 204 Processing helix chain 'G' and resid 249 through 256 Processing helix chain 'G' and resid 256 through 261 removed outlier: 3.550A pdb=" N ASN G 260 " --> pdb=" O CYS G 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 50 removed outlier: 3.552A pdb=" N ILE H 42 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE H 49 " --> pdb=" O MET H 45 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU H 50 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 66 Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 102 through 109 removed outlier: 4.126A pdb=" N LEU H 106 " --> pdb=" O ASN H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 123 Processing helix chain 'H' and resid 127 through 131 Processing helix chain 'H' and resid 232 through 236 removed outlier: 4.000A pdb=" N TYR H 236 " --> pdb=" O ASN H 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 232 through 236' Processing helix chain 'H' and resid 271 through 279 removed outlier: 4.277A pdb=" N ASP H 275 " --> pdb=" O ARG H 271 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE H 276 " --> pdb=" O SER H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 295 removed outlier: 3.854A pdb=" N ILE H 295 " --> pdb=" O LYS H 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 17 removed outlier: 4.766A pdb=" N LEU I 10 " --> pdb=" O LEU I 6 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU I 11 " --> pdb=" O VAL I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 35 removed outlier: 3.931A pdb=" N ILE I 31 " --> pdb=" O SER I 27 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 41 Processing helix chain 'I' and resid 53 through 58 removed outlier: 4.169A pdb=" N ILE I 57 " --> pdb=" O LEU I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 88 removed outlier: 3.540A pdb=" N ASN I 74 " --> pdb=" O GLU I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 109 Processing helix chain 'I' and resid 133 through 138 Processing helix chain 'I' and resid 153 through 179 removed outlier: 7.675A pdb=" N GLU I 171 " --> pdb=" O GLY I 167 " (cutoff:3.500A) removed outlier: 9.353A pdb=" N GLN I 172 " --> pdb=" O LYS I 168 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU I 173 " --> pdb=" O LEU I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 244 through 246 No H-bonds generated for 'chain 'I' and resid 244 through 246' Processing helix chain 'I' and resid 247 through 259 removed outlier: 3.641A pdb=" N ILE I 251 " --> pdb=" O VAL I 247 " (cutoff:3.500A) Proline residue: I 256 - end of helix removed outlier: 3.652A pdb=" N LEU I 259 " --> pdb=" O MET I 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 59 Processing helix chain 'J' and resid 63 through 71 Processing helix chain 'J' and resid 71 through 76 Processing helix chain 'J' and resid 107 through 113 Processing helix chain 'J' and resid 150 through 158 Processing helix chain 'J' and resid 161 through 166 Processing helix chain 'J' and resid 167 through 171 removed outlier: 3.877A pdb=" N LYS J 170 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER J 171 " --> pdb=" O GLY J 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 167 through 171' Processing helix chain 'J' and resid 181 through 198 Processing helix chain 'J' and resid 199 through 201 No H-bonds generated for 'chain 'J' and resid 199 through 201' Processing helix chain 'J' and resid 223 through 241 removed outlier: 3.687A pdb=" N LYS J 227 " --> pdb=" O ASN J 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 277 removed outlier: 3.558A pdb=" N LYS J 269 " --> pdb=" O ASN J 265 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LYS J 270 " --> pdb=" O SER J 266 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ILE J 271 " --> pdb=" O ILE J 267 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU J 274 " --> pdb=" O LYS J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 278 through 280 No H-bonds generated for 'chain 'J' and resid 278 through 280' Processing helix chain 'J' and resid 283 through 300 Processing helix chain 'J' and resid 338 through 351 removed outlier: 4.719A pdb=" N TYR J 347 " --> pdb=" O LEU J 343 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS J 348 " --> pdb=" O ALA J 344 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA J 349 " --> pdb=" O ASN J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 354 through 359 removed outlier: 3.578A pdb=" N SER J 359 " --> pdb=" O CYS J 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 366 through 375 Processing helix chain 'J' and resid 389 through 396 removed outlier: 3.896A pdb=" N ASN J 393 " --> pdb=" O GLY J 389 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR J 394 " --> pdb=" O PHE J 390 " (cutoff:3.500A) Processing helix chain 'J' and resid 417 through 424 Processing helix chain 'J' and resid 460 through 475 Processing helix chain 'K' and resid 14 through 20 Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.569A pdb=" N GLY K 31 " --> pdb=" O VAL K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 38 removed outlier: 3.780A pdb=" N THR K 37 " --> pdb=" O ARG K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 57 Processing helix chain 'K' and resid 69 through 78 removed outlier: 3.563A pdb=" N SER K 77 " --> pdb=" O ASP K 73 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER K 78 " --> pdb=" O LYS K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 90 Processing helix chain 'K' and resid 124 through 132 removed outlier: 3.680A pdb=" N ILE K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU K 129 " --> pdb=" O ASP K 125 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLU K 130 " --> pdb=" O ASN K 126 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR K 131 " --> pdb=" O LEU K 127 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS K 132 " --> pdb=" O ILE K 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 124 through 132' Processing helix chain 'K' and resid 146 through 150 Processing helix chain 'K' and resid 152 through 160 removed outlier: 3.666A pdb=" N LEU K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 194 removed outlier: 3.877A pdb=" N ASN K 189 " --> pdb=" O ALA K 185 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TRP K 190 " --> pdb=" O ALA K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 215 Processing helix chain 'K' and resid 220 through 243 removed outlier: 3.672A pdb=" N SER K 231 " --> pdb=" O SER K 227 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU K 234 " --> pdb=" O VAL K 230 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL K 237 " --> pdb=" O LEU K 233 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE K 238 " --> pdb=" O LEU K 234 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU K 243 " --> pdb=" O THR K 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 269 removed outlier: 3.935A pdb=" N PHE K 263 " --> pdb=" O GLN K 259 " (cutoff:3.500A) Processing helix chain 'K' and resid 276 through 290 removed outlier: 3.839A pdb=" N GLU K 284 " --> pdb=" O ASP K 280 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR K 289 " --> pdb=" O LEU K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 361 Processing helix chain 'K' and resid 364 through 377 removed outlier: 3.809A pdb=" N VAL K 370 " --> pdb=" O PHE K 366 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG K 372 " --> pdb=" O ASN K 368 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS K 375 " --> pdb=" O CYS K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 379 through 383 removed outlier: 3.586A pdb=" N GLN K 382 " --> pdb=" O ASP K 379 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR K 383 " --> pdb=" O LEU K 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 379 through 383' Processing helix chain 'K' and resid 396 through 399 Processing helix chain 'K' and resid 409 through 429 removed outlier: 4.619A pdb=" N TYR K 414 " --> pdb=" O SER K 410 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP K 415 " --> pdb=" O TRP K 411 " (cutoff:3.500A) Processing helix chain 'K' and resid 435 through 439 Processing helix chain 'K' and resid 483 through 489 removed outlier: 3.876A pdb=" N ILE K 487 " --> pdb=" O GLU K 483 " (cutoff:3.500A) Processing helix chain 'K' and resid 497 through 505 Processing helix chain 'K' and resid 512 through 523 Processing helix chain 'K' and resid 524 through 527 removed outlier: 3.598A pdb=" N LEU K 527 " --> pdb=" O GLU K 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 524 through 527' Processing helix chain 'K' and resid 528 through 533 Processing helix chain 'K' and resid 540 through 548 Processing helix chain 'K' and resid 557 through 562 Processing helix chain 'K' and resid 563 through 573 Processing helix chain 'K' and resid 573 through 578 removed outlier: 4.105A pdb=" N CYS K 578 " --> pdb=" O LYS K 574 " (cutoff:3.500A) Processing helix chain 'K' and resid 598 through 603 Processing helix chain 'K' and resid 614 through 619 removed outlier: 3.558A pdb=" N TYR K 618 " --> pdb=" O ASP K 614 " (cutoff:3.500A) Processing helix chain 'K' and resid 624 through 634 removed outlier: 3.831A pdb=" N SER K 630 " --> pdb=" O ARG K 626 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 658 Processing helix chain 'K' and resid 672 through 676 Processing helix chain 'K' and resid 677 through 680 Processing helix chain 'K' and resid 681 through 696 removed outlier: 3.622A pdb=" N VAL K 685 " --> pdb=" O LYS K 681 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS K 687 " --> pdb=" O GLU K 683 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU K 691 " --> pdb=" O LYS K 687 " (cutoff:3.500A) Processing helix chain 'K' and resid 701 through 709 removed outlier: 3.567A pdb=" N LYS K 706 " --> pdb=" O VAL K 702 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR K 707 " --> pdb=" O ASP K 703 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL K 708 " --> pdb=" O TYR K 704 " (cutoff:3.500A) Processing helix chain 'K' and resid 720 through 725 Processing helix chain 'K' and resid 728 through 732 Processing helix chain 'K' and resid 744 through 748 Processing helix chain 'K' and resid 750 through 762 Processing helix chain 'K' and resid 767 through 792 Processing helix chain 'K' and resid 813 through 825 removed outlier: 3.529A pdb=" N ARG K 822 " --> pdb=" O LYS K 818 " (cutoff:3.500A) Processing helix chain 'K' and resid 869 through 887 removed outlier: 3.649A pdb=" N LEU K 881 " --> pdb=" O SER K 877 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY K 884 " --> pdb=" O LEU K 880 " (cutoff:3.500A) Processing helix chain 'K' and resid 931 through 935 Processing helix chain 'K' and resid 936 through 951 removed outlier: 3.582A pdb=" N ASP K 940 " --> pdb=" O ALA K 936 " (cutoff:3.500A) Processing helix chain 'K' and resid 955 through 960 Processing helix chain 'K' and resid 961 through 972 removed outlier: 4.133A pdb=" N TYR K 965 " --> pdb=" O ASP K 961 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N HIS K 967 " --> pdb=" O GLU K 963 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU K 968 " --> pdb=" O LYS K 964 " (cutoff:3.500A) Processing helix chain 'K' and resid 974 through 989 removed outlier: 3.645A pdb=" N THR K 978 " --> pdb=" O GLU K 974 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN K 989 " --> pdb=" O TRP K 985 " (cutoff:3.500A) Processing helix chain 'K' and resid 1020 through 1036 Processing helix chain 'X' and resid 130 through 141 removed outlier: 3.844A pdb=" N VAL X 134 " --> pdb=" O ASP X 130 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS X 139 " --> pdb=" O ASN X 135 " (cutoff:3.500A) Processing helix chain 'X' and resid 155 through 160 removed outlier: 3.519A pdb=" N VAL X 159 " --> pdb=" O LYS X 155 " (cutoff:3.500A) Processing helix chain 'X' and resid 160 through 166 Processing helix chain 'x' and resid 130 through 143 removed outlier: 3.956A pdb=" N LYS x 139 " --> pdb=" O ASN x 135 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU x 140 " --> pdb=" O ASN x 136 " (cutoff:3.500A) Processing helix chain 'x' and resid 157 through 166 removed outlier: 3.772A pdb=" N GLU x 161 " --> pdb=" O GLU x 157 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP x 162 " --> pdb=" O LYS x 158 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE x 163 " --> pdb=" O VAL x 159 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS x 164 " --> pdb=" O LYS x 160 " (cutoff:3.500A) Processing helix chain 'T' and resid 131 through 141 removed outlier: 3.555A pdb=" N ASN T 136 " --> pdb=" O THR T 132 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE T 137 " --> pdb=" O ILE T 133 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS T 139 " --> pdb=" O ASN T 135 " (cutoff:3.500A) Processing helix chain 'T' and resid 155 through 167 removed outlier: 3.873A pdb=" N VAL T 159 " --> pdb=" O LYS T 155 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE T 163 " --> pdb=" O VAL T 159 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LYS T 164 " --> pdb=" O LYS T 160 " (cutoff:3.500A) Processing helix chain 'W' and resid 131 through 141 removed outlier: 3.876A pdb=" N LYS W 139 " --> pdb=" O ASN W 135 " (cutoff:3.500A) Processing helix chain 'W' and resid 155 through 167 removed outlier: 3.647A pdb=" N VAL W 159 " --> pdb=" O LYS W 155 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE W 163 " --> pdb=" O VAL W 159 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE W 167 " --> pdb=" O ILE W 163 " (cutoff:3.500A) Processing helix chain 't' and resid 130 through 141 removed outlier: 3.635A pdb=" N VAL t 134 " --> pdb=" O ASP t 130 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE t 138 " --> pdb=" O VAL t 134 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS t 139 " --> pdb=" O ASN t 135 " (cutoff:3.500A) Processing helix chain 't' and resid 155 through 166 removed outlier: 3.858A pdb=" N VAL t 159 " --> pdb=" O LYS t 155 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE t 163 " --> pdb=" O VAL t 159 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS t 164 " --> pdb=" O LYS t 160 " (cutoff:3.500A) Processing helix chain 'w' and resid 130 through 140 removed outlier: 3.625A pdb=" N ILE w 137 " --> pdb=" O ILE w 133 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE w 138 " --> pdb=" O VAL w 134 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS w 139 " --> pdb=" O ASN w 135 " (cutoff:3.500A) Processing helix chain 'w' and resid 141 through 146 Processing helix chain 'w' and resid 155 through 167 removed outlier: 3.841A pdb=" N VAL w 159 " --> pdb=" O LYS w 155 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS w 164 " --> pdb=" O LYS w 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 141 removed outlier: 3.714A pdb=" N LYS L 139 " --> pdb=" O ASN L 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 155 through 162 removed outlier: 4.030A pdb=" N VAL L 159 " --> pdb=" O LYS L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 167 removed outlier: 3.660A pdb=" N PHE L 167 " --> pdb=" O ILE L 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 141 removed outlier: 3.519A pdb=" N VAL M 134 " --> pdb=" O ASP M 130 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS M 139 " --> pdb=" O ASN M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 167 removed outlier: 4.506A pdb=" N VAL M 159 " --> pdb=" O LYS M 155 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE M 167 " --> pdb=" O ILE M 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 141 removed outlier: 3.785A pdb=" N VAL O 134 " --> pdb=" O ASP O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 155 through 165 removed outlier: 3.613A pdb=" N VAL O 159 " --> pdb=" O LYS O 155 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE O 163 " --> pdb=" O VAL O 159 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 141 removed outlier: 3.572A pdb=" N LYS P 139 " --> pdb=" O ASN P 135 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL P 141 " --> pdb=" O ILE P 137 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 146 Processing helix chain 'P' and resid 155 through 167 removed outlier: 3.677A pdb=" N VAL P 159 " --> pdb=" O LYS P 155 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU P 161 " --> pdb=" O GLU P 157 " (cutoff:3.500A) Processing helix chain 'l' and resid 131 through 141 removed outlier: 3.907A pdb=" N ASN l 136 " --> pdb=" O THR l 132 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE l 137 " --> pdb=" O ILE l 133 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS l 139 " --> pdb=" O ASN l 135 " (cutoff:3.500A) Processing helix chain 'l' and resid 155 through 164 removed outlier: 3.873A pdb=" N ILE l 163 " --> pdb=" O VAL l 159 " (cutoff:3.500A) Processing helix chain 'm' and resid 130 through 141 removed outlier: 3.572A pdb=" N VAL m 134 " --> pdb=" O ASP m 130 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN m 136 " --> pdb=" O THR m 132 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE m 137 " --> pdb=" O ILE m 133 " (cutoff:3.500A) Processing helix chain 'm' and resid 141 through 146 Processing helix chain 'm' and resid 155 through 167 removed outlier: 3.933A pdb=" N ILE m 163 " --> pdb=" O VAL m 159 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS m 164 " --> pdb=" O LYS m 160 " (cutoff:3.500A) Processing helix chain 'o' and resid 131 through 141 removed outlier: 3.567A pdb=" N LYS o 139 " --> pdb=" O ASN o 135 " (cutoff:3.500A) Processing helix chain 'o' and resid 141 through 146 Processing helix chain 'o' and resid 155 through 167 removed outlier: 4.030A pdb=" N VAL o 159 " --> pdb=" O LYS o 155 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP o 162 " --> pdb=" O LYS o 158 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE o 163 " --> pdb=" O VAL o 159 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS o 164 " --> pdb=" O LYS o 160 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU o 165 " --> pdb=" O GLU o 161 " (cutoff:3.500A) Processing helix chain 'p' and resid 131 through 141 removed outlier: 3.744A pdb=" N ASN p 136 " --> pdb=" O THR p 132 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE p 137 " --> pdb=" O ILE p 133 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS p 139 " --> pdb=" O ASN p 135 " (cutoff:3.500A) Processing helix chain 'p' and resid 141 through 146 Processing helix chain 'p' and resid 155 through 166 removed outlier: 3.631A pdb=" N VAL p 159 " --> pdb=" O LYS p 155 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP p 162 " --> pdb=" O LYS p 158 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS p 164 " --> pdb=" O LYS p 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 139 removed outlier: 3.592A pdb=" N VAL N 134 " --> pdb=" O ASP N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 155 through 162 removed outlier: 3.544A pdb=" N VAL N 159 " --> pdb=" O LYS N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 167 removed outlier: 3.841A pdb=" N PHE N 167 " --> pdb=" O ILE N 163 " (cutoff:3.500A) Processing helix chain 'n' and resid 131 through 136 Processing helix chain 'n' and resid 136 through 141 Processing helix chain 'n' and resid 155 through 167 removed outlier: 3.525A pdb=" N VAL n 159 " --> pdb=" O LYS n 155 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE n 163 " --> pdb=" O VAL n 159 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS n 164 " --> pdb=" O LYS n 160 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU n 165 " --> pdb=" O GLU n 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 131 through 141 Processing helix chain 'Q' and resid 155 through 162 removed outlier: 3.885A pdb=" N VAL Q 159 " --> pdb=" O LYS Q 155 " (cutoff:3.500A) Processing helix chain 'Q' and resid 162 through 167 Processing helix chain 'R' and resid 131 through 141 Processing helix chain 'R' and resid 155 through 167 removed outlier: 3.572A pdb=" N GLU R 165 " --> pdb=" O GLU R 161 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE R 167 " --> pdb=" O ILE R 163 " (cutoff:3.500A) Processing helix chain 'S' and resid 130 through 141 removed outlier: 3.715A pdb=" N VAL S 134 " --> pdb=" O ASP S 130 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN S 136 " --> pdb=" O THR S 132 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE S 138 " --> pdb=" O VAL S 134 " (cutoff:3.500A) Processing helix chain 'S' and resid 155 through 167 removed outlier: 3.696A pdb=" N ILE S 163 " --> pdb=" O VAL S 159 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS S 164 " --> pdb=" O LYS S 160 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU S 165 " --> pdb=" O GLU S 161 " (cutoff:3.500A) Processing helix chain 'q' and resid 130 through 141 Processing helix chain 'q' and resid 156 through 167 removed outlier: 4.433A pdb=" N ASP q 162 " --> pdb=" O LYS q 158 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE q 163 " --> pdb=" O VAL q 159 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS q 164 " --> pdb=" O LYS q 160 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU q 165 " --> pdb=" O GLU q 161 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE q 167 " --> pdb=" O ILE q 163 " (cutoff:3.500A) Processing helix chain 'r' and resid 130 through 141 removed outlier: 3.514A pdb=" N VAL r 134 " --> pdb=" O ASP r 130 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN r 136 " --> pdb=" O THR r 132 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE r 138 " --> pdb=" O VAL r 134 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS r 139 " --> pdb=" O ASN r 135 " (cutoff:3.500A) Processing helix chain 'r' and resid 141 through 146 Processing helix chain 'r' and resid 155 through 166 removed outlier: 4.190A pdb=" N VAL r 159 " --> pdb=" O LYS r 155 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE r 163 " --> pdb=" O VAL r 159 " (cutoff:3.500A) Processing helix chain 's' and resid 130 through 141 removed outlier: 3.994A pdb=" N VAL s 134 " --> pdb=" O ASP s 130 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS s 139 " --> pdb=" O ASN s 135 " (cutoff:3.500A) Processing helix chain 's' and resid 155 through 166 removed outlier: 3.664A pdb=" N VAL s 159 " --> pdb=" O LYS s 155 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP s 162 " --> pdb=" O LYS s 158 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE s 163 " --> pdb=" O VAL s 159 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS s 164 " --> pdb=" O LYS s 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU s 165 " --> pdb=" O GLU s 161 " (cutoff:3.500A) 1207 hydrogen bonds defined for protein. 3546 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 13.70 Time building geometry restraints manager: 21.57 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: 14763 1.33 - 1.45: 12615 1.45 - 1.57: 35793 1.57 - 1.70: 180 1.70 - 1.82: 150 Bond restraints: 63501 Sorted by residual: bond pdb=" C1' C V 47 " pdb=" N1 C V 47 " ideal model delta sigma weight residual 1.480 1.578 -0.098 1.50e-02 4.44e+03 4.28e+01 bond pdb=" C VAL n 57 " pdb=" N PRO n 58 " ideal model delta sigma weight residual 1.335 1.318 0.017 8.70e-03 1.32e+04 3.85e+00 bond pdb=" CA TYR J 14 " pdb=" C TYR J 14 " ideal model delta sigma weight residual 1.531 1.517 0.014 7.40e-03 1.83e+04 3.47e+00 bond pdb=" CG1 ILE K 225 " pdb=" CD1 ILE K 225 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.34e+00 bond pdb=" CB ARG D 204 " pdb=" CG ARG D 204 " ideal model delta sigma weight residual 1.520 1.468 0.052 3.00e-02 1.11e+03 2.98e+00 ... (remaining 63496 not shown) Histogram of bond angle deviations from ideal: 90.22 - 99.01: 2 99.01 - 107.81: 2661 107.81 - 116.60: 43115 116.60 - 125.39: 39649 125.39 - 134.18: 893 Bond angle restraints: 86320 Sorted by residual: angle pdb=" O3' A V 46 " pdb=" P C V 47 " pdb=" O5' C V 47 " ideal model delta sigma weight residual 104.00 90.22 13.78 1.50e+00 4.44e-01 8.44e+01 angle pdb=" C ARG J 218 " pdb=" N GLU J 219 " pdb=" CA GLU J 219 " ideal model delta sigma weight residual 121.54 130.57 -9.03 1.91e+00 2.74e-01 2.23e+01 angle pdb=" N LYS S 21 " pdb=" CA LYS S 21 " pdb=" C LYS S 21 " ideal model delta sigma weight residual 114.62 109.39 5.23 1.14e+00 7.69e-01 2.10e+01 angle pdb=" O3' A V 46 " pdb=" P C V 47 " pdb=" OP2 C V 47 " ideal model delta sigma weight residual 108.00 121.30 -13.30 3.00e+00 1.11e-01 1.97e+01 angle pdb=" N LYS Q 151 " pdb=" CA LYS Q 151 " pdb=" C LYS Q 151 " ideal model delta sigma weight residual 114.04 108.95 5.09 1.24e+00 6.50e-01 1.69e+01 ... (remaining 86315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.33: 38094 34.33 - 68.66: 895 68.66 - 102.99: 117 102.99 - 137.32: 5 137.32 - 171.65: 3 Dihedral angle restraints: 39114 sinusoidal: 16959 harmonic: 22155 Sorted by residual: dihedral pdb=" CB CYS J 262 " pdb=" SG CYS J 262 " pdb=" SG CYS J 268 " pdb=" CB CYS J 268 " ideal model delta sinusoidal sigma weight residual 93.00 176.19 -83.19 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYS J 111 " pdb=" SG CYS J 111 " pdb=" SG CYS t 63 " pdb=" CB CYS t 63 " ideal model delta sinusoidal sigma weight residual 93.00 165.10 -72.10 1 1.00e+01 1.00e-02 6.65e+01 dihedral pdb=" O4' U V 2 " pdb=" C1' U V 2 " pdb=" N1 U V 2 " pdb=" C2 U V 2 " ideal model delta sinusoidal sigma weight residual -128.00 43.65 -171.65 1 1.70e+01 3.46e-03 6.61e+01 ... (remaining 39111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 7464 0.053 - 0.107: 2259 0.107 - 0.160: 351 0.160 - 0.213: 21 0.213 - 0.266: 4 Chirality restraints: 10099 Sorted by residual: chirality pdb=" CB ILE r 18 " pdb=" CA ILE r 18 " pdb=" CG1 ILE r 18 " pdb=" CG2 ILE r 18 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB VAL D 232 " pdb=" CA VAL D 232 " pdb=" CG1 VAL D 232 " pdb=" CG2 VAL D 232 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB ILE M 18 " pdb=" CA ILE M 18 " pdb=" CG1 ILE M 18 " pdb=" CG2 ILE M 18 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 10096 not shown) Planarity restraints: 10563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 19 " 0.035 2.00e-02 2.50e+03 1.60e-02 7.04e+00 pdb=" N9 A V 19 " -0.036 2.00e-02 2.50e+03 pdb=" C8 A V 19 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A V 19 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A V 19 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A V 19 " 0.008 2.00e-02 2.50e+03 pdb=" N6 A V 19 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A V 19 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A V 19 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A V 19 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A V 19 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A V 13 " -0.036 2.00e-02 2.50e+03 1.54e-02 6.49e+00 pdb=" N9 A V 13 " 0.033 2.00e-02 2.50e+03 pdb=" C8 A V 13 " 0.005 2.00e-02 2.50e+03 pdb=" N7 A V 13 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 13 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A V 13 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A V 13 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A V 13 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A V 13 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A V 13 " 0.007 2.00e-02 2.50e+03 pdb=" C4 A V 13 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G U 12 " -0.033 2.00e-02 2.50e+03 1.47e-02 6.48e+00 pdb=" N9 G U 12 " 0.035 2.00e-02 2.50e+03 pdb=" C8 G U 12 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G U 12 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G U 12 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G U 12 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G U 12 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G U 12 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G U 12 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G U 12 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G U 12 " 0.006 2.00e-02 2.50e+03 pdb=" C4 G U 12 " 0.011 2.00e-02 2.50e+03 ... (remaining 10560 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 1315 2.62 - 3.19: 61436 3.19 - 3.76: 97953 3.76 - 4.33: 143926 4.33 - 4.90: 226350 Nonbonded interactions: 530980 Sorted by model distance: nonbonded pdb=" OH TYR J 473 " pdb=" O PRO W 62 " model vdw 2.055 2.440 nonbonded pdb=" O TYR H 72 " pdb=" OG1 THR H 299 " model vdw 2.060 2.440 nonbonded pdb=" OE2 GLU E 270 " pdb=" NZ LYS F 219 " model vdw 2.076 2.520 nonbonded pdb=" OG SER I 142 " pdb=" O TYR I 151 " model vdw 2.084 2.440 nonbonded pdb=" OH TYR I 55 " pdb=" OE1 GLU I 79 " model vdw 2.087 2.440 ... (remaining 530975 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'w' selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 23.850 Check model and map are aligned: 0.690 Set scattering table: 0.450 Process input model: 134.500 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.560 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:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 63501 Z= 0.410 Angle : 0.751 13.778 86320 Z= 0.419 Chirality : 0.049 0.266 10099 Planarity : 0.004 0.049 10563 Dihedral : 15.641 171.653 24775 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.81 % Favored : 84.95 % Rotamer: Outliers : 0.16 % Allowed : 9.65 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -4.68 (0.08), residues: 7434 helix: -2.80 (0.09), residues: 1966 sheet: -1.99 (0.14), residues: 1097 loop : -3.76 (0.07), residues: 4371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 281 HIS 0.008 0.001 HIS H 99 PHE 0.027 0.002 PHE H 188 TYR 0.027 0.002 TYR B 42 ARG 0.008 0.001 ARG K 923 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2545 residues out of total 6825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 2534 time to evaluate : 5.473 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: 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: 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 6 ASP cc_start: 0.7212 (m-30) cc_final: 0.6993 (m-30) REVERT: A 52 TYR cc_start: 0.8682 (t80) cc_final: 0.8457 (t80) REVERT: A 111 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7584 (tm-30) REVERT: D 45 TYR cc_start: 0.8323 (m-10) cc_final: 0.8117 (m-80) REVERT: E 63 ASP cc_start: 0.6803 (p0) cc_final: 0.6416 (p0) REVERT: E 77 ASN cc_start: 0.8008 (m-40) cc_final: 0.7680 (p0) REVERT: E 258 LEU cc_start: 0.8049 (mt) cc_final: 0.7781 (mt) REVERT: F 63 ASP cc_start: 0.7469 (p0) cc_final: 0.6863 (p0) REVERT: F 102 ASP cc_start: 0.7320 (p0) cc_final: 0.6865 (p0) REVERT: G 138 ASN cc_start: 0.8035 (p0) cc_final: 0.7793 (p0) REVERT: I 271 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7299 (m-10) REVERT: J 148 ILE cc_start: 0.7909 (mp) cc_final: 0.7434 (mt) REVERT: J 292 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6065 (mt-10) REVERT: J 390 PHE cc_start: 0.7662 (m-80) cc_final: 0.7350 (m-80) REVERT: K 162 LYS cc_start: 0.7926 (pttt) cc_final: 0.7533 (mttm) REVERT: K 188 MET cc_start: 0.8978 (mmm) cc_final: 0.8702 (mmm) REVERT: K 201 TYR cc_start: 0.6398 (m-80) cc_final: 0.6084 (m-80) REVERT: K 228 TYR cc_start: 0.6756 (t80) cc_final: 0.6514 (t80) REVERT: K 681 LYS cc_start: 0.8292 (mmtt) cc_final: 0.8079 (mmtt) REVERT: K 684 GLU cc_start: 0.8056 (mp0) cc_final: 0.7817 (mp0) REVERT: K 686 ASN cc_start: 0.8692 (m110) cc_final: 0.8073 (m110) REVERT: K 793 LYS cc_start: 0.8935 (mttp) cc_final: 0.8704 (mttt) REVERT: X 86 LEU cc_start: 0.7072 (tp) cc_final: 0.6842 (tp) REVERT: X 109 TYR cc_start: 0.6588 (m-80) cc_final: 0.6275 (m-10) REVERT: X 110 ILE cc_start: 0.7560 (mm) cc_final: 0.7127 (mm) REVERT: x 65 TYR cc_start: 0.8479 (p90) cc_final: 0.8135 (p90) REVERT: x 139 LYS cc_start: 0.8658 (ttmt) cc_final: 0.8445 (tptt) REVERT: W 64 ASP cc_start: 0.7456 (m-30) cc_final: 0.7092 (m-30) REVERT: W 131 ASP cc_start: 0.8412 (p0) cc_final: 0.7872 (p0) REVERT: W 142 PHE cc_start: 0.8897 (m-80) cc_final: 0.8687 (m-80) REVERT: t 79 GLN cc_start: 0.7179 (mm-40) cc_final: 0.6844 (mm110) REVERT: t 95 LEU cc_start: 0.8986 (mt) cc_final: 0.8621 (mt) REVERT: t 112 TYR cc_start: 0.7528 (t80) cc_final: 0.6696 (t80) REVERT: t 131 ASP cc_start: 0.8325 (p0) cc_final: 0.8035 (p0) REVERT: w 108 ILE cc_start: 0.8675 (mp) cc_final: 0.8435 (mm) REVERT: L 162 ASP cc_start: 0.7251 (p0) cc_final: 0.6646 (p0) REVERT: M 7 TYR cc_start: 0.7494 (t80) cc_final: 0.7145 (t80) REVERT: M 34 ASP cc_start: 0.7662 (t0) cc_final: 0.7287 (t0) REVERT: M 106 LEU cc_start: 0.8272 (mt) cc_final: 0.7944 (mt) REVERT: O 40 ASN cc_start: 0.8839 (m-40) cc_final: 0.8600 (m110) REVERT: O 47 TYR cc_start: 0.8160 (m-10) cc_final: 0.7950 (m-10) REVERT: O 147 ASN cc_start: 0.7462 (p0) cc_final: 0.7210 (p0) REVERT: O 172 LEU cc_start: 0.7955 (mp) cc_final: 0.7623 (mp) REVERT: P 11 PRO cc_start: 0.7882 (Cg_endo) cc_final: 0.7123 (Cg_exo) REVERT: P 31 THR cc_start: 0.9145 (p) cc_final: 0.8875 (p) REVERT: P 164 LYS cc_start: 0.8549 (mmtp) cc_final: 0.8328 (tptt) REVERT: P 169 TYR cc_start: 0.8599 (p90) cc_final: 0.8338 (p90) REVERT: l 167 PHE cc_start: 0.7934 (m-80) cc_final: 0.7702 (m-80) REVERT: o 9 PHE cc_start: 0.6905 (p90) cc_final: 0.6534 (p90) REVERT: o 11 PRO cc_start: 0.8538 (Cg_endo) cc_final: 0.7794 (Cg_exo) REVERT: o 112 TYR cc_start: 0.8189 (t80) cc_final: 0.7971 (t80) REVERT: o 172 LEU cc_start: 0.8789 (pt) cc_final: 0.7907 (pt) REVERT: p 35 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7622 (mp0) REVERT: p 65 TYR cc_start: 0.7958 (p90) cc_final: 0.7417 (p90) REVERT: p 67 LYS cc_start: 0.8483 (mttt) cc_final: 0.8130 (mttp) REVERT: p 97 ARG cc_start: 0.7948 (mtt180) cc_final: 0.7688 (mtt180) REVERT: p 131 ASP cc_start: 0.9100 (p0) cc_final: 0.8732 (p0) REVERT: p 167 PHE cc_start: 0.8325 (m-80) cc_final: 0.8030 (m-80) REVERT: N 166 LEU cc_start: 0.9182 (tt) cc_final: 0.8952 (mt) REVERT: n 112 TYR cc_start: 0.7976 (t80) cc_final: 0.7759 (t80) REVERT: n 166 LEU cc_start: 0.8777 (tp) cc_final: 0.8536 (tt) REVERT: Q 7 TYR cc_start: 0.8326 (t80) cc_final: 0.8122 (t80) REVERT: Q 95 LEU cc_start: 0.8889 (tp) cc_final: 0.8457 (tp) REVERT: Q 170 TYR cc_start: 0.7313 (m-80) cc_final: 0.7039 (m-80) REVERT: S 6 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7734 (tm-30) REVERT: S 31 THR cc_start: 0.8667 (p) cc_final: 0.8422 (p) REVERT: S 42 LEU cc_start: 0.9105 (tp) cc_final: 0.8902 (tt) REVERT: S 84 LEU cc_start: 0.8038 (mp) cc_final: 0.7826 (mp) REVERT: S 145 ILE cc_start: 0.7880 (mm) cc_final: 0.7607 (mm) REVERT: q 23 THR cc_start: 0.7083 (m) cc_final: 0.6772 (t) REVERT: q 32 ASN cc_start: 0.7879 (t0) cc_final: 0.7622 (t0) REVERT: q 86 LEU cc_start: 0.8567 (tp) cc_final: 0.8234 (tp) REVERT: q 170 TYR cc_start: 0.7189 (m-10) cc_final: 0.6866 (m-80) REVERT: s 6 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7879 (tm-30) REVERT: s 84 LEU cc_start: 0.8796 (mp) cc_final: 0.8364 (mp) REVERT: s 109 TYR cc_start: 0.6949 (m-80) cc_final: 0.6569 (m-80) REVERT: s 140 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8125 (mm-30) outliers start: 11 outliers final: 5 residues processed: 2541 average time/residue: 0.6258 time to fit residues: 2666.2883 Evaluate side-chains 1833 residues out of total 6825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1827 time to evaluate : 5.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain I residue 271 TYR Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain m residue 16 ILE Chi-restraints excluded: chain s residue 17 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 747 random chunks: chunk 630 optimal weight: 20.0000 chunk 566 optimal weight: 0.2980 chunk 314 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 381 optimal weight: 30.0000 chunk 302 optimal weight: 1.9990 chunk 585 optimal weight: 6.9990 chunk 226 optimal weight: 0.0370 chunk 356 optimal weight: 2.9990 chunk 435 optimal weight: 10.0000 chunk 678 optimal weight: 5.9990 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN C 84 ASN C 128 ASN D 141 ASN D 153 ASN E 77 ASN F 17 HIS F 141 ASN F 153 ASN F 177 ASN G 19 HIS G 166 ASN H 90 ASN H 135 GLN I 21 ASN I 44 GLN I 50 ASN I 74 ASN I 87 ASN I 97 ASN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 HIS J 96 ASN J 211 ASN J 265 ASN J 345 ASN ** J 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 440 ASN K 24 ASN K 38 GLN K 59 GLN K 96 ASN K 110 GLN K 175 HIS ** K 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 344 ASN ** K 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 387 ASN K 544 ASN K 602 ASN K 760 ASN K 846 ASN K 994 HIS X 4 GLN X 32 ASN ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 119 ASN T 40 ASN T 135 ASN t 14 ASN t 135 ASN t 174 GLN ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 GLN O 29 HIS O 76 GLN O 77 GLN O 150 GLN O 174 GLN ** P 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 14 ASN l 40 ASN l 76 GLN ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 4 GLN m 147 ASN o 147 ASN p 53 ASN N 4 GLN N 135 ASN ** N 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 119 ASN Q 39 HIS R 29 HIS R 39 HIS ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 4 GLN q 14 ASN q 40 ASN ** q 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 14 ASN r 40 ASN ** s 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 40 ASN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 63501 Z= 0.236 Angle : 0.744 14.025 86320 Z= 0.383 Chirality : 0.049 0.342 10099 Planarity : 0.005 0.062 10563 Dihedral : 11.559 178.544 9583 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.55 % Favored : 87.40 % Rotamer: Outliers : 3.69 % Allowed : 20.10 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.82 (0.08), residues: 7434 helix: -1.79 (0.10), residues: 2084 sheet: -1.50 (0.15), residues: 1107 loop : -3.38 (0.08), residues: 4243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 770 HIS 0.013 0.002 HIS K 175 PHE 0.027 0.002 PHE W 9 TYR 0.026 0.002 TYR N 109 ARG 0.012 0.001 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2368 residues out of total 6825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 2116 time to evaluate : 5.329 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: 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: 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 111 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7467 (tm-30) REVERT: D 77 ASN cc_start: 0.7293 (m-40) cc_final: 0.6971 (m-40) REVERT: E 63 ASP cc_start: 0.6386 (p0) cc_final: 0.5941 (p0) REVERT: G 66 ASP cc_start: 0.7494 (p0) cc_final: 0.7251 (p0) REVERT: G 138 ASN cc_start: 0.7755 (p0) cc_final: 0.7533 (p0) REVERT: G 155 THR cc_start: 0.8329 (t) cc_final: 0.8103 (p) REVERT: G 257 ILE cc_start: 0.8534 (mm) cc_final: 0.8291 (mm) REVERT: H 113 ARG cc_start: 0.7781 (mtp85) cc_final: 0.7405 (ttm170) REVERT: H 122 PHE cc_start: 0.7761 (m-80) cc_final: 0.7328 (m-80) REVERT: I 173 GLU cc_start: 0.6397 (tp30) cc_final: 0.5872 (tp30) REVERT: I 246 ASP cc_start: 0.7073 (p0) cc_final: 0.6805 (p0) REVERT: I 271 TYR cc_start: 0.7683 (OUTLIER) cc_final: 0.7106 (m-10) REVERT: J 148 ILE cc_start: 0.7841 (mp) cc_final: 0.7325 (mt) REVERT: J 171 SER cc_start: 0.8199 (m) cc_final: 0.7925 (p) REVERT: K 148 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8041 (tt0) REVERT: K 162 LYS cc_start: 0.7850 (pttt) cc_final: 0.7451 (mtpt) REVERT: K 188 MET cc_start: 0.8922 (mmm) cc_final: 0.8688 (mmm) REVERT: K 328 LYS cc_start: 0.7849 (mttm) cc_final: 0.7274 (mttm) REVERT: K 502 LYS cc_start: 0.8905 (pttt) cc_final: 0.8636 (pttm) REVERT: K 681 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8047 (mmmt) REVERT: K 682 LYS cc_start: 0.8796 (tppt) cc_final: 0.8458 (tppt) REVERT: K 686 ASN cc_start: 0.8519 (m110) cc_final: 0.7802 (m110) REVERT: K 793 LYS cc_start: 0.8853 (mttp) cc_final: 0.8463 (mttt) REVERT: K 926 VAL cc_start: 0.9386 (t) cc_final: 0.9061 (m) REVERT: X 4 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.6721 (pp30) REVERT: X 110 ILE cc_start: 0.7502 (mm) cc_final: 0.7100 (mm) REVERT: x 5 ARG cc_start: 0.6314 (mpt180) cc_final: 0.6052 (mmm-85) REVERT: x 49 VAL cc_start: 0.8619 (p) cc_final: 0.8329 (p) REVERT: x 65 TYR cc_start: 0.8394 (p90) cc_final: 0.7475 (p90) REVERT: x 139 LYS cc_start: 0.8612 (ttmt) cc_final: 0.8375 (tptt) REVERT: T 6 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7087 (mt-10) REVERT: W 7 TYR cc_start: 0.7961 (t80) cc_final: 0.7658 (t80) REVERT: W 97 ARG cc_start: 0.9047 (mtp85) cc_final: 0.8755 (mtp85) REVERT: W 167 PHE cc_start: 0.7966 (m-80) cc_final: 0.7746 (m-80) REVERT: t 52 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7692 (ptpp) REVERT: t 79 GLN cc_start: 0.7682 (mm-40) cc_final: 0.7076 (mm-40) REVERT: t 135 ASN cc_start: 0.8187 (m-40) cc_final: 0.7979 (m110) REVERT: M 12 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8116 (mm) REVERT: O 34 ASP cc_start: 0.7660 (p0) cc_final: 0.7287 (p0) REVERT: O 47 TYR cc_start: 0.7944 (m-10) cc_final: 0.7717 (m-10) REVERT: O 147 ASN cc_start: 0.7486 (p0) cc_final: 0.7251 (p0) REVERT: O 150 GLN cc_start: 0.8312 (mt0) cc_final: 0.8038 (mp10) REVERT: P 31 THR cc_start: 0.9104 (p) cc_final: 0.8837 (p) REVERT: P 169 TYR cc_start: 0.8476 (p90) cc_final: 0.8217 (p90) REVERT: o 9 PHE cc_start: 0.6828 (p90) cc_final: 0.6474 (p90) REVERT: o 11 PRO cc_start: 0.8549 (Cg_endo) cc_final: 0.7743 (Cg_exo) REVERT: o 112 TYR cc_start: 0.8161 (t80) cc_final: 0.7774 (t80) REVERT: p 35 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7572 (mp0) REVERT: p 65 TYR cc_start: 0.8145 (p90) cc_final: 0.7751 (p90) REVERT: p 97 ARG cc_start: 0.7947 (mtt180) cc_final: 0.7699 (mtt180) REVERT: p 167 PHE cc_start: 0.8225 (m-80) cc_final: 0.7975 (m-80) REVERT: N 106 LEU cc_start: 0.8499 (tt) cc_final: 0.7974 (mp) REVERT: N 166 LEU cc_start: 0.9024 (tt) cc_final: 0.8745 (mt) REVERT: Q 86 LEU cc_start: 0.8693 (pt) cc_final: 0.8395 (pt) REVERT: Q 105 ASP cc_start: 0.7320 (t0) cc_final: 0.6807 (p0) REVERT: S 166 LEU cc_start: 0.8418 (tt) cc_final: 0.7676 (mm) REVERT: q 170 TYR cc_start: 0.7042 (m-10) cc_final: 0.6721 (m-10) REVERT: s 6 GLU cc_start: 0.8294 (tm-30) cc_final: 0.8001 (tm-30) REVERT: s 84 LEU cc_start: 0.8779 (mp) cc_final: 0.8485 (mp) REVERT: s 109 TYR cc_start: 0.7002 (m-80) cc_final: 0.6667 (m-80) outliers start: 252 outliers final: 151 residues processed: 2230 average time/residue: 0.5709 time to fit residues: 2165.0468 Evaluate side-chains 1996 residues out of total 6825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1841 time to evaluate : 5.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 218 LYS Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 HIS Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 185 ILE Chi-restraints excluded: chain H residue 227 ASP Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain I residue 229 THR Chi-restraints excluded: chain I residue 271 TYR Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 188 ILE Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 169 ASP Chi-restraints excluded: chain K residue 175 HIS Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 212 ASP Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 290 ILE Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 616 GLU Chi-restraints excluded: chain K residue 752 LEU Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain K residue 916 VAL Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 984 ASP Chi-restraints excluded: chain K residue 1031 ILE Chi-restraints excluded: chain X residue 4 GLN Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 59 THR Chi-restraints excluded: chain x residue 147 ASN Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 163 ILE Chi-restraints excluded: chain T residue 170 TYR Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 126 VAL Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 154 VAL Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain t residue 16 ILE Chi-restraints excluded: chain t residue 52 LYS Chi-restraints excluded: chain t residue 81 ASN Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain t residue 102 ILE Chi-restraints excluded: chain w residue 123 THR Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 69 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 140 GLU Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 14 ASN Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain P residue 34 ASP Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 101 ASN Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 70 LEU Chi-restraints excluded: chain l residue 134 VAL Chi-restraints excluded: chain m residue 16 ILE Chi-restraints excluded: chain m residue 31 THR Chi-restraints excluded: chain m residue 127 SER Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain o residue 134 VAL Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain R residue 21 LYS Chi-restraints excluded: chain R residue 101 ASN Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain S residue 33 ILE Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 124 LYS Chi-restraints excluded: chain q residue 45 THR Chi-restraints excluded: chain q residue 66 VAL Chi-restraints excluded: chain q residue 159 VAL Chi-restraints excluded: chain r residue 34 ASP Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 44 ILE Chi-restraints excluded: chain s residue 59 THR Chi-restraints excluded: chain s residue 148 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 747 random chunks: chunk 377 optimal weight: 20.0000 chunk 210 optimal weight: 2.9990 chunk 564 optimal weight: 8.9990 chunk 461 optimal weight: 2.9990 chunk 187 optimal weight: 0.1980 chunk 679 optimal weight: 6.9990 chunk 734 optimal weight: 6.9990 chunk 605 optimal weight: 3.9990 chunk 673 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 545 optimal weight: 0.0770 overall best weight: 2.0544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 HIS ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 135 GLN H 167 ASN ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 HIS ** K 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 39 HIS ** x 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 174 GLN ** t 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 GLN ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 32 ASN ** o 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 101 ASN ** N 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 53 ASN q 14 ASN ** s 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 63501 Z= 0.295 Angle : 0.715 11.357 86320 Z= 0.371 Chirality : 0.049 0.286 10099 Planarity : 0.004 0.067 10563 Dihedral : 11.443 177.955 9583 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.73 % Favored : 87.23 % Rotamer: Outliers : 5.10 % Allowed : 22.85 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.48 (0.09), residues: 7434 helix: -1.42 (0.11), residues: 2090 sheet: -1.50 (0.14), residues: 1360 loop : -3.22 (0.08), residues: 3984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 770 HIS 0.018 0.001 HIS K 175 PHE 0.029 0.002 PHE J 331 TYR 0.040 0.002 TYR B 87 ARG 0.016 0.001 ARG t 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2251 residues out of total 6825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 1903 time to evaluate : 5.441 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: 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 111 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7565 (tp40) REVERT: E 63 ASP cc_start: 0.6637 (p0) cc_final: 0.6133 (p0) REVERT: F 63 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.6973 (p0) REVERT: G 138 ASN cc_start: 0.7736 (p0) cc_final: 0.7492 (p0) REVERT: H 102 ASN cc_start: 0.7755 (p0) cc_final: 0.7435 (p0) REVERT: H 122 PHE cc_start: 0.7818 (m-80) cc_final: 0.7536 (m-80) REVERT: I 271 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.7345 (m-10) REVERT: K 134 LEU cc_start: 0.5780 (OUTLIER) cc_final: 0.5163 (pp) REVERT: K 162 LYS cc_start: 0.7854 (pttt) cc_final: 0.7461 (mtpt) REVERT: K 188 MET cc_start: 0.8969 (mmm) cc_final: 0.8702 (mmm) REVERT: K 328 LYS cc_start: 0.7861 (mttm) cc_final: 0.7338 (mttm) REVERT: K 406 LEU cc_start: 0.7866 (tp) cc_final: 0.7414 (tp) REVERT: K 502 LYS cc_start: 0.8950 (pttt) cc_final: 0.8669 (pttm) REVERT: K 682 LYS cc_start: 0.8943 (tppt) cc_final: 0.8564 (tppt) REVERT: K 686 ASN cc_start: 0.8638 (m110) cc_final: 0.8143 (m110) REVERT: K 793 LYS cc_start: 0.8872 (mttp) cc_final: 0.8591 (mttt) REVERT: K 926 VAL cc_start: 0.9404 (t) cc_final: 0.9091 (m) REVERT: X 70 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8883 (mp) REVERT: X 110 ILE cc_start: 0.7607 (mm) cc_final: 0.7210 (mm) REVERT: x 5 ARG cc_start: 0.6230 (mpt180) cc_final: 0.5725 (mmm160) REVERT: x 49 VAL cc_start: 0.8787 (p) cc_final: 0.8490 (p) REVERT: x 139 LYS cc_start: 0.8678 (ttmt) cc_final: 0.8452 (tptt) REVERT: T 6 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7097 (mt-10) REVERT: T 172 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7993 (mm) REVERT: W 7 TYR cc_start: 0.8084 (t80) cc_final: 0.7624 (t80) REVERT: W 97 ARG cc_start: 0.9073 (mtp85) cc_final: 0.8757 (mtp85) REVERT: W 131 ASP cc_start: 0.8401 (p0) cc_final: 0.8131 (p0) REVERT: W 167 PHE cc_start: 0.7944 (m-80) cc_final: 0.7709 (m-80) REVERT: t 5 ARG cc_start: 0.8209 (mmt90) cc_final: 0.7836 (mmt180) REVERT: t 52 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7618 (ptpp) REVERT: t 79 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7140 (mm110) REVERT: t 95 LEU cc_start: 0.8849 (mt) cc_final: 0.8623 (mt) REVERT: w 79 GLN cc_start: 0.5610 (OUTLIER) cc_final: 0.5260 (pm20) REVERT: w 95 LEU cc_start: 0.8530 (pp) cc_final: 0.8135 (mm) REVERT: w 108 ILE cc_start: 0.8694 (mm) cc_final: 0.8488 (mm) REVERT: L 79 GLN cc_start: 0.7316 (mm-40) cc_final: 0.7110 (mm-40) REVERT: M 12 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8099 (mm) REVERT: O 147 ASN cc_start: 0.7581 (p0) cc_final: 0.7342 (p0) REVERT: O 150 GLN cc_start: 0.8361 (mt0) cc_final: 0.8142 (mp10) REVERT: P 22 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7262 (mp) REVERT: P 31 THR cc_start: 0.9056 (p) cc_final: 0.8825 (p) REVERT: P 169 TYR cc_start: 0.8489 (p90) cc_final: 0.8220 (p90) REVERT: o 9 PHE cc_start: 0.6845 (p90) cc_final: 0.6423 (p90) REVERT: o 11 PRO cc_start: 0.8517 (Cg_endo) cc_final: 0.7843 (Cg_exo) REVERT: p 35 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7568 (mp0) REVERT: p 65 TYR cc_start: 0.8215 (p90) cc_final: 0.7681 (p90) REVERT: p 67 LYS cc_start: 0.8499 (mttt) cc_final: 0.8149 (mttp) REVERT: p 85 THR cc_start: 0.7919 (p) cc_final: 0.7517 (p) REVERT: p 86 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7697 (mt) REVERT: N 106 LEU cc_start: 0.8406 (tt) cc_final: 0.7954 (mp) REVERT: N 166 LEU cc_start: 0.9035 (tt) cc_final: 0.8737 (mt) REVERT: n 5 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.6741 (mmt180) REVERT: n 169 TYR cc_start: 0.7594 (p90) cc_final: 0.7374 (p90) REVERT: Q 7 TYR cc_start: 0.8032 (t80) cc_final: 0.7781 (t80) REVERT: Q 94 TYR cc_start: 0.7958 (t80) cc_final: 0.7559 (t80) REVERT: Q 105 ASP cc_start: 0.7248 (t0) cc_final: 0.6815 (p0) REVERT: Q 170 TYR cc_start: 0.7214 (m-10) cc_final: 0.6906 (m-80) REVERT: S 104 ASP cc_start: 0.6516 (t0) cc_final: 0.6236 (t0) REVERT: S 144 LYS cc_start: 0.8685 (mptt) cc_final: 0.8002 (tptp) REVERT: q 57 VAL cc_start: 0.8462 (t) cc_final: 0.8173 (p) REVERT: q 170 TYR cc_start: 0.7086 (m-10) cc_final: 0.6737 (m-10) REVERT: s 6 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8030 (tm-30) REVERT: s 109 TYR cc_start: 0.7168 (m-80) cc_final: 0.6868 (m-80) REVERT: s 140 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8455 (mm-30) outliers start: 348 outliers final: 226 residues processed: 2079 average time/residue: 0.5771 time to fit residues: 2055.8446 Evaluate side-chains 1984 residues out of total 6825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 1747 time to evaluate : 5.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 218 LYS Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 185 ILE Chi-restraints excluded: chain H residue 227 ASP Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain H residue 303 LEU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain I residue 229 THR Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain I residue 271 TYR Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 171 SER Chi-restraints excluded: chain J residue 188 ILE Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain K residue 20 HIS Chi-restraints excluded: chain K residue 59 GLN Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 169 ASP Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 212 ASP Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 290 ILE Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 532 LEU Chi-restraints excluded: chain K residue 616 GLU Chi-restraints excluded: chain K residue 752 LEU Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain K residue 811 ASP Chi-restraints excluded: chain K residue 815 ASP Chi-restraints excluded: chain K residue 838 GLU Chi-restraints excluded: chain K residue 895 ASN Chi-restraints excluded: chain K residue 905 VAL Chi-restraints excluded: chain K residue 959 LEU Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 984 ASP Chi-restraints excluded: chain K residue 1031 ILE Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 147 ASN Chi-restraints excluded: chain x residue 162 ASP Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 61 ASP Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 163 ILE Chi-restraints excluded: chain T residue 170 TYR Chi-restraints excluded: chain T residue 172 LEU Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 126 VAL Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 154 VAL Chi-restraints excluded: chain t residue 16 ILE Chi-restraints excluded: chain t residue 52 LYS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 59 THR Chi-restraints excluded: chain t residue 81 ASN Chi-restraints excluded: chain t residue 102 ILE Chi-restraints excluded: chain t residue 106 LEU Chi-restraints excluded: chain t residue 132 THR Chi-restraints excluded: chain t residue 138 ILE Chi-restraints excluded: chain w residue 8 VAL Chi-restraints excluded: chain w residue 79 GLN Chi-restraints excluded: chain w residue 84 LEU Chi-restraints excluded: chain w residue 85 THR Chi-restraints excluded: chain w residue 123 THR Chi-restraints excluded: chain w residue 141 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 14 ASN Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 34 ASP Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 70 LEU Chi-restraints excluded: chain l residue 93 LEU Chi-restraints excluded: chain l residue 114 SER Chi-restraints excluded: chain l residue 128 ILE Chi-restraints excluded: chain l residue 158 LYS Chi-restraints excluded: chain m residue 16 ILE Chi-restraints excluded: chain m residue 31 THR Chi-restraints excluded: chain m residue 38 ILE Chi-restraints excluded: chain m residue 127 SER Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 38 ILE Chi-restraints excluded: chain o residue 59 THR Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain o residue 123 THR Chi-restraints excluded: chain o residue 127 SER Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 16 ILE Chi-restraints excluded: chain p residue 60 LEU Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 101 ASN Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain n residue 5 ARG Chi-restraints excluded: chain n residue 23 THR Chi-restraints excluded: chain n residue 42 LEU Chi-restraints excluded: chain n residue 86 LEU Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 84 LEU Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 21 LYS Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 101 ASN Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain S residue 19 ASP Chi-restraints excluded: chain S residue 33 ILE Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 124 LYS Chi-restraints excluded: chain S residue 136 ASN Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain q residue 59 THR Chi-restraints excluded: chain q residue 63 CYS Chi-restraints excluded: chain q residue 66 VAL Chi-restraints excluded: chain q residue 102 ILE Chi-restraints excluded: chain q residue 132 THR Chi-restraints excluded: chain q residue 140 GLU Chi-restraints excluded: chain q residue 147 ASN Chi-restraints excluded: chain q residue 159 VAL Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 34 ASP Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 59 THR Chi-restraints excluded: chain s residue 69 ILE Chi-restraints excluded: chain s residue 148 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 747 random chunks: chunk 671 optimal weight: 4.9990 chunk 510 optimal weight: 0.8980 chunk 352 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 324 optimal weight: 10.0000 chunk 456 optimal weight: 6.9990 chunk 682 optimal weight: 20.0000 chunk 722 optimal weight: 5.9990 chunk 356 optimal weight: 3.9990 chunk 646 optimal weight: 0.0020 chunk 194 optimal weight: 1.9990 overall best weight: 1.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 HIS D 35 GLN ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 HIS ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 135 GLN H 187 ASN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 285 ASN ** J 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 HIS ** K 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 994 HIS ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 GLN l 4 GLN ** m 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 150 GLN p 101 ASN ** N 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 135 ASN ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 63501 Z= 0.268 Angle : 0.706 10.902 86320 Z= 0.363 Chirality : 0.048 0.265 10099 Planarity : 0.004 0.070 10563 Dihedral : 11.380 178.914 9583 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.42 % Favored : 87.56 % Rotamer: Outliers : 5.54 % Allowed : 24.11 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.25 (0.09), residues: 7434 helix: -1.22 (0.11), residues: 2102 sheet: -1.30 (0.14), residues: 1338 loop : -3.11 (0.08), residues: 3994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 770 HIS 0.009 0.001 HIS K 994 PHE 0.018 0.002 PHE m 9 TYR 0.037 0.002 TYR N 112 ARG 0.008 0.001 ARG l 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2234 residues out of total 6825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 1856 time to evaluate : 5.440 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7451 (tp-100) REVERT: E 63 ASP cc_start: 0.6540 (p0) cc_final: 0.6090 (p0) REVERT: E 195 ASP cc_start: 0.6188 (m-30) cc_final: 0.5773 (m-30) REVERT: E 258 LEU cc_start: 0.8106 (mt) cc_final: 0.7895 (mt) REVERT: F 63 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.6891 (p0) REVERT: H 102 ASN cc_start: 0.7734 (p0) cc_final: 0.7408 (p0) REVERT: H 113 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7340 (ttm170) REVERT: I 271 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.7304 (m-10) REVERT: J 171 SER cc_start: 0.8276 (m) cc_final: 0.7961 (p) REVERT: K 188 MET cc_start: 0.8957 (mmm) cc_final: 0.8723 (mmm) REVERT: K 241 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7966 (t80) REVERT: K 328 LYS cc_start: 0.7821 (mttm) cc_final: 0.7322 (mttm) REVERT: K 650 ASP cc_start: 0.7974 (t0) cc_final: 0.7770 (t0) REVERT: K 682 LYS cc_start: 0.8924 (tppt) cc_final: 0.8474 (tppt) REVERT: K 686 ASN cc_start: 0.8680 (m110) cc_final: 0.8081 (m110) REVERT: K 782 LEU cc_start: 0.8917 (mt) cc_final: 0.8713 (mt) REVERT: K 793 LYS cc_start: 0.8871 (mttp) cc_final: 0.8592 (mttt) REVERT: K 819 GLU cc_start: 0.7260 (tp30) cc_final: 0.7043 (tp30) REVERT: K 926 VAL cc_start: 0.9367 (t) cc_final: 0.9061 (m) REVERT: X 110 ILE cc_start: 0.7637 (mm) cc_final: 0.7245 (mm) REVERT: x 5 ARG cc_start: 0.6145 (mpt180) cc_final: 0.5627 (mmt-90) REVERT: x 139 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8370 (tptt) REVERT: T 6 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7014 (mt-10) REVERT: T 65 TYR cc_start: 0.8252 (p90) cc_final: 0.8015 (p90) REVERT: T 79 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.6244 (tm-30) REVERT: T 172 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8010 (mm) REVERT: W 7 TYR cc_start: 0.8124 (t80) cc_final: 0.7554 (t80) REVERT: W 97 ARG cc_start: 0.9034 (mtp85) cc_final: 0.8671 (mtp85) REVERT: W 140 GLU cc_start: 0.7454 (tp30) cc_final: 0.6890 (tm-30) REVERT: W 167 PHE cc_start: 0.7931 (m-80) cc_final: 0.7708 (m-80) REVERT: t 79 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7271 (mm-40) REVERT: t 95 LEU cc_start: 0.8879 (mt) cc_final: 0.8596 (mt) REVERT: w 79 GLN cc_start: 0.5353 (pm20) cc_final: 0.5021 (pm20) REVERT: w 134 VAL cc_start: 0.8940 (t) cc_final: 0.8722 (t) REVERT: L 79 GLN cc_start: 0.7380 (mm-40) cc_final: 0.7136 (mm-40) REVERT: M 12 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8100 (mm) REVERT: O 77 GLN cc_start: 0.6816 (OUTLIER) cc_final: 0.6494 (mm-40) REVERT: O 147 ASN cc_start: 0.7603 (p0) cc_final: 0.7350 (p0) REVERT: P 22 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7287 (mp) REVERT: P 31 THR cc_start: 0.9007 (p) cc_final: 0.8681 (p) REVERT: P 169 TYR cc_start: 0.8413 (p90) cc_final: 0.8204 (p90) REVERT: o 9 PHE cc_start: 0.6812 (p90) cc_final: 0.6437 (p90) REVERT: o 11 PRO cc_start: 0.8498 (Cg_endo) cc_final: 0.7797 (Cg_exo) REVERT: o 36 ARG cc_start: 0.8712 (mmm-85) cc_final: 0.8392 (mmm-85) REVERT: p 35 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7528 (mp0) REVERT: p 65 TYR cc_start: 0.8244 (p90) cc_final: 0.7801 (p90) REVERT: p 67 LYS cc_start: 0.8568 (mttt) cc_final: 0.8143 (mttp) REVERT: p 85 THR cc_start: 0.8004 (p) cc_final: 0.7614 (p) REVERT: p 86 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7903 (mt) REVERT: N 106 LEU cc_start: 0.8454 (tt) cc_final: 0.7979 (mp) REVERT: N 166 LEU cc_start: 0.9045 (tt) cc_final: 0.8737 (mt) REVERT: Q 7 TYR cc_start: 0.8104 (t80) cc_final: 0.7805 (t80) REVERT: Q 105 ASP cc_start: 0.7277 (t0) cc_final: 0.6945 (p0) REVERT: S 104 ASP cc_start: 0.6523 (t0) cc_final: 0.6301 (t0) REVERT: S 144 LYS cc_start: 0.8696 (mptt) cc_final: 0.7993 (tptp) REVERT: q 57 VAL cc_start: 0.8459 (t) cc_final: 0.8200 (p) REVERT: q 170 TYR cc_start: 0.7020 (m-10) cc_final: 0.6677 (m-10) REVERT: r 67 LYS cc_start: 0.7805 (ptpt) cc_final: 0.7586 (mttt) REVERT: s 6 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8055 (tm-30) REVERT: s 84 LEU cc_start: 0.8798 (mt) cc_final: 0.8583 (mp) REVERT: s 109 TYR cc_start: 0.7172 (m-80) cc_final: 0.6888 (m-80) REVERT: s 140 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8427 (mm-30) REVERT: s 164 LYS cc_start: 0.8392 (mmmm) cc_final: 0.8160 (mmtt) outliers start: 378 outliers final: 250 residues processed: 2061 average time/residue: 0.5617 time to fit residues: 1996.7851 Evaluate side-chains 2009 residues out of total 6825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1750 time to evaluate : 5.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 218 LYS Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 185 ILE Chi-restraints excluded: chain H residue 227 ASP Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain I residue 229 THR Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain I residue 271 TYR Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 188 ILE Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 262 CYS Chi-restraints excluded: chain J residue 285 ASN Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain K residue 20 HIS Chi-restraints excluded: chain K residue 59 GLN Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 169 ASP Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 212 ASP Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 241 PHE Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 290 ILE Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 450 LEU Chi-restraints excluded: chain K residue 532 LEU Chi-restraints excluded: chain K residue 536 LEU Chi-restraints excluded: chain K residue 616 GLU Chi-restraints excluded: chain K residue 752 LEU Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain K residue 811 ASP Chi-restraints excluded: chain K residue 815 ASP Chi-restraints excluded: chain K residue 838 GLU Chi-restraints excluded: chain K residue 895 ASN Chi-restraints excluded: chain K residue 905 VAL Chi-restraints excluded: chain K residue 915 SER Chi-restraints excluded: chain K residue 959 LEU Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 984 ASP Chi-restraints excluded: chain K residue 1031 ILE Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 34 ASP Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 105 ASP Chi-restraints excluded: chain X residue 143 ASP Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 23 THR Chi-restraints excluded: chain x residue 70 LEU Chi-restraints excluded: chain x residue 147 ASN Chi-restraints excluded: chain x residue 162 ASP Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 61 ASP Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain T residue 79 GLN Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 163 ILE Chi-restraints excluded: chain T residue 170 TYR Chi-restraints excluded: chain T residue 172 LEU Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 19 ASP Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 126 VAL Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 154 VAL Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain t residue 16 ILE Chi-restraints excluded: chain t residue 52 LYS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 59 THR Chi-restraints excluded: chain t residue 81 ASN Chi-restraints excluded: chain t residue 102 ILE Chi-restraints excluded: chain t residue 106 LEU Chi-restraints excluded: chain t residue 132 THR Chi-restraints excluded: chain t residue 138 ILE Chi-restraints excluded: chain w residue 8 VAL Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain w residue 85 THR Chi-restraints excluded: chain w residue 123 THR Chi-restraints excluded: chain w residue 156 ILE Chi-restraints excluded: chain w residue 172 LEU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 69 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 14 ASN Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 77 GLN Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 34 ASP Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 59 THR Chi-restraints excluded: chain l residue 84 LEU Chi-restraints excluded: chain l residue 114 SER Chi-restraints excluded: chain l residue 158 LYS Chi-restraints excluded: chain m residue 16 ILE Chi-restraints excluded: chain m residue 18 ILE Chi-restraints excluded: chain m residue 31 THR Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 150 GLN Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 59 THR Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain o residue 123 THR Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 16 ILE Chi-restraints excluded: chain p residue 60 LEU Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 101 ASN Chi-restraints excluded: chain p residue 134 VAL Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain n residue 42 LEU Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 86 LEU Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 84 LEU Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain R residue 21 LYS Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 101 ASN Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 33 ILE Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 124 LYS Chi-restraints excluded: chain S residue 136 ASN Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain q residue 45 THR Chi-restraints excluded: chain q residue 59 THR Chi-restraints excluded: chain q residue 63 CYS Chi-restraints excluded: chain q residue 66 VAL Chi-restraints excluded: chain q residue 102 ILE Chi-restraints excluded: chain q residue 140 GLU Chi-restraints excluded: chain q residue 147 ASN Chi-restraints excluded: chain q residue 159 VAL Chi-restraints excluded: chain r residue 5 ARG Chi-restraints excluded: chain r residue 8 VAL Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 34 ASP Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 44 ILE Chi-restraints excluded: chain s residue 59 THR Chi-restraints excluded: chain s residue 69 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 747 random chunks: chunk 601 optimal weight: 6.9990 chunk 409 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 537 optimal weight: 9.9990 chunk 297 optimal weight: 6.9990 chunk 616 optimal weight: 6.9990 chunk 499 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 368 optimal weight: 5.9990 chunk 648 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 ASN H 91 HIS H 135 GLN ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 HIS ** J 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 HIS ** K 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 879 ASN ** K 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 29 HIS M 150 GLN ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 GLN ** P 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 GLN ** m 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 76 GLN p 101 ASN ** N 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 81 ASN Q 32 ASN ** Q 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN ** S 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.109 63501 Z= 0.623 Angle : 0.868 11.997 86320 Z= 0.451 Chirality : 0.052 0.246 10099 Planarity : 0.005 0.079 10563 Dihedral : 11.549 177.382 9583 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 28.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.23 % Favored : 85.66 % Rotamer: Outliers : 6.86 % Allowed : 25.71 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.45 (0.09), residues: 7434 helix: -1.34 (0.11), residues: 2095 sheet: -1.36 (0.17), residues: 948 loop : -3.16 (0.08), residues: 4391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP F 281 HIS 0.011 0.002 HIS D 19 PHE 0.031 0.002 PHE J 98 TYR 0.048 0.003 TYR B 87 ARG 0.008 0.001 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2136 residues out of total 6825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 468 poor density : 1668 time to evaluate : 6.179 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.9019 (tt) cc_final: 0.8772 (tp) REVERT: A 111 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7815 (tp40) REVERT: E 45 TYR cc_start: 0.8374 (m-80) cc_final: 0.8165 (m-80) REVERT: E 63 ASP cc_start: 0.7205 (p0) cc_final: 0.6562 (p0) REVERT: F 63 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7306 (p0) REVERT: H 102 ASN cc_start: 0.8052 (p0) cc_final: 0.7693 (p0) REVERT: H 122 PHE cc_start: 0.7860 (m-80) cc_final: 0.7495 (m-80) REVERT: H 250 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7764 (p0) REVERT: K 162 LYS cc_start: 0.8011 (pttt) cc_final: 0.7604 (mtpt) REVERT: K 188 MET cc_start: 0.8971 (mmm) cc_final: 0.8617 (mmm) REVERT: K 288 LYS cc_start: 0.8823 (tptt) cc_final: 0.8618 (tptt) REVERT: K 682 LYS cc_start: 0.8985 (tppt) cc_final: 0.8531 (tppt) REVERT: K 686 ASN cc_start: 0.8703 (m110) cc_final: 0.8156 (m110) REVERT: K 782 LEU cc_start: 0.9032 (mt) cc_final: 0.8810 (mt) REVERT: K 793 LYS cc_start: 0.8957 (mttp) cc_final: 0.8613 (mttt) REVERT: K 819 GLU cc_start: 0.7525 (tp30) cc_final: 0.7283 (tp30) REVERT: K 926 VAL cc_start: 0.9462 (t) cc_final: 0.9213 (m) REVERT: X 110 ILE cc_start: 0.7845 (mm) cc_final: 0.7455 (mm) REVERT: x 5 ARG cc_start: 0.6209 (mpt180) cc_final: 0.5673 (mmt-90) REVERT: x 139 LYS cc_start: 0.8672 (ttmt) cc_final: 0.8400 (tptt) REVERT: T 6 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7050 (tt0) REVERT: W 7 TYR cc_start: 0.8264 (t80) cc_final: 0.7757 (t80) REVERT: W 97 ARG cc_start: 0.9106 (mtp85) cc_final: 0.8707 (mtp85) REVERT: W 140 GLU cc_start: 0.7438 (tp30) cc_final: 0.6940 (tm-30) REVERT: t 79 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7215 (mm110) REVERT: t 95 LEU cc_start: 0.9083 (mt) cc_final: 0.8806 (mt) REVERT: t 147 ASN cc_start: 0.7011 (p0) cc_final: 0.6716 (p0) REVERT: w 14 ASN cc_start: 0.6776 (m110) cc_final: 0.6556 (m-40) REVERT: w 29 HIS cc_start: 0.4491 (OUTLIER) cc_final: 0.3949 (m-70) REVERT: w 79 GLN cc_start: 0.5494 (OUTLIER) cc_final: 0.5172 (pm20) REVERT: M 12 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8498 (mm) REVERT: M 88 LEU cc_start: 0.8543 (mt) cc_final: 0.8249 (mt) REVERT: O 150 GLN cc_start: 0.8442 (mt0) cc_final: 0.8225 (mp10) REVERT: O 165 GLU cc_start: 0.7675 (mp0) cc_final: 0.7303 (mp0) REVERT: O 169 TYR cc_start: 0.8130 (p90) cc_final: 0.7827 (p90) REVERT: P 22 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7423 (mp) REVERT: P 31 THR cc_start: 0.9016 (p) cc_final: 0.8680 (p) REVERT: P 169 TYR cc_start: 0.8613 (p90) cc_final: 0.8354 (p90) REVERT: l 160 LYS cc_start: 0.8623 (mtpt) cc_final: 0.8413 (mttp) REVERT: o 9 PHE cc_start: 0.7002 (p90) cc_final: 0.6547 (p90) REVERT: o 11 PRO cc_start: 0.8637 (Cg_endo) cc_final: 0.7714 (Cg_exo) REVERT: o 112 TYR cc_start: 0.8061 (t80) cc_final: 0.7628 (t80) REVERT: p 35 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7554 (mp0) REVERT: p 63 CYS cc_start: 0.6530 (m) cc_final: 0.6309 (m) REVERT: p 65 TYR cc_start: 0.8357 (p90) cc_final: 0.7638 (p90) REVERT: p 67 LYS cc_start: 0.8563 (mttt) cc_final: 0.8098 (mttp) REVERT: p 85 THR cc_start: 0.8035 (p) cc_final: 0.7741 (p) REVERT: p 97 ARG cc_start: 0.8069 (mtt180) cc_final: 0.7443 (mtm-85) REVERT: N 112 TYR cc_start: 0.7999 (t80) cc_final: 0.7768 (t80) REVERT: N 166 LEU cc_start: 0.9235 (tt) cc_final: 0.8962 (mt) REVERT: Q 7 TYR cc_start: 0.8268 (t80) cc_final: 0.7866 (t80) REVERT: Q 105 ASP cc_start: 0.7501 (t0) cc_final: 0.6902 (p0) REVERT: Q 106 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7751 (tt) REVERT: S 144 LYS cc_start: 0.8817 (mptt) cc_final: 0.8041 (tptp) REVERT: q 170 TYR cc_start: 0.7483 (m-10) cc_final: 0.6918 (m-10) REVERT: r 84 LEU cc_start: 0.8671 (mt) cc_final: 0.8465 (mp) REVERT: s 6 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8032 (tm-30) REVERT: s 84 LEU cc_start: 0.8848 (mt) cc_final: 0.8602 (mp) REVERT: s 109 TYR cc_start: 0.7228 (m-80) cc_final: 0.6908 (m-80) REVERT: s 140 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8544 (mm-30) outliers start: 468 outliers final: 339 residues processed: 1935 average time/residue: 0.5743 time to fit residues: 1905.4110 Evaluate side-chains 1926 residues out of total 6825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 1579 time to evaluate : 5.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 218 LYS Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 98 GLN Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 227 ASP Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain I residue 229 THR Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain I residue 271 TYR Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 171 SER Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 188 ILE Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain K residue 20 HIS Chi-restraints excluded: chain K residue 59 GLN Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 169 ASP Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 212 ASP Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 241 PHE Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 290 ILE Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 409 ASP Chi-restraints excluded: chain K residue 450 LEU Chi-restraints excluded: chain K residue 532 LEU Chi-restraints excluded: chain K residue 616 GLU Chi-restraints excluded: chain K residue 652 ASP Chi-restraints excluded: chain K residue 670 ILE Chi-restraints excluded: chain K residue 752 LEU Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain K residue 796 VAL Chi-restraints excluded: chain K residue 811 ASP Chi-restraints excluded: chain K residue 815 ASP Chi-restraints excluded: chain K residue 838 GLU Chi-restraints excluded: chain K residue 895 ASN Chi-restraints excluded: chain K residue 915 SER Chi-restraints excluded: chain K residue 916 VAL Chi-restraints excluded: chain K residue 959 LEU Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 984 ASP Chi-restraints excluded: chain K residue 1031 ILE Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 34 ASP Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 105 ASP Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 138 ILE Chi-restraints excluded: chain X residue 143 ASP Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 23 THR Chi-restraints excluded: chain x residue 59 THR Chi-restraints excluded: chain x residue 69 ILE Chi-restraints excluded: chain x residue 70 LEU Chi-restraints excluded: chain x residue 93 LEU Chi-restraints excluded: chain x residue 106 LEU Chi-restraints excluded: chain x residue 147 ASN Chi-restraints excluded: chain x residue 162 ASP Chi-restraints excluded: chain T residue 6 GLU Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 16 ILE Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 61 ASP Chi-restraints excluded: chain T residue 63 CYS Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 147 ASN Chi-restraints excluded: chain T residue 163 ILE Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 19 ASP Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 126 VAL Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 154 VAL Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain t residue 16 ILE Chi-restraints excluded: chain t residue 52 LYS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 59 THR Chi-restraints excluded: chain t residue 69 ILE Chi-restraints excluded: chain t residue 81 ASN Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain t residue 102 ILE Chi-restraints excluded: chain t residue 106 LEU Chi-restraints excluded: chain t residue 119 ASN Chi-restraints excluded: chain t residue 132 THR Chi-restraints excluded: chain t residue 138 ILE Chi-restraints excluded: chain t residue 145 ILE Chi-restraints excluded: chain w residue 8 VAL Chi-restraints excluded: chain w residue 9 PHE Chi-restraints excluded: chain w residue 29 HIS Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain w residue 74 THR Chi-restraints excluded: chain w residue 79 GLN Chi-restraints excluded: chain w residue 85 THR Chi-restraints excluded: chain w residue 101 ASN Chi-restraints excluded: chain w residue 123 THR Chi-restraints excluded: chain w residue 141 VAL Chi-restraints excluded: chain w residue 156 ILE Chi-restraints excluded: chain w residue 172 LEU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 69 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 14 ASN Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 108 ILE Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 150 GLN Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain O residue 6 GLU Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 91 ASN Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 34 ASP Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain l residue 4 GLN Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 9 PHE Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 28 ASP Chi-restraints excluded: chain l residue 42 LEU Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 59 THR Chi-restraints excluded: chain l residue 84 LEU Chi-restraints excluded: chain l residue 114 SER Chi-restraints excluded: chain l residue 127 SER Chi-restraints excluded: chain m residue 16 ILE Chi-restraints excluded: chain m residue 18 ILE Chi-restraints excluded: chain m residue 31 THR Chi-restraints excluded: chain m residue 38 ILE Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 96 ILE Chi-restraints excluded: chain m residue 127 SER Chi-restraints excluded: chain m residue 150 GLN Chi-restraints excluded: chain m residue 173 GLU Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 59 THR Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain o residue 123 THR Chi-restraints excluded: chain o residue 127 SER Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 60 LEU Chi-restraints excluded: chain p residue 101 ASN Chi-restraints excluded: chain p residue 141 VAL Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 34 ASP Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain n residue 23 THR Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain n residue 42 LEU Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 86 LEU Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain n residue 101 ASN Chi-restraints excluded: chain n residue 135 ASN Chi-restraints excluded: chain n residue 163 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 21 LYS Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 101 ASN Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 33 ILE Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 124 LYS Chi-restraints excluded: chain S residue 136 ASN Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain q residue 59 THR Chi-restraints excluded: chain q residue 63 CYS Chi-restraints excluded: chain q residue 66 VAL Chi-restraints excluded: chain q residue 70 LEU Chi-restraints excluded: chain q residue 94 TYR Chi-restraints excluded: chain q residue 140 GLU Chi-restraints excluded: chain q residue 147 ASN Chi-restraints excluded: chain q residue 159 VAL Chi-restraints excluded: chain r residue 5 ARG Chi-restraints excluded: chain r residue 8 VAL Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 34 ASP Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 86 LEU Chi-restraints excluded: chain r residue 134 VAL Chi-restraints excluded: chain r residue 168 SER Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 23 THR Chi-restraints excluded: chain s residue 28 ASP Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 59 THR Chi-restraints excluded: chain s residue 69 ILE Chi-restraints excluded: chain s residue 126 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 747 random chunks: chunk 242 optimal weight: 0.9980 chunk 650 optimal weight: 1.9990 chunk 142 optimal weight: 0.1980 chunk 423 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 722 optimal weight: 4.9990 chunk 599 optimal weight: 20.0000 chunk 334 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 239 optimal weight: 0.8980 chunk 379 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 178 ASN H 91 HIS H 135 GLN H 167 ASN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 174 GLN ** W 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 29 HIS ** O 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 4 GLN m 147 ASN ** o 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 101 ASN ** N 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 63501 Z= 0.227 Angle : 0.727 12.506 86320 Z= 0.371 Chirality : 0.049 0.243 10099 Planarity : 0.004 0.075 10563 Dihedral : 11.479 179.808 9583 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.17 % Favored : 87.77 % Rotamer: Outliers : 5.26 % Allowed : 28.28 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.05 (0.09), residues: 7434 helix: -0.99 (0.11), residues: 2094 sheet: -1.26 (0.14), residues: 1283 loop : -2.97 (0.09), residues: 4057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 281 HIS 0.009 0.001 HIS w 29 PHE 0.018 0.002 PHE l 167 TYR 0.033 0.002 TYR J 347 ARG 0.011 0.001 ARG H 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2192 residues out of total 6825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 359 poor density : 1833 time to evaluate : 5.373 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: 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 111 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7642 (tp40) REVERT: E 63 ASP cc_start: 0.6468 (p0) cc_final: 0.5944 (p0) REVERT: E 124 TYR cc_start: 0.8436 (m-80) cc_final: 0.8216 (m-80) REVERT: F 63 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.6938 (p0) REVERT: H 102 ASN cc_start: 0.7875 (p0) cc_final: 0.7532 (p0) REVERT: I 44 GLN cc_start: 0.6417 (OUTLIER) cc_final: 0.6023 (pt0) REVERT: I 271 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.7180 (m-10) REVERT: K 162 LYS cc_start: 0.7898 (pttt) cc_final: 0.7476 (mtpt) REVERT: K 188 MET cc_start: 0.8801 (mmm) cc_final: 0.8477 (mmm) REVERT: K 241 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8266 (t80) REVERT: K 328 LYS cc_start: 0.7842 (mttm) cc_final: 0.7011 (mttm) REVERT: K 682 LYS cc_start: 0.8927 (tppt) cc_final: 0.8448 (tppt) REVERT: K 686 ASN cc_start: 0.8688 (m110) cc_final: 0.7988 (m110) REVERT: K 782 LEU cc_start: 0.8763 (mt) cc_final: 0.8469 (mt) REVERT: K 793 LYS cc_start: 0.8851 (mttp) cc_final: 0.8534 (mttt) REVERT: K 819 GLU cc_start: 0.7231 (tp30) cc_final: 0.6972 (tp30) REVERT: K 885 LYS cc_start: 0.7928 (tttt) cc_final: 0.7719 (ttpt) REVERT: K 926 VAL cc_start: 0.9373 (t) cc_final: 0.9117 (m) REVERT: X 110 ILE cc_start: 0.7723 (mm) cc_final: 0.7341 (mm) REVERT: X 121 MET cc_start: 0.6144 (mmm) cc_final: 0.5767 (tpt) REVERT: x 5 ARG cc_start: 0.6136 (mpt180) cc_final: 0.5638 (mmt-90) REVERT: x 139 LYS cc_start: 0.8654 (ttmt) cc_final: 0.8427 (tptt) REVERT: T 6 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7083 (mt-10) REVERT: T 65 TYR cc_start: 0.8386 (p90) cc_final: 0.8111 (p90) REVERT: T 79 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6567 (tm-30) REVERT: W 7 TYR cc_start: 0.8180 (t80) cc_final: 0.7657 (t80) REVERT: W 97 ARG cc_start: 0.9060 (mtp85) cc_final: 0.8542 (mtp85) REVERT: W 106 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8519 (tp) REVERT: W 140 GLU cc_start: 0.7526 (tp30) cc_final: 0.7161 (tm-30) REVERT: W 167 PHE cc_start: 0.7715 (m-80) cc_final: 0.7376 (m-80) REVERT: t 52 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7548 (ptpp) REVERT: t 79 GLN cc_start: 0.7482 (mm-40) cc_final: 0.7092 (mm-40) REVERT: t 147 ASN cc_start: 0.7110 (p0) cc_final: 0.6803 (p0) REVERT: w 36 ARG cc_start: 0.8792 (tpp80) cc_final: 0.8474 (tpt170) REVERT: M 12 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8255 (mm) REVERT: O 97 ARG cc_start: 0.8667 (mmm-85) cc_final: 0.8128 (mmm-85) REVERT: O 165 GLU cc_start: 0.7764 (mp0) cc_final: 0.7399 (mp0) REVERT: P 22 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7287 (mp) REVERT: P 31 THR cc_start: 0.8979 (p) cc_final: 0.8660 (p) REVERT: o 9 PHE cc_start: 0.6836 (p90) cc_final: 0.6437 (p90) REVERT: o 11 PRO cc_start: 0.8536 (Cg_endo) cc_final: 0.7779 (Cg_exo) REVERT: o 122 LYS cc_start: 0.8554 (mmmt) cc_final: 0.8341 (mptt) REVERT: o 166 LEU cc_start: 0.8841 (tt) cc_final: 0.8555 (mp) REVERT: p 35 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7537 (mp0) REVERT: p 63 CYS cc_start: 0.6372 (m) cc_final: 0.6135 (m) REVERT: p 65 TYR cc_start: 0.8243 (p90) cc_final: 0.7676 (p90) REVERT: p 67 LYS cc_start: 0.8498 (mttt) cc_final: 0.7928 (mttp) REVERT: p 85 THR cc_start: 0.7980 (p) cc_final: 0.7633 (p) REVERT: p 97 ARG cc_start: 0.8090 (mtt180) cc_final: 0.7489 (mtm-85) REVERT: N 106 LEU cc_start: 0.8620 (tt) cc_final: 0.8023 (mp) REVERT: N 112 TYR cc_start: 0.7944 (t80) cc_final: 0.7573 (t80) REVERT: Q 7 TYR cc_start: 0.8188 (t80) cc_final: 0.7912 (t80) REVERT: Q 105 ASP cc_start: 0.7269 (t0) cc_final: 0.6961 (p0) REVERT: S 144 LYS cc_start: 0.8636 (mptt) cc_final: 0.7977 (tptp) REVERT: q 57 VAL cc_start: 0.8503 (t) cc_final: 0.8242 (p) REVERT: q 170 TYR cc_start: 0.7000 (m-10) cc_final: 0.6574 (m-10) REVERT: s 6 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8092 (tm-30) REVERT: s 109 TYR cc_start: 0.7176 (m-80) cc_final: 0.6885 (m-80) REVERT: s 140 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8570 (mm-30) outliers start: 359 outliers final: 261 residues processed: 2018 average time/residue: 0.5735 time to fit residues: 1984.4130 Evaluate side-chains 2004 residues out of total 6825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1733 time to evaluate : 5.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 218 LYS Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 227 ASP Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 44 GLN Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain I residue 271 TYR Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 188 ILE Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 262 CYS Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 453 SER Chi-restraints excluded: chain K residue 20 HIS Chi-restraints excluded: chain K residue 59 GLN Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 169 ASP Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 212 ASP Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 241 PHE Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 290 ILE Chi-restraints excluded: chain K residue 292 ASN Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 320 ILE Chi-restraints excluded: chain K residue 450 LEU Chi-restraints excluded: chain K residue 506 SER Chi-restraints excluded: chain K residue 536 LEU Chi-restraints excluded: chain K residue 616 GLU Chi-restraints excluded: chain K residue 652 ASP Chi-restraints excluded: chain K residue 688 LEU Chi-restraints excluded: chain K residue 752 LEU Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain K residue 767 THR Chi-restraints excluded: chain K residue 797 ILE Chi-restraints excluded: chain K residue 811 ASP Chi-restraints excluded: chain K residue 815 ASP Chi-restraints excluded: chain K residue 838 GLU Chi-restraints excluded: chain K residue 895 ASN Chi-restraints excluded: chain K residue 915 SER Chi-restraints excluded: chain K residue 916 VAL Chi-restraints excluded: chain K residue 959 LEU Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 980 PHE Chi-restraints excluded: chain K residue 984 ASP Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 34 ASP Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 143 ASP Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 70 LEU Chi-restraints excluded: chain x residue 93 LEU Chi-restraints excluded: chain x residue 106 LEU Chi-restraints excluded: chain x residue 136 ASN Chi-restraints excluded: chain x residue 147 ASN Chi-restraints excluded: chain x residue 162 ASP Chi-restraints excluded: chain T residue 6 GLU Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 61 ASP Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain T residue 79 GLN Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 147 ASN Chi-restraints excluded: chain T residue 163 ILE Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 19 ASP Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 106 LEU Chi-restraints excluded: chain W residue 126 VAL Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 154 VAL Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain t residue 16 ILE Chi-restraints excluded: chain t residue 52 LYS Chi-restraints excluded: chain t residue 59 THR Chi-restraints excluded: chain t residue 69 ILE Chi-restraints excluded: chain t residue 81 ASN Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain t residue 102 ILE Chi-restraints excluded: chain t residue 106 LEU Chi-restraints excluded: chain t residue 132 THR Chi-restraints excluded: chain w residue 8 VAL Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain w residue 74 THR Chi-restraints excluded: chain w residue 84 LEU Chi-restraints excluded: chain w residue 123 THR Chi-restraints excluded: chain w residue 156 ILE Chi-restraints excluded: chain w residue 172 LEU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 14 ASN Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 34 ASP Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 9 PHE Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 59 THR Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 77 GLN Chi-restraints excluded: chain l residue 84 LEU Chi-restraints excluded: chain l residue 93 LEU Chi-restraints excluded: chain l residue 127 SER Chi-restraints excluded: chain m residue 16 ILE Chi-restraints excluded: chain m residue 31 THR Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 106 LEU Chi-restraints excluded: chain m residue 127 SER Chi-restraints excluded: chain m residue 173 GLU Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain o residue 123 THR Chi-restraints excluded: chain o residue 127 SER Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 60 LEU Chi-restraints excluded: chain p residue 101 ASN Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain n residue 42 LEU Chi-restraints excluded: chain n residue 86 LEU Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain n residue 163 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 21 LYS Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 101 ASN Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain S residue 19 ASP Chi-restraints excluded: chain S residue 33 ILE Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 124 LYS Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain q residue 45 THR Chi-restraints excluded: chain q residue 66 VAL Chi-restraints excluded: chain q residue 70 LEU Chi-restraints excluded: chain q residue 91 ASN Chi-restraints excluded: chain q residue 102 ILE Chi-restraints excluded: chain q residue 140 GLU Chi-restraints excluded: chain q residue 147 ASN Chi-restraints excluded: chain q residue 159 VAL Chi-restraints excluded: chain r residue 8 VAL Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 34 ASP Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 86 LEU Chi-restraints excluded: chain r residue 134 VAL Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 59 THR Chi-restraints excluded: chain s residue 69 ILE Chi-restraints excluded: chain s residue 86 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 747 random chunks: chunk 696 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 411 optimal weight: 1.9990 chunk 527 optimal weight: 8.9990 chunk 408 optimal weight: 3.9990 chunk 608 optimal weight: 2.9990 chunk 403 optimal weight: 1.9990 chunk 719 optimal weight: 4.9990 chunk 450 optimal weight: 7.9990 chunk 438 optimal weight: 0.2980 chunk 332 optimal weight: 7.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN G 13 HIS G 178 ASN H 91 HIS ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 HIS ** K 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 GLN ** O 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 GLN m 135 ASN p 76 GLN p 101 ASN ** N 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 14 ASN ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN ** s 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 63501 Z= 0.266 Angle : 0.732 12.575 86320 Z= 0.373 Chirality : 0.049 0.281 10099 Planarity : 0.004 0.077 10563 Dihedral : 11.377 179.682 9583 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.46 % Favored : 87.49 % Rotamer: Outliers : 5.31 % Allowed : 28.92 % Favored : 65.77 % 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: -2.96 (0.09), residues: 7434 helix: -0.91 (0.11), residues: 2114 sheet: -1.19 (0.14), residues: 1302 loop : -2.94 (0.09), residues: 4018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 27 HIS 0.007 0.001 HIS X 29 PHE 0.028 0.002 PHE m 167 TYR 0.055 0.002 TYR B 87 ARG 0.008 0.001 ARG X 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2134 residues out of total 6825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 362 poor density : 1772 time to evaluate : 5.436 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: 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 111 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7595 (tp40) REVERT: E 45 TYR cc_start: 0.8116 (m-80) cc_final: 0.7825 (m-80) REVERT: E 63 ASP cc_start: 0.6573 (p0) cc_final: 0.6033 (p0) REVERT: F 63 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7043 (p0) REVERT: H 102 ASN cc_start: 0.7865 (p0) cc_final: 0.7521 (p0) REVERT: I 271 TYR cc_start: 0.7827 (OUTLIER) cc_final: 0.7105 (m-10) REVERT: K 89 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8389 (mmtt) REVERT: K 162 LYS cc_start: 0.7856 (pttt) cc_final: 0.7451 (mtpt) REVERT: K 188 MET cc_start: 0.8780 (mmm) cc_final: 0.8486 (mmm) REVERT: K 241 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.8215 (t80) REVERT: K 328 LYS cc_start: 0.7736 (mttm) cc_final: 0.7056 (mttm) REVERT: K 682 LYS cc_start: 0.8938 (tppt) cc_final: 0.8458 (tppt) REVERT: K 686 ASN cc_start: 0.8687 (m110) cc_final: 0.7952 (m110) REVERT: K 782 LEU cc_start: 0.8819 (mt) cc_final: 0.8464 (mt) REVERT: K 793 LYS cc_start: 0.8870 (mttp) cc_final: 0.8562 (mttt) REVERT: K 819 GLU cc_start: 0.7292 (tp30) cc_final: 0.7072 (tp30) REVERT: K 923 ARG cc_start: 0.8453 (tpp-160) cc_final: 0.8181 (tpp-160) REVERT: K 926 VAL cc_start: 0.9367 (t) cc_final: 0.9096 (m) REVERT: X 110 ILE cc_start: 0.7742 (mm) cc_final: 0.7365 (mm) REVERT: x 5 ARG cc_start: 0.6099 (mpt180) cc_final: 0.5620 (mmt-90) REVERT: x 139 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8442 (tptt) REVERT: T 65 TYR cc_start: 0.8345 (p90) cc_final: 0.8110 (p90) REVERT: T 79 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6648 (tm-30) REVERT: W 7 TYR cc_start: 0.8135 (t80) cc_final: 0.7570 (t80) REVERT: W 97 ARG cc_start: 0.9040 (mtp85) cc_final: 0.8802 (mtp85) REVERT: W 140 GLU cc_start: 0.7523 (tp30) cc_final: 0.7224 (tm-30) REVERT: W 167 PHE cc_start: 0.7813 (m-80) cc_final: 0.7362 (m-80) REVERT: t 83 PHE cc_start: 0.6358 (m-10) cc_final: 0.5948 (m-80) REVERT: t 97 ARG cc_start: 0.8449 (mpp80) cc_final: 0.8218 (mpp80) REVERT: M 12 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8301 (mm) REVERT: O 130 ASP cc_start: 0.7273 (m-30) cc_final: 0.7065 (m-30) REVERT: O 165 GLU cc_start: 0.7718 (mp0) cc_final: 0.7427 (mp0) REVERT: P 22 ILE cc_start: 0.7365 (OUTLIER) cc_final: 0.7128 (mp) REVERT: P 31 THR cc_start: 0.8961 (p) cc_final: 0.8639 (p) REVERT: P 64 ASP cc_start: 0.7521 (m-30) cc_final: 0.7089 (m-30) REVERT: l 4 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7105 (pp30) REVERT: m 134 VAL cc_start: 0.8749 (t) cc_final: 0.8381 (t) REVERT: o 9 PHE cc_start: 0.6846 (p90) cc_final: 0.6453 (p90) REVERT: o 11 PRO cc_start: 0.8540 (Cg_endo) cc_final: 0.7788 (Cg_exo) REVERT: o 95 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8672 (mm) REVERT: o 122 LYS cc_start: 0.8553 (mmmt) cc_final: 0.8334 (mmmt) REVERT: o 166 LEU cc_start: 0.8840 (tt) cc_final: 0.8512 (mp) REVERT: p 35 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7500 (mp0) REVERT: p 65 TYR cc_start: 0.8225 (p90) cc_final: 0.7863 (p90) REVERT: p 85 THR cc_start: 0.7834 (p) cc_final: 0.7465 (p) REVERT: p 97 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7548 (mtm-85) REVERT: N 106 LEU cc_start: 0.8696 (tt) cc_final: 0.8153 (mp) REVERT: N 112 TYR cc_start: 0.7993 (t80) cc_final: 0.7585 (t80) REVERT: n 9 PHE cc_start: 0.7471 (p90) cc_final: 0.7182 (p90) REVERT: Q 7 TYR cc_start: 0.8226 (t80) cc_final: 0.7807 (t80) REVERT: Q 105 ASP cc_start: 0.7307 (t0) cc_final: 0.7050 (p0) REVERT: Q 106 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7651 (tt) REVERT: R 63 CYS cc_start: 0.5595 (m) cc_final: 0.5204 (m) REVERT: S 74 THR cc_start: 0.6787 (t) cc_final: 0.6547 (m) REVERT: S 144 LYS cc_start: 0.8700 (mptt) cc_final: 0.8007 (tptp) REVERT: q 23 THR cc_start: 0.6948 (m) cc_final: 0.6643 (t) REVERT: q 57 VAL cc_start: 0.8479 (t) cc_final: 0.8245 (p) REVERT: q 170 TYR cc_start: 0.7042 (m-10) cc_final: 0.6690 (m-10) REVERT: s 6 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8115 (tm-30) REVERT: s 109 TYR cc_start: 0.7174 (m-80) cc_final: 0.6669 (m-80) REVERT: s 140 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8581 (mm-30) outliers start: 362 outliers final: 271 residues processed: 1969 average time/residue: 0.5694 time to fit residues: 1918.3175 Evaluate side-chains 1972 residues out of total 6825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1692 time to evaluate : 5.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 227 ASP Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain I residue 271 TYR Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 188 ILE Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 371 LEU Chi-restraints excluded: chain J residue 420 ASP Chi-restraints excluded: chain J residue 453 SER Chi-restraints excluded: chain K residue 20 HIS Chi-restraints excluded: chain K residue 59 GLN Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 212 ASP Chi-restraints excluded: chain K residue 241 PHE Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 290 ILE Chi-restraints excluded: chain K residue 292 ASN Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 320 ILE Chi-restraints excluded: chain K residue 450 LEU Chi-restraints excluded: chain K residue 506 SER Chi-restraints excluded: chain K residue 536 LEU Chi-restraints excluded: chain K residue 616 GLU Chi-restraints excluded: chain K residue 652 ASP Chi-restraints excluded: chain K residue 688 LEU Chi-restraints excluded: chain K residue 744 VAL Chi-restraints excluded: chain K residue 752 LEU Chi-restraints excluded: chain K residue 767 THR Chi-restraints excluded: chain K residue 811 ASP Chi-restraints excluded: chain K residue 815 ASP Chi-restraints excluded: chain K residue 838 GLU Chi-restraints excluded: chain K residue 883 GLU Chi-restraints excluded: chain K residue 895 ASN Chi-restraints excluded: chain K residue 915 SER Chi-restraints excluded: chain K residue 916 VAL Chi-restraints excluded: chain K residue 959 LEU Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 980 PHE Chi-restraints excluded: chain K residue 984 ASP Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 34 ASP Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 143 ASP Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 59 THR Chi-restraints excluded: chain x residue 69 ILE Chi-restraints excluded: chain x residue 70 LEU Chi-restraints excluded: chain x residue 93 LEU Chi-restraints excluded: chain x residue 106 LEU Chi-restraints excluded: chain x residue 136 ASN Chi-restraints excluded: chain x residue 147 ASN Chi-restraints excluded: chain x residue 162 ASP Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 16 ILE Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 61 ASP Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain T residue 79 GLN Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 121 MET Chi-restraints excluded: chain T residue 147 ASN Chi-restraints excluded: chain T residue 163 ILE Chi-restraints excluded: chain T residue 170 TYR Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 19 ASP Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 154 VAL Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain t residue 16 ILE Chi-restraints excluded: chain t residue 52 LYS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 59 THR Chi-restraints excluded: chain t residue 69 ILE Chi-restraints excluded: chain t residue 81 ASN Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain t residue 102 ILE Chi-restraints excluded: chain t residue 106 LEU Chi-restraints excluded: chain t residue 132 THR Chi-restraints excluded: chain w residue 8 VAL Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain w residue 84 LEU Chi-restraints excluded: chain w residue 85 THR Chi-restraints excluded: chain w residue 123 THR Chi-restraints excluded: chain w residue 156 ILE Chi-restraints excluded: chain w residue 172 LEU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 14 ASN Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 150 GLN Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 34 ASP Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain l residue 4 GLN Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 9 PHE Chi-restraints excluded: chain l residue 59 THR Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 84 LEU Chi-restraints excluded: chain l residue 127 SER Chi-restraints excluded: chain m residue 16 ILE Chi-restraints excluded: chain m residue 18 ILE Chi-restraints excluded: chain m residue 31 THR Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 127 SER Chi-restraints excluded: chain m residue 173 GLU Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 59 THR Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain o residue 95 LEU Chi-restraints excluded: chain o residue 123 THR Chi-restraints excluded: chain o residue 127 SER Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 60 LEU Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain n residue 23 THR Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain n residue 42 LEU Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 86 LEU Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain n residue 163 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 21 LYS Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 101 ASN Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain S residue 19 ASP Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 33 ILE Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 124 LYS Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain q residue 66 VAL Chi-restraints excluded: chain q residue 70 LEU Chi-restraints excluded: chain q residue 91 ASN Chi-restraints excluded: chain q residue 102 ILE Chi-restraints excluded: chain q residue 147 ASN Chi-restraints excluded: chain q residue 159 VAL Chi-restraints excluded: chain q residue 166 LEU Chi-restraints excluded: chain r residue 8 VAL Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 34 ASP Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 86 LEU Chi-restraints excluded: chain r residue 134 VAL Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 59 THR Chi-restraints excluded: chain s residue 69 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 747 random chunks: chunk 445 optimal weight: 6.9990 chunk 287 optimal weight: 1.9990 chunk 430 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 457 optimal weight: 1.9990 chunk 490 optimal weight: 2.9990 chunk 355 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 565 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN G 13 HIS ** G 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 GLN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 148 GLN ** K 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 53 ASN ** p 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 101 ASN ** N 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 63501 Z= 0.264 Angle : 0.748 15.997 86320 Z= 0.379 Chirality : 0.049 0.275 10099 Planarity : 0.004 0.077 10563 Dihedral : 11.357 179.673 9583 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.36 % Favored : 87.60 % Rotamer: Outliers : 5.20 % Allowed : 29.51 % Favored : 65.29 % 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: -2.80 (0.09), residues: 7434 helix: -0.88 (0.11), residues: 2092 sheet: -1.31 (0.15), residues: 1168 loop : -2.65 (0.09), residues: 4174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 367 HIS 0.005 0.001 HIS t 39 PHE 0.024 0.001 PHE m 167 TYR 0.061 0.002 TYR G 45 ARG 0.013 0.001 ARG X 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2110 residues out of total 6825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 355 poor density : 1755 time to evaluate : 5.422 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: 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: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.7987 (tm-30) cc_final: 0.7623 (tp40) REVERT: B 4 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6439 (pm20) REVERT: E 63 ASP cc_start: 0.6415 (p0) cc_final: 0.5971 (p0) REVERT: F 63 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7047 (p0) REVERT: G 63 ASP cc_start: 0.7940 (p0) cc_final: 0.7725 (p0) REVERT: G 66 ASP cc_start: 0.7561 (p0) cc_final: 0.7305 (p0) REVERT: H 102 ASN cc_start: 0.7822 (p0) cc_final: 0.7489 (p0) REVERT: I 271 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7155 (m-10) REVERT: K 162 LYS cc_start: 0.7776 (pttt) cc_final: 0.7342 (mtpt) REVERT: K 188 MET cc_start: 0.8752 (mmm) cc_final: 0.8530 (mmm) REVERT: K 241 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7957 (t80) REVERT: K 328 LYS cc_start: 0.7776 (mttm) cc_final: 0.7125 (mttm) REVERT: K 682 LYS cc_start: 0.8925 (tppt) cc_final: 0.8447 (tppt) REVERT: K 686 ASN cc_start: 0.8694 (m110) cc_final: 0.7956 (m110) REVERT: K 713 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.5940 (tmt170) REVERT: K 793 LYS cc_start: 0.8864 (mttp) cc_final: 0.8628 (mttt) REVERT: K 819 GLU cc_start: 0.7286 (tp30) cc_final: 0.7059 (tp30) REVERT: K 923 ARG cc_start: 0.8461 (tpp-160) cc_final: 0.8199 (tpp-160) REVERT: K 926 VAL cc_start: 0.9353 (t) cc_final: 0.9089 (m) REVERT: X 5 ARG cc_start: 0.7182 (tpp-160) cc_final: 0.6815 (tpp-160) REVERT: X 110 ILE cc_start: 0.7736 (mm) cc_final: 0.7364 (mm) REVERT: X 121 MET cc_start: 0.5818 (OUTLIER) cc_final: 0.5344 (mmt) REVERT: x 5 ARG cc_start: 0.6084 (mpt180) cc_final: 0.5613 (mmt-90) REVERT: x 65 TYR cc_start: 0.8236 (p90) cc_final: 0.7863 (p90) REVERT: T 65 TYR cc_start: 0.8360 (p90) cc_final: 0.8092 (p90) REVERT: T 79 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6643 (tm-30) REVERT: W 7 TYR cc_start: 0.8163 (t80) cc_final: 0.7595 (t80) REVERT: W 140 GLU cc_start: 0.7550 (tp30) cc_final: 0.7296 (tm-30) REVERT: W 167 PHE cc_start: 0.7769 (m-80) cc_final: 0.7296 (m-80) REVERT: t 83 PHE cc_start: 0.6150 (m-10) cc_final: 0.5741 (m-80) REVERT: t 94 TYR cc_start: 0.8466 (t80) cc_final: 0.8259 (t80) REVERT: t 121 MET cc_start: 0.7950 (tpp) cc_final: 0.7739 (tpp) REVERT: O 97 ARG cc_start: 0.8693 (mmm-85) cc_final: 0.8322 (mmm-85) REVERT: O 147 ASN cc_start: 0.7625 (p0) cc_final: 0.7398 (p0) REVERT: O 165 GLU cc_start: 0.7760 (mp0) cc_final: 0.7446 (mp0) REVERT: P 22 ILE cc_start: 0.7363 (OUTLIER) cc_final: 0.7125 (mp) REVERT: P 31 THR cc_start: 0.8976 (p) cc_final: 0.8639 (p) REVERT: P 64 ASP cc_start: 0.7496 (m-30) cc_final: 0.7121 (m-30) REVERT: l 4 GLN cc_start: 0.7255 (pp30) cc_final: 0.6972 (pp30) REVERT: o 9 PHE cc_start: 0.6835 (p90) cc_final: 0.6441 (p90) REVERT: o 11 PRO cc_start: 0.8526 (Cg_endo) cc_final: 0.7748 (Cg_exo) REVERT: p 35 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7490 (mp0) REVERT: p 65 TYR cc_start: 0.8268 (p90) cc_final: 0.7852 (p90) REVERT: p 85 THR cc_start: 0.7814 (p) cc_final: 0.7488 (p) REVERT: p 97 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7586 (mtm-85) REVERT: N 106 LEU cc_start: 0.8746 (tt) cc_final: 0.8193 (mp) REVERT: N 112 TYR cc_start: 0.8047 (t80) cc_final: 0.7564 (t80) REVERT: n 9 PHE cc_start: 0.7548 (p90) cc_final: 0.7226 (p90) REVERT: Q 7 TYR cc_start: 0.8251 (t80) cc_final: 0.7889 (t80) REVERT: Q 106 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7651 (tt) REVERT: R 63 CYS cc_start: 0.5750 (m) cc_final: 0.5378 (m) REVERT: S 5 ARG cc_start: 0.6975 (mmt180) cc_final: 0.6761 (tpt170) REVERT: S 98 LYS cc_start: 0.7592 (mmtm) cc_final: 0.6956 (mmtt) REVERT: S 144 LYS cc_start: 0.8730 (mptt) cc_final: 0.8027 (tptp) REVERT: q 23 THR cc_start: 0.6953 (m) cc_final: 0.6653 (t) REVERT: q 57 VAL cc_start: 0.8442 (t) cc_final: 0.8218 (p) REVERT: q 170 TYR cc_start: 0.6996 (m-10) cc_final: 0.6618 (m-10) REVERT: s 6 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8164 (tm-30) REVERT: s 109 TYR cc_start: 0.7053 (m-80) cc_final: 0.6833 (m-80) outliers start: 355 outliers final: 289 residues processed: 1948 average time/residue: 0.5869 time to fit residues: 1963.7987 Evaluate side-chains 1980 residues out of total 6825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1682 time to evaluate : 5.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 185 ILE Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 227 ASP Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain I residue 271 TYR Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 188 ILE Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 262 CYS Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 371 LEU Chi-restraints excluded: chain J residue 453 SER Chi-restraints excluded: chain K residue 20 HIS Chi-restraints excluded: chain K residue 59 GLN Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 212 ASP Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 241 PHE Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 290 ILE Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 320 ILE Chi-restraints excluded: chain K residue 450 LEU Chi-restraints excluded: chain K residue 506 SER Chi-restraints excluded: chain K residue 536 LEU Chi-restraints excluded: chain K residue 538 SER Chi-restraints excluded: chain K residue 616 GLU Chi-restraints excluded: chain K residue 688 LEU Chi-restraints excluded: chain K residue 713 ARG Chi-restraints excluded: chain K residue 744 VAL Chi-restraints excluded: chain K residue 752 LEU Chi-restraints excluded: chain K residue 811 ASP Chi-restraints excluded: chain K residue 815 ASP Chi-restraints excluded: chain K residue 838 GLU Chi-restraints excluded: chain K residue 883 GLU Chi-restraints excluded: chain K residue 885 LYS Chi-restraints excluded: chain K residue 895 ASN Chi-restraints excluded: chain K residue 915 SER Chi-restraints excluded: chain K residue 916 VAL Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 980 PHE Chi-restraints excluded: chain K residue 984 ASP Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 34 ASP Chi-restraints excluded: chain X residue 55 ARG Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 71 VAL Chi-restraints excluded: chain X residue 121 MET Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 143 ASP Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 16 ILE Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 59 THR Chi-restraints excluded: chain x residue 69 ILE Chi-restraints excluded: chain x residue 70 LEU Chi-restraints excluded: chain x residue 93 LEU Chi-restraints excluded: chain x residue 106 LEU Chi-restraints excluded: chain x residue 136 ASN Chi-restraints excluded: chain x residue 147 ASN Chi-restraints excluded: chain x residue 162 ASP Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 61 ASP Chi-restraints excluded: chain T residue 79 GLN Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 121 MET Chi-restraints excluded: chain T residue 147 ASN Chi-restraints excluded: chain T residue 163 ILE Chi-restraints excluded: chain T residue 170 TYR Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 19 ASP Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 154 VAL Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain t residue 16 ILE Chi-restraints excluded: chain t residue 52 LYS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 59 THR Chi-restraints excluded: chain t residue 69 ILE Chi-restraints excluded: chain t residue 81 ASN Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain t residue 102 ILE Chi-restraints excluded: chain t residue 106 LEU Chi-restraints excluded: chain t residue 119 ASN Chi-restraints excluded: chain t residue 132 THR Chi-restraints excluded: chain t residue 174 GLN Chi-restraints excluded: chain w residue 8 VAL Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain w residue 84 LEU Chi-restraints excluded: chain w residue 85 THR Chi-restraints excluded: chain w residue 123 THR Chi-restraints excluded: chain w residue 156 ILE Chi-restraints excluded: chain w residue 172 LEU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 34 ASP Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 9 PHE Chi-restraints excluded: chain l residue 28 ASP Chi-restraints excluded: chain l residue 59 THR Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 84 LEU Chi-restraints excluded: chain l residue 127 SER Chi-restraints excluded: chain m residue 16 ILE Chi-restraints excluded: chain m residue 18 ILE Chi-restraints excluded: chain m residue 31 THR Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 106 LEU Chi-restraints excluded: chain m residue 127 SER Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 24 ILE Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 59 THR Chi-restraints excluded: chain o residue 123 THR Chi-restraints excluded: chain o residue 127 SER Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 16 ILE Chi-restraints excluded: chain p residue 53 ASN Chi-restraints excluded: chain p residue 60 LEU Chi-restraints excluded: chain p residue 101 ASN Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain n residue 23 THR Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain n residue 42 LEU Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 86 LEU Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 21 LYS Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 101 ASN Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain S residue 19 ASP Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 33 ILE Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 124 LYS Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain q residue 66 VAL Chi-restraints excluded: chain q residue 70 LEU Chi-restraints excluded: chain q residue 102 ILE Chi-restraints excluded: chain q residue 140 GLU Chi-restraints excluded: chain q residue 147 ASN Chi-restraints excluded: chain q residue 159 VAL Chi-restraints excluded: chain q residue 166 LEU Chi-restraints excluded: chain r residue 8 VAL Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 34 ASP Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 86 LEU Chi-restraints excluded: chain r residue 93 LEU Chi-restraints excluded: chain r residue 134 VAL Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 59 THR Chi-restraints excluded: chain s residue 69 ILE Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 108 ILE Chi-restraints excluded: chain s residue 113 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 747 random chunks: chunk 654 optimal weight: 4.9990 chunk 689 optimal weight: 6.9990 chunk 629 optimal weight: 50.0000 chunk 670 optimal weight: 4.9990 chunk 403 optimal weight: 6.9990 chunk 292 optimal weight: 0.2980 chunk 526 optimal weight: 5.9990 chunk 205 optimal weight: 0.9990 chunk 606 optimal weight: 8.9990 chunk 634 optimal weight: 0.2980 chunk 668 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN F 13 HIS G 13 HIS I 172 GLN ** J 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 135 ASN ** O 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 GLN p 53 ASN ** p 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 101 ASN ** N 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 63501 Z= 0.257 Angle : 0.760 14.451 86320 Z= 0.384 Chirality : 0.049 0.254 10099 Planarity : 0.004 0.075 10563 Dihedral : 11.318 179.696 9582 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.19 % Favored : 87.76 % Rotamer: Outliers : 5.07 % Allowed : 30.46 % Favored : 64.47 % 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: -2.77 (0.09), residues: 7434 helix: -0.82 (0.11), residues: 2089 sheet: -1.34 (0.16), residues: 1117 loop : -2.62 (0.09), residues: 4228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 367 HIS 0.005 0.001 HIS t 39 PHE 0.024 0.001 PHE m 167 TYR 0.069 0.002 TYR G 45 ARG 0.008 0.001 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2084 residues out of total 6825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 1738 time to evaluate : 6.146 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: 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 111 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7621 (tp40) REVERT: B 4 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6426 (pm20) REVERT: E 45 TYR cc_start: 0.8153 (m-80) cc_final: 0.7871 (m-80) REVERT: E 63 ASP cc_start: 0.6523 (p0) cc_final: 0.5996 (p0) REVERT: F 63 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7098 (p0) REVERT: F 195 ASP cc_start: 0.6013 (OUTLIER) cc_final: 0.5811 (m-30) REVERT: G 66 ASP cc_start: 0.7520 (p0) cc_final: 0.7267 (p0) REVERT: H 102 ASN cc_start: 0.7841 (p0) cc_final: 0.7504 (p0) REVERT: I 271 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.7081 (m-10) REVERT: K 162 LYS cc_start: 0.7695 (pttt) cc_final: 0.7285 (mtpt) REVERT: K 241 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7871 (t80) REVERT: K 328 LYS cc_start: 0.7783 (mttm) cc_final: 0.7137 (mttm) REVERT: K 682 LYS cc_start: 0.8906 (tppt) cc_final: 0.8437 (tppt) REVERT: K 686 ASN cc_start: 0.8677 (m110) cc_final: 0.7936 (m110) REVERT: K 713 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.5907 (tmt170) REVERT: K 793 LYS cc_start: 0.8856 (mttp) cc_final: 0.8620 (mttt) REVERT: K 819 GLU cc_start: 0.7259 (tp30) cc_final: 0.7042 (tp30) REVERT: K 923 ARG cc_start: 0.8413 (tpp-160) cc_final: 0.8175 (tpp-160) REVERT: K 926 VAL cc_start: 0.9353 (t) cc_final: 0.9093 (m) REVERT: X 5 ARG cc_start: 0.7135 (tpp-160) cc_final: 0.6785 (tpp-160) REVERT: X 94 TYR cc_start: 0.6735 (t80) cc_final: 0.6428 (t80) REVERT: X 110 ILE cc_start: 0.7701 (mm) cc_final: 0.7319 (mm) REVERT: X 121 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.5891 (mmt) REVERT: x 5 ARG cc_start: 0.6077 (mpt180) cc_final: 0.5576 (mmt-90) REVERT: x 65 TYR cc_start: 0.8223 (p90) cc_final: 0.7881 (p90) REVERT: T 28 ASP cc_start: 0.7011 (m-30) cc_final: 0.6590 (m-30) REVERT: T 65 TYR cc_start: 0.8331 (p90) cc_final: 0.8079 (p90) REVERT: T 79 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6639 (tm-30) REVERT: W 7 TYR cc_start: 0.8207 (t80) cc_final: 0.7614 (t80) REVERT: W 140 GLU cc_start: 0.7704 (tp30) cc_final: 0.7489 (tm-30) REVERT: W 167 PHE cc_start: 0.7744 (m-80) cc_final: 0.7306 (m-80) REVERT: t 83 PHE cc_start: 0.6114 (m-10) cc_final: 0.5712 (m-80) REVERT: t 94 TYR cc_start: 0.8558 (t80) cc_final: 0.8325 (t80) REVERT: t 121 MET cc_start: 0.7926 (tpp) cc_final: 0.7711 (tpp) REVERT: w 36 ARG cc_start: 0.8764 (tpp80) cc_final: 0.8420 (tpp80) REVERT: O 97 ARG cc_start: 0.8679 (mmm-85) cc_final: 0.8362 (mmm-85) REVERT: O 147 ASN cc_start: 0.7607 (p0) cc_final: 0.7392 (p0) REVERT: O 165 GLU cc_start: 0.7880 (mp0) cc_final: 0.7537 (mp0) REVERT: P 22 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.7155 (mp) REVERT: P 31 THR cc_start: 0.8949 (p) cc_final: 0.8603 (p) REVERT: P 64 ASP cc_start: 0.7466 (m-30) cc_final: 0.7136 (m-30) REVERT: m 21 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6446 (tptp) REVERT: o 9 PHE cc_start: 0.6827 (p90) cc_final: 0.6440 (p90) REVERT: o 11 PRO cc_start: 0.8532 (Cg_endo) cc_final: 0.7749 (Cg_exo) REVERT: p 35 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7561 (mp0) REVERT: p 65 TYR cc_start: 0.8251 (p90) cc_final: 0.7846 (p90) REVERT: p 85 THR cc_start: 0.7802 (p) cc_final: 0.7486 (p) REVERT: p 97 ARG cc_start: 0.8106 (mtt180) cc_final: 0.7585 (mtm-85) REVERT: p 131 ASP cc_start: 0.9047 (p0) cc_final: 0.8803 (p0) REVERT: N 106 LEU cc_start: 0.8732 (tt) cc_final: 0.8183 (mp) REVERT: n 9 PHE cc_start: 0.7554 (p90) cc_final: 0.7195 (p90) REVERT: Q 7 TYR cc_start: 0.8257 (t80) cc_final: 0.7908 (t80) REVERT: R 63 CYS cc_start: 0.5752 (m) cc_final: 0.5392 (m) REVERT: S 98 LYS cc_start: 0.7643 (mmtm) cc_final: 0.6977 (mmtt) REVERT: S 144 LYS cc_start: 0.8698 (mptt) cc_final: 0.8060 (tptp) REVERT: q 16 ILE cc_start: 0.7013 (tp) cc_final: 0.6686 (tp) REVERT: q 23 THR cc_start: 0.6974 (m) cc_final: 0.6686 (t) REVERT: q 170 TYR cc_start: 0.6961 (m-10) cc_final: 0.6520 (m-10) REVERT: s 6 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8173 (tm-30) REVERT: s 113 SER cc_start: 0.8682 (OUTLIER) cc_final: 0.8417 (p) outliers start: 346 outliers final: 291 residues processed: 1924 average time/residue: 0.5790 time to fit residues: 1912.3397 Evaluate side-chains 1975 residues out of total 6825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 1673 time to evaluate : 5.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 185 ILE Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 227 ASP Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain I residue 271 TYR Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 188 ILE Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 262 CYS Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 371 LEU Chi-restraints excluded: chain J residue 453 SER Chi-restraints excluded: chain K residue 20 HIS Chi-restraints excluded: chain K residue 59 GLN Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 212 ASP Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 241 PHE Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 290 ILE Chi-restraints excluded: chain K residue 292 ASN Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 320 ILE Chi-restraints excluded: chain K residue 450 LEU Chi-restraints excluded: chain K residue 532 LEU Chi-restraints excluded: chain K residue 538 SER Chi-restraints excluded: chain K residue 616 GLU Chi-restraints excluded: chain K residue 652 ASP Chi-restraints excluded: chain K residue 688 LEU Chi-restraints excluded: chain K residue 713 ARG Chi-restraints excluded: chain K residue 744 VAL Chi-restraints excluded: chain K residue 752 LEU Chi-restraints excluded: chain K residue 767 THR Chi-restraints excluded: chain K residue 811 ASP Chi-restraints excluded: chain K residue 815 ASP Chi-restraints excluded: chain K residue 838 GLU Chi-restraints excluded: chain K residue 883 GLU Chi-restraints excluded: chain K residue 885 LYS Chi-restraints excluded: chain K residue 895 ASN Chi-restraints excluded: chain K residue 915 SER Chi-restraints excluded: chain K residue 916 VAL Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 980 PHE Chi-restraints excluded: chain K residue 984 ASP Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 34 ASP Chi-restraints excluded: chain X residue 55 ARG Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 71 VAL Chi-restraints excluded: chain X residue 121 MET Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 143 ASP Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 59 THR Chi-restraints excluded: chain x residue 69 ILE Chi-restraints excluded: chain x residue 70 LEU Chi-restraints excluded: chain x residue 93 LEU Chi-restraints excluded: chain x residue 106 LEU Chi-restraints excluded: chain x residue 136 ASN Chi-restraints excluded: chain x residue 147 ASN Chi-restraints excluded: chain x residue 162 ASP Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 16 ILE Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 61 ASP Chi-restraints excluded: chain T residue 79 GLN Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 121 MET Chi-restraints excluded: chain T residue 147 ASN Chi-restraints excluded: chain T residue 163 ILE Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 19 ASP Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 154 VAL Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain t residue 16 ILE Chi-restraints excluded: chain t residue 52 LYS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 59 THR Chi-restraints excluded: chain t residue 69 ILE Chi-restraints excluded: chain t residue 81 ASN Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain t residue 102 ILE Chi-restraints excluded: chain t residue 106 LEU Chi-restraints excluded: chain t residue 119 ASN Chi-restraints excluded: chain t residue 132 THR Chi-restraints excluded: chain t residue 174 GLN Chi-restraints excluded: chain w residue 8 VAL Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain w residue 84 LEU Chi-restraints excluded: chain w residue 85 THR Chi-restraints excluded: chain w residue 123 THR Chi-restraints excluded: chain w residue 156 ILE Chi-restraints excluded: chain w residue 172 LEU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain M residue 14 ASN Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain O residue 6 GLU Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 34 ASP Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain l residue 4 GLN Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 59 THR Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 77 GLN Chi-restraints excluded: chain m residue 16 ILE Chi-restraints excluded: chain m residue 18 ILE Chi-restraints excluded: chain m residue 21 LYS Chi-restraints excluded: chain m residue 31 THR Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 106 LEU Chi-restraints excluded: chain m residue 143 ASP Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 24 ILE Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 59 THR Chi-restraints excluded: chain o residue 123 THR Chi-restraints excluded: chain o residue 127 SER Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 16 ILE Chi-restraints excluded: chain p residue 53 ASN Chi-restraints excluded: chain p residue 60 LEU Chi-restraints excluded: chain p residue 101 ASN Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain n residue 23 THR Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain n residue 42 LEU Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 86 LEU Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain n residue 163 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 21 LYS Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 101 ASN Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain S residue 19 ASP Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 33 ILE Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 124 LYS Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain q residue 66 VAL Chi-restraints excluded: chain q residue 70 LEU Chi-restraints excluded: chain q residue 102 ILE Chi-restraints excluded: chain q residue 147 ASN Chi-restraints excluded: chain q residue 159 VAL Chi-restraints excluded: chain q residue 166 LEU Chi-restraints excluded: chain r residue 8 VAL Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 34 ASP Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 86 LEU Chi-restraints excluded: chain r residue 93 LEU Chi-restraints excluded: chain r residue 134 VAL Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 59 THR Chi-restraints excluded: chain s residue 69 ILE Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 108 ILE Chi-restraints excluded: chain s residue 113 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 747 random chunks: chunk 440 optimal weight: 6.9990 chunk 709 optimal weight: 3.9990 chunk 433 optimal weight: 7.9990 chunk 336 optimal weight: 0.9980 chunk 493 optimal weight: 1.9990 chunk 744 optimal weight: 0.7980 chunk 684 optimal weight: 7.9990 chunk 592 optimal weight: 6.9990 chunk 61 optimal weight: 0.0170 chunk 457 optimal weight: 2.9990 chunk 363 optimal weight: 0.4980 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 43 ASN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN F 130 GLN G 13 HIS ** G 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 212 ASN ** J 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 101 ASN ** N 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 77 GLN Q 32 ASN ** Q 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 63501 Z= 0.221 Angle : 0.772 13.980 86320 Z= 0.388 Chirality : 0.049 0.271 10099 Planarity : 0.004 0.082 10563 Dihedral : 11.272 179.578 9582 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.84 % Favored : 88.11 % Rotamer: Outliers : 4.43 % Allowed : 31.40 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.70 (0.09), residues: 7434 helix: -0.83 (0.11), residues: 2102 sheet: -1.27 (0.16), residues: 1111 loop : -2.56 (0.09), residues: 4221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 235 HIS 0.005 0.001 HIS t 39 PHE 0.018 0.001 PHE m 167 TYR 0.042 0.002 TYR B 87 ARG 0.020 0.001 ARG l 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14868 Ramachandran restraints generated. 7434 Oldfield, 0 Emsley, 7434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2053 residues out of total 6825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 1751 time to evaluate : 5.568 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: 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 111 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7396 (tp-100) REVERT: B 4 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6407 (pm20) REVERT: E 63 ASP cc_start: 0.6416 (p0) cc_final: 0.5869 (p0) REVERT: F 63 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7000 (p0) REVERT: G 66 ASP cc_start: 0.7478 (p0) cc_final: 0.7234 (p0) REVERT: H 102 ASN cc_start: 0.7848 (p0) cc_final: 0.7516 (p0) REVERT: I 271 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.7143 (m-10) REVERT: J 171 SER cc_start: 0.8243 (m) cc_final: 0.7919 (p) REVERT: K 162 LYS cc_start: 0.7699 (pttt) cc_final: 0.7296 (mtpt) REVERT: K 241 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7634 (t80) REVERT: K 328 LYS cc_start: 0.7804 (mttm) cc_final: 0.7271 (mttm) REVERT: K 682 LYS cc_start: 0.8880 (tppt) cc_final: 0.8409 (tppt) REVERT: K 686 ASN cc_start: 0.8710 (m110) cc_final: 0.7969 (m110) REVERT: K 713 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.5843 (tmt170) REVERT: K 793 LYS cc_start: 0.8813 (mttp) cc_final: 0.8568 (mttt) REVERT: K 819 GLU cc_start: 0.7225 (tp30) cc_final: 0.7015 (tp30) REVERT: K 923 ARG cc_start: 0.8356 (tpp-160) cc_final: 0.8146 (tpp-160) REVERT: K 926 VAL cc_start: 0.9290 (t) cc_final: 0.9042 (m) REVERT: X 5 ARG cc_start: 0.7053 (tpp-160) cc_final: 0.6702 (tpp-160) REVERT: X 94 TYR cc_start: 0.6689 (t80) cc_final: 0.6387 (t80) REVERT: X 110 ILE cc_start: 0.7680 (mm) cc_final: 0.7307 (mm) REVERT: X 121 MET cc_start: 0.6066 (OUTLIER) cc_final: 0.5584 (mmt) REVERT: x 5 ARG cc_start: 0.6032 (mpt180) cc_final: 0.5532 (mmt-90) REVERT: x 65 TYR cc_start: 0.8157 (p90) cc_final: 0.7854 (p90) REVERT: T 6 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6489 (tp30) REVERT: T 65 TYR cc_start: 0.8329 (p90) cc_final: 0.8073 (p90) REVERT: T 79 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6737 (tm-30) REVERT: W 7 TYR cc_start: 0.8175 (t80) cc_final: 0.7569 (t80) REVERT: W 167 PHE cc_start: 0.7734 (m-80) cc_final: 0.7315 (m-80) REVERT: t 83 PHE cc_start: 0.6111 (m-10) cc_final: 0.5690 (m-80) REVERT: t 121 MET cc_start: 0.7907 (tpp) cc_final: 0.7658 (tpp) REVERT: w 36 ARG cc_start: 0.8643 (tpp80) cc_final: 0.8293 (tpp80) REVERT: L 173 GLU cc_start: 0.8410 (pp20) cc_final: 0.8128 (pp20) REVERT: O 147 ASN cc_start: 0.7583 (p0) cc_final: 0.7364 (p0) REVERT: O 165 GLU cc_start: 0.7819 (mp0) cc_final: 0.7504 (mp0) REVERT: P 22 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.7105 (mp) REVERT: P 31 THR cc_start: 0.8935 (p) cc_final: 0.8611 (p) REVERT: P 64 ASP cc_start: 0.7455 (m-30) cc_final: 0.7209 (m-30) REVERT: o 9 PHE cc_start: 0.6819 (p90) cc_final: 0.6427 (p90) REVERT: o 11 PRO cc_start: 0.8404 (Cg_endo) cc_final: 0.7599 (Cg_exo) REVERT: o 122 LYS cc_start: 0.8445 (mmmt) cc_final: 0.8001 (mmtm) REVERT: p 35 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7580 (mp0) REVERT: p 65 TYR cc_start: 0.8157 (p90) cc_final: 0.7767 (p90) REVERT: p 85 THR cc_start: 0.7766 (p) cc_final: 0.7467 (p) REVERT: N 106 LEU cc_start: 0.8696 (tt) cc_final: 0.8181 (mp) REVERT: n 9 PHE cc_start: 0.7575 (p90) cc_final: 0.7196 (p90) REVERT: Q 7 TYR cc_start: 0.8200 (t80) cc_final: 0.7896 (t80) REVERT: R 63 CYS cc_start: 0.5389 (m) cc_final: 0.4940 (m) REVERT: S 5 ARG cc_start: 0.6268 (tpt170) cc_final: 0.5935 (tpt170) REVERT: S 144 LYS cc_start: 0.8673 (mptt) cc_final: 0.8077 (tptp) REVERT: q 16 ILE cc_start: 0.6963 (tp) cc_final: 0.6651 (tp) REVERT: q 23 THR cc_start: 0.6990 (m) cc_final: 0.6720 (t) REVERT: q 170 TYR cc_start: 0.6881 (m-10) cc_final: 0.6395 (m-10) REVERT: r 161 GLU cc_start: 0.7911 (pp20) cc_final: 0.7673 (pp20) REVERT: s 6 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8135 (tm-30) outliers start: 302 outliers final: 263 residues processed: 1913 average time/residue: 0.5790 time to fit residues: 1905.3321 Evaluate side-chains 1961 residues out of total 6825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1690 time to evaluate : 5.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 227 ASP Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain I residue 212 ASN Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain I residue 271 TYR Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 188 ILE Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 262 CYS Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 336 ILE Chi-restraints excluded: chain J residue 453 SER Chi-restraints excluded: chain K residue 20 HIS Chi-restraints excluded: chain K residue 59 GLN Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 212 ASP Chi-restraints excluded: chain K residue 241 PHE Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 290 ILE Chi-restraints excluded: chain K residue 292 ASN Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 320 ILE Chi-restraints excluded: chain K residue 450 LEU Chi-restraints excluded: chain K residue 538 SER Chi-restraints excluded: chain K residue 688 LEU Chi-restraints excluded: chain K residue 713 ARG Chi-restraints excluded: chain K residue 744 VAL Chi-restraints excluded: chain K residue 767 THR Chi-restraints excluded: chain K residue 811 ASP Chi-restraints excluded: chain K residue 815 ASP Chi-restraints excluded: chain K residue 883 GLU Chi-restraints excluded: chain K residue 885 LYS Chi-restraints excluded: chain K residue 895 ASN Chi-restraints excluded: chain K residue 916 VAL Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 984 ASP Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 71 VAL Chi-restraints excluded: chain X residue 121 MET Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 143 ASP Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 69 ILE Chi-restraints excluded: chain x residue 70 LEU Chi-restraints excluded: chain x residue 93 LEU Chi-restraints excluded: chain x residue 106 LEU Chi-restraints excluded: chain x residue 136 ASN Chi-restraints excluded: chain x residue 147 ASN Chi-restraints excluded: chain x residue 162 ASP Chi-restraints excluded: chain x residue 172 LEU Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 16 ILE Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 61 ASP Chi-restraints excluded: chain T residue 79 GLN Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 121 MET Chi-restraints excluded: chain T residue 147 ASN Chi-restraints excluded: chain T residue 163 ILE Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 19 ASP Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 154 VAL Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain t residue 16 ILE Chi-restraints excluded: chain t residue 52 LYS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 59 THR Chi-restraints excluded: chain t residue 81 ASN Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain t residue 102 ILE Chi-restraints excluded: chain t residue 106 LEU Chi-restraints excluded: chain t residue 119 ASN Chi-restraints excluded: chain t residue 132 THR Chi-restraints excluded: chain t residue 174 GLN Chi-restraints excluded: chain w residue 8 VAL Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain w residue 84 LEU Chi-restraints excluded: chain w residue 85 THR Chi-restraints excluded: chain w residue 123 THR Chi-restraints excluded: chain w residue 156 ILE Chi-restraints excluded: chain w residue 172 LEU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain O residue 6 GLU Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 32 ASN Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 34 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 59 THR Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 77 GLN Chi-restraints excluded: chain m residue 16 ILE Chi-restraints excluded: chain m residue 18 ILE Chi-restraints excluded: chain m residue 21 LYS Chi-restraints excluded: chain m residue 31 THR Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 143 ASP Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 59 THR Chi-restraints excluded: chain o residue 123 THR Chi-restraints excluded: chain o residue 127 SER Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 16 ILE Chi-restraints excluded: chain p residue 60 LEU Chi-restraints excluded: chain p residue 101 ASN Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain n residue 23 THR Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain n residue 42 LEU Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 86 LEU Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain n residue 163 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 21 LYS Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 101 ASN Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 33 ILE Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 124 LYS Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain q residue 66 VAL Chi-restraints excluded: chain q residue 70 LEU Chi-restraints excluded: chain q residue 91 ASN Chi-restraints excluded: chain q residue 102 ILE Chi-restraints excluded: chain q residue 140 GLU Chi-restraints excluded: chain q residue 147 ASN Chi-restraints excluded: chain q residue 159 VAL Chi-restraints excluded: chain q residue 166 LEU Chi-restraints excluded: chain r residue 8 VAL Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 34 ASP Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 86 LEU Chi-restraints excluded: chain r residue 93 LEU Chi-restraints excluded: chain r residue 134 VAL Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 59 THR Chi-restraints excluded: chain s residue 69 ILE Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 108 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 747 random chunks: chunk 470 optimal weight: 10.0000 chunk 631 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 546 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 164 optimal weight: 4.9990 chunk 593 optimal weight: 0.4980 chunk 248 optimal weight: 0.5980 chunk 609 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN G 13 HIS ** G 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 ASN I 172 GLN I 212 ASN ** J 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 53 ASN ** W 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 GLN ** m 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 101 ASN ** N 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN ** s 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.125963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.083688 restraints weight = 146129.285| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 4.41 r_work: 0.3038 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 63501 Z= 0.237 Angle : 0.776 13.848 86320 Z= 0.391 Chirality : 0.049 0.297 10099 Planarity : 0.004 0.084 10563 Dihedral : 11.227 179.805 9582 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.96 % Favored : 88.01 % Rotamer: Outliers : 4.50 % Allowed : 31.66 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.67 (0.09), residues: 7434 helix: -0.81 (0.11), residues: 2108 sheet: -1.23 (0.16), residues: 1113 loop : -2.53 (0.09), residues: 4213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 770 HIS 0.008 0.001 HIS I 210 PHE 0.018 0.001 PHE t 167 TYR 0.063 0.002 TYR B 87 ARG 0.009 0.001 ARG P 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27045.55 seconds wall clock time: 469 minutes 39.46 seconds (28179.46 seconds total)