Starting phenix.real_space_refine on Sat Jul 20 20:55:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqh_23486/07_2024/7lqh_23486.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqh_23486/07_2024/7lqh_23486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqh_23486/07_2024/7lqh_23486.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqh_23486/07_2024/7lqh_23486.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqh_23486/07_2024/7lqh_23486.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqh_23486/07_2024/7lqh_23486.cif" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.029 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: 3 Type Number sf(0) Gaussians C 8640 2.51 5 N 1584 2.21 5 O 1872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 204": "OE1" <-> "OE2" Residue "K PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 304": "OE1" <-> "OE2" Residue "L PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 1204": "OE1" <-> "OE2" Residue "O PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 1304": "OE1" <-> "OE2" Residue "P PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 304": "OE1" <-> "OE2" Residue "S PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 1204": "OE1" <-> "OE2" Residue "V PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 1304": "OE1" <-> "OE2" Residue "W PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 204": "OE1" <-> "OE2" Residue "Y PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 304": "OE1" <-> "OE2" Residue "Z PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 1204": "OE1" <-> "OE2" Residue "l PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 1304": "OE1" <-> "OE2" Residue "m PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 204": "OE1" <-> "OE2" Residue "o PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 304": "OE1" <-> "OE2" Residue "p PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 1204": "OE1" <-> "OE2" Residue "s PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 1304": "OE1" <-> "OE2" Residue "t PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 204": "OE1" <-> "OE2" Residue "v PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 304": "OE1" <-> "OE2" Residue "w PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 1204": "OE1" <-> "OE2" Residue "z PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 1304": "OE1" <-> "OE2" Residue "0 PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 204": "OE1" <-> "OE2" Residue "2 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 304": "OE1" <-> "OE2" Residue "3 PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 1204": "OE1" <-> "OE2" Residue "6 PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 1304": "OE1" <-> "OE2" Residue "7 PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 204": "OE1" <-> "OE2" Residue "9 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA GLU 304": "OE1" <-> "OE2" Residue "AA PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA GLU 1204": "OE1" <-> "OE2" Residue "DA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EA PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EA GLU 1304": "OE1" <-> "OE2" Residue "EA PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GA GLU 204": "OE1" <-> "OE2" Residue "GA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HA PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HA GLU 304": "OE1" <-> "OE2" Residue "HA PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JA PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JA PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KA GLU 1204": "OE1" <-> "OE2" Residue "KA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA GLU 1304": "OE1" <-> "OE2" Residue "LA PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MA PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MA PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA GLU 204": "OE1" <-> "OE2" Residue "NA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OA PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OA GLU 304": "OE1" <-> "OE2" Residue "OA PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "QA PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "QA PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RA GLU 1204": "OE1" <-> "OE2" Residue "RA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA GLU 1304": "OE1" <-> "OE2" Residue "SA PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "UA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "UA GLU 204": "OE1" <-> "OE2" Residue "UA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "UA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VA GLU 304": "OE1" <-> "OE2" Residue "WA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "WA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YA GLU 1204": "OE1" <-> "OE2" Residue "YA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ZA GLU 1304": "OE1" <-> "OE2" Residue "b PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bA GLU 204": "OE1" <-> "OE2" Residue "bA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "cA GLU 304": "OE1" <-> "OE2" Residue "dA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "dA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "fA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "fA GLU 1204": "OE1" <-> "OE2" Residue "fA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "fA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "gA GLU 1304": "OE1" <-> "OE2" Residue "c PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "iA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "iA GLU 204": "OE1" <-> "OE2" Residue "iA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "iA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "jA GLU 304": "OE1" <-> "OE2" Residue "kA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "kA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "mA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "mA GLU 1204": "OE1" <-> "OE2" Residue "mA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "mA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "nA GLU 1304": "OE1" <-> "OE2" Residue "d PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "pA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "pA GLU 204": "OE1" <-> "OE2" Residue "pA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "pA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "qA GLU 304": "OE1" <-> "OE2" Residue "rA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "rA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "tA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "tA GLU 1204": "OE1" <-> "OE2" Residue "tA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "tA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "uA GLU 1304": "OE1" <-> "OE2" Residue "e PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "wA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "wA GLU 204": "OE1" <-> "OE2" Residue "wA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "wA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "xA GLU 304": "OE1" <-> "OE2" Residue "yA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "yA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0A PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0A GLU 1204": "OE1" <-> "OE2" Residue "0A PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0A PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A GLU 1304": "OE1" <-> "OE2" Residue "f PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A GLU 204": "OE1" <-> "OE2" Residue "3A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A GLU 304": "OE1" <-> "OE2" Residue "5A PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7A PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7A GLU 1204": "OE1" <-> "OE2" Residue "7A PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7A PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8A GLU 1304": "OE1" <-> "OE2" Residue "g PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB GLU 204": "OE1" <-> "OE2" Residue "AB PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BB GLU 304": "OE1" <-> "OE2" Residue "CB PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EB PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EB GLU 1204": "OE1" <-> "OE2" Residue "EB PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EB PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FB GLU 1304": "OE1" <-> "OE2" Residue "h PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HB PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HB GLU 204": "OE1" <-> "OE2" Residue "HB PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HB PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IB GLU 304": "OE1" <-> "OE2" Residue "JB PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JB PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB GLU 1204": "OE1" <-> "OE2" Residue "LB PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MB GLU 1304": "OE1" <-> "OE2" Residue "i PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OB PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OB GLU 204": "OE1" <-> "OE2" Residue "OB PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OB PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PB GLU 304": "OE1" <-> "OE2" Residue "QB PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "QB PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB GLU 1204": "OE1" <-> "OE2" Residue "SB PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TB GLU 1304": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 12096 Number of models: 1 Model: "" Number of chains: 144 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "u" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "9" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "AA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "BA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "CA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "DA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "EA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "FA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "GA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "HA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "IA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "JA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "KA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "LA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "MA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "NA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "OA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "PA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "QA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "RA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "SA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "TA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "UA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "VA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "WA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "XA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "YA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "ZA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "aA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "bA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "cA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "dA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "eA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "fA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "gA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "hA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "iA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "jA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "kA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "lA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "mA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "nA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "oA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "pA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "qA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "rA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "sA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "tA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "uA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "vA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "wA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "xA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "yA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "zA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "0A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "1A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "2A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "3A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "4A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "5A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "6A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "8A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "9A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "AB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "BB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "CB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "DB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "EB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "FB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "GB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "HB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "IB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "JB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "KB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "LB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "MB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "NB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "OB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "PB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "QB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "RB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "SB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "TB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 6.17, per 1000 atoms: 0.51 Number of scatterers: 12096 At special positions: 0 Unit cell: (89.64, 89.64, 111.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1872 8.00 N 1584 7.00 C 8640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=35, symmetry=0 Number of additional bonds: simple=35, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.17 Conformation dependent library (CDL) restraints added in 997.4 milliseconds 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 22 sheets defined 0.0% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'M' and resid 1006 through 1007 Processing sheet with id=AA3, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AA4, first strand: chain 'T' and resid 1006 through 1007 Processing sheet with id=AA5, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'j' and resid 1006 through 1007 Processing sheet with id=AA7, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AA8, first strand: chain 'q' and resid 1006 through 1007 Processing sheet with id=AA9, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'x' and resid 1006 through 1007 Processing sheet with id=AB2, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AB3, first strand: chain '4' and resid 1006 through 1007 Processing sheet with id=AB4, first strand: chain 'G' and resid 6 through 7 Processing sheet with id=AB5, first strand: chain 'BA' and resid 1006 through 1007 Processing sheet with id=AB6, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AB7, first strand: chain 'IA' and resid 1006 through 1007 Processing sheet with id=AB8, first strand: chain 'I' and resid 6 through 7 Processing sheet with id=AB9, first strand: chain 'PA' and resid 1006 through 1007 Processing sheet with id=AC1, first strand: chain 'h' and resid 2 through 6 removed outlier: 3.535A pdb=" N PHEGB 105 " --> pdb=" O PHE h 3 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE h 5 " --> pdb=" O PHEGB 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE2A 105 " --> pdb=" O PHE f 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE f 5 " --> pdb=" O PHE2A 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEoA 105 " --> pdb=" O PHE d 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE d 5 " --> pdb=" O PHEoA 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEaA 105 " --> pdb=" O PHE b 3 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE b 5 " --> pdb=" O PHEaA 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHETA 105 " --> pdb=" O PHE a 3 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE a 5 " --> pdb=" O PHETA 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHEhA 105 " --> pdb=" O PHE c 3 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE c 5 " --> pdb=" O PHEhA 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEvA 105 " --> pdb=" O PHE e 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE e 5 " --> pdb=" O PHEvA 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE9A 105 " --> pdb=" O PHE g 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE g 5 " --> pdb=" O PHE9A 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHENB 105 " --> pdb=" O PHE i 3 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE i 5 " --> pdb=" O PHENB 103 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'HB' and resid 202 through 206 removed outlier: 3.521A pdb=" N LYSIB 302 " --> pdb=" O GMA3A 208 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS3A 206 " --> pdb=" O GLUIB 304 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GMAIB 308 " --> pdb=" O LYS3A 202 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS4A 302 " --> pdb=" O GMApA 208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYSpA 206 " --> pdb=" O GLU4A 304 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYSqA 302 " --> pdb=" O GMAbA 208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYSbA 206 " --> pdb=" O GLUqA 304 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYScA 302 " --> pdb=" O GMAUA 208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYSUA 206 " --> pdb=" O GLUcA 304 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GMAcA 308 " --> pdb=" O LYSUA 202 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYSVA 302 " --> pdb=" O GMAiA 208 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYSiA 206 " --> pdb=" O GLUVA 304 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GMAVA 308 " --> pdb=" O LYSiA 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYSjA 302 " --> pdb=" O GMAwA 208 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYSwA 206 " --> pdb=" O GLUjA 304 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYSxA 302 " --> pdb=" O GMAAB 208 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYSAB 206 " --> pdb=" O GLUxA 304 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GMAxA 308 " --> pdb=" O LYSAB 202 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYSBB 302 " --> pdb=" O GMAOB 208 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYSOB 206 " --> pdb=" O GLUBB 304 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'JB' and resid 1002 through 1006 removed outlier: 3.536A pdb=" N PHEKB1105 " --> pdb=" O PHEJB1003 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHEJB1005 " --> pdb=" O PHEKB1103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE6A1105 " --> pdb=" O PHE5A1003 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE5A1005 " --> pdb=" O PHE6A1103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEsA1105 " --> pdb=" O PHErA1003 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHErA1005 " --> pdb=" O PHEsA1103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEeA1105 " --> pdb=" O PHEdA1003 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHEdA1005 " --> pdb=" O PHEeA1103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEXA1105 " --> pdb=" O PHEWA1003 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHEWA1005 " --> pdb=" O PHEXA1103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHElA1105 " --> pdb=" O PHEkA1003 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHEkA1005 " --> pdb=" O PHElA1103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEzA1105 " --> pdb=" O PHEyA1003 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHEyA1005 " --> pdb=" O PHEzA1103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEDB1105 " --> pdb=" O PHECB1003 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHECB1005 " --> pdb=" O PHEDB1103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHERB1105 " --> pdb=" O PHEQB1003 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHEQB1005 " --> pdb=" O PHERB1103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'LB' and resid 1202 through 1206 removed outlier: 3.521A pdb=" N LYSMB1302 " --> pdb=" O GMA7A1208 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS7A1206 " --> pdb=" O GLUMB1304 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GMAMB1308 " --> pdb=" O LYS7A1202 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS8A1302 " --> pdb=" O GMAtA1208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYStA1206 " --> pdb=" O GLU8A1304 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYSuA1302 " --> pdb=" O GMAfA1208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYSfA1206 " --> pdb=" O GLUuA1304 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYSgA1302 " --> pdb=" O GMAYA1208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYSYA1206 " --> pdb=" O GLUgA1304 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GMAgA1308 " --> pdb=" O LYSYA1202 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYSZA1302 " --> pdb=" O GMAmA1208 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYSmA1206 " --> pdb=" O GLUZA1304 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GMAZA1308 " --> pdb=" O LYSmA1202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYSnA1302 " --> pdb=" O GMA0A1208 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS0A1206 " --> pdb=" O GLUnA1304 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS1A1302 " --> pdb=" O GMAEB1208 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYSEB1206 " --> pdb=" O GLU1A1304 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GMA1A1308 " --> pdb=" O LYSEB1202 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYSFB1302 " --> pdb=" O GMASB1208 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYSSB1206 " --> pdb=" O GLUFB1304 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 786 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 6.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 1489 1.26 - 1.33: 1391 1.33 - 1.41: 3600 1.41 - 1.48: 1308 1.48 - 1.56: 4740 Bond restraints: 12528 Sorted by residual: bond pdb=" N 5CR d 1 " pdb=" CAL 5CR d 1 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" N 5CR e 1 " pdb=" CAL 5CR e 1 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" N 5CRrA1001 " pdb=" CAL 5CRrA1001 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" N 5CRyA1001 " pdb=" CAL 5CRyA1001 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" N 5CR i 1 " pdb=" CAL 5CR i 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+01 ... (remaining 12523 not shown) Histogram of bond angle deviations from ideal: 105.41 - 109.75: 1131 109.75 - 114.08: 4107 114.08 - 118.42: 2126 118.42 - 122.76: 7479 122.76 - 127.10: 1429 Bond angle restraints: 16272 Sorted by residual: angle pdb=" N 5CR b 1 " pdb=" CAL 5CR b 1 " pdb=" CAA 5CR b 1 " ideal model delta sigma weight residual 114.91 124.81 -9.90 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " pdb=" CAA 5CR f 1 " ideal model delta sigma weight residual 114.91 124.80 -9.89 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR5A1001 " pdb=" CAL 5CR5A1001 " pdb=" CAA 5CR5A1001 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR a 1 " pdb=" CAL 5CR a 1 " pdb=" CAA 5CR a 1 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CRWA1001 " pdb=" CAL 5CRWA1001 " pdb=" CAA 5CRWA1001 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.08e+01 ... (remaining 16267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 4844 15.26 - 30.52: 790 30.52 - 45.79: 342 45.79 - 61.05: 198 61.05 - 76.31: 18 Dihedral angle restraints: 6192 sinusoidal: 2880 harmonic: 3312 Sorted by residual: dihedral pdb=" CA LYSMA 106 " pdb=" CB LYSMA 106 " pdb=" CG LYSMA 106 " pdb=" CD LYSMA 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.26 58.74 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYSQA1106 " pdb=" CB LYSQA1106 " pdb=" CG LYSQA1106 " pdb=" CD LYSQA1106 " ideal model delta sinusoidal sigma weight residual 60.00 1.29 58.71 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYS 1 106 " pdb=" CB LYS 1 106 " pdb=" CG LYS 1 106 " pdb=" CD LYS 1 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.29 58.71 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 6189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.018: 407 0.018 - 0.036: 334 0.036 - 0.054: 299 0.054 - 0.073: 89 0.073 - 0.091: 23 Chirality restraints: 1152 Sorted by residual: chirality pdb=" CA LYS R 202 " pdb=" N LYS R 202 " pdb=" C LYS R 202 " pdb=" CB LYS R 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.06e-01 chirality pdb=" CA LYS V1202 " pdb=" N LYS V1202 " pdb=" C LYS V1202 " pdb=" CB LYS V1202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.02e-01 chirality pdb=" CA LYS Y 202 " pdb=" N LYS Y 202 " pdb=" C LYS Y 202 " pdb=" CB LYS Y 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.86e-01 ... (remaining 1149 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHEUA 205 " -0.008 2.00e-02 2.50e+03 7.00e-03 8.57e-01 pdb=" CG PHEUA 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEUA 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHEUA 205 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHEUA 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEUA 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHEUA 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEYA1205 " -0.009 2.00e-02 2.50e+03 6.98e-03 8.53e-01 pdb=" CG PHEYA1205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEYA1205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHEYA1205 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHEYA1205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEYA1205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHEYA1205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEAB 205 " -0.009 2.00e-02 2.50e+03 6.97e-03 8.51e-01 pdb=" CG PHEAB 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEAB 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHEAB 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHEAB 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEAB 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHEAB 205 " -0.003 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 281 2.66 - 3.22: 10092 3.22 - 3.78: 19029 3.78 - 4.34: 28093 4.34 - 4.90: 46315 Nonbonded interactions: 103810 Sorted by model distance: nonbonded pdb=" CD LYS N1102 " pdb=" OE2 GMA 9 208 " model vdw 2.098 2.752 nonbonded pdb=" OE2 GMA Y 208 " pdb=" CD LYS r1102 " model vdw 2.116 2.752 nonbonded pdb=" CD LYS U1102 " pdb=" OE2 GMA v 208 " model vdw 2.116 2.752 nonbonded pdb=" CD LYS k1102 " pdb=" OE2 GMANA 208 " model vdw 2.117 2.752 nonbonded pdb=" CD LYS Q 102 " pdb=" OE2 GMADA1208 " model vdw 2.118 2.752 ... (remaining 103805 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 '0' selection = chain '0A' selection = chain '1' selection = chain '1A' selection = chain '2' selection = chain '2A' selection = chain '3' selection = chain '3A' selection = chain '4' selection = chain '4A' selection = chain '5' selection = chain '5A' selection = chain '6' selection = chain '6A' selection = chain '7' selection = chain '7A' selection = chain '8' selection = chain '8A' selection = chain '9' selection = chain '9A' selection = chain 'A' selection = chain 'AA' selection = chain 'AB' selection = chain 'B' selection = chain 'BA' selection = chain 'BB' selection = chain 'C' selection = chain 'CA' selection = chain 'CB' selection = chain 'D' selection = chain 'DA' selection = chain 'DB' selection = chain 'E' selection = chain 'EA' selection = chain 'EB' selection = chain 'F' selection = chain 'FA' selection = chain 'FB' selection = chain 'G' selection = chain 'GA' selection = chain 'GB' selection = chain 'H' selection = chain 'HA' selection = chain 'HB' selection = chain 'I' selection = chain 'IA' selection = chain 'IB' selection = chain 'J' selection = chain 'JA' selection = chain 'JB' selection = chain 'K' selection = chain 'KA' selection = chain 'KB' selection = chain 'L' selection = chain 'LA' selection = chain 'LB' selection = chain 'M' selection = chain 'MA' selection = chain 'MB' selection = chain 'N' selection = chain 'NA' selection = chain 'NB' selection = chain 'O' selection = chain 'OA' selection = chain 'OB' selection = chain 'P' selection = chain 'PA' selection = chain 'PB' selection = chain 'Q' selection = chain 'QA' selection = chain 'QB' selection = chain 'R' selection = chain 'RA' selection = chain 'RB' selection = chain 'S' selection = chain 'SA' selection = chain 'SB' selection = chain 'T' selection = chain 'TA' selection = chain 'TB' selection = chain 'U' selection = chain 'UA' selection = chain 'V' selection = chain 'VA' selection = chain 'W' selection = chain 'WA' selection = chain 'X' selection = chain 'XA' selection = chain 'Y' selection = chain 'YA' selection = chain 'Z' selection = chain 'ZA' selection = chain 'a' selection = chain 'aA' selection = chain 'b' selection = chain 'bA' selection = chain 'c' selection = chain 'cA' selection = chain 'd' selection = chain 'dA' selection = chain 'e' selection = chain 'eA' selection = chain 'f' selection = chain 'fA' selection = chain 'g' selection = chain 'gA' selection = chain 'h' selection = chain 'hA' selection = chain 'i' selection = chain 'iA' selection = chain 'j' selection = chain 'jA' selection = chain 'k' selection = chain 'kA' selection = chain 'l' selection = chain 'lA' selection = chain 'm' selection = chain 'mA' selection = chain 'n' selection = chain 'nA' selection = chain 'o' selection = chain 'oA' selection = chain 'p' selection = chain 'pA' selection = chain 'q' selection = chain 'qA' selection = chain 'r' selection = chain 'rA' selection = chain 's' selection = chain 'sA' selection = chain 't' selection = chain 'tA' selection = chain 'u' selection = chain 'uA' selection = chain 'v' selection = chain 'vA' selection = chain 'w' selection = chain 'wA' selection = chain 'x' selection = chain 'xA' selection = chain 'y' selection = chain 'yA' selection = chain 'z' selection = chain 'zA' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.950 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.190 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: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 0.016 0.118 12528 Z= 0.917 Angle : 1.417 9.902 16272 Z= 0.592 Chirality : 0.035 0.091 1152 Planarity : 0.002 0.009 2160 Dihedral : 20.718 76.311 3888 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 31.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 14.58 % Allowed : 14.58 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.94 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHEUA 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 472 time to evaluate : 1.246 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: A 4 GLU cc_start: 0.7369 (mp0) cc_final: 0.6755 (pm20) REVERT: B 4 GLU cc_start: 0.7493 (mp0) cc_final: 0.6748 (pm20) REVERT: S 306 LYS cc_start: 0.8629 (tttt) cc_final: 0.8357 (mttt) REVERT: Y 206 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8180 (ttmm) REVERT: Z 306 LYS cc_start: 0.8563 (tttt) cc_final: 0.8262 (tttt) REVERT: j 1006 LYS cc_start: 0.8500 (mtmt) cc_final: 0.8034 (mtmt) REVERT: m 1306 LYS cc_start: 0.8633 (tttt) cc_final: 0.8339 (mttt) REVERT: o 204 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7064 (mt-10) REVERT: s 1206 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8228 (ttmm) REVERT: t 1306 LYS cc_start: 0.8695 (tttt) cc_final: 0.8441 (mttt) REVERT: v 206 LYS cc_start: 0.8477 (ttmm) cc_final: 0.8231 (ttmm) REVERT: w 304 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7091 (mm-30) REVERT: w 306 LYS cc_start: 0.8689 (tttt) cc_final: 0.8339 (mttt) REVERT: x 1004 GLU cc_start: 0.7152 (mp0) cc_final: 0.6745 (mp0) REVERT: 0 1304 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7144 (mm-30) REVERT: 0 1306 LYS cc_start: 0.8594 (tttt) cc_final: 0.8264 (tttt) REVERT: F 4 GLU cc_start: 0.7397 (mp0) cc_final: 0.6657 (pm20) REVERT: 3 304 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7148 (mm-30) REVERT: 6 1204 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6808 (mt-10) REVERT: 6 1206 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8366 (ttmm) REVERT: 7 1306 LYS cc_start: 0.8772 (tttt) cc_final: 0.8420 (mttt) REVERT: G 4 GLU cc_start: 0.7313 (mp0) cc_final: 0.6485 (pm20) REVERT: 9 204 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6532 (mt-10) REVERT: AA 306 LYS cc_start: 0.8673 (tttt) cc_final: 0.8387 (mttt) REVERT: DA 1204 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7037 (mt-10) REVERT: EA 1306 LYS cc_start: 0.8705 (tttt) cc_final: 0.8431 (mttt) REVERT: HA 306 LYS cc_start: 0.8699 (tttt) cc_final: 0.8363 (mttt) REVERT: LA 1306 LYS cc_start: 0.8705 (tttt) cc_final: 0.8323 (mttt) REVERT: OA 306 LYS cc_start: 0.8570 (tttt) cc_final: 0.8318 (mttt) REVERT: SA 1306 LYS cc_start: 0.8648 (tttt) cc_final: 0.8295 (tttt) REVERT: a 2 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8344 (ttpt) REVERT: TA 104 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: TA 105 PHE cc_start: 0.9072 (t80) cc_final: 0.8761 (t80) REVERT: UA 202 LYS cc_start: 0.8784 (tttm) cc_final: 0.8340 (ttmm) REVERT: VA 305 PHE cc_start: 0.8549 (t80) cc_final: 0.8266 (t80) REVERT: WA 1003 PHE cc_start: 0.9115 (t80) cc_final: 0.8755 (t80) REVERT: WA 1005 PHE cc_start: 0.8951 (t80) cc_final: 0.8609 (t80) REVERT: WA 1007 PHE cc_start: 0.9301 (t80) cc_final: 0.8997 (t80) REVERT: XA 1103 PHE cc_start: 0.8930 (t80) cc_final: 0.8678 (t80) REVERT: XA 1107 PHE cc_start: 0.8921 (t80) cc_final: 0.8714 (t80) REVERT: YA 1202 LYS cc_start: 0.8788 (tttm) cc_final: 0.8391 (tttm) REVERT: ZA 1304 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8190 (tm-30) REVERT: aA 103 PHE cc_start: 0.9101 (t80) cc_final: 0.8425 (t80) REVERT: aA 106 LYS cc_start: 0.8822 (tttp) cc_final: 0.8564 (tttp) REVERT: bA 202 LYS cc_start: 0.8841 (tttm) cc_final: 0.8397 (ttmm) REVERT: cA 303 PHE cc_start: 0.9015 (t80) cc_final: 0.8654 (t80) REVERT: cA 304 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8429 (tm-30) REVERT: fA 1202 LYS cc_start: 0.8656 (tttm) cc_final: 0.8373 (tttm) REVERT: c 5 PHE cc_start: 0.8932 (t80) cc_final: 0.8452 (t80) REVERT: c 7 PHE cc_start: 0.9209 (t80) cc_final: 0.8995 (t80) REVERT: hA 106 LYS cc_start: 0.8870 (tttp) cc_final: 0.8657 (tttp) REVERT: iA 202 LYS cc_start: 0.8878 (tttm) cc_final: 0.8562 (ttmm) REVERT: jA 306 LYS cc_start: 0.8334 (tptp) cc_final: 0.8046 (tptp) REVERT: kA 1005 PHE cc_start: 0.9077 (t80) cc_final: 0.8703 (t80) REVERT: lA 1103 PHE cc_start: 0.8901 (t80) cc_final: 0.8521 (t80) REVERT: mA 1206 LYS cc_start: 0.8797 (tttt) cc_final: 0.8582 (tttt) REVERT: nA 1305 PHE cc_start: 0.8662 (t80) cc_final: 0.8453 (t80) REVERT: d 3 PHE cc_start: 0.9295 (t80) cc_final: 0.8996 (t80) REVERT: d 5 PHE cc_start: 0.9090 (t80) cc_final: 0.8869 (t80) REVERT: d 7 PHE cc_start: 0.9253 (t80) cc_final: 0.8845 (t80) REVERT: oA 107 PHE cc_start: 0.8813 (t80) cc_final: 0.8347 (t80) REVERT: pA 202 LYS cc_start: 0.8916 (tttm) cc_final: 0.8524 (mmmm) REVERT: pA 206 LYS cc_start: 0.8826 (tttt) cc_final: 0.8593 (tttt) REVERT: qA 305 PHE cc_start: 0.8722 (t80) cc_final: 0.8402 (t80) REVERT: rA 1005 PHE cc_start: 0.8915 (t80) cc_final: 0.8588 (t80) REVERT: sA 1103 PHE cc_start: 0.9020 (t80) cc_final: 0.8784 (t80) REVERT: tA 1206 LYS cc_start: 0.8812 (tttt) cc_final: 0.8431 (tttt) REVERT: vA 106 LYS cc_start: 0.8825 (tttp) cc_final: 0.8561 (tttp) REVERT: wA 202 LYS cc_start: 0.8733 (tttm) cc_final: 0.8401 (mmmm) REVERT: wA 206 LYS cc_start: 0.8797 (tttt) cc_final: 0.8503 (tttt) REVERT: xA 303 PHE cc_start: 0.8927 (t80) cc_final: 0.8677 (t80) REVERT: zA 1106 LYS cc_start: 0.8767 (tttp) cc_final: 0.8557 (tttp) REVERT: 1A 1303 PHE cc_start: 0.8829 (t80) cc_final: 0.8602 (t80) REVERT: 1A 1305 PHE cc_start: 0.8465 (t80) cc_final: 0.8239 (t80) REVERT: 3A 202 LYS cc_start: 0.8922 (tttm) cc_final: 0.8551 (mmmm) REVERT: 3A 206 LYS cc_start: 0.8739 (tttt) cc_final: 0.8527 (tttt) REVERT: 4A 306 LYS cc_start: 0.8459 (tptp) cc_final: 0.8229 (tptp) REVERT: 4A 307 PHE cc_start: 0.8508 (t80) cc_final: 0.8127 (t80) REVERT: 5A 1003 PHE cc_start: 0.9169 (t80) cc_final: 0.8731 (t80) REVERT: 5A 1005 PHE cc_start: 0.9041 (t80) cc_final: 0.8732 (t80) REVERT: 5A 1007 PHE cc_start: 0.9152 (t80) cc_final: 0.8671 (t80) REVERT: 6A 1106 LYS cc_start: 0.8863 (tttp) cc_final: 0.8585 (tttp) REVERT: 7A 1205 PHE cc_start: 0.8502 (t80) cc_final: 0.8271 (t80) REVERT: 7A 1206 LYS cc_start: 0.8695 (tttt) cc_final: 0.8343 (tttm) REVERT: 9A 104 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: 9A 106 LYS cc_start: 0.8906 (tttp) cc_final: 0.8655 (tttm) REVERT: BB 305 PHE cc_start: 0.8766 (t80) cc_final: 0.8355 (t80) REVERT: BB 307 PHE cc_start: 0.8514 (t80) cc_final: 0.8208 (t80) REVERT: CB 1003 PHE cc_start: 0.9123 (t80) cc_final: 0.8740 (t80) REVERT: CB 1005 PHE cc_start: 0.9008 (t80) cc_final: 0.8652 (t80) REVERT: CB 1007 PHE cc_start: 0.9161 (t80) cc_final: 0.8929 (t80) REVERT: DB 1106 LYS cc_start: 0.8792 (tttp) cc_final: 0.8527 (tttp) REVERT: EB 1202 LYS cc_start: 0.8867 (tttm) cc_final: 0.8491 (tttm) REVERT: EB 1206 LYS cc_start: 0.8740 (tttt) cc_final: 0.8538 (tttm) REVERT: FB 1304 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8667 (tm-30) REVERT: GB 103 PHE cc_start: 0.9078 (t80) cc_final: 0.8876 (t80) REVERT: GB 106 LYS cc_start: 0.8643 (tttp) cc_final: 0.8431 (tttm) REVERT: HB 206 LYS cc_start: 0.8809 (tttt) cc_final: 0.8555 (tttm) REVERT: IB 303 PHE cc_start: 0.8906 (t80) cc_final: 0.8678 (t80) REVERT: IB 304 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8429 (tm-30) REVERT: KB 1105 PHE cc_start: 0.8731 (t80) cc_final: 0.8308 (t80) REVERT: KB 1106 LYS cc_start: 0.8655 (tttp) cc_final: 0.8378 (tttp) REVERT: MB 1303 PHE cc_start: 0.8794 (t80) cc_final: 0.8553 (t80) REVERT: i 6 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8467 (ttpt) REVERT: NB 104 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: OB 206 LYS cc_start: 0.8866 (tttt) cc_final: 0.8654 (tttt) REVERT: PB 304 GLU cc_start: 0.8840 (tm-30) cc_final: 0.6113 (pm20) REVERT: PB 305 PHE cc_start: 0.8434 (t80) cc_final: 0.7272 (t80) REVERT: TB 1305 PHE cc_start: 0.8317 (t80) cc_final: 0.8019 (t80) REVERT: TB 1307 PHE cc_start: 0.8067 (t80) cc_final: 0.7620 (t80) outliers start: 126 outliers final: 85 residues processed: 495 average time/residue: 0.4503 time to fit residues: 272.6089 Evaluate side-chains 550 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 460 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain N residue 1102 LYS Chi-restraints excluded: chain N residue 1106 LYS Chi-restraints excluded: chain Q residue 106 LYS Chi-restraints excluded: chain U residue 1102 LYS Chi-restraints excluded: chain U residue 1106 LYS Chi-restraints excluded: chain W residue 1302 LYS Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 106 LYS Chi-restraints excluded: chain k residue 1102 LYS Chi-restraints excluded: chain k residue 1106 LYS Chi-restraints excluded: chain n residue 102 LYS Chi-restraints excluded: chain n residue 106 LYS Chi-restraints excluded: chain p residue 302 LYS Chi-restraints excluded: chain r residue 1102 LYS Chi-restraints excluded: chain r residue 1106 LYS Chi-restraints excluded: chain t residue 1302 LYS Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain y residue 1102 LYS Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain 1 residue 102 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 3 residue 302 LYS Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain CA residue 1102 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain FA residue 102 LYS Chi-restraints excluded: chain FA residue 106 LYS Chi-restraints excluded: chain JA residue 1102 LYS Chi-restraints excluded: chain JA residue 1106 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain QA residue 1102 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 104 GLU Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain dA residue 1002 LYS Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain kA residue 1004 GLU Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain rA residue 1004 GLU Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain yA residue 1006 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 5A residue 1006 LYS Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain 9A residue 104 GLU Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain CB residue 1006 LYS Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain JB residue 1006 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.6980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.6563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.343 12528 Z= 6.056 Angle : 3.929 32.601 16272 Z= 1.767 Chirality : 0.302 1.031 1152 Planarity : 0.018 0.055 2160 Dihedral : 22.150 100.810 1779 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 104.10 Ramachandran Plot: Outliers : 0.35 % Allowed : 15.28 % Favored : 84.38 % Rotamer: Outliers : 15.86 % Allowed : 18.63 % Favored : 65.51 % Cbeta Deviations : 12.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.69 % 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: -6.67 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.08 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.113 0.018 PHETA 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 451 time to evaluate : 1.219 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: A 6 LYS cc_start: 0.8997 (mtmt) cc_final: 0.8558 (mtmt) REVERT: J 106 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8636 (mmmm) REVERT: M 1006 LYS cc_start: 0.9060 (mtmt) cc_final: 0.8851 (mtmt) REVERT: N 1104 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7704 (mm-30) REVERT: N 1106 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8480 (mmmm) REVERT: B 4 GLU cc_start: 0.8269 (mp0) cc_final: 0.7446 (mp0) REVERT: Q 104 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7483 (mm-30) REVERT: Q 106 LYS cc_start: 0.9031 (mmmm) cc_final: 0.8644 (mmmm) REVERT: T 1006 LYS cc_start: 0.8986 (mtmt) cc_final: 0.8514 (mtmt) REVERT: U 1104 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7747 (mm-30) REVERT: U 1106 LYS cc_start: 0.8692 (tptm) cc_final: 0.8336 (tptm) REVERT: W 1302 LYS cc_start: 0.9160 (ttpt) cc_final: 0.8938 (mtpt) REVERT: C 6 LYS cc_start: 0.9013 (mtmt) cc_final: 0.8777 (mtmt) REVERT: X 104 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7684 (mm-30) REVERT: X 106 LYS cc_start: 0.8926 (mmmm) cc_final: 0.8586 (mmmm) REVERT: Y 206 LYS cc_start: 0.9104 (ttmm) cc_final: 0.8825 (mtpp) REVERT: j 1004 GLU cc_start: 0.8139 (mp0) cc_final: 0.7287 (mp0) REVERT: j 1006 LYS cc_start: 0.8987 (mtmt) cc_final: 0.8652 (mtmt) REVERT: k 1102 LYS cc_start: 0.7994 (ttpt) cc_final: 0.7371 (ttpt) REVERT: k 1106 LYS cc_start: 0.8842 (mmmm) cc_final: 0.8633 (mmmm) REVERT: l 1206 LYS cc_start: 0.8940 (ttmm) cc_final: 0.8702 (ttmm) REVERT: n 106 LYS cc_start: 0.8866 (mmmm) cc_final: 0.8354 (mmmm) REVERT: o 204 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7539 (mt-10) REVERT: q 1004 GLU cc_start: 0.8428 (mp0) cc_final: 0.8124 (mp0) REVERT: r 1106 LYS cc_start: 0.9029 (mmmm) cc_final: 0.8742 (mmmm) REVERT: s 1204 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7457 (mt-10) REVERT: t 1304 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7526 (mm-30) REVERT: u 102 LYS cc_start: 0.9042 (ttpt) cc_final: 0.8647 (ttpt) REVERT: u 104 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7762 (mm-30) REVERT: u 106 LYS cc_start: 0.8774 (mmmm) cc_final: 0.8398 (mmmm) REVERT: v 202 LYS cc_start: 0.9196 (mtpt) cc_final: 0.8871 (mmmm) REVERT: y 1102 LYS cc_start: 0.9076 (ttpt) cc_final: 0.8702 (ttpt) REVERT: y 1106 LYS cc_start: 0.8983 (mmmm) cc_final: 0.8680 (mmmm) REVERT: 1 106 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8596 (mmmm) REVERT: 3 304 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7710 (mm-30) REVERT: 4 1004 GLU cc_start: 0.7806 (mp0) cc_final: 0.7471 (mp0) REVERT: 5 1104 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7792 (mm-30) REVERT: 6 1202 LYS cc_start: 0.9289 (mtpt) cc_final: 0.8719 (mmmm) REVERT: 6 1204 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7276 (mt-10) REVERT: 7 1304 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7373 (mm-30) REVERT: G 4 GLU cc_start: 0.8063 (mp0) cc_final: 0.7164 (mp0) REVERT: G 6 LYS cc_start: 0.9064 (mtmt) cc_final: 0.8775 (mtmt) REVERT: 8 102 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8710 (ttpt) REVERT: 8 106 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8645 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8024 (mp0) cc_final: 0.7405 (mp0) REVERT: BA 1006 LYS cc_start: 0.8958 (mtmt) cc_final: 0.8722 (mtmt) REVERT: CA 1104 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7502 (mm-30) REVERT: CA 1106 LYS cc_start: 0.8886 (mmmm) cc_final: 0.8548 (mmmm) REVERT: DA 1206 LYS cc_start: 0.9015 (ttmm) cc_final: 0.8785 (ttmm) REVERT: EA 1304 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7770 (mm-30) REVERT: EA 1306 LYS cc_start: 0.9020 (tttt) cc_final: 0.8764 (mttt) REVERT: FA 104 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7449 (mm-30) REVERT: FA 106 LYS cc_start: 0.8763 (mmmm) cc_final: 0.8354 (mmmm) REVERT: JA 1106 LYS cc_start: 0.8919 (mmmm) cc_final: 0.8597 (mmmm) REVERT: LA 1304 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7134 (mm-30) REVERT: I 6 LYS cc_start: 0.8948 (mtmt) cc_final: 0.8734 (mtmt) REVERT: MA 106 LYS cc_start: 0.8867 (mmmm) cc_final: 0.8648 (mmmt) REVERT: PA 1004 GLU cc_start: 0.7922 (mp0) cc_final: 0.7006 (mp0) REVERT: QA 1102 LYS cc_start: 0.8983 (mtmt) cc_final: 0.8653 (mmmt) REVERT: RA 1202 LYS cc_start: 0.9185 (mtpt) cc_final: 0.8765 (mtpp) REVERT: RA 1204 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7796 (mt-10) REVERT: SA 1304 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8144 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9018 (tttt) cc_final: 0.8787 (tttt) REVERT: a 2 LYS cc_start: 0.9118 (tppt) cc_final: 0.8658 (tppt) REVERT: a 4 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8247 (tp30) REVERT: TA 106 LYS cc_start: 0.9029 (tttp) cc_final: 0.8661 (ptmm) REVERT: UA 202 LYS cc_start: 0.9328 (tttm) cc_final: 0.8869 (ttmm) REVERT: UA 204 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7640 (tm-30) REVERT: VA 302 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8836 (tptp) REVERT: VA 306 LYS cc_start: 0.9071 (tptp) cc_final: 0.8842 (tptp) REVERT: YA 1202 LYS cc_start: 0.9187 (tttm) cc_final: 0.8875 (tttm) REVERT: ZA 1304 GLU cc_start: 0.9117 (tm-30) cc_final: 0.8462 (tm-30) REVERT: aA 106 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8750 (ptmm) REVERT: bA 202 LYS cc_start: 0.9276 (tttm) cc_final: 0.8796 (ttmm) REVERT: dA 1002 LYS cc_start: 0.9119 (ttmt) cc_final: 0.8915 (ttmt) REVERT: iA 202 LYS cc_start: 0.9334 (tttm) cc_final: 0.8996 (tppp) REVERT: lA 1103 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.9127 (t80) REVERT: d 2 LYS cc_start: 0.9088 (tppt) cc_final: 0.8582 (tppt) REVERT: d 6 LYS cc_start: 0.9128 (ttpt) cc_final: 0.8920 (ttpt) REVERT: pA 202 LYS cc_start: 0.9276 (tttm) cc_final: 0.8994 (tttm) REVERT: qA 306 LYS cc_start: 0.8996 (tptp) cc_final: 0.8760 (tptp) REVERT: sA 1103 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8919 (t80) REVERT: vA 104 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8364 (tm-30) REVERT: wA 202 LYS cc_start: 0.9308 (tttm) cc_final: 0.8889 (tppp) REVERT: wA 204 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7771 (tm-30) REVERT: wA 206 LYS cc_start: 0.9136 (tttt) cc_final: 0.8932 (tttt) REVERT: yA 1002 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8935 (tppt) REVERT: 1A 1302 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8685 (tptp) REVERT: f 2 LYS cc_start: 0.9118 (ttmt) cc_final: 0.8768 (ttmt) REVERT: 3A 202 LYS cc_start: 0.9275 (tttm) cc_final: 0.8866 (ttmm) REVERT: 3A 204 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7602 (tm-30) REVERT: 4A 302 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8679 (tptp) REVERT: 4A 306 LYS cc_start: 0.8949 (tptp) cc_final: 0.8714 (tptp) REVERT: 5A 1002 LYS cc_start: 0.9165 (ptpt) cc_final: 0.8936 (ptpt) REVERT: 8A 1304 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8301 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.8733 (tptp) cc_final: 0.8517 (tptp) REVERT: g 2 LYS cc_start: 0.9051 (tppt) cc_final: 0.8572 (tppt) REVERT: AB 202 LYS cc_start: 0.9320 (tttm) cc_final: 0.8937 (ttmm) REVERT: BB 302 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8855 (tptp) REVERT: CB 1004 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8302 (tp30) REVERT: DB 1102 LYS cc_start: 0.9191 (tptm) cc_final: 0.8944 (tptm) REVERT: FB 1302 LYS cc_start: 0.8855 (tptp) cc_final: 0.8642 (tptp) REVERT: FB 1303 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8472 (t80) REVERT: FB 1306 LYS cc_start: 0.8945 (tptp) cc_final: 0.8736 (tptp) REVERT: HB 202 LYS cc_start: 0.9387 (tttm) cc_final: 0.8953 (pttm) REVERT: IB 306 LYS cc_start: 0.8846 (tptp) cc_final: 0.8604 (tptp) REVERT: IB 307 PHE cc_start: 0.9329 (t80) cc_final: 0.9075 (t80) REVERT: KB 1106 LYS cc_start: 0.9107 (tttp) cc_final: 0.8872 (tttm) REVERT: LB 1202 LYS cc_start: 0.9154 (tttm) cc_final: 0.8876 (pptt) REVERT: NB 102 LYS cc_start: 0.9241 (tptm) cc_final: 0.9030 (pttt) REVERT: NB 104 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: OB 202 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8994 (mmmm) REVERT: PB 306 LYS cc_start: 0.8846 (tptp) cc_final: 0.8645 (tptp) outliers start: 137 outliers final: 84 residues processed: 496 average time/residue: 0.4691 time to fit residues: 282.0450 Evaluate side-chains 551 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 450 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain kA residue 1004 GLU Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain rA residue 1004 GLU Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 7A residue 1204 GLU Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.7163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.334 12528 Z= 6.071 Angle : 4.020 38.958 16272 Z= 1.810 Chirality : 0.298 0.937 1152 Planarity : 0.018 0.056 2160 Dihedral : 22.152 116.666 1537 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 110.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 18.58 % Favored : 81.25 % Rotamer: Outliers : 21.88 % Allowed : 22.11 % Favored : 56.02 % Cbeta Deviations : 14.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.69 % 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: -6.18 (0.23), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.70 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.125 0.017 PHE 2 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 428 time to evaluate : 1.185 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: A 6 LYS cc_start: 0.9002 (mtmt) cc_final: 0.8626 (mtmt) REVERT: K 206 LYS cc_start: 0.9014 (ttmm) cc_final: 0.8793 (ttmm) REVERT: M 1004 GLU cc_start: 0.7924 (mp0) cc_final: 0.6998 (mp0) REVERT: M 1006 LYS cc_start: 0.9049 (mtmt) cc_final: 0.8836 (mtmt) REVERT: N 1104 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7949 (mm-30) REVERT: N 1106 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8470 (mmmm) REVERT: P 1304 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8428 (mm-30) REVERT: B 4 GLU cc_start: 0.8399 (mp0) cc_final: 0.7977 (mp0) REVERT: Q 104 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7440 (mm-30) REVERT: Q 106 LYS cc_start: 0.8968 (mmmm) cc_final: 0.8590 (mmmm) REVERT: S 307 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.9066 (m-80) REVERT: T 1006 LYS cc_start: 0.9047 (mtmt) cc_final: 0.8782 (mtmt) REVERT: U 1104 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7477 (mm-30) REVERT: U 1106 LYS cc_start: 0.8799 (tptm) cc_final: 0.8468 (tptm) REVERT: X 104 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7837 (mm-30) REVERT: X 106 LYS cc_start: 0.8891 (mmmm) cc_final: 0.8530 (mmmm) REVERT: j 1004 GLU cc_start: 0.8134 (mp0) cc_final: 0.7437 (mp0) REVERT: j 1006 LYS cc_start: 0.9017 (mtmt) cc_final: 0.8676 (mtmt) REVERT: k 1106 LYS cc_start: 0.8867 (mmmm) cc_final: 0.8545 (mmmm) REVERT: l 1202 LYS cc_start: 0.9195 (mtpt) cc_final: 0.8876 (mtpp) REVERT: l 1204 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8086 (mm-30) REVERT: l 1206 LYS cc_start: 0.9007 (ttmm) cc_final: 0.8716 (ttmm) REVERT: m 1306 LYS cc_start: 0.9164 (tttt) cc_final: 0.8925 (mttt) REVERT: D 4 GLU cc_start: 0.8018 (mp0) cc_final: 0.7069 (mp0) REVERT: n 106 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8379 (mmmm) REVERT: o 202 LYS cc_start: 0.9195 (ttpt) cc_final: 0.8929 (ttpt) REVERT: o 204 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7854 (mt-10) REVERT: q 1004 GLU cc_start: 0.8343 (mp0) cc_final: 0.8060 (mp0) REVERT: r 1106 LYS cc_start: 0.8910 (mmmm) cc_final: 0.8651 (mmmm) REVERT: s 1204 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7812 (mt-10) REVERT: E 6 LYS cc_start: 0.8961 (mtmt) cc_final: 0.8649 (mtmt) REVERT: u 106 LYS cc_start: 0.8802 (mmmm) cc_final: 0.8345 (mmmm) REVERT: v 206 LYS cc_start: 0.9232 (ttmm) cc_final: 0.9006 (ttmm) REVERT: w 307 PHE cc_start: 0.9499 (OUTLIER) cc_final: 0.9022 (m-80) REVERT: x 1003 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8208 (m-80) REVERT: y 1102 LYS cc_start: 0.9068 (ttpt) cc_final: 0.8650 (ttpt) REVERT: y 1104 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7840 (mm-30) REVERT: y 1106 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8685 (mmmm) REVERT: 1 104 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7265 (mm-30) REVERT: 1 106 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8434 (mmmm) REVERT: 3 304 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8073 (mm-30) REVERT: 4 1006 LYS cc_start: 0.9042 (ttmt) cc_final: 0.8822 (ttmt) REVERT: 6 1202 LYS cc_start: 0.9258 (mtpt) cc_final: 0.8786 (mtpp) REVERT: 7 1304 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7801 (mm-30) REVERT: G 4 GLU cc_start: 0.8155 (mp0) cc_final: 0.7397 (mp0) REVERT: G 6 LYS cc_start: 0.9077 (mtmt) cc_final: 0.8870 (mtmt) REVERT: 8 106 LYS cc_start: 0.8839 (mmmm) cc_final: 0.8267 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8077 (mp0) cc_final: 0.7278 (mp0) REVERT: CA 1104 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7271 (mm-30) REVERT: CA 1106 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8663 (mmmm) REVERT: DA 1206 LYS cc_start: 0.9049 (ttmm) cc_final: 0.8775 (ttmm) REVERT: EA 1306 LYS cc_start: 0.9074 (mttt) cc_final: 0.8655 (mttt) REVERT: FA 104 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7373 (mm-30) REVERT: FA 106 LYS cc_start: 0.8825 (mmmm) cc_final: 0.8398 (mmmm) REVERT: GA 204 GLU cc_start: 0.6083 (OUTLIER) cc_final: 0.5444 (pm20) REVERT: HA 302 LYS cc_start: 0.9114 (mtpt) cc_final: 0.8666 (mmmm) REVERT: JA 1106 LYS cc_start: 0.8974 (mmmm) cc_final: 0.8617 (mmmm) REVERT: KA 1207 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8717 (t80) REVERT: I 4 GLU cc_start: 0.7805 (mp0) cc_final: 0.7151 (mp0) REVERT: NA 202 LYS cc_start: 0.9166 (mtpt) cc_final: 0.8718 (mptt) REVERT: PA 1004 GLU cc_start: 0.7801 (mp0) cc_final: 0.6904 (mp0) REVERT: QA 1106 LYS cc_start: 0.4827 (tptt) cc_final: 0.4216 (tptp) REVERT: RA 1202 LYS cc_start: 0.9134 (mtpt) cc_final: 0.8812 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8234 (mm-30) REVERT: a 2 LYS cc_start: 0.9135 (tppt) cc_final: 0.8769 (tppt) REVERT: a 4 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8153 (tp30) REVERT: TA 106 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8689 (ptmm) REVERT: UA 202 LYS cc_start: 0.9376 (tttm) cc_final: 0.8911 (ttmm) REVERT: WA 1002 LYS cc_start: 0.9207 (tppt) cc_final: 0.8852 (tppt) REVERT: YA 1202 LYS cc_start: 0.9261 (tttm) cc_final: 0.8989 (tttm) REVERT: YA 1204 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7800 (tm-30) REVERT: ZA 1302 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8898 (tptp) REVERT: ZA 1304 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8704 (tm-30) REVERT: aA 104 GLU cc_start: 0.8747 (tm-30) cc_final: 0.7871 (tm-30) REVERT: bA 202 LYS cc_start: 0.9266 (tttm) cc_final: 0.8874 (ttmm) REVERT: bA 204 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7648 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9124 (ttmt) cc_final: 0.8904 (ttmt) REVERT: iA 202 LYS cc_start: 0.9371 (tttm) cc_final: 0.8986 (tppp) REVERT: lA 1103 PHE cc_start: 0.9429 (OUTLIER) cc_final: 0.9224 (t80) REVERT: d 6 LYS cc_start: 0.9162 (ttpt) cc_final: 0.8950 (ttpt) REVERT: oA 102 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8951 (tptm) REVERT: pA 204 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7767 (tm-30) REVERT: qA 306 LYS cc_start: 0.8990 (tptp) cc_final: 0.8716 (tptp) REVERT: rA 1006 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8869 (ttpt) REVERT: tA 1204 GLU cc_start: 0.8387 (tm-30) cc_final: 0.8035 (tm-30) REVERT: e 6 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8731 (ttpt) REVERT: vA 104 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8303 (tm-30) REVERT: wA 202 LYS cc_start: 0.9311 (tttm) cc_final: 0.8863 (tppp) REVERT: yA 1002 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8798 (tppt) REVERT: yA 1004 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8247 (tp30) REVERT: 1A 1302 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8797 (tptp) REVERT: f 2 LYS cc_start: 0.9121 (ttmt) cc_final: 0.8769 (ttmt) REVERT: 3A 202 LYS cc_start: 0.9256 (tttm) cc_final: 0.8899 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7669 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8688 (tptp) REVERT: 5A 1002 LYS cc_start: 0.9131 (ptpt) cc_final: 0.8920 (ptpt) REVERT: 8A 1302 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8772 (tptp) REVERT: g 2 LYS cc_start: 0.9028 (tppt) cc_final: 0.8532 (tppt) REVERT: 9A 105 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.9082 (t80) REVERT: AB 202 LYS cc_start: 0.9331 (tttm) cc_final: 0.9012 (ttmm) REVERT: AB 204 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7861 (tm-30) REVERT: BB 302 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8913 (tptp) REVERT: CB 1004 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8403 (tp30) REVERT: EB 1204 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7435 (tm-30) REVERT: FB 1302 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8657 (tptp) REVERT: FB 1306 LYS cc_start: 0.8935 (tptp) cc_final: 0.8732 (tptp) REVERT: h 2 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8958 (ttpt) REVERT: HB 202 LYS cc_start: 0.9388 (tttm) cc_final: 0.8982 (pttt) REVERT: IB 306 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8696 (tptp) REVERT: NB 104 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.7972 (pm20) REVERT: OB 202 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.9013 (mmmm) REVERT: PB 307 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.8946 (t80) outliers start: 189 outliers final: 128 residues processed: 503 average time/residue: 0.4681 time to fit residues: 285.6750 Evaluate side-chains 583 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 427 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 304 GLU Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 6 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain hA residue 106 LYS Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain kA residue 1004 GLU Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1004 GLU Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 7A residue 1204 GLU Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.7489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.395 12528 Z= 6.076 Angle : 4.066 34.182 16272 Z= 1.834 Chirality : 0.298 0.923 1152 Planarity : 0.018 0.058 2160 Dihedral : 22.331 115.470 1525 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 111.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 20.49 % Favored : 79.34 % Rotamer: Outliers : 25.00 % Allowed : 22.45 % Favored : 52.55 % Cbeta Deviations : 14.93 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.69 % 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: -6.36 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.84 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.131 0.017 PHE 2 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 422 time to evaluate : 1.334 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: A 6 LYS cc_start: 0.9013 (mtmt) cc_final: 0.8752 (mtmt) REVERT: K 206 LYS cc_start: 0.9034 (ttmm) cc_final: 0.8815 (ttmm) REVERT: M 1004 GLU cc_start: 0.7991 (mp0) cc_final: 0.7071 (mp0) REVERT: N 1104 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8062 (mm-30) REVERT: N 1106 LYS cc_start: 0.8872 (mmmm) cc_final: 0.8366 (mmmm) REVERT: B 4 GLU cc_start: 0.8369 (mp0) cc_final: 0.7767 (mp0) REVERT: B 5 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8999 (m-80) REVERT: Q 104 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7422 (mm-30) REVERT: Q 106 LYS cc_start: 0.8992 (mmmm) cc_final: 0.8602 (mmmm) REVERT: S 307 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8971 (m-80) REVERT: T 1006 LYS cc_start: 0.9060 (mtmt) cc_final: 0.8787 (mtmt) REVERT: U 1104 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7587 (mm-30) REVERT: U 1106 LYS cc_start: 0.8819 (tptm) cc_final: 0.8441 (tptm) REVERT: W 1302 LYS cc_start: 0.9238 (mtpt) cc_final: 0.8793 (mtpp) REVERT: C 4 GLU cc_start: 0.8034 (mp0) cc_final: 0.7424 (mp0) REVERT: X 106 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8527 (mmmm) REVERT: j 1004 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: j 1006 LYS cc_start: 0.9004 (mtmt) cc_final: 0.8564 (mtmt) REVERT: k 1106 LYS cc_start: 0.8908 (mmmm) cc_final: 0.8593 (mmmm) REVERT: l 1202 LYS cc_start: 0.9179 (mtpt) cc_final: 0.8806 (mtpp) REVERT: l 1204 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8047 (mm-30) REVERT: l 1206 LYS cc_start: 0.9022 (ttmm) cc_final: 0.8795 (ttmm) REVERT: m 1306 LYS cc_start: 0.9157 (tttt) cc_final: 0.8953 (mttt) REVERT: D 4 GLU cc_start: 0.7982 (mp0) cc_final: 0.7082 (mp0) REVERT: D 6 LYS cc_start: 0.8986 (mtmt) cc_final: 0.8402 (mtmt) REVERT: n 104 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7875 (mm-30) REVERT: n 106 LYS cc_start: 0.8946 (mmmm) cc_final: 0.8403 (mmmm) REVERT: o 202 LYS cc_start: 0.9214 (ttpt) cc_final: 0.8949 (ttpt) REVERT: q 1004 GLU cc_start: 0.8350 (mp0) cc_final: 0.8083 (mp0) REVERT: r 1104 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7744 (mm-30) REVERT: r 1106 LYS cc_start: 0.8873 (mmmm) cc_final: 0.8555 (mmmm) REVERT: s 1204 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7807 (mt-10) REVERT: E 6 LYS cc_start: 0.9015 (mtmt) cc_final: 0.8669 (mtmt) REVERT: u 106 LYS cc_start: 0.8718 (mmmm) cc_final: 0.8256 (mmmm) REVERT: v 206 LYS cc_start: 0.9259 (ttmm) cc_final: 0.9018 (ttmm) REVERT: x 1003 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8457 (m-80) REVERT: x 1006 LYS cc_start: 0.8892 (mtmt) cc_final: 0.8287 (mtmt) REVERT: y 1102 LYS cc_start: 0.9051 (ttpt) cc_final: 0.8626 (ttpt) REVERT: y 1104 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7938 (mm-30) REVERT: y 1106 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8717 (mmmm) REVERT: 1 104 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7253 (mm-30) REVERT: 1 106 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8357 (mmmm) REVERT: 3 304 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8143 (mm-30) REVERT: 4 1004 GLU cc_start: 0.8056 (mp0) cc_final: 0.7322 (mp0) REVERT: 4 1006 LYS cc_start: 0.9013 (ttmt) cc_final: 0.8794 (ttmt) REVERT: 5 1104 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8028 (mm-30) REVERT: 5 1106 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8503 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9248 (mtpt) cc_final: 0.8777 (mtpp) REVERT: 7 1304 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7773 (mm-30) REVERT: G 3 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8271 (m-80) REVERT: G 4 GLU cc_start: 0.8202 (mp0) cc_final: 0.7495 (mp0) REVERT: G 6 LYS cc_start: 0.9077 (mtmt) cc_final: 0.8838 (mtmt) REVERT: 8 106 LYS cc_start: 0.8778 (mmmm) cc_final: 0.8296 (mmmm) REVERT: AA 306 LYS cc_start: 0.9060 (mttt) cc_final: 0.8725 (mttm) REVERT: BA 1004 GLU cc_start: 0.8108 (mp0) cc_final: 0.7313 (mp0) REVERT: CA 1104 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7371 (mm-30) REVERT: CA 1106 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8560 (mmmm) REVERT: DA 1206 LYS cc_start: 0.9176 (ttmm) cc_final: 0.8950 (ttmm) REVERT: EA 1306 LYS cc_start: 0.9089 (mttt) cc_final: 0.8669 (mttt) REVERT: H 4 GLU cc_start: 0.2874 (OUTLIER) cc_final: 0.1982 (pm20) REVERT: FA 106 LYS cc_start: 0.8860 (mmmm) cc_final: 0.8502 (mmmm) REVERT: HA 302 LYS cc_start: 0.9093 (mtpt) cc_final: 0.8693 (mmmm) REVERT: JA 1104 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7627 (mm-30) REVERT: JA 1106 LYS cc_start: 0.8941 (mmmm) cc_final: 0.8601 (mmmm) REVERT: I 4 GLU cc_start: 0.7775 (mp0) cc_final: 0.7149 (mp0) REVERT: MA 106 LYS cc_start: 0.3071 (OUTLIER) cc_final: 0.2854 (tptp) REVERT: PA 1004 GLU cc_start: 0.7760 (mp0) cc_final: 0.6995 (mp0) REVERT: QA 1106 LYS cc_start: 0.3251 (OUTLIER) cc_final: 0.1469 (mmmt) REVERT: RA 1202 LYS cc_start: 0.9156 (mtpt) cc_final: 0.8834 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8265 (mm-30) REVERT: SA 1307 PHE cc_start: 0.9371 (OUTLIER) cc_final: 0.8608 (m-80) REVERT: a 2 LYS cc_start: 0.9143 (tppt) cc_final: 0.8845 (tppt) REVERT: a 4 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8208 (tp30) REVERT: TA 106 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8678 (ptmm) REVERT: UA 204 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7809 (tm-30) REVERT: VA 302 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8917 (tptp) REVERT: WA 1002 LYS cc_start: 0.9207 (tppt) cc_final: 0.8844 (tppt) REVERT: YA 1204 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7923 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8690 (t80) REVERT: ZA 1304 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8728 (tm-30) REVERT: aA 104 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8059 (tm-30) REVERT: aA 106 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8662 (ptmm) REVERT: bA 202 LYS cc_start: 0.9262 (tttm) cc_final: 0.8887 (ttmm) REVERT: dA 1002 LYS cc_start: 0.9137 (ttmt) cc_final: 0.8917 (ttmt) REVERT: eA 1104 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8015 (tm-30) REVERT: iA 202 LYS cc_start: 0.9393 (tttm) cc_final: 0.8999 (tppp) REVERT: lA 1103 PHE cc_start: 0.9450 (OUTLIER) cc_final: 0.9248 (t80) REVERT: nA 1306 LYS cc_start: 0.9046 (tptp) cc_final: 0.8813 (tptp) REVERT: d 2 LYS cc_start: 0.9115 (tppt) cc_final: 0.8867 (tppt) REVERT: oA 102 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8943 (tptm) REVERT: pA 204 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7630 (tm-30) REVERT: qA 306 LYS cc_start: 0.8919 (tptp) cc_final: 0.8662 (tptp) REVERT: rA 1006 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8871 (ttpt) REVERT: sA 1103 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8907 (t80) REVERT: tA 1206 LYS cc_start: 0.9092 (tttt) cc_final: 0.8879 (tmtt) REVERT: uA 1307 PHE cc_start: 0.9432 (OUTLIER) cc_final: 0.9048 (t80) REVERT: e 6 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8616 (ttpt) REVERT: wA 202 LYS cc_start: 0.9284 (tttm) cc_final: 0.8895 (ttmm) REVERT: wA 204 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7880 (tm-30) REVERT: zA 1104 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8234 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9315 (OUTLIER) cc_final: 0.9066 (t80) REVERT: f 2 LYS cc_start: 0.9133 (ttmt) cc_final: 0.8771 (ttmt) REVERT: f 4 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8334 (tp30) REVERT: 3A 202 LYS cc_start: 0.9262 (tttm) cc_final: 0.8921 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7649 (tm-30) REVERT: 4A 302 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8664 (tptp) REVERT: 5A 1002 LYS cc_start: 0.9138 (ptpt) cc_final: 0.8906 (ptpt) REVERT: 8A 1302 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8705 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8530 (tm-30) REVERT: g 2 LYS cc_start: 0.9044 (tppt) cc_final: 0.8514 (tppt) REVERT: 9A 105 PHE cc_start: 0.9426 (OUTLIER) cc_final: 0.9070 (t80) REVERT: AB 202 LYS cc_start: 0.9354 (tttm) cc_final: 0.9038 (ttmm) REVERT: AB 204 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7837 (tm-30) REVERT: BB 302 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8922 (tptp) REVERT: CB 1004 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8248 (tp30) REVERT: DB 1102 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8986 (tptm) REVERT: FB 1302 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8492 (tptp) REVERT: FB 1305 PHE cc_start: 0.9079 (t80) cc_final: 0.8848 (t80) REVERT: FB 1306 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8713 (tptp) REVERT: h 2 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8952 (ttpt) REVERT: GB 103 PHE cc_start: 0.9462 (OUTLIER) cc_final: 0.9118 (t80) REVERT: HB 202 LYS cc_start: 0.9395 (tttm) cc_final: 0.8981 (pttt) REVERT: IB 306 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8690 (tptp) REVERT: NB 102 LYS cc_start: 0.4145 (OUTLIER) cc_final: 0.3939 (pttm) REVERT: NB 103 PHE cc_start: 0.9155 (t80) cc_final: 0.8848 (t80) REVERT: NB 104 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.7973 (pm20) REVERT: NB 106 LYS cc_start: 0.9134 (tttp) cc_final: 0.8533 (pptt) REVERT: OB 202 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.9003 (mmmm) REVERT: PB 306 LYS cc_start: 0.8772 (tptp) cc_final: 0.8556 (tptp) outliers start: 216 outliers final: 146 residues processed: 510 average time/residue: 0.4450 time to fit residues: 276.4566 Evaluate side-chains 606 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 420 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain AA residue 304 GLU Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain QA residue 1104 GLU Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 6 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain hA residue 106 LYS Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain kA residue 1004 GLU Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1004 GLU Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 7A residue 1204 GLU Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1306 LYS Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.7607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.355 12528 Z= 6.078 Angle : 4.073 31.154 16272 Z= 1.839 Chirality : 0.298 0.919 1152 Planarity : 0.018 0.057 2160 Dihedral : 22.122 114.971 1518 Min Nonbonded Distance : 1.562 Molprobity Statistics. All-atom Clashscore : 111.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 21.18 % Favored : 78.65 % Rotamer: Outliers : 25.81 % Allowed : 24.88 % Favored : 49.31 % Cbeta Deviations : 14.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.98 % 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: -6.37 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.85 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.130 0.017 PHE 2 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 422 time to evaluate : 1.374 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: K 206 LYS cc_start: 0.9010 (ttmm) cc_final: 0.8810 (ttmm) REVERT: M 1004 GLU cc_start: 0.7892 (mp0) cc_final: 0.6942 (mp0) REVERT: N 1104 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8113 (mm-30) REVERT: N 1106 LYS cc_start: 0.8861 (mmmm) cc_final: 0.8391 (mmmm) REVERT: B 4 GLU cc_start: 0.8383 (mp0) cc_final: 0.7806 (mp0) REVERT: Q 104 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7445 (mm-30) REVERT: Q 106 LYS cc_start: 0.8998 (mmmm) cc_final: 0.8669 (mmmm) REVERT: S 307 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.8979 (m-80) REVERT: T 1006 LYS cc_start: 0.9033 (mtmt) cc_final: 0.8733 (mtmt) REVERT: U 1104 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7538 (mm-30) REVERT: U 1106 LYS cc_start: 0.8784 (tptm) cc_final: 0.8372 (tptm) REVERT: W 1302 LYS cc_start: 0.9265 (mtpt) cc_final: 0.8783 (mtpp) REVERT: C 4 GLU cc_start: 0.8022 (mp0) cc_final: 0.7411 (mp0) REVERT: X 106 LYS cc_start: 0.8971 (mmmm) cc_final: 0.8541 (mmmm) REVERT: j 1004 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: j 1006 LYS cc_start: 0.9028 (mtmt) cc_final: 0.8637 (mtmt) REVERT: k 1106 LYS cc_start: 0.8943 (mmmm) cc_final: 0.8614 (mmmm) REVERT: l 1202 LYS cc_start: 0.9163 (mtpt) cc_final: 0.8802 (mtpp) REVERT: l 1206 LYS cc_start: 0.9022 (ttmm) cc_final: 0.8805 (ttmm) REVERT: m 1306 LYS cc_start: 0.9149 (tttt) cc_final: 0.8946 (mttt) REVERT: D 4 GLU cc_start: 0.8025 (mp0) cc_final: 0.7007 (mp0) REVERT: D 6 LYS cc_start: 0.8997 (mtmt) cc_final: 0.8469 (mtmt) REVERT: D 7 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.8677 (t80) REVERT: n 104 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7930 (mm-30) REVERT: n 106 LYS cc_start: 0.8892 (mmmm) cc_final: 0.8347 (mmmm) REVERT: o 202 LYS cc_start: 0.9232 (ttpt) cc_final: 0.9016 (ttpt) REVERT: q 1004 GLU cc_start: 0.8313 (mp0) cc_final: 0.8079 (mp0) REVERT: r 1106 LYS cc_start: 0.8868 (mmmm) cc_final: 0.8492 (mmmm) REVERT: E 6 LYS cc_start: 0.9008 (mtmt) cc_final: 0.8663 (mtmt) REVERT: u 106 LYS cc_start: 0.8733 (mmmm) cc_final: 0.8262 (mmmm) REVERT: v 206 LYS cc_start: 0.9275 (ttmm) cc_final: 0.9005 (ttmm) REVERT: w 307 PHE cc_start: 0.9457 (OUTLIER) cc_final: 0.8696 (m-80) REVERT: x 1003 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8401 (m-80) REVERT: x 1006 LYS cc_start: 0.8886 (mtmt) cc_final: 0.8414 (mtmt) REVERT: y 1106 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8765 (mmmm) REVERT: F 6 LYS cc_start: 0.9005 (mtmt) cc_final: 0.8761 (mtmt) REVERT: 1 104 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7267 (mm-30) REVERT: 1 106 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8380 (mmmm) REVERT: 4 1004 GLU cc_start: 0.7977 (mp0) cc_final: 0.7623 (mp0) REVERT: 5 1106 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8437 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9220 (mtpt) cc_final: 0.8771 (mtpp) REVERT: G 3 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8320 (m-80) REVERT: G 4 GLU cc_start: 0.8174 (mp0) cc_final: 0.7440 (mp0) REVERT: G 6 LYS cc_start: 0.9079 (mtmt) cc_final: 0.8868 (mtmt) REVERT: 8 106 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8299 (mmmm) REVERT: AA 306 LYS cc_start: 0.9059 (mttt) cc_final: 0.8681 (mttm) REVERT: BA 1004 GLU cc_start: 0.8039 (mp0) cc_final: 0.7662 (mp0) REVERT: CA 1104 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7241 (mm-30) REVERT: CA 1106 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8497 (mmmm) REVERT: DA 1206 LYS cc_start: 0.9254 (ttmm) cc_final: 0.9026 (ttmm) REVERT: EA 1306 LYS cc_start: 0.9091 (mttt) cc_final: 0.8704 (mttt) REVERT: H 4 GLU cc_start: 0.2923 (OUTLIER) cc_final: 0.2038 (pm20) REVERT: FA 106 LYS cc_start: 0.8862 (mmmm) cc_final: 0.8515 (mmmm) REVERT: HA 302 LYS cc_start: 0.9107 (mtpt) cc_final: 0.8717 (mmmm) REVERT: JA 1104 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7914 (mm-30) REVERT: JA 1106 LYS cc_start: 0.8962 (mmmm) cc_final: 0.8618 (mmmm) REVERT: I 4 GLU cc_start: 0.7816 (mp0) cc_final: 0.7239 (mp0) REVERT: I 6 LYS cc_start: 0.8968 (mtmt) cc_final: 0.8587 (ttmt) REVERT: PA 1004 GLU cc_start: 0.7743 (mp0) cc_final: 0.6993 (mp0) REVERT: PA 1006 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8289 (ttmt) REVERT: RA 1202 LYS cc_start: 0.9141 (mtpt) cc_final: 0.8811 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8250 (mm-30) REVERT: SA 1307 PHE cc_start: 0.9373 (OUTLIER) cc_final: 0.8563 (m-80) REVERT: a 2 LYS cc_start: 0.9154 (tppt) cc_final: 0.8871 (tppt) REVERT: a 4 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8222 (tp30) REVERT: TA 106 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8689 (ptmm) REVERT: WA 1002 LYS cc_start: 0.9218 (tppt) cc_final: 0.8839 (tppt) REVERT: YA 1204 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7986 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8794 (t80) REVERT: ZA 1304 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8661 (tm-30) REVERT: aA 104 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8279 (tm-30) REVERT: bA 202 LYS cc_start: 0.9243 (tttm) cc_final: 0.8826 (ttmm) REVERT: dA 1002 LYS cc_start: 0.9135 (ttmt) cc_final: 0.8914 (ttmt) REVERT: eA 1104 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8071 (tm-30) REVERT: c 4 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7984 (tp30) REVERT: lA 1103 PHE cc_start: 0.9446 (OUTLIER) cc_final: 0.9245 (t80) REVERT: nA 1306 LYS cc_start: 0.9041 (tptp) cc_final: 0.8825 (tptp) REVERT: d 2 LYS cc_start: 0.9111 (tppt) cc_final: 0.8899 (tppt) REVERT: oA 102 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8949 (tptm) REVERT: pA 204 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7742 (tm-30) REVERT: qA 306 LYS cc_start: 0.8939 (tptp) cc_final: 0.8668 (tptp) REVERT: rA 1006 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8877 (ttpt) REVERT: tA 1204 GLU cc_start: 0.8509 (tm-30) cc_final: 0.7608 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9106 (tttt) cc_final: 0.8899 (tmtt) REVERT: e 6 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8722 (ttpt) REVERT: wA 202 LYS cc_start: 0.9287 (tttm) cc_final: 0.8884 (ttmm) REVERT: zA 1104 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8278 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9322 (OUTLIER) cc_final: 0.9059 (t80) REVERT: f 2 LYS cc_start: 0.9132 (ttmt) cc_final: 0.8769 (ttmt) REVERT: f 4 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8364 (tp30) REVERT: 3A 202 LYS cc_start: 0.9244 (tttm) cc_final: 0.8923 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7632 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8667 (tptp) REVERT: 4A 307 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.9087 (t80) REVERT: 5A 1002 LYS cc_start: 0.9126 (ptpt) cc_final: 0.8886 (ptpt) REVERT: 8A 1302 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8672 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8253 (tm-30) REVERT: g 2 LYS cc_start: 0.9044 (tppt) cc_final: 0.8516 (tppt) REVERT: AB 202 LYS cc_start: 0.9362 (tttm) cc_final: 0.8958 (ttmm) REVERT: AB 204 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7859 (tm-30) REVERT: BB 302 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8921 (tptp) REVERT: CB 1004 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8246 (tp30) REVERT: DB 1102 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8992 (tptm) REVERT: EB 1204 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7561 (tm-30) REVERT: FB 1302 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8650 (tptp) REVERT: h 2 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8964 (ttpt) REVERT: GB 103 PHE cc_start: 0.9448 (OUTLIER) cc_final: 0.8997 (t80) REVERT: HB 202 LYS cc_start: 0.9374 (tttm) cc_final: 0.8981 (pttt) REVERT: IB 306 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8732 (tptp) REVERT: KB 1105 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.9016 (t80) REVERT: NB 103 PHE cc_start: 0.9178 (t80) cc_final: 0.8902 (t80) REVERT: NB 104 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.7978 (pm20) REVERT: NB 106 LYS cc_start: 0.9154 (tttp) cc_final: 0.8608 (pptt) REVERT: OB 202 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.9015 (mmmm) outliers start: 223 outliers final: 168 residues processed: 520 average time/residue: 0.4664 time to fit residues: 299.3403 Evaluate side-chains 625 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 421 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 304 GLU Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1202 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain dA residue 1006 LYS Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 6 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain hA residue 106 LYS Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain kA residue 1004 GLU Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1004 GLU Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 7A residue 1204 GLU Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.7659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.351 12528 Z= 6.076 Angle : 4.076 30.142 16272 Z= 1.841 Chirality : 0.299 0.921 1152 Planarity : 0.018 0.057 2160 Dihedral : 22.080 115.172 1518 Min Nonbonded Distance : 1.585 Molprobity Statistics. All-atom Clashscore : 112.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 21.88 % Favored : 77.95 % Rotamer: Outliers : 26.62 % Allowed : 25.69 % Favored : 47.69 % Cbeta Deviations : 14.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.79 % 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: -6.38 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.86 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.130 0.017 PHE 2 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 420 time to evaluate : 1.812 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: J 106 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8535 (tmmm) REVERT: M 1004 GLU cc_start: 0.8103 (mp0) cc_final: 0.7129 (mp0) REVERT: N 1104 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8117 (mm-30) REVERT: N 1106 LYS cc_start: 0.8859 (mmmm) cc_final: 0.8344 (mmmm) REVERT: O 1206 LYS cc_start: 0.8893 (ttmm) cc_final: 0.8654 (ttmm) REVERT: P 1304 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8246 (mm-30) REVERT: B 4 GLU cc_start: 0.8368 (mp0) cc_final: 0.7734 (mp0) REVERT: B 5 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.9022 (m-80) REVERT: Q 104 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7455 (mm-30) REVERT: Q 106 LYS cc_start: 0.8996 (mmmm) cc_final: 0.8725 (mmmm) REVERT: T 1006 LYS cc_start: 0.9027 (mtmt) cc_final: 0.8651 (mtmt) REVERT: U 1104 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7635 (mm-30) REVERT: U 1106 LYS cc_start: 0.8790 (tptm) cc_final: 0.8380 (tptm) REVERT: W 1302 LYS cc_start: 0.9262 (mtpt) cc_final: 0.8779 (mtpp) REVERT: C 4 GLU cc_start: 0.8047 (mp0) cc_final: 0.7459 (mp0) REVERT: X 106 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8547 (mmmm) REVERT: j 1004 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: j 1006 LYS cc_start: 0.9029 (mtmt) cc_final: 0.8652 (mtmt) REVERT: k 1106 LYS cc_start: 0.8955 (mmmm) cc_final: 0.8580 (mmmm) REVERT: l 1202 LYS cc_start: 0.9151 (mtpt) cc_final: 0.8807 (mtpp) REVERT: l 1204 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8053 (mm-30) REVERT: D 4 GLU cc_start: 0.8030 (mp0) cc_final: 0.7100 (mp0) REVERT: D 6 LYS cc_start: 0.8962 (mtmt) cc_final: 0.8409 (mtmt) REVERT: D 7 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.8724 (t80) REVERT: n 104 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7942 (mm-30) REVERT: n 106 LYS cc_start: 0.8896 (mmmm) cc_final: 0.8344 (mmmm) REVERT: o 202 LYS cc_start: 0.9240 (ttpt) cc_final: 0.9026 (ttpt) REVERT: q 1004 GLU cc_start: 0.8296 (mp0) cc_final: 0.8062 (mp0) REVERT: r 1106 LYS cc_start: 0.8884 (mmmm) cc_final: 0.8459 (mmmm) REVERT: E 6 LYS cc_start: 0.9004 (mtmt) cc_final: 0.8658 (mtmt) REVERT: u 106 LYS cc_start: 0.8735 (mmmm) cc_final: 0.8254 (mmmm) REVERT: v 206 LYS cc_start: 0.9281 (ttmm) cc_final: 0.8992 (ttmm) REVERT: w 307 PHE cc_start: 0.9475 (OUTLIER) cc_final: 0.8752 (m-80) REVERT: x 1006 LYS cc_start: 0.8886 (mtmt) cc_final: 0.8278 (mtmt) REVERT: y 1106 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8775 (mmmm) REVERT: F 6 LYS cc_start: 0.9009 (mtmt) cc_final: 0.8775 (mtmt) REVERT: 1 104 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7346 (mm-30) REVERT: 1 106 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8395 (mmmm) REVERT: 4 1004 GLU cc_start: 0.8078 (mp0) cc_final: 0.7724 (mp0) REVERT: 5 1106 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8490 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9210 (mtpt) cc_final: 0.8749 (mtpp) REVERT: G 3 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: G 4 GLU cc_start: 0.8199 (mp0) cc_final: 0.7495 (mp0) REVERT: 8 106 LYS cc_start: 0.8746 (mmmm) cc_final: 0.8279 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8044 (mp0) cc_final: 0.7674 (mp0) REVERT: CA 1104 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7201 (mm-30) REVERT: CA 1106 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8661 (mmmm) REVERT: DA 1206 LYS cc_start: 0.9289 (ttmm) cc_final: 0.9043 (ttmm) REVERT: EA 1306 LYS cc_start: 0.9094 (mttt) cc_final: 0.8724 (mttt) REVERT: H 4 GLU cc_start: 0.2904 (OUTLIER) cc_final: 0.2016 (pm20) REVERT: FA 106 LYS cc_start: 0.8856 (mmmm) cc_final: 0.8511 (mmmm) REVERT: HA 302 LYS cc_start: 0.9106 (mtpt) cc_final: 0.8716 (mmmm) REVERT: JA 1106 LYS cc_start: 0.8948 (mmmm) cc_final: 0.8606 (mmmm) REVERT: LA 1306 LYS cc_start: 0.8990 (pttp) cc_final: 0.8727 (pttp) REVERT: I 4 GLU cc_start: 0.7811 (mp0) cc_final: 0.7262 (mp0) REVERT: I 6 LYS cc_start: 0.8983 (mtmt) cc_final: 0.8624 (ttmt) REVERT: MA 106 LYS cc_start: 0.2981 (OUTLIER) cc_final: 0.2488 (tptt) REVERT: PA 1004 GLU cc_start: 0.7754 (mp0) cc_final: 0.6982 (mp0) REVERT: PA 1006 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8682 (ttmt) REVERT: RA 1202 LYS cc_start: 0.9148 (mtpt) cc_final: 0.8821 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8170 (mm-30) REVERT: SA 1307 PHE cc_start: 0.9373 (OUTLIER) cc_final: 0.8541 (m-80) REVERT: a 2 LYS cc_start: 0.9144 (tppt) cc_final: 0.8859 (tppt) REVERT: a 4 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8240 (tp30) REVERT: TA 106 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8722 (ptmm) REVERT: UA 202 LYS cc_start: 0.9380 (tttm) cc_final: 0.8947 (ttmm) REVERT: VA 302 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8931 (tptp) REVERT: WA 1002 LYS cc_start: 0.9231 (tppt) cc_final: 0.8850 (tppt) REVERT: YA 1204 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7996 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8914 (t80) REVERT: ZA 1304 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8629 (tm-30) REVERT: aA 104 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8338 (tm-30) REVERT: bA 202 LYS cc_start: 0.9243 (tttm) cc_final: 0.8835 (ttmm) REVERT: dA 1002 LYS cc_start: 0.9137 (ttmt) cc_final: 0.8909 (ttmt) REVERT: eA 1104 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8058 (tm-30) REVERT: nA 1306 LYS cc_start: 0.9008 (tptp) cc_final: 0.8777 (tptp) REVERT: oA 102 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8948 (tptm) REVERT: pA 204 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7795 (tm-30) REVERT: qA 306 LYS cc_start: 0.8926 (tptp) cc_final: 0.8668 (tptp) REVERT: rA 1006 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8875 (ttpt) REVERT: tA 1204 GLU cc_start: 0.8494 (tm-30) cc_final: 0.7718 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9123 (tttt) cc_final: 0.8906 (tmtt) REVERT: wA 202 LYS cc_start: 0.9288 (tttm) cc_final: 0.8887 (ttmm) REVERT: wA 204 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7678 (tm-30) REVERT: zA 1104 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8288 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.9053 (t80) REVERT: f 2 LYS cc_start: 0.9133 (ttmt) cc_final: 0.8772 (ttmt) REVERT: f 4 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8382 (tp30) REVERT: 3A 202 LYS cc_start: 0.9257 (tttm) cc_final: 0.8946 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7622 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8673 (tptp) REVERT: 5A 1002 LYS cc_start: 0.9126 (ptpt) cc_final: 0.8884 (ptpt) REVERT: 8A 1302 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8680 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8275 (tm-30) REVERT: g 2 LYS cc_start: 0.9023 (tppt) cc_final: 0.8512 (tppt) REVERT: 9A 105 PHE cc_start: 0.9411 (OUTLIER) cc_final: 0.9077 (t80) REVERT: AB 202 LYS cc_start: 0.9358 (tttm) cc_final: 0.8983 (ttmm) REVERT: AB 204 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7876 (tm-30) REVERT: CB 1004 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8247 (tp30) REVERT: DB 1102 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8998 (tptm) REVERT: EB 1204 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7573 (tm-30) REVERT: FB 1302 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8642 (tptp) REVERT: h 2 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8965 (ttpt) REVERT: GB 103 PHE cc_start: 0.9449 (OUTLIER) cc_final: 0.9053 (t80) REVERT: HB 202 LYS cc_start: 0.9381 (tttm) cc_final: 0.8977 (pttt) REVERT: IB 306 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8736 (tptp) REVERT: i 4 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8210 (tp30) REVERT: NB 104 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8042 (pm20) REVERT: NB 106 LYS cc_start: 0.9155 (tttp) cc_final: 0.8612 (pptt) REVERT: OB 202 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.9016 (mmmm) REVERT: QB 1006 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8816 (ttpt) outliers start: 230 outliers final: 179 residues processed: 523 average time/residue: 0.4595 time to fit residues: 295.0449 Evaluate side-chains 635 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 421 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain M residue 1007 PHE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain q residue 1006 LYS Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 304 GLU Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain LA residue 1304 GLU Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain dA residue 1006 LYS Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 6 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain hA residue 106 LYS Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain kA residue 1004 GLU Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1004 GLU Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 7A residue 1204 GLU Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.7701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.346 12528 Z= 6.079 Angle : 4.088 30.151 16272 Z= 1.846 Chirality : 0.300 0.924 1152 Planarity : 0.018 0.057 2160 Dihedral : 22.040 115.112 1518 Min Nonbonded Distance : 1.631 Molprobity Statistics. All-atom Clashscore : 113.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 22.22 % Favored : 77.60 % Rotamer: Outliers : 28.24 % Allowed : 24.54 % Favored : 47.22 % Cbeta Deviations : 14.76 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.08 % 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: -6.37 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.85 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.130 0.017 PHE 2 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 421 time to evaluate : 1.373 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: J 106 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8512 (tmmm) REVERT: M 1004 GLU cc_start: 0.8091 (mp0) cc_final: 0.7132 (mp0) REVERT: N 1104 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8144 (mm-30) REVERT: N 1106 LYS cc_start: 0.8859 (mmmm) cc_final: 0.8340 (mmmm) REVERT: O 1206 LYS cc_start: 0.8897 (ttmm) cc_final: 0.8655 (ttmm) REVERT: P 1304 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8275 (mm-30) REVERT: B 4 GLU cc_start: 0.8363 (mp0) cc_final: 0.7711 (mp0) REVERT: B 5 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.8970 (m-80) REVERT: Q 104 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7452 (mm-30) REVERT: Q 106 LYS cc_start: 0.9013 (mmmm) cc_final: 0.8732 (mmmm) REVERT: T 1006 LYS cc_start: 0.9008 (mtmt) cc_final: 0.8592 (mtmt) REVERT: U 1106 LYS cc_start: 0.8796 (tptm) cc_final: 0.8402 (tptm) REVERT: W 1302 LYS cc_start: 0.9259 (mtpt) cc_final: 0.8777 (mtpp) REVERT: C 4 GLU cc_start: 0.8069 (mp0) cc_final: 0.7487 (mp0) REVERT: X 106 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8545 (mmmm) REVERT: j 1004 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: j 1006 LYS cc_start: 0.9031 (mtmt) cc_final: 0.8618 (mtmt) REVERT: k 1106 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8610 (mmmm) REVERT: l 1202 LYS cc_start: 0.9136 (mtpt) cc_final: 0.8831 (mtpp) REVERT: l 1204 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7995 (mm-30) REVERT: D 4 GLU cc_start: 0.8034 (mp0) cc_final: 0.7166 (mp0) REVERT: D 6 LYS cc_start: 0.8976 (mtmt) cc_final: 0.8418 (mtmt) REVERT: D 7 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.8720 (t80) REVERT: n 104 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7924 (mm-30) REVERT: n 106 LYS cc_start: 0.8874 (mmmm) cc_final: 0.8315 (mmmm) REVERT: o 202 LYS cc_start: 0.9252 (ttpt) cc_final: 0.9032 (ttpt) REVERT: q 1004 GLU cc_start: 0.8259 (mp0) cc_final: 0.8041 (mp0) REVERT: r 1106 LYS cc_start: 0.8888 (mmmm) cc_final: 0.8429 (mmmm) REVERT: E 6 LYS cc_start: 0.9013 (mtmt) cc_final: 0.8696 (mtmt) REVERT: u 106 LYS cc_start: 0.8741 (mmmm) cc_final: 0.8211 (mmmm) REVERT: v 206 LYS cc_start: 0.9283 (ttmm) cc_final: 0.9000 (ttmm) REVERT: w 307 PHE cc_start: 0.9448 (OUTLIER) cc_final: 0.8943 (m-80) REVERT: x 1003 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8780 (m-80) REVERT: x 1006 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8291 (mtmt) REVERT: y 1106 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8792 (mmmm) REVERT: F 6 LYS cc_start: 0.9023 (mtmt) cc_final: 0.8789 (mtmt) REVERT: 1 104 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7408 (mm-30) REVERT: 1 106 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8387 (mmmm) REVERT: 5 1106 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8463 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9204 (mtpt) cc_final: 0.8725 (mtpp) REVERT: 7 1304 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8038 (mm-30) REVERT: G 3 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8250 (m-80) REVERT: G 4 GLU cc_start: 0.8199 (mp0) cc_final: 0.7503 (mp0) REVERT: 8 106 LYS cc_start: 0.8753 (mmmm) cc_final: 0.8273 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8040 (mp0) cc_final: 0.7702 (mp0) REVERT: CA 1104 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7248 (mm-30) REVERT: CA 1106 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8671 (mmmm) REVERT: DA 1206 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.9047 (ttmm) REVERT: EA 1306 LYS cc_start: 0.9108 (mttt) cc_final: 0.8772 (mttt) REVERT: H 4 GLU cc_start: 0.2908 (OUTLIER) cc_final: 0.2009 (pm20) REVERT: FA 106 LYS cc_start: 0.8848 (mmmm) cc_final: 0.8511 (mmmm) REVERT: HA 302 LYS cc_start: 0.9107 (mtpt) cc_final: 0.8719 (mmmm) REVERT: JA 1104 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8085 (mm-30) REVERT: JA 1106 LYS cc_start: 0.8955 (mmmm) cc_final: 0.8603 (mmmm) REVERT: LA 1306 LYS cc_start: 0.9010 (pttp) cc_final: 0.8659 (pttp) REVERT: I 4 GLU cc_start: 0.7809 (mp0) cc_final: 0.7260 (mp0) REVERT: I 6 LYS cc_start: 0.8981 (mtmt) cc_final: 0.8617 (ttmt) REVERT: MA 103 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8699 (m-80) REVERT: MA 106 LYS cc_start: 0.2994 (OUTLIER) cc_final: 0.2501 (tptt) REVERT: PA 1004 GLU cc_start: 0.7745 (mp0) cc_final: 0.7011 (mp0) REVERT: PA 1006 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8688 (ttmt) REVERT: RA 1202 LYS cc_start: 0.9150 (mtpt) cc_final: 0.8809 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8157 (mm-30) REVERT: SA 1307 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8542 (m-80) REVERT: a 2 LYS cc_start: 0.9147 (tppt) cc_final: 0.8878 (tppt) REVERT: a 4 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8236 (tp30) REVERT: TA 106 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8726 (ptmm) REVERT: UA 202 LYS cc_start: 0.9381 (tttm) cc_final: 0.8957 (ttmm) REVERT: VA 302 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8935 (tptp) REVERT: WA 1002 LYS cc_start: 0.9231 (tppt) cc_final: 0.8842 (tppt) REVERT: YA 1204 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8096 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8851 (t80) REVERT: ZA 1304 GLU cc_start: 0.9112 (tm-30) cc_final: 0.8656 (tm-30) REVERT: ZA 1305 PHE cc_start: 0.9156 (t80) cc_final: 0.8947 (t80) REVERT: aA 104 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8386 (tm-30) REVERT: bA 202 LYS cc_start: 0.9248 (tttm) cc_final: 0.8873 (ttmm) REVERT: dA 1002 LYS cc_start: 0.9136 (ttmt) cc_final: 0.8907 (ttmt) REVERT: eA 1104 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8061 (tm-30) REVERT: c 4 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7984 (tp30) REVERT: lA 1103 PHE cc_start: 0.9370 (OUTLIER) cc_final: 0.9031 (t80) REVERT: nA 1306 LYS cc_start: 0.9028 (tptp) cc_final: 0.8770 (tptp) REVERT: d 2 LYS cc_start: 0.9067 (tppt) cc_final: 0.8811 (tppt) REVERT: oA 102 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8950 (tptm) REVERT: pA 204 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7817 (tm-30) REVERT: qA 306 LYS cc_start: 0.8930 (tptp) cc_final: 0.8672 (tptp) REVERT: rA 1006 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8879 (ttpt) REVERT: tA 1204 GLU cc_start: 0.8506 (tm-30) cc_final: 0.7738 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9124 (tttt) cc_final: 0.8900 (tmtt) REVERT: wA 202 LYS cc_start: 0.9289 (tttm) cc_final: 0.8883 (ttmm) REVERT: wA 204 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7683 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.9049 (t80) REVERT: f 2 LYS cc_start: 0.9132 (ttmt) cc_final: 0.8772 (ttmt) REVERT: f 4 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8382 (tp30) REVERT: 3A 202 LYS cc_start: 0.9252 (tttm) cc_final: 0.8954 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7622 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8678 (tptp) REVERT: 5A 1002 LYS cc_start: 0.9138 (ptpt) cc_final: 0.8893 (ptpt) REVERT: 8A 1302 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8695 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8276 (tm-30) REVERT: g 2 LYS cc_start: 0.9021 (tppt) cc_final: 0.8508 (tppt) REVERT: 9A 105 PHE cc_start: 0.9408 (OUTLIER) cc_final: 0.9054 (t80) REVERT: AB 202 LYS cc_start: 0.9358 (tttm) cc_final: 0.8983 (ttmm) REVERT: CB 1004 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8258 (tp30) REVERT: DB 1102 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.9006 (tptm) REVERT: EB 1204 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7608 (tm-30) REVERT: FB 1302 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8635 (tptp) REVERT: h 2 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8987 (ttpt) REVERT: GB 103 PHE cc_start: 0.9450 (OUTLIER) cc_final: 0.9053 (t80) REVERT: HB 202 LYS cc_start: 0.9381 (tttm) cc_final: 0.8977 (pttt) REVERT: IB 306 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8712 (tptp) REVERT: i 4 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8211 (tp30) REVERT: NB 104 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8037 (pm20) REVERT: NB 106 LYS cc_start: 0.9151 (tttp) cc_final: 0.8624 (pptt) REVERT: OB 202 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.9013 (mmmm) REVERT: QB 1006 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8833 (ttpt) outliers start: 244 outliers final: 183 residues processed: 528 average time/residue: 0.4534 time to fit residues: 291.9755 Evaluate side-chains 644 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 421 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain M residue 1007 PHE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain q residue 1006 LYS Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 304 GLU Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain DA residue 1206 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1202 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain LA residue 1307 PHE Chi-restraints excluded: chain MA residue 103 PHE Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 304 GLU Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain dA residue 1006 LYS Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 LYS Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1306 LYS Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 6 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain hA residue 106 LYS Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain kA residue 1004 GLU Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain pA residue 203 PHE Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1004 GLU Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 7A residue 1204 GLU Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1106 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.7733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.348 12528 Z= 6.081 Angle : 4.099 30.178 16272 Z= 1.850 Chirality : 0.300 0.926 1152 Planarity : 0.018 0.057 2160 Dihedral : 21.794 115.165 1515 Min Nonbonded Distance : 1.626 Molprobity Statistics. All-atom Clashscore : 113.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 21.70 % Favored : 78.12 % Rotamer: Outliers : 27.43 % Allowed : 26.39 % Favored : 46.18 % Cbeta Deviations : 14.84 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.98 % 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: -6.37 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.85 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.130 0.017 PHE 2 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 420 time to evaluate : 1.405 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: J 106 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8496 (tmmm) REVERT: M 1004 GLU cc_start: 0.8241 (mp0) cc_final: 0.7644 (mp0) REVERT: N 1106 LYS cc_start: 0.8857 (mmmm) cc_final: 0.8337 (mmmm) REVERT: O 1206 LYS cc_start: 0.8897 (ttmm) cc_final: 0.8656 (ttmm) REVERT: B 4 GLU cc_start: 0.8350 (mp0) cc_final: 0.7716 (mp0) REVERT: B 5 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.8969 (m-80) REVERT: Q 104 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7357 (mm-30) REVERT: Q 106 LYS cc_start: 0.9017 (mmmm) cc_final: 0.8773 (mmmm) REVERT: S 307 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.8891 (m-80) REVERT: T 1006 LYS cc_start: 0.9015 (mtmt) cc_final: 0.8539 (mtmt) REVERT: U 1104 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7424 (mm-30) REVERT: U 1106 LYS cc_start: 0.8828 (tptm) cc_final: 0.8406 (tptm) REVERT: W 1302 LYS cc_start: 0.9254 (mtpt) cc_final: 0.8777 (mtpp) REVERT: C 4 GLU cc_start: 0.8077 (mp0) cc_final: 0.7505 (mp0) REVERT: X 106 LYS cc_start: 0.9013 (mmmm) cc_final: 0.8544 (mmmm) REVERT: j 1004 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: j 1006 LYS cc_start: 0.9035 (mtmt) cc_final: 0.8611 (mtmt) REVERT: k 1106 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8618 (mmmm) REVERT: l 1202 LYS cc_start: 0.9126 (mtpt) cc_final: 0.8820 (mtpp) REVERT: l 1204 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8009 (mm-30) REVERT: D 4 GLU cc_start: 0.8027 (mp0) cc_final: 0.7192 (mp0) REVERT: D 6 LYS cc_start: 0.8980 (mtmt) cc_final: 0.8443 (mtmt) REVERT: D 7 PHE cc_start: 0.9289 (OUTLIER) cc_final: 0.8719 (t80) REVERT: n 104 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7899 (mm-30) REVERT: n 106 LYS cc_start: 0.8875 (mmmm) cc_final: 0.8309 (mmmm) REVERT: o 202 LYS cc_start: 0.9256 (ttpt) cc_final: 0.9034 (ttpt) REVERT: q 1004 GLU cc_start: 0.8258 (mp0) cc_final: 0.8013 (mp0) REVERT: r 1106 LYS cc_start: 0.8858 (mmmm) cc_final: 0.8372 (mmmm) REVERT: E 6 LYS cc_start: 0.9019 (mtmt) cc_final: 0.8692 (mtmt) REVERT: u 106 LYS cc_start: 0.8767 (mmmm) cc_final: 0.8383 (mmmm) REVERT: v 206 LYS cc_start: 0.9283 (ttmm) cc_final: 0.8984 (ttmm) REVERT: w 307 PHE cc_start: 0.9477 (OUTLIER) cc_final: 0.8821 (m-80) REVERT: x 1003 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.8751 (m-80) REVERT: x 1006 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8298 (mtmt) REVERT: y 1106 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8792 (mmmm) REVERT: F 6 LYS cc_start: 0.9026 (mtmt) cc_final: 0.8807 (mtmt) REVERT: 1 104 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7409 (mm-30) REVERT: 1 106 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8404 (mmmm) REVERT: 5 1106 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8412 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9196 (mtpt) cc_final: 0.8724 (mtpp) REVERT: 7 1304 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8013 (mm-30) REVERT: G 3 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8240 (m-80) REVERT: G 4 GLU cc_start: 0.8202 (mp0) cc_final: 0.7520 (mp0) REVERT: 8 106 LYS cc_start: 0.8736 (mmmm) cc_final: 0.8291 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8041 (mp0) cc_final: 0.7698 (mp0) REVERT: CA 1104 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7200 (mm-30) REVERT: CA 1106 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8687 (mmmm) REVERT: DA 1206 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.9057 (ttmm) REVERT: EA 1306 LYS cc_start: 0.9107 (mttt) cc_final: 0.8763 (mttt) REVERT: H 4 GLU cc_start: 0.2901 (OUTLIER) cc_final: 0.2001 (pm20) REVERT: FA 106 LYS cc_start: 0.8861 (mmmm) cc_final: 0.8500 (mmmm) REVERT: HA 302 LYS cc_start: 0.9102 (mtpt) cc_final: 0.8727 (mmmm) REVERT: JA 1104 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8073 (mm-30) REVERT: JA 1106 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8596 (mmmm) REVERT: LA 1306 LYS cc_start: 0.8983 (pttp) cc_final: 0.8623 (pttp) REVERT: I 4 GLU cc_start: 0.7808 (mp0) cc_final: 0.7272 (mp0) REVERT: I 6 LYS cc_start: 0.8986 (mtmt) cc_final: 0.8643 (ttmt) REVERT: MA 106 LYS cc_start: 0.2980 (OUTLIER) cc_final: 0.2384 (tptt) REVERT: PA 1004 GLU cc_start: 0.7734 (mp0) cc_final: 0.6973 (mp0) REVERT: PA 1006 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8684 (ttmt) REVERT: PA 1007 PHE cc_start: 0.9437 (OUTLIER) cc_final: 0.8837 (m-80) REVERT: RA 1202 LYS cc_start: 0.9149 (mtpt) cc_final: 0.8810 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8183 (mm-30) REVERT: SA 1307 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.8544 (m-80) REVERT: a 2 LYS cc_start: 0.9152 (tppt) cc_final: 0.8877 (tppt) REVERT: a 4 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8242 (tp30) REVERT: TA 106 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8722 (ptmm) REVERT: UA 202 LYS cc_start: 0.9378 (tttm) cc_final: 0.8955 (ttmm) REVERT: VA 302 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8947 (tptp) REVERT: WA 1002 LYS cc_start: 0.9218 (tppt) cc_final: 0.8832 (tppt) REVERT: ZA 1303 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8853 (t80) REVERT: ZA 1304 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8658 (tm-30) REVERT: aA 104 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8423 (tm-30) REVERT: bA 202 LYS cc_start: 0.9247 (tttm) cc_final: 0.8833 (ttmm) REVERT: dA 1002 LYS cc_start: 0.9137 (ttmt) cc_final: 0.8909 (ttmt) REVERT: eA 1104 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8062 (tm-30) REVERT: c 4 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7989 (tp30) REVERT: lA 1103 PHE cc_start: 0.9450 (OUTLIER) cc_final: 0.9160 (t80) REVERT: nA 1306 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8775 (tptp) REVERT: d 2 LYS cc_start: 0.9084 (tppt) cc_final: 0.8771 (tppt) REVERT: oA 102 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8953 (tptm) REVERT: pA 204 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7824 (tm-30) REVERT: qA 306 LYS cc_start: 0.8933 (tptp) cc_final: 0.8676 (tptp) REVERT: rA 1006 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8879 (ttpt) REVERT: tA 1204 GLU cc_start: 0.8507 (tm-30) cc_final: 0.7727 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9132 (tttt) cc_final: 0.8917 (tmtt) REVERT: uA 1307 PHE cc_start: 0.9431 (OUTLIER) cc_final: 0.9106 (t80) REVERT: vA 105 PHE cc_start: 0.9396 (OUTLIER) cc_final: 0.8334 (t80) REVERT: wA 202 LYS cc_start: 0.9286 (tttm) cc_final: 0.8883 (ttmm) REVERT: wA 204 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7721 (tm-30) REVERT: 0A 1204 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7897 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.9099 (t80) REVERT: f 2 LYS cc_start: 0.9124 (ttmt) cc_final: 0.8765 (ttmt) REVERT: f 4 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8400 (tp30) REVERT: 3A 202 LYS cc_start: 0.9238 (tttm) cc_final: 0.8951 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7622 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8682 (tptp) REVERT: 5A 1002 LYS cc_start: 0.9136 (ptpt) cc_final: 0.8894 (ptpt) REVERT: 8A 1302 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8701 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8279 (tm-30) REVERT: g 2 LYS cc_start: 0.9018 (tppt) cc_final: 0.8508 (tppt) REVERT: 9A 105 PHE cc_start: 0.9405 (OUTLIER) cc_final: 0.9062 (t80) REVERT: AB 202 LYS cc_start: 0.9346 (tttm) cc_final: 0.8969 (ttmm) REVERT: CB 1004 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8311 (tp30) REVERT: DB 1102 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.9008 (tptm) REVERT: EB 1204 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7613 (tm-30) REVERT: FB 1302 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8628 (tptp) REVERT: GB 103 PHE cc_start: 0.9465 (OUTLIER) cc_final: 0.9063 (t80) REVERT: HB 202 LYS cc_start: 0.9381 (tttm) cc_final: 0.8978 (pttt) REVERT: IB 306 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8712 (tptp) REVERT: KB 1105 PHE cc_start: 0.9199 (t80) cc_final: 0.8980 (t80) REVERT: i 4 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8231 (tp30) REVERT: NB 104 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8039 (pm20) REVERT: NB 106 LYS cc_start: 0.9151 (tttp) cc_final: 0.8623 (pptt) REVERT: OB 202 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.9012 (mmmm) REVERT: QB 1006 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8843 (ttpt) outliers start: 237 outliers final: 183 residues processed: 527 average time/residue: 0.4432 time to fit residues: 285.4714 Evaluate side-chains 646 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 420 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain M residue 1007 PHE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 304 GLU Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain DA residue 1206 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1202 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain LA residue 1307 PHE Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 304 GLU Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain PA residue 1007 PHE Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain dA residue 1006 LYS Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 LYS Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1306 LYS Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 6 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain hA residue 106 LYS Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain kA residue 1004 GLU Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain pA residue 203 PHE Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1004 GLU Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 7A residue 1204 GLU Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1106 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.7750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.347 12528 Z= 6.087 Angle : 4.103 30.226 16272 Z= 1.853 Chirality : 0.300 0.929 1152 Planarity : 0.018 0.057 2160 Dihedral : 21.734 115.056 1511 Min Nonbonded Distance : 1.630 Molprobity Statistics. All-atom Clashscore : 112.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.88 % Favored : 78.12 % Rotamer: Outliers : 27.55 % Allowed : 26.16 % Favored : 46.30 % Cbeta Deviations : 15.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.08 % 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: -6.36 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.84 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.130 0.017 PHE 2 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 420 time to evaluate : 1.268 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: J 106 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8502 (tmmm) REVERT: M 1004 GLU cc_start: 0.8271 (mp0) cc_final: 0.7803 (mp0) REVERT: N 1104 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8068 (mm-30) REVERT: N 1106 LYS cc_start: 0.8857 (mmmm) cc_final: 0.8336 (mmmm) REVERT: O 1206 LYS cc_start: 0.8893 (ttmm) cc_final: 0.8652 (ttmm) REVERT: B 4 GLU cc_start: 0.8338 (mp0) cc_final: 0.7697 (mp0) REVERT: B 5 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8968 (m-80) REVERT: Q 104 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7386 (mm-30) REVERT: Q 106 LYS cc_start: 0.9020 (mmmm) cc_final: 0.8799 (mmmm) REVERT: S 307 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.8956 (m-80) REVERT: T 1006 LYS cc_start: 0.9005 (mtmt) cc_final: 0.8527 (mtmt) REVERT: U 1106 LYS cc_start: 0.8823 (tptm) cc_final: 0.8386 (tptm) REVERT: W 1302 LYS cc_start: 0.9249 (mtpt) cc_final: 0.8779 (mtpp) REVERT: C 4 GLU cc_start: 0.8089 (mp0) cc_final: 0.7513 (mp0) REVERT: X 106 LYS cc_start: 0.9067 (mmmm) cc_final: 0.8594 (mmmm) REVERT: j 1004 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: j 1006 LYS cc_start: 0.9032 (mtmt) cc_final: 0.8598 (mtmt) REVERT: k 1106 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8623 (mmmm) REVERT: l 1202 LYS cc_start: 0.9122 (mtpt) cc_final: 0.8817 (mtpp) REVERT: l 1204 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8021 (mm-30) REVERT: D 4 GLU cc_start: 0.8025 (mp0) cc_final: 0.6978 (mp0) REVERT: D 6 LYS cc_start: 0.8980 (mtmt) cc_final: 0.8446 (mtmt) REVERT: D 7 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8784 (t80) REVERT: n 104 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7895 (mm-30) REVERT: n 106 LYS cc_start: 0.8880 (mmmm) cc_final: 0.8308 (mmmm) REVERT: o 202 LYS cc_start: 0.9254 (ttpt) cc_final: 0.9034 (ttpt) REVERT: r 1106 LYS cc_start: 0.8857 (mmmm) cc_final: 0.8366 (mmmm) REVERT: E 6 LYS cc_start: 0.9089 (mtmt) cc_final: 0.8762 (mtmt) REVERT: u 106 LYS cc_start: 0.8774 (mmmm) cc_final: 0.8391 (mmmm) REVERT: v 206 LYS cc_start: 0.9279 (ttmm) cc_final: 0.8975 (ttmm) REVERT: w 307 PHE cc_start: 0.9445 (OUTLIER) cc_final: 0.8790 (m-80) REVERT: x 1003 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8801 (m-80) REVERT: x 1006 LYS cc_start: 0.8877 (mtmt) cc_final: 0.8323 (mtmt) REVERT: y 1106 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8797 (mmmm) REVERT: F 6 LYS cc_start: 0.9014 (mtmt) cc_final: 0.8791 (mtmt) REVERT: 1 104 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7290 (mm-30) REVERT: 1 106 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8420 (mmmm) REVERT: 5 1106 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8443 (mmmm) REVERT: G 3 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8245 (m-80) REVERT: G 4 GLU cc_start: 0.8206 (mp0) cc_final: 0.7533 (mp0) REVERT: 8 106 LYS cc_start: 0.8724 (mmmm) cc_final: 0.8291 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8041 (mp0) cc_final: 0.7701 (mp0) REVERT: CA 1104 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7204 (mm-30) REVERT: CA 1106 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8700 (mmmm) REVERT: DA 1206 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.9047 (ttmm) REVERT: EA 1306 LYS cc_start: 0.9109 (mttt) cc_final: 0.8756 (mttt) REVERT: H 4 GLU cc_start: 0.2899 (OUTLIER) cc_final: 0.2003 (pm20) REVERT: FA 106 LYS cc_start: 0.8862 (mmmm) cc_final: 0.8505 (mmmm) REVERT: HA 302 LYS cc_start: 0.9101 (mtpt) cc_final: 0.8728 (mmmm) REVERT: JA 1104 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7986 (tm-30) REVERT: JA 1106 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8589 (mmmm) REVERT: I 4 GLU cc_start: 0.7809 (mp0) cc_final: 0.7275 (mp0) REVERT: I 6 LYS cc_start: 0.8985 (mtmt) cc_final: 0.8640 (ttmt) REVERT: MA 103 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8657 (m-80) REVERT: MA 106 LYS cc_start: 0.2976 (OUTLIER) cc_final: 0.2389 (tptt) REVERT: PA 1004 GLU cc_start: 0.7734 (mp0) cc_final: 0.6978 (mp0) REVERT: PA 1006 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8689 (ttmt) REVERT: PA 1007 PHE cc_start: 0.9439 (OUTLIER) cc_final: 0.8849 (m-80) REVERT: RA 1202 LYS cc_start: 0.9151 (mtpt) cc_final: 0.8816 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8180 (mm-30) REVERT: SA 1307 PHE cc_start: 0.9378 (OUTLIER) cc_final: 0.8546 (m-80) REVERT: a 2 LYS cc_start: 0.9154 (tppt) cc_final: 0.8879 (tppt) REVERT: a 4 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8248 (tp30) REVERT: TA 106 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8703 (ptmm) REVERT: UA 202 LYS cc_start: 0.9381 (tttm) cc_final: 0.8963 (ttmm) REVERT: VA 302 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8940 (tptp) REVERT: WA 1002 LYS cc_start: 0.9218 (tppt) cc_final: 0.8832 (tppt) REVERT: ZA 1303 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.8953 (t80) REVERT: ZA 1304 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8664 (tm-30) REVERT: aA 104 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8471 (tm-30) REVERT: bA 202 LYS cc_start: 0.9259 (tttm) cc_final: 0.8846 (ttmm) REVERT: dA 1002 LYS cc_start: 0.9136 (ttmt) cc_final: 0.8908 (ttmt) REVERT: eA 1104 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8061 (tm-30) REVERT: c 4 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7992 (tp30) REVERT: hA 104 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8311 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9439 (OUTLIER) cc_final: 0.9123 (t80) REVERT: nA 1306 LYS cc_start: 0.9021 (tptp) cc_final: 0.8775 (tptp) REVERT: d 2 LYS cc_start: 0.9085 (tppt) cc_final: 0.8772 (tppt) REVERT: oA 102 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8954 (tptm) REVERT: pA 204 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7823 (tm-30) REVERT: qA 306 LYS cc_start: 0.8931 (tptp) cc_final: 0.8678 (tptp) REVERT: rA 1006 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8878 (ttpt) REVERT: sA 1103 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8911 (t80) REVERT: tA 1204 GLU cc_start: 0.8512 (tm-30) cc_final: 0.7732 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8913 (tmtt) REVERT: uA 1307 PHE cc_start: 0.9409 (OUTLIER) cc_final: 0.9045 (t80) REVERT: vA 105 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.8329 (t80) REVERT: wA 202 LYS cc_start: 0.9286 (tttm) cc_final: 0.8882 (ttmm) REVERT: wA 204 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7729 (tm-30) REVERT: 0A 1204 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7903 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.9099 (t80) REVERT: f 2 LYS cc_start: 0.9124 (ttmt) cc_final: 0.8766 (ttmt) REVERT: f 4 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8399 (tp30) REVERT: 3A 202 LYS cc_start: 0.9237 (tttm) cc_final: 0.8954 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7623 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8685 (tptp) REVERT: 5A 1002 LYS cc_start: 0.9136 (ptpt) cc_final: 0.8900 (ptpt) REVERT: 8A 1302 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8708 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8292 (tm-30) REVERT: g 2 LYS cc_start: 0.9019 (tppt) cc_final: 0.8508 (tppt) REVERT: 9A 105 PHE cc_start: 0.9407 (OUTLIER) cc_final: 0.9049 (t80) REVERT: AB 202 LYS cc_start: 0.9346 (tttm) cc_final: 0.8968 (ttmm) REVERT: CB 1004 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8293 (tp30) REVERT: DB 1102 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.9008 (tptm) REVERT: EB 1204 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7619 (tm-30) REVERT: FB 1302 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8625 (tptp) REVERT: GB 103 PHE cc_start: 0.9465 (OUTLIER) cc_final: 0.9064 (t80) REVERT: HB 202 LYS cc_start: 0.9382 (tttm) cc_final: 0.8977 (pttt) REVERT: IB 306 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8760 (tptp) REVERT: KB 1105 PHE cc_start: 0.9216 (t80) cc_final: 0.8966 (t80) REVERT: i 4 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8241 (tp30) REVERT: NB 104 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8038 (pm20) REVERT: NB 106 LYS cc_start: 0.9153 (tttp) cc_final: 0.8623 (pptt) REVERT: OB 202 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9013 (mmmm) REVERT: QB 1006 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8847 (ttpt) outliers start: 238 outliers final: 184 residues processed: 527 average time/residue: 0.4944 time to fit residues: 321.6005 Evaluate side-chains 649 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 420 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain M residue 1007 PHE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 304 GLU Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain DA residue 1206 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1202 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain LA residue 1307 PHE Chi-restraints excluded: chain MA residue 103 PHE Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 304 GLU Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain PA residue 1007 PHE Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain dA residue 1006 LYS Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 LYS Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1306 LYS Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 6 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain hA residue 106 LYS Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain kA residue 1004 GLU Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain pA residue 203 PHE Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1004 GLU Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 7A residue 1204 GLU Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1106 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.7763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.344 12528 Z= 6.084 Angle : 4.103 30.368 16272 Z= 1.854 Chirality : 0.300 0.931 1152 Planarity : 0.018 0.057 2160 Dihedral : 21.739 115.140 1511 Min Nonbonded Distance : 1.633 Molprobity Statistics. All-atom Clashscore : 113.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.70 % Favored : 78.30 % Rotamer: Outliers : 27.78 % Allowed : 26.39 % Favored : 45.83 % Cbeta Deviations : 15.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.98 % 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: -6.38 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.86 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.130 0.017 PHE 2 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 421 time to evaluate : 1.387 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: J 106 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8481 (tmmm) REVERT: M 1004 GLU cc_start: 0.8368 (mp0) cc_final: 0.7783 (mp0) REVERT: N 1106 LYS cc_start: 0.8870 (mmmm) cc_final: 0.8344 (mmmm) REVERT: O 1206 LYS cc_start: 0.8890 (ttmm) cc_final: 0.8648 (ttmm) REVERT: B 4 GLU cc_start: 0.8333 (mp0) cc_final: 0.7690 (mp0) REVERT: B 5 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8972 (m-80) REVERT: Q 104 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7394 (mm-30) REVERT: Q 106 LYS cc_start: 0.9023 (mmmm) cc_final: 0.8806 (mmmm) REVERT: S 307 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.8972 (m-80) REVERT: T 1006 LYS cc_start: 0.9008 (mtmt) cc_final: 0.8537 (mtmt) REVERT: U 1106 LYS cc_start: 0.8835 (tptm) cc_final: 0.8393 (tptm) REVERT: W 1302 LYS cc_start: 0.9243 (mtpt) cc_final: 0.8780 (mtpp) REVERT: C 4 GLU cc_start: 0.8090 (mp0) cc_final: 0.7514 (mp0) REVERT: X 106 LYS cc_start: 0.9064 (mmmm) cc_final: 0.8595 (mmmm) REVERT: j 1004 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: j 1006 LYS cc_start: 0.9033 (mtmt) cc_final: 0.8627 (mtmt) REVERT: k 1106 LYS cc_start: 0.8964 (mmmm) cc_final: 0.8629 (mmmm) REVERT: l 1202 LYS cc_start: 0.9116 (mtpt) cc_final: 0.8823 (mtpp) REVERT: l 1204 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7982 (mm-30) REVERT: D 4 GLU cc_start: 0.8022 (mp0) cc_final: 0.6971 (mp0) REVERT: D 6 LYS cc_start: 0.8982 (mtmt) cc_final: 0.8447 (mtmt) REVERT: D 7 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8724 (t80) REVERT: n 104 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7911 (mm-30) REVERT: n 106 LYS cc_start: 0.8879 (mmmm) cc_final: 0.8305 (mmmm) REVERT: o 202 LYS cc_start: 0.9257 (ttpt) cc_final: 0.9038 (ttpt) REVERT: q 1004 GLU cc_start: 0.8134 (mp0) cc_final: 0.7886 (mp0) REVERT: r 1106 LYS cc_start: 0.8863 (mmmm) cc_final: 0.8357 (mmmm) REVERT: E 6 LYS cc_start: 0.9082 (mtmt) cc_final: 0.8775 (mtmt) REVERT: u 106 LYS cc_start: 0.8784 (mmmm) cc_final: 0.8395 (mmmm) REVERT: v 206 LYS cc_start: 0.9277 (ttmm) cc_final: 0.8984 (ttmm) REVERT: w 307 PHE cc_start: 0.9441 (OUTLIER) cc_final: 0.8786 (m-80) REVERT: x 1003 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8818 (m-80) REVERT: x 1006 LYS cc_start: 0.8875 (mtmt) cc_final: 0.8313 (mtmt) REVERT: y 1106 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8814 (mmmm) REVERT: F 6 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8769 (mtmt) REVERT: 1 104 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7295 (mm-30) REVERT: 1 106 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8436 (mmmm) REVERT: 5 1106 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8469 (mmmm) REVERT: 7 1304 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8062 (mm-30) REVERT: G 3 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8243 (m-80) REVERT: G 4 GLU cc_start: 0.8199 (mp0) cc_final: 0.7540 (mp0) REVERT: 8 106 LYS cc_start: 0.8720 (mmmm) cc_final: 0.8291 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8037 (mp0) cc_final: 0.7697 (mp0) REVERT: CA 1104 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7205 (mm-30) REVERT: DA 1206 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.9056 (ttmm) REVERT: EA 1306 LYS cc_start: 0.9113 (mttt) cc_final: 0.8766 (mttt) REVERT: H 4 GLU cc_start: 0.2899 (OUTLIER) cc_final: 0.2002 (pm20) REVERT: FA 106 LYS cc_start: 0.8858 (mmmm) cc_final: 0.8498 (mmmm) REVERT: HA 302 LYS cc_start: 0.9101 (mtpt) cc_final: 0.8730 (mmmm) REVERT: JA 1106 LYS cc_start: 0.8951 (mmmm) cc_final: 0.8586 (mmmm) REVERT: I 4 GLU cc_start: 0.7805 (mp0) cc_final: 0.7269 (mp0) REVERT: I 6 LYS cc_start: 0.8985 (mtmt) cc_final: 0.8642 (ttmt) REVERT: MA 103 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8656 (m-80) REVERT: MA 106 LYS cc_start: 0.2975 (OUTLIER) cc_final: 0.2384 (tptt) REVERT: PA 1004 GLU cc_start: 0.7727 (mp0) cc_final: 0.7010 (mp0) REVERT: PA 1007 PHE cc_start: 0.9440 (OUTLIER) cc_final: 0.8841 (m-80) REVERT: RA 1202 LYS cc_start: 0.9153 (mtpt) cc_final: 0.8822 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8153 (mm-30) REVERT: SA 1307 PHE cc_start: 0.9377 (OUTLIER) cc_final: 0.8542 (m-80) REVERT: a 2 LYS cc_start: 0.9138 (tppt) cc_final: 0.8873 (tppt) REVERT: a 4 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8250 (tp30) REVERT: TA 106 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8709 (ptmm) REVERT: UA 202 LYS cc_start: 0.9383 (tttm) cc_final: 0.8947 (ttmm) REVERT: UA 204 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7808 (tm-30) REVERT: WA 1002 LYS cc_start: 0.9218 (tppt) cc_final: 0.8831 (tppt) REVERT: ZA 1303 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8843 (t80) REVERT: ZA 1304 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8668 (tm-30) REVERT: aA 104 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8456 (tm-30) REVERT: bA 202 LYS cc_start: 0.9263 (tttm) cc_final: 0.8849 (ttmm) REVERT: dA 1002 LYS cc_start: 0.9135 (ttmt) cc_final: 0.8907 (ttmt) REVERT: eA 1104 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8062 (tm-30) REVERT: c 4 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7998 (tp30) REVERT: lA 1103 PHE cc_start: 0.9441 (OUTLIER) cc_final: 0.9128 (t80) REVERT: nA 1306 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8774 (tptp) REVERT: d 2 LYS cc_start: 0.9087 (tppt) cc_final: 0.8768 (tppt) REVERT: oA 102 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8933 (tptm) REVERT: pA 204 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7832 (tm-30) REVERT: qA 306 LYS cc_start: 0.8944 (tptp) cc_final: 0.8680 (tptp) REVERT: rA 1006 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8879 (ttpt) REVERT: sA 1103 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8908 (t80) REVERT: tA 1204 GLU cc_start: 0.8512 (tm-30) cc_final: 0.7743 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8913 (tmtt) REVERT: uA 1307 PHE cc_start: 0.9418 (OUTLIER) cc_final: 0.9065 (t80) REVERT: vA 105 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.8334 (t80) REVERT: wA 202 LYS cc_start: 0.9287 (tttm) cc_final: 0.8883 (ttmm) REVERT: wA 204 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7733 (tm-30) REVERT: 0A 1204 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7885 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.9100 (t80) REVERT: f 2 LYS cc_start: 0.9125 (ttmt) cc_final: 0.8767 (ttmt) REVERT: f 4 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8396 (tp30) REVERT: 3A 202 LYS cc_start: 0.9236 (tttm) cc_final: 0.8948 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7621 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8687 (tptp) REVERT: 5A 1002 LYS cc_start: 0.9137 (ptpt) cc_final: 0.8894 (ptpt) REVERT: 8A 1302 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8711 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8288 (tm-30) REVERT: g 2 LYS cc_start: 0.9019 (tppt) cc_final: 0.8509 (tppt) REVERT: 9A 105 PHE cc_start: 0.9399 (OUTLIER) cc_final: 0.9057 (t80) REVERT: AB 202 LYS cc_start: 0.9345 (tttm) cc_final: 0.8970 (ttmm) REVERT: CB 1004 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8311 (tp30) REVERT: DB 1102 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.9008 (tptm) REVERT: EB 1204 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7630 (tm-30) REVERT: FB 1302 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8615 (tptp) REVERT: GB 103 PHE cc_start: 0.9466 (OUTLIER) cc_final: 0.9068 (t80) REVERT: HB 202 LYS cc_start: 0.9381 (tttm) cc_final: 0.8979 (pttt) REVERT: IB 306 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8731 (tptp) REVERT: i 4 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8245 (tp30) REVERT: NB 104 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8038 (pm20) REVERT: NB 106 LYS cc_start: 0.9153 (tttp) cc_final: 0.8624 (pptt) REVERT: OB 202 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.9015 (mmmm) REVERT: QB 1006 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8849 (ttpt) outliers start: 240 outliers final: 187 residues processed: 529 average time/residue: 0.4498 time to fit residues: 290.7925 Evaluate side-chains 651 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 421 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain M residue 1007 PHE Chi-restraints excluded: chain N residue 1102 LYS Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 304 GLU Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain DA residue 1206 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1202 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain LA residue 1307 PHE Chi-restraints excluded: chain MA residue 103 PHE Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 304 GLU Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1007 PHE Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain dA residue 1006 LYS Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 LYS Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 6 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain hA residue 106 LYS Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain kA residue 1004 GLU Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain pA residue 203 PHE Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1004 GLU Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 7A residue 1204 GLU Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain CB residue 1006 LYS Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1106 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.072577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.062500 restraints weight = 33929.000| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.08 r_work: 0.2736 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.7775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.342 12528 Z= 6.084 Angle : 4.108 30.377 16272 Z= 1.856 Chirality : 0.300 0.934 1152 Planarity : 0.018 0.057 2160 Dihedral : 21.742 115.072 1511 Min Nonbonded Distance : 1.633 Molprobity Statistics. All-atom Clashscore : 113.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.05 % Favored : 77.95 % Rotamer: Outliers : 27.55 % Allowed : 26.85 % Favored : 45.60 % Cbeta Deviations : 15.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.18 % 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: -6.41 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.88 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.130 0.017 PHE 2 205 =============================================================================== Job complete usr+sys time: 4089.38 seconds wall clock time: 73 minutes 12.41 seconds (4392.41 seconds total)