Starting phenix.real_space_refine on Fri Mar 15 16:01:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqg_23485/03_2024/7lqg_23485_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqg_23485/03_2024/7lqg_23485.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/7lqg_23485/03_2024/7lqg_23485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqg_23485/03_2024/7lqg_23485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqg_23485/03_2024/7lqg_23485_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqg_23485/03_2024/7lqg_23485_updated.pdb" } 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= 0.030 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.71, per 1000 atoms: 0.47 Number of scatterers: 12096 At special positions: 0 Unit cell: (89.64, 89.64, 108, 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=36, symmetry=0 Number of additional bonds: simple=36, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.36 Conformation dependent library (CDL) restraints added in 1.0 seconds 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... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... No hydrogen bonds 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: 0.01 Time building geometry restraints manager: 5.73 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: 1530 1.26 - 1.33: 1350 1.33 - 1.41: 3600 1.41 - 1.48: 1300 1.48 - 1.56: 4748 Bond restraints: 12528 Sorted by residual: 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 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 3.48e+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 3.46e+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 5CRQB1001 " pdb=" CAL 5CRQB1001 " 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: 105.44 - 109.77: 1156 109.77 - 114.09: 4084 114.09 - 118.42: 2116 118.42 - 122.74: 7470 122.74 - 127.06: 1446 Bond angle restraints: 16272 Sorted by residual: 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 f 1 " pdb=" CAL 5CR f 1 " pdb=" CAA 5CR f 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 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 1.08e+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 angle pdb=" N 5CR i 1 " pdb=" CAL 5CR i 1 " pdb=" CAA 5CR i 1 " 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: 4840 15.26 - 30.52: 794 30.52 - 45.78: 342 45.78 - 61.04: 198 61.04 - 76.30: 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 1.29 58.71 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 8 106 " pdb=" CB LYS 8 106 " pdb=" CG LYS 8 106 " pdb=" CD LYS 8 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.30 58.70 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: 404 0.018 - 0.036: 326 0.036 - 0.054: 308 0.054 - 0.072: 88 0.072 - 0.090: 26 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 2.02e-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 l1202 " pdb=" N LYS l1202 " pdb=" C LYS l1202 " pdb=" CB LYS l1202 " 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 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 PHEUA 205 " -0.009 2.00e-02 2.50e+03 6.98e-03 8.53e-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 PHESB1205 " -0.008 2.00e-02 2.50e+03 6.92e-03 8.39e-01 pdb=" CG PHESB1205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHESB1205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHESB1205 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHESB1205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHESB1205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHESB1205 " -0.002 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 48 2.45 - 3.07: 6948 3.07 - 3.68: 18344 3.68 - 4.29: 30140 4.29 - 4.90: 49410 Nonbonded interactions: 104890 Sorted by model distance: nonbonded pdb=" CD LYS A 2 " pdb=" OE2 GMADA1208 " model vdw 1.842 2.752 nonbonded pdb=" CD LYS M1002 " pdb=" OE2 GMA 9 208 " model vdw 1.842 2.752 nonbonded pdb=" OE2 GMA V1208 " pdb=" CD LYS H 2 " model vdw 1.868 2.752 nonbonded pdb=" OE2 GMA R 208 " pdb=" CD LYSIA1002 " model vdw 1.868 2.752 nonbonded pdb=" OE2 GMA l1208 " pdb=" NZ LYS D 2 " model vdw 1.870 2.496 ... (remaining 104885 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.110 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 28.270 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.390 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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= 0.844 Angle : 1.417 9.883 16272 Z= 0.592 Chirality : 0.035 0.090 1152 Planarity : 0.002 0.009 2160 Dihedral : 20.718 76.303 3888 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 31.02 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 628 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 502 time to evaluate : 1.267 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: 0.7489 (mp0) cc_final: 0.6990 (pm20) REVERT: A 6 LYS cc_start: 0.8409 (mtmt) cc_final: 0.7960 (mtmt) REVERT: M 1004 GLU cc_start: 0.7511 (mp0) cc_final: 0.7009 (pm20) REVERT: M 1006 LYS cc_start: 0.8412 (mtmt) cc_final: 0.7962 (mtmt) REVERT: P 1302 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8557 (ttmm) REVERT: B 4 GLU cc_start: 0.7387 (mp0) cc_final: 0.6353 (pm20) REVERT: T 1004 GLU cc_start: 0.7416 (mp0) cc_final: 0.6368 (pm20) REVERT: W 1302 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8394 (ttmm) REVERT: C 6 LYS cc_start: 0.8478 (mtmt) cc_final: 0.8165 (mtmt) REVERT: Z 306 LYS cc_start: 0.8670 (tttt) cc_final: 0.8389 (tttt) REVERT: j 1006 LYS cc_start: 0.8483 (mtmt) cc_final: 0.8135 (mtmt) REVERT: m 1306 LYS cc_start: 0.8682 (tttt) cc_final: 0.8400 (tttt) REVERT: n 104 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6300 (mm-30) REVERT: p 306 LYS cc_start: 0.8718 (tttt) cc_final: 0.8460 (tttt) REVERT: r 1104 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6343 (mm-30) REVERT: t 1306 LYS cc_start: 0.8723 (tttt) cc_final: 0.8465 (tttt) REVERT: E 4 GLU cc_start: 0.7451 (mp0) cc_final: 0.7098 (mp0) REVERT: E 6 LYS cc_start: 0.8375 (mtmt) cc_final: 0.8101 (mtmt) REVERT: u 102 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8440 (mtpp) REVERT: u 104 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7138 (mm-30) REVERT: w 304 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7102 (mm-30) REVERT: w 306 LYS cc_start: 0.8688 (tttt) cc_final: 0.8359 (tttt) REVERT: x 1004 GLU cc_start: 0.7477 (mp0) cc_final: 0.7137 (mp0) REVERT: x 1006 LYS cc_start: 0.8388 (mtmt) cc_final: 0.8120 (mtmt) REVERT: y 1102 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8447 (mtpp) REVERT: y 1104 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7164 (mm-30) REVERT: z 1202 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8300 (mtpt) REVERT: 0 1302 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8519 (ttmm) REVERT: 0 1304 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7083 (mm-30) REVERT: 0 1306 LYS cc_start: 0.8695 (tttt) cc_final: 0.8386 (tttt) REVERT: F 4 GLU cc_start: 0.7394 (mp0) cc_final: 0.6855 (pm20) REVERT: 2 206 LYS cc_start: 0.8439 (ttmm) cc_final: 0.8190 (ttmm) REVERT: 3 306 LYS cc_start: 0.8751 (tttt) cc_final: 0.8443 (tttt) REVERT: 4 1004 GLU cc_start: 0.7422 (mp0) cc_final: 0.6862 (pm20) REVERT: 6 1206 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8193 (ttmm) REVERT: 7 1306 LYS cc_start: 0.8759 (tttt) cc_final: 0.8423 (tttt) REVERT: G 4 GLU cc_start: 0.7500 (mp0) cc_final: 0.6448 (mp0) REVERT: 9 202 LYS cc_start: 0.8499 (mtpt) cc_final: 0.8271 (mtpt) REVERT: 9 204 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6821 (mt-10) REVERT: AA 306 LYS cc_start: 0.8758 (tttt) cc_final: 0.8472 (tttt) REVERT: BA 1004 GLU cc_start: 0.7518 (mp0) cc_final: 0.6466 (mp0) REVERT: DA 1202 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8302 (mtpt) REVERT: DA 1204 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6823 (mt-10) REVERT: EA 1302 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8628 (ttmm) REVERT: EA 1304 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6981 (mm-30) REVERT: EA 1306 LYS cc_start: 0.8759 (tttt) cc_final: 0.8463 (tttt) REVERT: I 4 GLU cc_start: 0.7640 (mp0) cc_final: 0.7418 (mp0) REVERT: OA 306 LYS cc_start: 0.8620 (tttt) cc_final: 0.8202 (tttt) REVERT: RA 1204 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7135 (mt-10) REVERT: SA 1306 LYS cc_start: 0.8631 (tttt) cc_final: 0.8225 (tttt) REVERT: a 3 PHE cc_start: 0.9235 (t80) cc_final: 0.9009 (t80) REVERT: a 5 PHE cc_start: 0.9036 (t80) cc_final: 0.8632 (t80) REVERT: a 7 PHE cc_start: 0.9251 (t80) cc_final: 0.8950 (t80) REVERT: TA 103 PHE cc_start: 0.9011 (t80) cc_final: 0.8762 (t80) REVERT: TA 107 PHE cc_start: 0.8855 (t80) cc_final: 0.8646 (t80) REVERT: UA 202 LYS cc_start: 0.8743 (tttm) cc_final: 0.8497 (mmmm) REVERT: UA 206 LYS cc_start: 0.8907 (tttt) cc_final: 0.8690 (tttt) REVERT: VA 304 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8172 (tm-30) REVERT: WA 1003 PHE cc_start: 0.9235 (t80) cc_final: 0.9018 (t80) REVERT: WA 1005 PHE cc_start: 0.9054 (t80) cc_final: 0.8645 (t80) REVERT: WA 1007 PHE cc_start: 0.9255 (t80) cc_final: 0.8980 (t80) REVERT: XA 1103 PHE cc_start: 0.8981 (t80) cc_final: 0.8746 (t80) REVERT: XA 1107 PHE cc_start: 0.8879 (t80) cc_final: 0.8668 (t80) REVERT: YA 1202 LYS cc_start: 0.8721 (tttm) cc_final: 0.8423 (tttm) REVERT: YA 1206 LYS cc_start: 0.8893 (tttt) cc_final: 0.8671 (tttt) REVERT: ZA 1304 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8173 (tm-30) REVERT: bA 202 LYS cc_start: 0.8657 (tttm) cc_final: 0.8266 (mmmm) REVERT: fA 1202 LYS cc_start: 0.8629 (tttm) cc_final: 0.8364 (tttm) REVERT: hA 103 PHE cc_start: 0.8994 (t80) cc_final: 0.8567 (t80) REVERT: hA 107 PHE cc_start: 0.8728 (t80) cc_final: 0.8372 (t80) REVERT: iA 202 LYS cc_start: 0.8724 (tttm) cc_final: 0.8388 (ttmm) REVERT: iA 204 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6966 (tm-30) REVERT: iA 206 LYS cc_start: 0.8950 (tttt) cc_final: 0.8476 (tttm) REVERT: jA 305 PHE cc_start: 0.8812 (t80) cc_final: 0.8586 (t80) REVERT: lA 1103 PHE cc_start: 0.8962 (t80) cc_final: 0.8549 (t80) REVERT: lA 1107 PHE cc_start: 0.8750 (t80) cc_final: 0.8441 (t80) REVERT: mA 1204 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6925 (tm-30) REVERT: mA 1206 LYS cc_start: 0.8933 (tttt) cc_final: 0.8409 (tttt) REVERT: nA 1305 PHE cc_start: 0.8820 (t80) cc_final: 0.8601 (t80) REVERT: d 5 PHE cc_start: 0.9042 (t80) cc_final: 0.8631 (t80) REVERT: oA 103 PHE cc_start: 0.9060 (t80) cc_final: 0.8390 (t80) REVERT: pA 202 LYS cc_start: 0.8764 (tttm) cc_final: 0.8397 (mmmm) REVERT: pA 206 LYS cc_start: 0.8962 (tttt) cc_final: 0.8485 (tttt) REVERT: rA 1005 PHE cc_start: 0.9060 (t80) cc_final: 0.8811 (t80) REVERT: sA 1103 PHE cc_start: 0.9029 (t80) cc_final: 0.8378 (t80) REVERT: tA 1202 LYS cc_start: 0.8745 (tttm) cc_final: 0.8479 (tttm) REVERT: tA 1206 LYS cc_start: 0.8945 (tttt) cc_final: 0.8470 (tttt) REVERT: e 5 PHE cc_start: 0.9202 (t80) cc_final: 0.8927 (t80) REVERT: wA 202 LYS cc_start: 0.8607 (tttm) cc_final: 0.8262 (tppp) REVERT: wA 206 LYS cc_start: 0.8849 (tttt) cc_final: 0.8513 (tttm) REVERT: xA 303 PHE cc_start: 0.8785 (t80) cc_final: 0.8524 (t80) REVERT: xA 305 PHE cc_start: 0.8647 (t80) cc_final: 0.8384 (t80) REVERT: yA 1005 PHE cc_start: 0.9221 (t80) cc_final: 0.8952 (t80) REVERT: 1A 1303 PHE cc_start: 0.8787 (t80) cc_final: 0.8526 (t80) REVERT: 1A 1305 PHE cc_start: 0.8655 (t80) cc_final: 0.8381 (t80) REVERT: f 3 PHE cc_start: 0.9281 (t80) cc_final: 0.9054 (t80) REVERT: f 7 PHE cc_start: 0.9110 (t80) cc_final: 0.8576 (t80) REVERT: 2A 102 LYS cc_start: 0.8748 (tptm) cc_final: 0.8306 (tptm) REVERT: 2A 106 LYS cc_start: 0.8921 (tttp) cc_final: 0.8703 (tttp) REVERT: 2A 107 PHE cc_start: 0.8737 (t80) cc_final: 0.8278 (t80) REVERT: 3A 202 LYS cc_start: 0.8895 (tttm) cc_final: 0.8665 (tttm) REVERT: 3A 206 LYS cc_start: 0.8908 (tttt) cc_final: 0.8676 (tttm) REVERT: 4A 304 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8244 (tm-30) REVERT: 5A 1003 PHE cc_start: 0.9280 (t80) cc_final: 0.9058 (t80) REVERT: 5A 1007 PHE cc_start: 0.9117 (t80) cc_final: 0.8615 (t80) REVERT: 6A 1102 LYS cc_start: 0.8733 (tptm) cc_final: 0.8313 (tptm) REVERT: 6A 1106 LYS cc_start: 0.8924 (tttp) cc_final: 0.8702 (tttp) REVERT: 6A 1107 PHE cc_start: 0.8759 (t80) cc_final: 0.8326 (t80) REVERT: 7A 1202 LYS cc_start: 0.8870 (tttm) cc_final: 0.8637 (tttm) REVERT: 8A 1304 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8244 (tm-30) REVERT: g 7 PHE cc_start: 0.9090 (t80) cc_final: 0.8841 (t80) REVERT: 9A 102 LYS cc_start: 0.8870 (tptm) cc_final: 0.8366 (tptm) REVERT: 9A 106 LYS cc_start: 0.8870 (tttp) cc_final: 0.8562 (tttm) REVERT: 9A 107 PHE cc_start: 0.8870 (t80) cc_final: 0.8327 (t80) REVERT: AB 202 LYS cc_start: 0.8868 (tttm) cc_final: 0.8520 (mtpp) REVERT: AB 206 LYS cc_start: 0.8933 (tttt) cc_final: 0.8727 (tttm) REVERT: BB 304 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8195 (tm-30) REVERT: BB 306 LYS cc_start: 0.8697 (tptp) cc_final: 0.8278 (tptp) REVERT: CB 1003 PHE cc_start: 0.9292 (t80) cc_final: 0.9085 (t80) REVERT: CB 1005 PHE cc_start: 0.9156 (t80) cc_final: 0.8841 (t80) REVERT: CB 1007 PHE cc_start: 0.9095 (t80) cc_final: 0.8865 (t80) REVERT: DB 1106 LYS cc_start: 0.8873 (tttp) cc_final: 0.8662 (tttp) REVERT: DB 1107 PHE cc_start: 0.8889 (t80) cc_final: 0.8278 (t80) REVERT: FB 1304 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8168 (tm-30) REVERT: FB 1306 LYS cc_start: 0.8682 (tptp) cc_final: 0.8280 (tptp) REVERT: GB 102 LYS cc_start: 0.8922 (tptm) cc_final: 0.8611 (tptm) REVERT: GB 106 LYS cc_start: 0.8740 (tttp) cc_final: 0.8378 (tttm) REVERT: HB 202 LYS cc_start: 0.8580 (tttm) cc_final: 0.8274 (mmmm) REVERT: IB 303 PHE cc_start: 0.8740 (t80) cc_final: 0.8458 (t80) REVERT: IB 304 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8502 (tm-30) REVERT: IB 306 LYS cc_start: 0.8770 (tptp) cc_final: 0.8563 (tptp) REVERT: KB 1102 LYS cc_start: 0.8919 (tptm) cc_final: 0.8618 (tptm) REVERT: MB 1303 PHE cc_start: 0.8741 (t80) cc_final: 0.8454 (t80) REVERT: MB 1306 LYS cc_start: 0.8749 (tptp) cc_final: 0.8547 (tptp) REVERT: OB 204 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7337 (tm-30) REVERT: OB 206 LYS cc_start: 0.8959 (tttt) cc_final: 0.8503 (tttt) REVERT: PB 305 PHE cc_start: 0.8500 (t80) cc_final: 0.8208 (t80) REVERT: PB 307 PHE cc_start: 0.8157 (t80) cc_final: 0.7803 (t80) REVERT: SB 1204 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7295 (tm-30) REVERT: SB 1206 LYS cc_start: 0.8938 (tttt) cc_final: 0.8487 (tttt) REVERT: TB 1305 PHE cc_start: 0.8512 (t80) cc_final: 0.8219 (t80) REVERT: TB 1307 PHE cc_start: 0.8172 (t80) cc_final: 0.7811 (t80) outliers start: 126 outliers final: 85 residues processed: 528 average time/residue: 0.4499 time to fit residues: 291.2926 Evaluate side-chains 583 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 492 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain N residue 1102 LYS Chi-restraints excluded: chain N residue 1106 LYS Chi-restraints excluded: chain P residue 1302 LYS Chi-restraints excluded: chain Q residue 106 LYS Chi-restraints excluded: chain S residue 302 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 0 residue 1302 LYS Chi-restraints excluded: chain 1 residue 102 LYS Chi-restraints excluded: chain 1 residue 106 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 EA residue 1302 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 102 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain QA residue 1102 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 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 dA residue 1006 LYS 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 e residue 6 LYS 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 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 4 GLU Chi-restraints excluded: chain h residue 6 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 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: 0.7980 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: 0.8574 moved from start: 0.6526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.319 12528 Z= 6.066 Angle : 3.967 31.667 16272 Z= 1.754 Chirality : 0.298 0.787 1152 Planarity : 0.017 0.060 2160 Dihedral : 21.933 92.588 1786 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 105.43 Ramachandran Plot: Outliers : 0.52 % Allowed : 21.88 % Favored : 77.60 % Rotamer: Outliers : 11.34 % Allowed : 21.06 % Favored : 67.59 % Cbeta Deviations : 12.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -7.13 (0.19), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.43 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.115 0.018 PHE G 7 *********************** 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 561 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 463 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8250 (mp0) cc_final: 0.7920 (mp0) REVERT: J 106 LYS cc_start: 0.8966 (mmmm) cc_final: 0.8528 (mmmm) REVERT: K 204 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7950 (mt-10) REVERT: M 1004 GLU cc_start: 0.8280 (mp0) cc_final: 0.8000 (mp0) REVERT: N 1106 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8538 (mmmm) REVERT: O 1204 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8038 (mt-10) REVERT: P 1304 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8173 (mm-30) REVERT: B 6 LYS cc_start: 0.9056 (mtmt) cc_final: 0.8670 (mtmt) REVERT: Q 106 LYS cc_start: 0.8793 (mmmm) cc_final: 0.8490 (mmmm) REVERT: R 202 LYS cc_start: 0.9204 (mtpt) cc_final: 0.8881 (mtpt) REVERT: R 204 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7545 (mt-10) REVERT: S 302 LYS cc_start: 0.9255 (ttpt) cc_final: 0.8879 (ttmm) REVERT: T 1006 LYS cc_start: 0.9026 (mtmt) cc_final: 0.8598 (mtmt) REVERT: U 1106 LYS cc_start: 0.8790 (mmmm) cc_final: 0.8464 (mmmm) REVERT: V 1202 LYS cc_start: 0.9127 (mtpt) cc_final: 0.8799 (mtpt) REVERT: W 1302 LYS cc_start: 0.9256 (ttpt) cc_final: 0.8886 (ttmm) REVERT: C 6 LYS cc_start: 0.9030 (mtmt) cc_final: 0.8645 (mtmt) REVERT: X 106 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8592 (mmmm) REVERT: j 1006 LYS cc_start: 0.9022 (mtmt) cc_final: 0.8645 (mtmt) REVERT: k 1106 LYS cc_start: 0.8922 (mmmm) cc_final: 0.8524 (mmmm) REVERT: l 1202 LYS cc_start: 0.9131 (mtpt) cc_final: 0.8680 (mmmm) REVERT: m 1302 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8746 (ttpt) REVERT: n 106 LYS cc_start: 0.9117 (mmmm) cc_final: 0.8821 (mmmm) REVERT: o 202 LYS cc_start: 0.9111 (mtpt) cc_final: 0.8588 (mmmm) REVERT: o 206 LYS cc_start: 0.8849 (ttmm) cc_final: 0.8648 (ttmm) REVERT: p 302 LYS cc_start: 0.9180 (ttpt) cc_final: 0.8730 (ttpp) REVERT: p 304 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7494 (mm-30) REVERT: p 306 LYS cc_start: 0.9005 (tttt) cc_final: 0.8799 (tttt) REVERT: r 1106 LYS cc_start: 0.9115 (mmmm) cc_final: 0.8818 (mmmm) REVERT: t 1304 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7807 (mm-30) REVERT: u 104 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7784 (mm-30) REVERT: u 106 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8797 (mmmm) REVERT: w 302 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8906 (ttmm) REVERT: x 1006 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8224 (mtmt) REVERT: y 1102 LYS cc_start: 0.9189 (ttpt) cc_final: 0.8611 (ttmm) REVERT: y 1104 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7773 (mm-30) REVERT: y 1106 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8628 (mmmm) REVERT: 0 1302 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8926 (ttmm) REVERT: F 4 GLU cc_start: 0.8097 (mp0) cc_final: 0.7166 (mp0) REVERT: 2 202 LYS cc_start: 0.9186 (mtpt) cc_final: 0.8860 (mtpt) REVERT: 2 204 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7385 (mt-10) REVERT: 4 1004 GLU cc_start: 0.8123 (mp0) cc_final: 0.7257 (mp0) REVERT: 6 1202 LYS cc_start: 0.9182 (mtpt) cc_final: 0.8853 (mtpt) REVERT: G 6 LYS cc_start: 0.8954 (mtmt) cc_final: 0.8746 (mtmt) REVERT: 8 106 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8581 (mmmm) REVERT: AA 306 LYS cc_start: 0.8989 (tttt) cc_final: 0.8780 (tttt) REVERT: BA 1006 LYS cc_start: 0.8957 (mtmt) cc_final: 0.8691 (mtmt) REVERT: CA 1106 LYS cc_start: 0.8909 (mmmm) cc_final: 0.8617 (mmmm) REVERT: EA 1304 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7894 (mm-30) REVERT: EA 1306 LYS cc_start: 0.8992 (tttt) cc_final: 0.8748 (tttt) REVERT: FA 104 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7537 (mm-30) REVERT: FA 106 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8762 (mmmm) REVERT: HA 304 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7337 (mm-30) REVERT: JA 1104 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7530 (mm-30) REVERT: JA 1106 LYS cc_start: 0.9016 (mmmm) cc_final: 0.8775 (mmmm) REVERT: I 6 LYS cc_start: 0.8953 (mtmt) cc_final: 0.8465 (mtmt) REVERT: MA 102 LYS cc_start: 0.9050 (ttpt) cc_final: 0.8726 (mmtt) REVERT: NA 202 LYS cc_start: 0.9074 (mtpt) cc_final: 0.8823 (mtpt) REVERT: OA 302 LYS cc_start: 0.9313 (ttpt) cc_final: 0.8867 (tptt) REVERT: OA 304 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8035 (mm-30) REVERT: PA 1006 LYS cc_start: 0.8924 (mtmt) cc_final: 0.8480 (mtmt) REVERT: QA 1102 LYS cc_start: 0.9066 (ttpt) cc_final: 0.8719 (tptt) REVERT: SA 1302 LYS cc_start: 0.9313 (ttpt) cc_final: 0.8875 (tptt) REVERT: SA 1304 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8086 (mm-30) REVERT: TA 102 LYS cc_start: 0.9196 (tptm) cc_final: 0.8991 (tptm) REVERT: TA 105 PHE cc_start: 0.9377 (OUTLIER) cc_final: 0.8867 (p90) REVERT: XA 1105 PHE cc_start: 0.9379 (OUTLIER) cc_final: 0.8707 (p90) REVERT: b 2 LYS cc_start: 0.9073 (ttmt) cc_final: 0.8844 (ttmt) REVERT: b 6 LYS cc_start: 0.9182 (ttpt) cc_final: 0.8914 (ttpt) REVERT: aA 102 LYS cc_start: 0.9233 (tptm) cc_final: 0.9015 (tptm) REVERT: bA 202 LYS cc_start: 0.9367 (tttm) cc_final: 0.8923 (ttmm) REVERT: cA 307 PHE cc_start: 0.9198 (t80) cc_final: 0.8943 (t80) REVERT: dA 1006 LYS cc_start: 0.9138 (ttpt) cc_final: 0.8893 (ttpt) REVERT: eA 1102 LYS cc_start: 0.9237 (tptm) cc_final: 0.9033 (tptm) REVERT: eA 1104 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8087 (tm-30) REVERT: gA 1306 LYS cc_start: 0.8865 (tptp) cc_final: 0.8658 (tptp) REVERT: gA 1307 PHE cc_start: 0.9164 (t80) cc_final: 0.8876 (t80) REVERT: iA 202 LYS cc_start: 0.9379 (tttm) cc_final: 0.8999 (ttmm) REVERT: iA 206 LYS cc_start: 0.9355 (tttt) cc_final: 0.9150 (tttm) REVERT: jA 305 PHE cc_start: 0.9326 (t80) cc_final: 0.9020 (t80) REVERT: jA 306 LYS cc_start: 0.9194 (tptp) cc_final: 0.8905 (tptp) REVERT: lA 1102 LYS cc_start: 0.9319 (tptm) cc_final: 0.9029 (tptm) REVERT: mA 1206 LYS cc_start: 0.9329 (tttt) cc_final: 0.9113 (tttm) REVERT: nA 1305 PHE cc_start: 0.9300 (t80) cc_final: 0.8986 (t80) REVERT: nA 1306 LYS cc_start: 0.9186 (tptp) cc_final: 0.8887 (tptp) REVERT: d 2 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8911 (ptpt) REVERT: oA 104 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8276 (tm-30) REVERT: pA 202 LYS cc_start: 0.9364 (tttm) cc_final: 0.8907 (ttmm) REVERT: pA 206 LYS cc_start: 0.9309 (tttt) cc_final: 0.9071 (tttt) REVERT: qA 302 LYS cc_start: 0.9126 (tptp) cc_final: 0.8901 (tptp) REVERT: sA 1103 PHE cc_start: 0.9375 (t80) cc_final: 0.9162 (t80) REVERT: sA 1104 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8173 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9271 (tttt) cc_final: 0.9061 (tttt) REVERT: uA 1302 LYS cc_start: 0.9119 (tptp) cc_final: 0.8895 (tptp) REVERT: e 4 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8339 (tp30) REVERT: vA 104 GLU cc_start: 0.8679 (tm-30) cc_final: 0.7695 (tm-30) REVERT: vA 105 PHE cc_start: 0.9275 (t80) cc_final: 0.9030 (t80) REVERT: wA 202 LYS cc_start: 0.9292 (tttm) cc_final: 0.8798 (ttmm) REVERT: yA 1004 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8269 (tp30) REVERT: zA 1104 GLU cc_start: 0.8663 (tm-30) cc_final: 0.7687 (tm-30) REVERT: zA 1105 PHE cc_start: 0.9283 (t80) cc_final: 0.9032 (t80) REVERT: 0A 1202 LYS cc_start: 0.9213 (tttm) cc_final: 0.8746 (ttmm) REVERT: 3A 202 LYS cc_start: 0.9377 (tttm) cc_final: 0.8863 (tppp) REVERT: 4A 306 LYS cc_start: 0.9012 (tptp) cc_final: 0.8725 (tptp) REVERT: 9A 102 LYS cc_start: 0.9306 (tptm) cc_final: 0.9041 (tptm) REVERT: 9A 106 LYS cc_start: 0.9141 (tttp) cc_final: 0.8861 (tttm) REVERT: AB 202 LYS cc_start: 0.9401 (tttm) cc_final: 0.9032 (ttmm) REVERT: BB 306 LYS cc_start: 0.9262 (tptp) cc_final: 0.8954 (tptp) REVERT: DB 1102 LYS cc_start: 0.9299 (tptm) cc_final: 0.9057 (tptm) REVERT: FB 1306 LYS cc_start: 0.9255 (tptp) cc_final: 0.8982 (tptp) REVERT: GB 102 LYS cc_start: 0.9224 (tptm) cc_final: 0.8954 (tptm) REVERT: HB 202 LYS cc_start: 0.9271 (tttm) cc_final: 0.8862 (ttmm) REVERT: KB 1102 LYS cc_start: 0.9233 (tptm) cc_final: 0.8969 (tptm) REVERT: MB 1306 LYS cc_start: 0.9235 (tptp) cc_final: 0.9033 (tptp) REVERT: OB 204 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8277 (tm-30) REVERT: OB 206 LYS cc_start: 0.9264 (tttt) cc_final: 0.8985 (tttm) REVERT: PB 302 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8778 (tptp) REVERT: PB 304 GLU cc_start: 0.8813 (tm-30) cc_final: 0.7739 (pm20) REVERT: PB 307 PHE cc_start: 0.9392 (t80) cc_final: 0.9143 (t80) REVERT: SB 1204 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8237 (tm-30) REVERT: TB 1302 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8752 (tptp) REVERT: TB 1304 GLU cc_start: 0.8783 (tm-30) cc_final: 0.7735 (pm20) REVERT: TB 1307 PHE cc_start: 0.9367 (t80) cc_final: 0.9095 (t80) outliers start: 98 outliers final: 66 residues processed: 475 average time/residue: 0.4699 time to fit residues: 270.5975 Evaluate side-chains 543 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 463 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain m residue 1302 LYS Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain UA residue 204 GLU Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1204 GLU Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain bA residue 204 GLU Chi-restraints excluded: chain bA residue 206 LYS Chi-restraints excluded: chain cA residue 302 LYS Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain fA residue 1206 LYS Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain iA residue 204 GLU Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain kA residue 1004 GLU Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1204 GLU Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain pA residue 204 GLU Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1004 GLU Chi-restraints excluded: chain tA residue 1204 GLU Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain wA residue 204 GLU Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain 0A residue 1204 GLU Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 204 GLU 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 g residue 4 GLU Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain EB residue 1204 GLU Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain IB residue 302 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1302 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain OB residue 204 GLU Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1204 GLU Chi-restraints excluded: chain TB residue 1302 LYS 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: 0.8496 moved from start: 0.7192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.311 12528 Z= 6.101 Angle : 4.166 63.214 16272 Z= 1.829 Chirality : 0.297 0.841 1152 Planarity : 0.016 0.063 2160 Dihedral : 21.616 95.806 1548 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 111.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 29.17 % Favored : 70.83 % Rotamer: Outliers : 15.51 % Allowed : 25.46 % Favored : 59.03 % Cbeta Deviations : 13.80 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.19 % 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: -7.63 (0.20), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.81 (0.15), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.102 0.017 PHE9A 103 *********************** 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 583 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 449 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 104 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7339 (mm-30) REVERT: J 106 LYS cc_start: 0.8974 (mmmm) cc_final: 0.8552 (mmmm) REVERT: K 204 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8052 (mt-10) REVERT: N 1104 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7583 (mm-30) REVERT: N 1106 LYS cc_start: 0.8965 (mmmm) cc_final: 0.8571 (mmmm) REVERT: O 1204 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8034 (mt-10) REVERT: B 6 LYS cc_start: 0.9051 (mtmt) cc_final: 0.8735 (mtmt) REVERT: Q 106 LYS cc_start: 0.8829 (mmmm) cc_final: 0.8481 (mmmm) REVERT: R 202 LYS cc_start: 0.9201 (mtpt) cc_final: 0.8808 (mtpt) REVERT: S 302 LYS cc_start: 0.9280 (ttpt) cc_final: 0.8924 (ttmm) REVERT: T 1006 LYS cc_start: 0.9008 (mtmt) cc_final: 0.8715 (mtmt) REVERT: U 1106 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8533 (mmmm) REVERT: V 1202 LYS cc_start: 0.9122 (mtpt) cc_final: 0.8840 (mtpt) REVERT: W 1302 LYS cc_start: 0.9285 (ttpt) cc_final: 0.8935 (ttmm) REVERT: C 4 GLU cc_start: 0.7491 (mp0) cc_final: 0.6661 (mp0) REVERT: C 6 LYS cc_start: 0.9039 (mtmt) cc_final: 0.8689 (mtmt) REVERT: X 106 LYS cc_start: 0.8969 (mmmm) cc_final: 0.8679 (mmmm) REVERT: Y 202 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8783 (mtpp) REVERT: Z 302 LYS cc_start: 0.9378 (ttpt) cc_final: 0.8892 (ttmm) REVERT: j 1004 GLU cc_start: 0.7526 (mp0) cc_final: 0.6869 (mp0) REVERT: j 1006 LYS cc_start: 0.8985 (mtmt) cc_final: 0.8687 (mtmt) REVERT: k 1106 LYS cc_start: 0.8978 (mmmm) cc_final: 0.8665 (mmmm) REVERT: l 1202 LYS cc_start: 0.9018 (mtpt) cc_final: 0.8640 (mmmm) REVERT: m 1302 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8866 (ttpt) REVERT: n 106 LYS cc_start: 0.9097 (mmmm) cc_final: 0.8769 (mmmm) REVERT: o 206 LYS cc_start: 0.8947 (ttmm) cc_final: 0.8740 (ttmm) REVERT: r 1106 LYS cc_start: 0.9109 (mmmm) cc_final: 0.8787 (mmmm) REVERT: E 6 LYS cc_start: 0.8783 (mtmt) cc_final: 0.8381 (mtmt) REVERT: u 104 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7757 (mm-30) REVERT: u 106 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8801 (mmmm) REVERT: w 302 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8865 (ttmm) REVERT: x 1006 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8361 (mtmt) REVERT: y 1104 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7720 (mm-30) REVERT: 0 1302 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8924 (ttmm) REVERT: F 4 GLU cc_start: 0.8063 (mp0) cc_final: 0.7273 (mp0) REVERT: F 6 LYS cc_start: 0.9004 (mtmt) cc_final: 0.8702 (mtmt) REVERT: 2 202 LYS cc_start: 0.9167 (mtpt) cc_final: 0.8832 (mtpt) REVERT: 2 204 GLU cc_start: 0.8235 (mt-10) cc_final: 0.8000 (mt-10) REVERT: 4 1004 GLU cc_start: 0.8077 (mp0) cc_final: 0.7260 (mp0) REVERT: 6 1202 LYS cc_start: 0.9166 (mtpt) cc_final: 0.8830 (mtpt) REVERT: G 6 LYS cc_start: 0.8993 (mtmt) cc_final: 0.8730 (mtmt) REVERT: 8 106 LYS cc_start: 0.8997 (mmmm) cc_final: 0.8669 (mmmm) REVERT: CA 1106 LYS cc_start: 0.8924 (mmmm) cc_final: 0.8637 (mmmm) REVERT: FA 104 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7575 (mm-30) REVERT: FA 106 LYS cc_start: 0.9003 (mmmm) cc_final: 0.8780 (mmmm) REVERT: GA 202 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8627 (mtpt) REVERT: JA 1104 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7531 (mm-30) REVERT: JA 1106 LYS cc_start: 0.8995 (mmmm) cc_final: 0.8762 (mmmm) REVERT: LA 1304 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8270 (mm-30) REVERT: LA 1306 LYS cc_start: 0.9059 (tttt) cc_final: 0.8832 (tttt) REVERT: I 6 LYS cc_start: 0.8954 (mtmt) cc_final: 0.8496 (mtmt) REVERT: MA 104 GLU cc_start: 0.6224 (OUTLIER) cc_final: 0.5936 (mm-30) REVERT: OA 302 LYS cc_start: 0.9312 (ttpt) cc_final: 0.8852 (tptt) REVERT: OA 304 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8208 (mm-30) REVERT: PA 1006 LYS cc_start: 0.8909 (mtmt) cc_final: 0.8494 (mtmt) REVERT: SA 1302 LYS cc_start: 0.9277 (ttpt) cc_final: 0.8894 (tptt) REVERT: SA 1304 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8294 (mm-30) REVERT: TA 105 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.8852 (p90) REVERT: TA 106 LYS cc_start: 0.9253 (tttp) cc_final: 0.8816 (tttp) REVERT: XA 1105 PHE cc_start: 0.9366 (OUTLIER) cc_final: 0.8712 (p90) REVERT: b 2 LYS cc_start: 0.9026 (ttmt) cc_final: 0.8791 (ttmt) REVERT: aA 104 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8239 (tm-30) REVERT: bA 202 LYS cc_start: 0.9356 (tttm) cc_final: 0.8961 (ttmm) REVERT: dA 1004 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8369 (tp30) REVERT: dA 1006 LYS cc_start: 0.9144 (ttpt) cc_final: 0.8921 (ttpt) REVERT: eA 1104 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8215 (tm-30) REVERT: gA 1306 LYS cc_start: 0.8923 (tptp) cc_final: 0.8641 (tptp) REVERT: iA 202 LYS cc_start: 0.9371 (tttm) cc_final: 0.9017 (ttmm) REVERT: iA 204 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8216 (tm-30) REVERT: jA 306 LYS cc_start: 0.9206 (tptp) cc_final: 0.8838 (tptp) REVERT: mA 1204 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8249 (tm-30) REVERT: nA 1306 LYS cc_start: 0.9190 (tptp) cc_final: 0.8824 (tptp) REVERT: oA 104 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8401 (tm-30) REVERT: pA 206 LYS cc_start: 0.9281 (tttt) cc_final: 0.9069 (tttt) REVERT: sA 1104 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8340 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9271 (tttt) cc_final: 0.9062 (tttt) REVERT: e 2 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8809 (tppt) REVERT: vA 104 GLU cc_start: 0.8708 (tm-30) cc_final: 0.7898 (tm-30) REVERT: vA 105 PHE cc_start: 0.9240 (t80) cc_final: 0.9039 (t80) REVERT: wA 202 LYS cc_start: 0.9319 (tttm) cc_final: 0.8901 (ttmm) REVERT: yA 1002 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8773 (tppt) REVERT: zA 1104 GLU cc_start: 0.8707 (tm-30) cc_final: 0.7769 (tm-30) REVERT: zA 1105 PHE cc_start: 0.9246 (t80) cc_final: 0.9010 (t80) REVERT: 0A 1202 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8885 (ttmm) REVERT: 3A 202 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.8755 (tppp) REVERT: 4A 302 LYS cc_start: 0.8891 (tptp) cc_final: 0.8399 (tptp) REVERT: 4A 306 LYS cc_start: 0.9057 (tptp) cc_final: 0.8757 (tptp) REVERT: 8A 1306 LYS cc_start: 0.9040 (tptp) cc_final: 0.8767 (tptp) REVERT: g 6 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8915 (ttpt) REVERT: 9A 106 LYS cc_start: 0.9149 (tttp) cc_final: 0.8837 (tttm) REVERT: AB 202 LYS cc_start: 0.9416 (tttm) cc_final: 0.9082 (ttmm) REVERT: BB 305 PHE cc_start: 0.9351 (t80) cc_final: 0.9036 (t80) REVERT: BB 306 LYS cc_start: 0.9252 (tptp) cc_final: 0.8945 (tptp) REVERT: DB 1102 LYS cc_start: 0.9294 (tptm) cc_final: 0.9060 (tptm) REVERT: EB 1202 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.8847 (tppp) REVERT: FB 1305 PHE cc_start: 0.9354 (t80) cc_final: 0.9077 (t80) REVERT: FB 1306 LYS cc_start: 0.9204 (tptp) cc_final: 0.8898 (tptp) REVERT: GB 102 LYS cc_start: 0.9238 (tptm) cc_final: 0.9009 (tptm) REVERT: KB 1102 LYS cc_start: 0.9261 (tptm) cc_final: 0.9026 (tptm) REVERT: MB 1306 LYS cc_start: 0.9253 (tptp) cc_final: 0.9049 (tptp) REVERT: NB 106 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8992 (ptmm) REVERT: OB 202 LYS cc_start: 0.9370 (tttm) cc_final: 0.9013 (tppp) REVERT: OB 206 LYS cc_start: 0.9287 (tttt) cc_final: 0.9023 (tttm) REVERT: PB 302 LYS cc_start: 0.8959 (tptp) cc_final: 0.8717 (tptp) REVERT: PB 304 GLU cc_start: 0.8811 (tm-30) cc_final: 0.7884 (pm20) REVERT: SB 1206 LYS cc_start: 0.9281 (tttt) cc_final: 0.9032 (pttt) REVERT: TB 1302 LYS cc_start: 0.8927 (tptp) cc_final: 0.8671 (tptp) REVERT: TB 1304 GLU cc_start: 0.8864 (tm-30) cc_final: 0.7742 (pm20) outliers start: 134 outliers final: 89 residues processed: 474 average time/residue: 0.4721 time to fit residues: 271.0844 Evaluate side-chains 555 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 449 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain m residue 1302 LYS Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain IA residue 1004 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain MA residue 104 GLU Chi-restraints excluded: chain QA residue 1104 GLU Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain UA residue 204 GLU 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 YA residue 1204 GLU Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain bA residue 204 GLU Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain iA residue 204 GLU Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1204 GLU Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 204 GLU Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1204 GLU Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain wA residue 204 GLU Chi-restraints excluded: chain xA residue 302 LYS 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 0A residue 1202 LYS Chi-restraints excluded: chain 0A residue 1204 GLU Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 3A residue 204 GLU Chi-restraints excluded: chain 5A residue 1002 LYS 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 g residue 4 GLU Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS 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 1202 LYS Chi-restraints excluded: chain EB residue 1204 GLU 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 IB residue 302 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1302 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain NB residue 106 LYS Chi-restraints excluded: chain OB residue 204 GLU Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1204 GLU 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: 0.8488 moved from start: 0.7457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.307 12528 Z= 6.112 Angle : 4.193 60.994 16272 Z= 1.841 Chirality : 0.297 0.790 1152 Planarity : 0.016 0.057 2160 Dihedral : 21.366 84.479 1525 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 112.33 Ramachandran Plot: Outliers : 0.35 % Allowed : 31.42 % Favored : 68.23 % Rotamer: Outliers : 16.78 % Allowed : 27.20 % Favored : 56.02 % Cbeta Deviations : 14.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.59 % 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: -7.85 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.98 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.106 0.016 PHEPB 303 *********************** 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 595 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 450 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8441 (mp0) cc_final: 0.8140 (mp0) REVERT: A 6 LYS cc_start: 0.8976 (mtmt) cc_final: 0.8710 (mmmt) REVERT: J 104 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7341 (mm-30) REVERT: J 106 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8555 (mmmm) REVERT: M 1004 GLU cc_start: 0.8434 (mp0) cc_final: 0.8101 (mp0) REVERT: N 1104 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7448 (mm-30) REVERT: N 1106 LYS cc_start: 0.8985 (mmmm) cc_final: 0.8571 (mmmm) REVERT: B 4 GLU cc_start: 0.8352 (mp0) cc_final: 0.7593 (mp0) REVERT: B 6 LYS cc_start: 0.9040 (mtmt) cc_final: 0.8726 (mtmt) REVERT: Q 106 LYS cc_start: 0.8903 (mmmm) cc_final: 0.8541 (mmmm) REVERT: R 202 LYS cc_start: 0.9226 (mtpt) cc_final: 0.8847 (mtpt) REVERT: S 302 LYS cc_start: 0.9287 (ttpt) cc_final: 0.8935 (ttmm) REVERT: T 1006 LYS cc_start: 0.8987 (mtmt) cc_final: 0.8698 (mtmt) REVERT: U 1104 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7835 (mm-30) REVERT: U 1106 LYS cc_start: 0.8878 (mmmm) cc_final: 0.8542 (mmmm) REVERT: V 1202 LYS cc_start: 0.9121 (mtpt) cc_final: 0.8857 (mtpt) REVERT: W 1302 LYS cc_start: 0.9286 (ttpt) cc_final: 0.8914 (ttmm) REVERT: C 4 GLU cc_start: 0.7315 (mp0) cc_final: 0.6355 (mp0) REVERT: C 6 LYS cc_start: 0.9008 (mtmt) cc_final: 0.8689 (mtmt) REVERT: X 106 LYS cc_start: 0.9010 (mmmm) cc_final: 0.8689 (mmmm) REVERT: Y 202 LYS cc_start: 0.9059 (mtpt) cc_final: 0.8804 (mtpp) REVERT: Z 302 LYS cc_start: 0.9398 (ttpt) cc_final: 0.8934 (ttmm) REVERT: j 1004 GLU cc_start: 0.7378 (mp0) cc_final: 0.6564 (mp0) REVERT: j 1006 LYS cc_start: 0.8980 (mtmt) cc_final: 0.8656 (mtmt) REVERT: k 1106 LYS cc_start: 0.8962 (mmmm) cc_final: 0.8646 (mmmm) REVERT: l 1202 LYS cc_start: 0.8993 (mtpt) cc_final: 0.8789 (mtpp) REVERT: D 4 GLU cc_start: 0.8438 (mp0) cc_final: 0.7818 (mp0) REVERT: n 104 GLU cc_start: 0.7760 (mm-30) cc_final: 0.6912 (mm-30) REVERT: n 106 LYS cc_start: 0.9075 (mmmm) cc_final: 0.8765 (mmmm) REVERT: o 202 LYS cc_start: 0.9167 (mtpt) cc_final: 0.8727 (mmmm) REVERT: o 206 LYS cc_start: 0.8959 (ttmm) cc_final: 0.8731 (ttmm) REVERT: q 1004 GLU cc_start: 0.8483 (mp0) cc_final: 0.7879 (mp0) REVERT: r 1106 LYS cc_start: 0.9065 (mmmm) cc_final: 0.8750 (mmmm) REVERT: E 2 LYS cc_start: 0.6735 (OUTLIER) cc_final: 0.6457 (mmtp) REVERT: E 6 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8398 (mtmt) REVERT: u 104 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7824 (mm-30) REVERT: u 106 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8954 (mmmm) REVERT: w 302 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8860 (ttmm) REVERT: x 1002 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.6437 (mmtp) REVERT: x 1006 LYS cc_start: 0.8768 (mtmt) cc_final: 0.8394 (mtmt) REVERT: y 1104 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7511 (mm-30) REVERT: y 1106 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8558 (mmmm) REVERT: 0 1302 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8924 (ttmm) REVERT: F 4 GLU cc_start: 0.8093 (mp0) cc_final: 0.7332 (mp0) REVERT: F 6 LYS cc_start: 0.8977 (mtmt) cc_final: 0.8701 (mtmt) REVERT: 1 104 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7935 (mm-30) REVERT: 1 106 LYS cc_start: 0.9001 (mmmm) cc_final: 0.8749 (mmmm) REVERT: 2 202 LYS cc_start: 0.9173 (mtpt) cc_final: 0.8843 (mtpt) REVERT: 2 206 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8656 (ptmm) REVERT: 4 1004 GLU cc_start: 0.8095 (mp0) cc_final: 0.7337 (mp0) REVERT: 5 1104 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7796 (mm-30) REVERT: 5 1106 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8728 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9158 (mtpt) cc_final: 0.8818 (mtpt) REVERT: 7 1304 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7874 (tp30) REVERT: 8 106 LYS cc_start: 0.8962 (mmmm) cc_final: 0.8661 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8045 (mp0) cc_final: 0.6831 (mp0) REVERT: CA 1106 LYS cc_start: 0.8908 (mmmm) cc_final: 0.8630 (mmmm) REVERT: FA 104 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7442 (mm-30) REVERT: FA 106 LYS cc_start: 0.9019 (mmmm) cc_final: 0.8759 (mmmm) REVERT: GA 202 LYS cc_start: 0.8926 (mtpt) cc_final: 0.8672 (mtpt) REVERT: HA 304 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8302 (mm-30) REVERT: JA 1104 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7433 (mm-30) REVERT: JA 1106 LYS cc_start: 0.9014 (mmmm) cc_final: 0.8779 (mmmm) REVERT: I 6 LYS cc_start: 0.8971 (mtmt) cc_final: 0.8503 (mtmt) REVERT: OA 302 LYS cc_start: 0.9291 (ttpt) cc_final: 0.8851 (tptt) REVERT: OA 304 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8327 (mm-30) REVERT: PA 1006 LYS cc_start: 0.8935 (mtmt) cc_final: 0.8680 (mtmt) REVERT: QA 1102 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8638 (tptt) REVERT: SA 1302 LYS cc_start: 0.9302 (ttpt) cc_final: 0.8876 (tptt) REVERT: SA 1304 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8397 (mm-30) REVERT: SA 1306 LYS cc_start: 0.6479 (OUTLIER) cc_final: 0.5962 (mmmt) REVERT: TA 105 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.8862 (p90) REVERT: XA 1105 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.8837 (p90) REVERT: b 2 LYS cc_start: 0.9026 (ttmt) cc_final: 0.8793 (ttmt) REVERT: bA 202 LYS cc_start: 0.9344 (tttm) cc_final: 0.8980 (ttmm) REVERT: gA 1306 LYS cc_start: 0.9013 (tptp) cc_final: 0.8716 (tptp) REVERT: iA 202 LYS cc_start: 0.9374 (tttm) cc_final: 0.9004 (ttmm) REVERT: iA 204 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8278 (tm-30) REVERT: jA 306 LYS cc_start: 0.9216 (tptp) cc_final: 0.8872 (ttpp) REVERT: mA 1204 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8255 (tm-30) REVERT: nA 1306 LYS cc_start: 0.9177 (tptp) cc_final: 0.8885 (ttpp) REVERT: oA 104 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8199 (tm-30) REVERT: sA 1104 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8120 (tm-30) REVERT: e 2 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8798 (tppt) REVERT: vA 104 GLU cc_start: 0.8656 (tm-30) cc_final: 0.7934 (tm-30) REVERT: vA 105 PHE cc_start: 0.9192 (t80) cc_final: 0.8974 (t80) REVERT: wA 202 LYS cc_start: 0.9323 (tttm) cc_final: 0.8883 (ttmm) REVERT: yA 1002 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8771 (tppt) REVERT: zA 1105 PHE cc_start: 0.9234 (t80) cc_final: 0.8965 (t80) REVERT: 0A 1202 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8849 (ttmm) REVERT: 3A 202 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.8761 (tppp) REVERT: 4A 302 LYS cc_start: 0.8857 (tptp) cc_final: 0.8410 (tptp) REVERT: 4A 306 LYS cc_start: 0.9009 (tptp) cc_final: 0.8708 (tptp) REVERT: g 6 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8930 (ttpt) REVERT: 9A 106 LYS cc_start: 0.9162 (tttp) cc_final: 0.8865 (tttm) REVERT: BB 302 LYS cc_start: 0.8918 (tptp) cc_final: 0.8603 (tptp) REVERT: BB 305 PHE cc_start: 0.9347 (t80) cc_final: 0.9076 (t80) REVERT: BB 306 LYS cc_start: 0.9230 (tptp) cc_final: 0.8925 (tptp) REVERT: EB 1202 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.8848 (tppp) REVERT: FB 1305 PHE cc_start: 0.9337 (t80) cc_final: 0.9030 (t80) REVERT: FB 1306 LYS cc_start: 0.9210 (tptp) cc_final: 0.8930 (tptp) REVERT: NB 106 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8973 (ptmm) REVERT: OB 202 LYS cc_start: 0.9358 (tttm) cc_final: 0.9015 (tppp) REVERT: OB 206 LYS cc_start: 0.9281 (tttt) cc_final: 0.9013 (tttm) REVERT: PB 302 LYS cc_start: 0.8970 (tptp) cc_final: 0.8741 (tptp) REVERT: PB 304 GLU cc_start: 0.8790 (tm-30) cc_final: 0.7861 (pm20) REVERT: TB 1302 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8696 (tptp) REVERT: TB 1304 GLU cc_start: 0.8834 (tm-30) cc_final: 0.7782 (pm20) outliers start: 145 outliers final: 105 residues processed: 481 average time/residue: 0.4607 time to fit residues: 269.1586 Evaluate side-chains 578 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 452 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain U residue 1107 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain X residue 104 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 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 p residue 307 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain IA residue 1004 GLU Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain UA residue 204 GLU 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 YA residue 1204 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain bA residue 204 GLU Chi-restraints excluded: chain cA residue 302 LYS Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain iA residue 204 GLU Chi-restraints excluded: chain iA residue 206 LYS Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1202 LYS Chi-restraints excluded: chain mA residue 1204 GLU Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 204 GLU Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1204 GLU Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain wA residue 204 GLU Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 0A residue 1204 GLU Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 3A residue 204 GLU Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 7A residue 1204 GLU Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS 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 1202 LYS Chi-restraints excluded: chain EB residue 1204 GLU 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 103 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 1202 LYS Chi-restraints excluded: chain MB residue 1302 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain NB residue 106 LYS Chi-restraints excluded: chain OB residue 204 GLU Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1204 GLU Chi-restraints excluded: chain TB residue 1302 LYS 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: 0.8490 moved from start: 0.7554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.308 12528 Z= 6.114 Angle : 4.203 62.537 16272 Z= 1.847 Chirality : 0.298 0.770 1152 Planarity : 0.016 0.056 2160 Dihedral : 21.343 89.078 1515 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 113.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 33.16 % Favored : 66.84 % Rotamer: Outliers : 17.59 % Allowed : 28.70 % Favored : 53.70 % Cbeta Deviations : 14.93 % 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: -7.87 (0.19), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.99 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.116 0.016 PHE V1207 *********************** 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 603 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 451 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8979 (mtmt) cc_final: 0.8745 (mmmt) REVERT: J 104 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7351 (mm-30) REVERT: J 106 LYS cc_start: 0.8997 (mmmm) cc_final: 0.8533 (mmmm) REVERT: L 304 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8006 (mm-30) REVERT: M 1006 LYS cc_start: 0.8964 (mtmt) cc_final: 0.8701 (mmmt) REVERT: N 1104 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7502 (mm-30) REVERT: N 1106 LYS cc_start: 0.8995 (mmmm) cc_final: 0.8562 (mmmm) REVERT: P 1304 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8061 (mm-30) REVERT: B 4 GLU cc_start: 0.8388 (mp0) cc_final: 0.7639 (mp0) REVERT: B 6 LYS cc_start: 0.9047 (mtmt) cc_final: 0.8703 (mtmt) REVERT: Q 106 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8522 (mmmm) REVERT: R 202 LYS cc_start: 0.9203 (mtpt) cc_final: 0.8829 (mtpt) REVERT: S 302 LYS cc_start: 0.9271 (ttpt) cc_final: 0.8928 (ttmm) REVERT: T 1004 GLU cc_start: 0.8401 (mp0) cc_final: 0.7676 (mp0) REVERT: T 1006 LYS cc_start: 0.9022 (mtmt) cc_final: 0.8703 (mtmt) REVERT: U 1106 LYS cc_start: 0.8878 (mmmm) cc_final: 0.8560 (mmmm) REVERT: V 1202 LYS cc_start: 0.9110 (mtpt) cc_final: 0.8843 (mtpt) REVERT: W 1302 LYS cc_start: 0.9292 (ttpt) cc_final: 0.8968 (ttmm) REVERT: C 4 GLU cc_start: 0.7261 (mp0) cc_final: 0.6409 (mp0) REVERT: C 6 LYS cc_start: 0.9001 (mtmt) cc_final: 0.8673 (mtmt) REVERT: X 106 LYS cc_start: 0.9022 (mmmm) cc_final: 0.8697 (mmmm) REVERT: Y 202 LYS cc_start: 0.9035 (mtpt) cc_final: 0.8662 (mmmm) REVERT: Z 302 LYS cc_start: 0.9418 (ttpt) cc_final: 0.8590 (ttpp) REVERT: j 1004 GLU cc_start: 0.7305 (mp0) cc_final: 0.6473 (mp0) REVERT: j 1006 LYS cc_start: 0.8997 (mtmt) cc_final: 0.8677 (mtmt) REVERT: k 1106 LYS cc_start: 0.8958 (mmmm) cc_final: 0.8626 (mmmm) REVERT: l 1202 LYS cc_start: 0.9017 (mtpt) cc_final: 0.8669 (mmmm) REVERT: D 4 GLU cc_start: 0.8387 (mp0) cc_final: 0.7875 (mp0) REVERT: n 104 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7027 (mm-30) REVERT: n 106 LYS cc_start: 0.9083 (mmmm) cc_final: 0.8705 (mmmm) REVERT: o 202 LYS cc_start: 0.9168 (mtpt) cc_final: 0.8757 (mmmm) REVERT: o 206 LYS cc_start: 0.8956 (ttmm) cc_final: 0.8713 (ttmm) REVERT: q 1002 LYS cc_start: 0.7673 (tttt) cc_final: 0.7371 (tptm) REVERT: q 1004 GLU cc_start: 0.8424 (mp0) cc_final: 0.7893 (mp0) REVERT: r 1104 GLU cc_start: 0.7749 (mm-30) cc_final: 0.6962 (mm-30) REVERT: r 1106 LYS cc_start: 0.9070 (mmmm) cc_final: 0.8724 (mmmm) REVERT: s 1202 LYS cc_start: 0.9087 (mtpt) cc_final: 0.8734 (mtpp) REVERT: E 2 LYS cc_start: 0.6696 (OUTLIER) cc_final: 0.6393 (mmtp) REVERT: E 6 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8414 (mtmt) REVERT: u 104 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7822 (mm-30) REVERT: u 106 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8936 (mmmm) REVERT: w 302 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8859 (ttmm) REVERT: x 1002 LYS cc_start: 0.6701 (OUTLIER) cc_final: 0.6404 (mmtp) REVERT: x 1006 LYS cc_start: 0.8758 (mtmt) cc_final: 0.8302 (mtmt) REVERT: y 1104 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7592 (mm-30) REVERT: y 1106 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8534 (mmmm) REVERT: 0 1302 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8911 (ttmm) REVERT: F 4 GLU cc_start: 0.8059 (mp0) cc_final: 0.6945 (mp0) REVERT: F 6 LYS cc_start: 0.8972 (mtmt) cc_final: 0.8718 (mtmt) REVERT: 1 104 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7737 (mm-30) REVERT: 1 106 LYS cc_start: 0.9007 (mmmm) cc_final: 0.8736 (mmmm) REVERT: 2 202 LYS cc_start: 0.9171 (mtpt) cc_final: 0.8945 (mtpt) REVERT: 4 1004 GLU cc_start: 0.8064 (mp0) cc_final: 0.6959 (mp0) REVERT: 4 1006 LYS cc_start: 0.8958 (mtmt) cc_final: 0.8694 (mtmt) REVERT: 5 1104 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7679 (mm-30) REVERT: 5 1106 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8718 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9154 (mtpt) cc_final: 0.8808 (mtpt) REVERT: 8 106 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8674 (mmmm) REVERT: AA 302 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.9031 (ttpt) REVERT: BA 1004 GLU cc_start: 0.8020 (mp0) cc_final: 0.6874 (mp0) REVERT: CA 1106 LYS cc_start: 0.8966 (mmmm) cc_final: 0.8670 (mmmm) REVERT: FA 104 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7356 (mm-30) REVERT: FA 106 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8746 (mmmm) REVERT: GA 202 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8693 (mtpt) REVERT: GA 204 GLU cc_start: 0.5127 (OUTLIER) cc_final: 0.4338 (pm20) REVERT: HA 304 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8373 (mm-30) REVERT: JA 1104 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7375 (mm-30) REVERT: JA 1106 LYS cc_start: 0.9030 (mmmm) cc_final: 0.8763 (mmmm) REVERT: I 6 LYS cc_start: 0.8981 (mtmt) cc_final: 0.8530 (mtmt) REVERT: OA 302 LYS cc_start: 0.9303 (ttpt) cc_final: 0.8836 (tptt) REVERT: OA 304 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8373 (mm-30) REVERT: OA 306 LYS cc_start: 0.5237 (OUTLIER) cc_final: 0.4721 (mmmt) REVERT: PA 1006 LYS cc_start: 0.8924 (mtmt) cc_final: 0.8662 (mtmt) REVERT: RA 1202 LYS cc_start: 0.9046 (ttpt) cc_final: 0.8650 (ttmm) REVERT: SA 1302 LYS cc_start: 0.9293 (ttpt) cc_final: 0.8831 (tptt) REVERT: SA 1306 LYS cc_start: 0.5688 (OUTLIER) cc_final: 0.5381 (mmmt) REVERT: TA 105 PHE cc_start: 0.9372 (OUTLIER) cc_final: 0.8843 (p90) REVERT: XA 1105 PHE cc_start: 0.9372 (OUTLIER) cc_final: 0.8839 (p90) REVERT: b 2 LYS cc_start: 0.9019 (ttmt) cc_final: 0.8785 (ttmt) REVERT: gA 1306 LYS cc_start: 0.9035 (tptp) cc_final: 0.8766 (tptp) REVERT: c 2 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8688 (ptpt) REVERT: hA 107 PHE cc_start: 0.9420 (OUTLIER) cc_final: 0.8963 (t80) REVERT: iA 202 LYS cc_start: 0.9383 (tttm) cc_final: 0.9008 (ttmm) REVERT: iA 204 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8233 (tm-30) REVERT: jA 306 LYS cc_start: 0.9218 (tptp) cc_final: 0.8844 (ttpp) REVERT: mA 1204 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8257 (tm-30) REVERT: nA 1306 LYS cc_start: 0.9187 (tptp) cc_final: 0.8885 (ttpp) REVERT: e 2 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8802 (tppt) REVERT: vA 104 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8009 (tm-30) REVERT: wA 202 LYS cc_start: 0.9327 (tttm) cc_final: 0.8848 (ttmm) REVERT: yA 1002 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8777 (tppt) REVERT: zA 1104 GLU cc_start: 0.8632 (tm-30) cc_final: 0.7943 (tm-30) REVERT: zA 1105 PHE cc_start: 0.9232 (t80) cc_final: 0.9000 (t80) REVERT: 0A 1202 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8845 (ttmm) REVERT: 3A 202 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8767 (tppp) REVERT: 4A 306 LYS cc_start: 0.9050 (tptp) cc_final: 0.8743 (tptp) REVERT: 8A 1302 LYS cc_start: 0.8773 (tptp) cc_final: 0.8305 (tptp) REVERT: 8A 1306 LYS cc_start: 0.9008 (tptp) cc_final: 0.8701 (tptp) REVERT: g 6 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8944 (ttpt) REVERT: 9A 102 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9105 (tptm) REVERT: AB 202 LYS cc_start: 0.9449 (tttm) cc_final: 0.9098 (tppp) REVERT: BB 302 LYS cc_start: 0.8950 (tptp) cc_final: 0.8640 (tptp) REVERT: BB 305 PHE cc_start: 0.9346 (t80) cc_final: 0.9064 (t80) REVERT: BB 306 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8950 (tptp) REVERT: EB 1202 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.8850 (tppp) REVERT: FB 1302 LYS cc_start: 0.8903 (tptp) cc_final: 0.8557 (tptp) REVERT: NB 106 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8992 (ptmm) REVERT: OB 202 LYS cc_start: 0.9354 (tttm) cc_final: 0.9019 (tppp) REVERT: OB 206 LYS cc_start: 0.9302 (tttt) cc_final: 0.9035 (tttm) REVERT: PB 302 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8743 (tptp) REVERT: PB 304 GLU cc_start: 0.8807 (tm-30) cc_final: 0.7868 (pm20) REVERT: TB 1302 LYS cc_start: 0.8925 (tptp) cc_final: 0.8673 (tptp) REVERT: TB 1304 GLU cc_start: 0.8834 (tm-30) cc_final: 0.7800 (pm20) outliers start: 152 outliers final: 115 residues processed: 484 average time/residue: 0.4610 time to fit residues: 271.2563 Evaluate side-chains 592 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 451 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain N residue 1102 LYS Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain U residue 1107 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain X residue 104 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 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 p residue 307 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain AA residue 302 LYS Chi-restraints excluded: chain H residue 4 GLU 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 IA residue 1004 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 NA residue 207 PHE Chi-restraints excluded: chain OA residue 306 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain UA residue 202 LYS Chi-restraints excluded: chain UA residue 204 GLU 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 1202 LYS Chi-restraints excluded: chain YA residue 1204 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain bA residue 204 GLU Chi-restraints excluded: chain cA residue 302 LYS Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain hA residue 107 PHE Chi-restraints excluded: chain iA residue 204 GLU Chi-restraints excluded: chain jA residue 302 LYS 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 lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1202 LYS Chi-restraints excluded: chain mA residue 1204 GLU Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 204 GLU Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1204 GLU Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain wA residue 204 GLU Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 0A residue 1204 GLU Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 3A residue 204 GLU Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 7A residue 1204 GLU Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 306 LYS Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS 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 1202 LYS Chi-restraints excluded: chain EB residue 1204 GLU 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 HB residue 206 LYS Chi-restraints excluded: chain IB residue 302 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 LB residue 1202 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain NB residue 106 LYS Chi-restraints excluded: chain OB residue 204 GLU Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1204 GLU 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: 0.8476 moved from start: 0.7639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.305 12528 Z= 6.121 Angle : 4.215 61.426 16272 Z= 1.852 Chirality : 0.298 0.767 1152 Planarity : 0.016 0.056 2160 Dihedral : 21.370 86.334 1503 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 114.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 33.16 % Favored : 66.84 % Rotamer: Outliers : 19.21 % Allowed : 29.17 % Favored : 51.62 % Cbeta Deviations : 14.50 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.28 % 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: -7.89 (0.19), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.01 (0.15), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.122 0.016 PHE V1207 *********************** 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 614 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 448 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8979 (mtmt) cc_final: 0.8770 (mmmt) REVERT: J 106 LYS cc_start: 0.9002 (mmmm) cc_final: 0.8532 (mmmm) REVERT: K 202 LYS cc_start: 0.9215 (mtpt) cc_final: 0.9006 (mtpt) REVERT: M 1006 LYS cc_start: 0.8971 (mtmt) cc_final: 0.8726 (mmmt) REVERT: N 1106 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8559 (mmmm) REVERT: B 4 GLU cc_start: 0.8405 (mp0) cc_final: 0.7617 (mp0) REVERT: B 6 LYS cc_start: 0.9084 (mtmt) cc_final: 0.8720 (mtmt) REVERT: Q 106 LYS cc_start: 0.8945 (mmmm) cc_final: 0.8513 (mmmm) REVERT: R 202 LYS cc_start: 0.9178 (mtpt) cc_final: 0.8849 (mtpt) REVERT: S 302 LYS cc_start: 0.9252 (ttpt) cc_final: 0.8920 (ttmm) REVERT: T 1004 GLU cc_start: 0.8400 (mp0) cc_final: 0.7659 (mp0) REVERT: T 1006 LYS cc_start: 0.9046 (mtmt) cc_final: 0.8697 (mtmt) REVERT: U 1106 LYS cc_start: 0.8881 (mmmm) cc_final: 0.8550 (mmmm) REVERT: V 1202 LYS cc_start: 0.9099 (mtpt) cc_final: 0.8836 (mtpt) REVERT: W 1302 LYS cc_start: 0.9280 (ttpt) cc_final: 0.8945 (ttmm) REVERT: C 6 LYS cc_start: 0.9000 (mtmt) cc_final: 0.8685 (mtmt) REVERT: X 106 LYS cc_start: 0.9016 (mmmm) cc_final: 0.8702 (mmmm) REVERT: Y 202 LYS cc_start: 0.9036 (mtpt) cc_final: 0.8740 (mtpp) REVERT: Z 302 LYS cc_start: 0.9374 (ttpt) cc_final: 0.8958 (ttpp) REVERT: j 1006 LYS cc_start: 0.9005 (mtmt) cc_final: 0.8665 (mtmt) REVERT: k 1106 LYS cc_start: 0.8964 (mmmm) cc_final: 0.8643 (mmmm) REVERT: l 1202 LYS cc_start: 0.9022 (mtpt) cc_final: 0.8719 (mtpp) REVERT: m 1302 LYS cc_start: 0.9368 (ttpt) cc_final: 0.8904 (ttpp) REVERT: m 1306 LYS cc_start: 0.9321 (tttt) cc_final: 0.8930 (mttt) REVERT: D 4 GLU cc_start: 0.8381 (mp0) cc_final: 0.7858 (mp0) REVERT: n 104 GLU cc_start: 0.7866 (mm-30) cc_final: 0.6970 (mm-30) REVERT: n 106 LYS cc_start: 0.9085 (mmmm) cc_final: 0.8686 (mmmm) REVERT: o 202 LYS cc_start: 0.9159 (mtpt) cc_final: 0.8750 (mmmm) REVERT: o 206 LYS cc_start: 0.8940 (ttmm) cc_final: 0.8719 (ttmm) REVERT: q 1002 LYS cc_start: 0.7745 (tttt) cc_final: 0.7440 (tptm) REVERT: q 1004 GLU cc_start: 0.8443 (mp0) cc_final: 0.7940 (mp0) REVERT: r 1104 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7032 (mm-30) REVERT: r 1106 LYS cc_start: 0.9077 (mmmm) cc_final: 0.8705 (mmmm) REVERT: s 1202 LYS cc_start: 0.9079 (mtpt) cc_final: 0.8708 (mtpp) REVERT: E 2 LYS cc_start: 0.6652 (OUTLIER) cc_final: 0.6382 (mmtp) REVERT: E 6 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8361 (mtmt) REVERT: u 104 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7614 (mm-30) REVERT: u 106 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8849 (mmmm) REVERT: w 302 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8859 (ttmm) REVERT: x 1002 LYS cc_start: 0.6718 (OUTLIER) cc_final: 0.6413 (mmtp) REVERT: y 1104 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7624 (mm-30) REVERT: y 1106 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8573 (mmmm) REVERT: 0 1302 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8903 (ttmm) REVERT: F 4 GLU cc_start: 0.8086 (mp0) cc_final: 0.7003 (mp0) REVERT: F 6 LYS cc_start: 0.8975 (mtmt) cc_final: 0.8726 (mtmt) REVERT: 1 104 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7844 (mm-30) REVERT: 1 106 LYS cc_start: 0.9002 (mmmm) cc_final: 0.8726 (mmmm) REVERT: 2 206 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8642 (ptmm) REVERT: 4 1004 GLU cc_start: 0.8096 (mp0) cc_final: 0.7020 (mp0) REVERT: 4 1006 LYS cc_start: 0.8967 (mtmt) cc_final: 0.8699 (mtmt) REVERT: 5 1104 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7831 (mm-30) REVERT: 5 1106 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8606 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9147 (mtpt) cc_final: 0.8809 (mtpt) REVERT: 6 1206 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8714 (ptmm) REVERT: G 4 GLU cc_start: 0.8015 (mp0) cc_final: 0.6851 (mp0) REVERT: 8 106 LYS cc_start: 0.8948 (mmmm) cc_final: 0.8682 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8006 (mp0) cc_final: 0.6904 (mp0) REVERT: BA 1006 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8690 (mtmt) REVERT: CA 1106 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8657 (mmmm) REVERT: FA 104 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7348 (mm-30) REVERT: FA 106 LYS cc_start: 0.8992 (mmmm) cc_final: 0.8732 (mmmm) REVERT: GA 202 LYS cc_start: 0.8920 (mtpt) cc_final: 0.8689 (mtpt) REVERT: GA 204 GLU cc_start: 0.5133 (OUTLIER) cc_final: 0.4445 (pm20) REVERT: HA 304 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8408 (mm-30) REVERT: JA 1104 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7375 (mm-30) REVERT: JA 1106 LYS cc_start: 0.8987 (mmmm) cc_final: 0.8750 (mmmm) REVERT: KA 1204 GLU cc_start: 0.5030 (OUTLIER) cc_final: 0.4339 (pm20) REVERT: I 6 LYS cc_start: 0.8973 (mtmt) cc_final: 0.8532 (mtmt) REVERT: OA 302 LYS cc_start: 0.9312 (ttpt) cc_final: 0.8831 (tptt) REVERT: PA 1006 LYS cc_start: 0.8935 (mtmt) cc_final: 0.8678 (mtmt) REVERT: RA 1202 LYS cc_start: 0.9045 (ttpt) cc_final: 0.8642 (ttmm) REVERT: SA 1302 LYS cc_start: 0.9314 (ttpt) cc_final: 0.8813 (tptt) REVERT: SA 1306 LYS cc_start: 0.5386 (OUTLIER) cc_final: 0.5020 (mmmt) REVERT: a 2 LYS cc_start: 0.9257 (ptpt) cc_final: 0.8937 (ptpt) REVERT: TA 105 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.8852 (p90) REVERT: XA 1105 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.8831 (p90) REVERT: b 2 LYS cc_start: 0.9020 (ttmt) cc_final: 0.8785 (ttmt) REVERT: gA 1306 LYS cc_start: 0.9033 (tptp) cc_final: 0.8757 (tptp) REVERT: c 2 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8684 (ptpt) REVERT: hA 107 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.8971 (t80) REVERT: iA 202 LYS cc_start: 0.9388 (tttm) cc_final: 0.9020 (ttmm) REVERT: iA 204 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: jA 306 LYS cc_start: 0.9201 (tptp) cc_final: 0.8865 (ttpp) REVERT: lA 1107 PHE cc_start: 0.9426 (OUTLIER) cc_final: 0.8921 (t80) REVERT: mA 1204 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8255 (tm-30) REVERT: nA 1306 LYS cc_start: 0.9173 (tptp) cc_final: 0.8878 (ttpp) REVERT: e 2 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8818 (tppt) REVERT: vA 104 GLU cc_start: 0.8605 (tm-30) cc_final: 0.7953 (tm-30) REVERT: wA 202 LYS cc_start: 0.9319 (tttm) cc_final: 0.8837 (ttmm) REVERT: yA 1002 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8767 (tppt) REVERT: zA 1105 PHE cc_start: 0.9203 (t80) cc_final: 0.8932 (t80) REVERT: 0A 1202 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8847 (ttmm) REVERT: 3A 202 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.8775 (tppp) REVERT: 4A 306 LYS cc_start: 0.9049 (tptp) cc_final: 0.8746 (tptp) REVERT: 8A 1302 LYS cc_start: 0.8712 (tptp) cc_final: 0.8274 (tptp) REVERT: 8A 1306 LYS cc_start: 0.8976 (tptp) cc_final: 0.8675 (tptp) REVERT: g 6 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8942 (ttpt) REVERT: 9A 102 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.9099 (tptm) REVERT: BB 302 LYS cc_start: 0.8888 (tptp) cc_final: 0.8567 (tptp) REVERT: BB 305 PHE cc_start: 0.9349 (t80) cc_final: 0.9071 (t80) REVERT: BB 306 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8947 (tptp) REVERT: EB 1202 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.8849 (tppp) REVERT: FB 1302 LYS cc_start: 0.8868 (tptp) cc_final: 0.8507 (tptp) REVERT: FB 1305 PHE cc_start: 0.9310 (t80) cc_final: 0.9014 (t80) REVERT: NB 106 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8972 (ptmm) REVERT: OB 202 LYS cc_start: 0.9349 (tttm) cc_final: 0.9015 (tppp) REVERT: OB 206 LYS cc_start: 0.9305 (tttt) cc_final: 0.9068 (tttm) REVERT: PB 302 LYS cc_start: 0.8974 (tptp) cc_final: 0.8743 (tptp) REVERT: PB 304 GLU cc_start: 0.8798 (tm-30) cc_final: 0.7886 (pm20) REVERT: TB 1302 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8692 (tptp) REVERT: TB 1304 GLU cc_start: 0.8837 (tm-30) cc_final: 0.7831 (pm20) outliers start: 166 outliers final: 120 residues processed: 487 average time/residue: 0.4808 time to fit residues: 283.6983 Evaluate side-chains 598 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 448 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain U residue 1107 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain X residue 104 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 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 o residue 207 PHE Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain s residue 1207 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain BA residue 1006 LYS Chi-restraints excluded: chain H residue 4 GLU 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 IA residue 1004 GLU 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 NA residue 207 PHE Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain UA residue 204 GLU 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 1202 LYS Chi-restraints excluded: chain YA residue 1204 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain bA residue 204 GLU Chi-restraints excluded: chain cA residue 302 LYS Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain hA residue 107 PHE Chi-restraints excluded: chain iA residue 204 GLU Chi-restraints excluded: chain jA residue 302 LYS 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 lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain lA residue 1107 PHE Chi-restraints excluded: chain mA residue 1202 LYS Chi-restraints excluded: chain mA residue 1204 GLU Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 204 GLU Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1204 GLU Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain wA residue 204 GLU Chi-restraints excluded: chain wA residue 206 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 0A residue 1204 GLU Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 3A residue 204 GLU Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 7A residue 1204 GLU Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 306 LYS Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS 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 1202 LYS Chi-restraints excluded: chain EB residue 1204 GLU 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 103 PHE Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain IB residue 302 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 LB residue 1202 LYS Chi-restraints excluded: chain MB residue 1302 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain NB residue 106 LYS Chi-restraints excluded: chain OB residue 204 GLU Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain RB residue 1102 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1204 GLU Chi-restraints excluded: chain TB residue 1302 LYS 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: 0.8477 moved from start: 0.7703 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= 6.111 Angle : 4.249 61.549 16272 Z= 1.863 Chirality : 0.298 0.768 1152 Planarity : 0.016 0.056 2160 Dihedral : 21.360 86.805 1499 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 114.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 34.20 % Favored : 65.80 % Rotamer: Outliers : 21.18 % Allowed : 29.28 % Favored : 49.54 % Cbeta Deviations : 14.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.58 % 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: -7.91 (0.19), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.02 (0.15), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.124 0.016 PHE V1207 *********************** 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 630 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 447 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8995 (mtmt) cc_final: 0.8769 (mmmt) REVERT: J 106 LYS cc_start: 0.9013 (mmmm) cc_final: 0.8534 (mmmm) REVERT: M 1006 LYS cc_start: 0.8965 (mtmt) cc_final: 0.8755 (mmmt) REVERT: N 1104 GLU cc_start: 0.7716 (mm-30) cc_final: 0.6072 (mm-30) REVERT: N 1106 LYS cc_start: 0.9008 (mmmm) cc_final: 0.8541 (mmmm) REVERT: O 1202 LYS cc_start: 0.9222 (mtpt) cc_final: 0.9016 (mtpt) REVERT: B 4 GLU cc_start: 0.8401 (mp0) cc_final: 0.7600 (mp0) REVERT: B 6 LYS cc_start: 0.9087 (mtmt) cc_final: 0.8713 (mtmt) REVERT: Q 106 LYS cc_start: 0.8945 (mmmm) cc_final: 0.8488 (mmmm) REVERT: R 202 LYS cc_start: 0.9155 (mtpt) cc_final: 0.8836 (mtpt) REVERT: S 302 LYS cc_start: 0.9222 (ttpt) cc_final: 0.8907 (mtpp) REVERT: T 1004 GLU cc_start: 0.8399 (mp0) cc_final: 0.7617 (mp0) REVERT: T 1006 LYS cc_start: 0.9064 (mtmt) cc_final: 0.8674 (mtmt) REVERT: U 1106 LYS cc_start: 0.8879 (mmmm) cc_final: 0.8545 (mmmm) REVERT: V 1202 LYS cc_start: 0.9095 (mtpt) cc_final: 0.8847 (mtpt) REVERT: W 1302 LYS cc_start: 0.9292 (ttpt) cc_final: 0.8941 (ttmm) REVERT: C 6 LYS cc_start: 0.8995 (mtmt) cc_final: 0.8670 (mtmt) REVERT: X 106 LYS cc_start: 0.9017 (mmmm) cc_final: 0.8686 (mmmm) REVERT: Y 202 LYS cc_start: 0.9036 (mtpt) cc_final: 0.8767 (mtpp) REVERT: Z 302 LYS cc_start: 0.9359 (ttpt) cc_final: 0.9004 (ttpp) REVERT: j 1004 GLU cc_start: 0.7403 (mp0) cc_final: 0.6772 (mp0) REVERT: j 1006 LYS cc_start: 0.8990 (mtmt) cc_final: 0.8645 (mtmt) REVERT: k 1106 LYS cc_start: 0.8973 (mmmm) cc_final: 0.8658 (mmmm) REVERT: l 1202 LYS cc_start: 0.9023 (mtpt) cc_final: 0.8715 (mtpp) REVERT: m 1302 LYS cc_start: 0.9377 (ttpt) cc_final: 0.8899 (ttpp) REVERT: m 1306 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.8943 (mttt) REVERT: D 4 GLU cc_start: 0.8390 (mp0) cc_final: 0.7907 (mp0) REVERT: n 104 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7043 (mm-30) REVERT: n 106 LYS cc_start: 0.9065 (mmmm) cc_final: 0.8659 (mmmm) REVERT: o 202 LYS cc_start: 0.9160 (mtpt) cc_final: 0.8759 (mmmm) REVERT: o 206 LYS cc_start: 0.8938 (ttmm) cc_final: 0.8706 (ttmm) REVERT: q 1002 LYS cc_start: 0.7774 (tttt) cc_final: 0.7491 (tptm) REVERT: q 1004 GLU cc_start: 0.8454 (mp0) cc_final: 0.7993 (mp0) REVERT: r 1104 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7095 (mm-30) REVERT: r 1106 LYS cc_start: 0.9054 (mmmm) cc_final: 0.8663 (mmmm) REVERT: s 1202 LYS cc_start: 0.9097 (mtpt) cc_final: 0.8725 (mtpp) REVERT: E 6 LYS cc_start: 0.8849 (mtmt) cc_final: 0.8416 (mtmt) REVERT: u 104 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7638 (mm-30) REVERT: u 106 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8889 (mmmm) REVERT: w 302 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8858 (ttmm) REVERT: x 1002 LYS cc_start: 0.6713 (OUTLIER) cc_final: 0.6431 (mmtp) REVERT: y 1104 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7643 (mm-30) REVERT: y 1106 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8280 (mmmm) REVERT: 0 1302 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8909 (ttmm) REVERT: F 4 GLU cc_start: 0.8087 (mp0) cc_final: 0.7007 (mp0) REVERT: F 6 LYS cc_start: 0.8973 (mtmt) cc_final: 0.8726 (mtmt) REVERT: 1 104 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7802 (mm-30) REVERT: 1 106 LYS cc_start: 0.9002 (mmmm) cc_final: 0.8716 (mmmm) REVERT: 2 206 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8638 (ptmm) REVERT: 4 1004 GLU cc_start: 0.8106 (mp0) cc_final: 0.7000 (mp0) REVERT: 4 1006 LYS cc_start: 0.8964 (mtmt) cc_final: 0.8700 (mtmt) REVERT: 5 1104 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7878 (mm-30) REVERT: 5 1106 LYS cc_start: 0.9000 (mmmm) cc_final: 0.8610 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9148 (mtpt) cc_final: 0.8822 (mtpt) REVERT: 6 1206 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8654 (ptmm) REVERT: G 4 GLU cc_start: 0.8025 (mp0) cc_final: 0.6899 (mp0) REVERT: G 6 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8663 (mtmt) REVERT: 8 106 LYS cc_start: 0.8933 (mmmm) cc_final: 0.8677 (mmmm) REVERT: AA 302 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8995 (ttpt) REVERT: BA 1004 GLU cc_start: 0.8005 (mp0) cc_final: 0.6911 (mp0) REVERT: BA 1006 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8503 (mtmt) REVERT: CA 1106 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8658 (mmmm) REVERT: FA 104 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7352 (mm-30) REVERT: FA 106 LYS cc_start: 0.8989 (mmmm) cc_final: 0.8735 (mmmm) REVERT: GA 202 LYS cc_start: 0.8911 (mtpt) cc_final: 0.8687 (mtpt) REVERT: HA 304 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8431 (mm-30) REVERT: JA 1104 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7343 (mm-30) REVERT: JA 1106 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8753 (mmmm) REVERT: KA 1204 GLU cc_start: 0.5053 (OUTLIER) cc_final: 0.4411 (pm20) REVERT: LA 1304 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8068 (mm-30) REVERT: I 6 LYS cc_start: 0.8973 (mtmt) cc_final: 0.8548 (mtmt) REVERT: OA 302 LYS cc_start: 0.9318 (ttpt) cc_final: 0.8794 (tptt) REVERT: OA 306 LYS cc_start: 0.3591 (OUTLIER) cc_final: 0.2282 (mmmt) REVERT: PA 1006 LYS cc_start: 0.8932 (mtmt) cc_final: 0.8676 (mtmt) REVERT: QA 1107 PHE cc_start: 0.9417 (OUTLIER) cc_final: 0.8022 (t80) REVERT: RA 1202 LYS cc_start: 0.9038 (ttpt) cc_final: 0.8649 (ttmm) REVERT: SA 1302 LYS cc_start: 0.9324 (ttpt) cc_final: 0.8817 (tptt) REVERT: SA 1306 LYS cc_start: 0.5350 (OUTLIER) cc_final: 0.4876 (mmmt) REVERT: a 2 LYS cc_start: 0.9277 (ptpt) cc_final: 0.9004 (ptpt) REVERT: TA 105 PHE cc_start: 0.9373 (OUTLIER) cc_final: 0.8848 (p90) REVERT: XA 1105 PHE cc_start: 0.9375 (OUTLIER) cc_final: 0.8836 (p90) REVERT: b 2 LYS cc_start: 0.9017 (ttmt) cc_final: 0.8779 (ttmt) REVERT: gA 1306 LYS cc_start: 0.9057 (tptp) cc_final: 0.8790 (tptp) REVERT: c 2 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8659 (ptpt) REVERT: hA 107 PHE cc_start: 0.9419 (OUTLIER) cc_final: 0.8968 (t80) REVERT: iA 202 LYS cc_start: 0.9397 (tttm) cc_final: 0.9017 (ttmm) REVERT: iA 204 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8247 (tm-30) REVERT: jA 306 LYS cc_start: 0.9203 (tptp) cc_final: 0.8879 (ttpp) REVERT: lA 1107 PHE cc_start: 0.9426 (OUTLIER) cc_final: 0.8972 (t80) REVERT: mA 1204 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8251 (tm-30) REVERT: nA 1306 LYS cc_start: 0.9172 (tptp) cc_final: 0.8876 (ttpp) REVERT: pA 202 LYS cc_start: 0.9411 (tttm) cc_final: 0.9169 (tttp) REVERT: e 2 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8816 (tppt) REVERT: wA 202 LYS cc_start: 0.9317 (tttm) cc_final: 0.8841 (ttmm) REVERT: yA 1002 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8770 (tppt) REVERT: zA 1105 PHE cc_start: 0.9235 (t80) cc_final: 0.8957 (t80) REVERT: 0A 1202 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8835 (ttmm) REVERT: 3A 202 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.8769 (tppp) REVERT: 4A 306 LYS cc_start: 0.9051 (tptp) cc_final: 0.8738 (tptp) REVERT: 8A 1306 LYS cc_start: 0.8933 (tptp) cc_final: 0.8620 (tptp) REVERT: g 6 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8951 (ttpt) REVERT: 9A 102 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9109 (tptm) REVERT: AB 202 LYS cc_start: 0.9448 (tttm) cc_final: 0.9085 (ttmm) REVERT: BB 302 LYS cc_start: 0.8838 (tptp) cc_final: 0.8493 (tptp) REVERT: BB 305 PHE cc_start: 0.9343 (t80) cc_final: 0.9065 (t80) REVERT: BB 306 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8946 (tptp) REVERT: EB 1202 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.8850 (tppp) REVERT: FB 1305 PHE cc_start: 0.9330 (t80) cc_final: 0.9082 (t80) REVERT: NB 106 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8972 (ptmm) REVERT: OB 202 LYS cc_start: 0.9341 (tttm) cc_final: 0.9010 (tppp) REVERT: OB 206 LYS cc_start: 0.9293 (tttt) cc_final: 0.9077 (tttm) REVERT: PB 302 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8745 (tptp) REVERT: PB 304 GLU cc_start: 0.8798 (tm-30) cc_final: 0.7890 (pm20) REVERT: TB 1302 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8691 (tptp) REVERT: TB 1304 GLU cc_start: 0.8827 (tm-30) cc_final: 0.7851 (pm20) outliers start: 183 outliers final: 129 residues processed: 490 average time/residue: 0.4603 time to fit residues: 273.9479 Evaluate side-chains 611 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 448 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain U residue 1104 GLU Chi-restraints excluded: chain U residue 1107 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain X residue 104 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 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 m residue 1306 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain s residue 1207 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain AA residue 302 LYS Chi-restraints excluded: chain BA residue 1006 LYS Chi-restraints excluded: chain H residue 4 GLU 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 304 GLU Chi-restraints excluded: chain IA residue 1002 LYS Chi-restraints excluded: chain IA residue 1004 GLU 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 NA residue 207 PHE Chi-restraints excluded: chain OA residue 306 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain QA residue 1107 PHE Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain UA residue 202 LYS Chi-restraints excluded: chain UA residue 204 GLU 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 1202 LYS Chi-restraints excluded: chain YA residue 1204 GLU Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain bA residue 204 GLU Chi-restraints excluded: chain cA residue 302 LYS Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain hA residue 107 PHE Chi-restraints excluded: chain iA residue 204 GLU Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain lA residue 1107 PHE Chi-restraints excluded: chain mA residue 1202 LYS Chi-restraints excluded: chain mA residue 1204 GLU Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 204 GLU Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1204 GLU Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain wA residue 204 GLU Chi-restraints excluded: chain wA residue 206 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 0A residue 1204 GLU Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 3A residue 204 GLU Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 7A residue 1204 GLU Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 306 LYS Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS 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 1202 LYS Chi-restraints excluded: chain EB residue 1204 GLU 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 103 PHE Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain IB residue 302 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 LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1302 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain NB residue 106 LYS Chi-restraints excluded: chain OB residue 204 GLU Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain RB residue 1102 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1204 GLU Chi-restraints excluded: chain TB residue 1302 LYS Chi-restraints excluded: chain TB residue 1306 LYS 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: 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: 0.8470 moved from start: 0.7744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.333 12528 Z= 6.112 Angle : 4.248 61.514 16272 Z= 1.864 Chirality : 0.298 0.792 1152 Planarity : 0.016 0.056 2160 Dihedral : 21.418 87.520 1495 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 114.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 33.85 % Favored : 66.15 % Rotamer: Outliers : 21.30 % Allowed : 29.63 % Favored : 49.07 % Cbeta Deviations : 14.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.28 % 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: -7.93 (0.19), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.04 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.121 0.016 PHEgA1307 *********************** 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 630 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 446 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8982 (mtmt) cc_final: 0.8761 (mmmt) REVERT: J 106 LYS cc_start: 0.9011 (mmmm) cc_final: 0.8534 (mmmm) REVERT: M 1006 LYS cc_start: 0.8972 (mtmt) cc_final: 0.8764 (mmmt) REVERT: N 1104 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7100 (mm-30) REVERT: N 1106 LYS cc_start: 0.9007 (mmmm) cc_final: 0.8543 (mmmm) REVERT: O 1202 LYS cc_start: 0.9223 (mtpt) cc_final: 0.9006 (mtpt) REVERT: B 4 GLU cc_start: 0.8451 (mp0) cc_final: 0.7614 (mp0) REVERT: B 6 LYS cc_start: 0.9092 (mtmt) cc_final: 0.8712 (mtmt) REVERT: Q 106 LYS cc_start: 0.8945 (mmmm) cc_final: 0.8503 (mmmm) REVERT: R 202 LYS cc_start: 0.9166 (mtpt) cc_final: 0.8842 (mtpt) REVERT: S 302 LYS cc_start: 0.9215 (ttpt) cc_final: 0.8890 (mtpp) REVERT: T 1004 GLU cc_start: 0.8410 (mp0) cc_final: 0.7612 (mp0) REVERT: T 1006 LYS cc_start: 0.9051 (mtmt) cc_final: 0.8662 (mtmt) REVERT: U 1106 LYS cc_start: 0.8873 (mmmm) cc_final: 0.8526 (mmmm) REVERT: V 1202 LYS cc_start: 0.9091 (mtpt) cc_final: 0.8863 (mtpt) REVERT: W 1302 LYS cc_start: 0.9302 (ttpt) cc_final: 0.8948 (ttmm) REVERT: C 4 GLU cc_start: 0.7479 (mp0) cc_final: 0.7060 (mp0) REVERT: C 6 LYS cc_start: 0.8995 (mtmt) cc_final: 0.8692 (mtmt) REVERT: X 106 LYS cc_start: 0.9048 (mmmm) cc_final: 0.8683 (mmmm) REVERT: Y 202 LYS cc_start: 0.9035 (mtpt) cc_final: 0.8721 (mtpp) REVERT: Y 206 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8797 (ttmm) REVERT: Z 302 LYS cc_start: 0.9355 (ttpt) cc_final: 0.8962 (ttpp) REVERT: j 1004 GLU cc_start: 0.7500 (mp0) cc_final: 0.6922 (mp0) REVERT: j 1006 LYS cc_start: 0.8991 (mtmt) cc_final: 0.8654 (mtmt) REVERT: k 1106 LYS cc_start: 0.8979 (mmmm) cc_final: 0.8660 (mmmm) REVERT: l 1202 LYS cc_start: 0.9041 (mtpt) cc_final: 0.8730 (mtpp) REVERT: m 1302 LYS cc_start: 0.9377 (ttpt) cc_final: 0.8906 (ttpp) REVERT: m 1306 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8949 (mttt) REVERT: D 4 GLU cc_start: 0.8392 (mp0) cc_final: 0.7897 (mp0) REVERT: n 104 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7278 (mm-30) REVERT: n 106 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8648 (mmmm) REVERT: o 202 LYS cc_start: 0.9156 (mtpt) cc_final: 0.8758 (mmmm) REVERT: o 206 LYS cc_start: 0.8943 (ttmm) cc_final: 0.8717 (ttmm) REVERT: q 1002 LYS cc_start: 0.7811 (tttt) cc_final: 0.7549 (tptm) REVERT: q 1004 GLU cc_start: 0.8454 (mp0) cc_final: 0.7997 (mp0) REVERT: r 1104 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7089 (mm-30) REVERT: r 1106 LYS cc_start: 0.9058 (mmmm) cc_final: 0.8664 (mmmm) REVERT: s 1202 LYS cc_start: 0.9099 (mtpt) cc_final: 0.8724 (mtpp) REVERT: E 6 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8425 (mtmt) REVERT: u 104 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7668 (mm-30) REVERT: u 106 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8895 (mmmm) REVERT: w 302 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8860 (ttmm) REVERT: x 1002 LYS cc_start: 0.6737 (OUTLIER) cc_final: 0.6434 (mmtp) REVERT: y 1104 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7679 (mm-30) REVERT: y 1106 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8321 (mmmm) REVERT: 0 1302 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8908 (ttmm) REVERT: F 4 GLU cc_start: 0.8100 (mp0) cc_final: 0.7005 (mp0) REVERT: F 6 LYS cc_start: 0.8973 (mtmt) cc_final: 0.8728 (mtmt) REVERT: 1 104 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7899 (mm-30) REVERT: 1 106 LYS cc_start: 0.9002 (mmmm) cc_final: 0.8706 (mmmm) REVERT: 2 206 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8634 (ptmm) REVERT: 4 1004 GLU cc_start: 0.8140 (mp0) cc_final: 0.7029 (mp0) REVERT: 4 1006 LYS cc_start: 0.8970 (mtmt) cc_final: 0.8712 (mtmt) REVERT: 5 1104 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7882 (mm-30) REVERT: 5 1106 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8615 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9150 (mtpt) cc_final: 0.8807 (mtpt) REVERT: 6 1206 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8663 (ptmm) REVERT: G 4 GLU cc_start: 0.8040 (mp0) cc_final: 0.6943 (mp0) REVERT: 8 106 LYS cc_start: 0.8942 (mmmm) cc_final: 0.8683 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8001 (mp0) cc_final: 0.6932 (mp0) REVERT: BA 1006 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8501 (mtmt) REVERT: CA 1106 LYS cc_start: 0.8921 (mmmm) cc_final: 0.8635 (mmmm) REVERT: FA 104 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7347 (mm-30) REVERT: FA 106 LYS cc_start: 0.8996 (mmmm) cc_final: 0.8736 (mmmm) REVERT: GA 202 LYS cc_start: 0.8911 (mtpt) cc_final: 0.8683 (mtpt) REVERT: HA 304 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8438 (mm-30) REVERT: JA 1104 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7367 (mm-30) REVERT: JA 1106 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8752 (mmmm) REVERT: LA 1306 LYS cc_start: 0.9171 (ttpt) cc_final: 0.8970 (ttpt) REVERT: I 6 LYS cc_start: 0.8958 (mtmt) cc_final: 0.8531 (mtmt) REVERT: OA 302 LYS cc_start: 0.9272 (ttpt) cc_final: 0.8782 (tptt) REVERT: PA 1006 LYS cc_start: 0.8922 (mtmt) cc_final: 0.8664 (mtmt) REVERT: QA 1107 PHE cc_start: 0.9366 (OUTLIER) cc_final: 0.8027 (t80) REVERT: RA 1202 LYS cc_start: 0.9036 (ttpt) cc_final: 0.8649 (ttmm) REVERT: SA 1302 LYS cc_start: 0.9331 (ttpt) cc_final: 0.8810 (tptt) REVERT: a 2 LYS cc_start: 0.9288 (ptpt) cc_final: 0.9009 (ptpt) REVERT: TA 105 PHE cc_start: 0.9377 (OUTLIER) cc_final: 0.8853 (p90) REVERT: XA 1105 PHE cc_start: 0.9372 (OUTLIER) cc_final: 0.8833 (p90) REVERT: b 2 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8779 (ttmt) REVERT: gA 1306 LYS cc_start: 0.9067 (tptp) cc_final: 0.8799 (tptp) REVERT: c 2 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8653 (ptpt) REVERT: hA 107 PHE cc_start: 0.9420 (OUTLIER) cc_final: 0.8965 (t80) REVERT: iA 202 LYS cc_start: 0.9385 (tttm) cc_final: 0.9016 (ttmm) REVERT: iA 204 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8285 (tm-30) REVERT: jA 306 LYS cc_start: 0.9198 (tptp) cc_final: 0.8895 (ttpp) REVERT: lA 1107 PHE cc_start: 0.9428 (OUTLIER) cc_final: 0.8976 (t80) REVERT: mA 1204 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8258 (tm-30) REVERT: nA 1306 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8874 (ttpp) REVERT: e 2 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8804 (tppt) REVERT: wA 202 LYS cc_start: 0.9315 (tttm) cc_final: 0.8799 (ttmm) REVERT: yA 1002 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8758 (tppt) REVERT: zA 1105 PHE cc_start: 0.9208 (t80) cc_final: 0.8938 (t80) REVERT: 0A 1202 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8834 (ttmm) REVERT: 3A 202 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.8771 (tppp) REVERT: 4A 306 LYS cc_start: 0.9050 (tptp) cc_final: 0.8747 (tptp) REVERT: 8A 1306 LYS cc_start: 0.8920 (tptp) cc_final: 0.8607 (tptp) REVERT: g 6 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8952 (ttpt) REVERT: 9A 102 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.9106 (tptm) REVERT: BB 305 PHE cc_start: 0.9342 (t80) cc_final: 0.9064 (t80) REVERT: BB 306 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8933 (tptp) REVERT: EB 1202 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.8852 (tppp) REVERT: FB 1305 PHE cc_start: 0.9316 (t80) cc_final: 0.9068 (t80) REVERT: NB 106 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8973 (ptmm) REVERT: OB 202 LYS cc_start: 0.9340 (tttm) cc_final: 0.9011 (tppp) REVERT: PB 302 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8749 (tptp) REVERT: PB 304 GLU cc_start: 0.8796 (tm-30) cc_final: 0.7895 (pm20) REVERT: TB 1302 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8697 (tptp) REVERT: TB 1304 GLU cc_start: 0.8822 (tm-30) cc_final: 0.7860 (pm20) outliers start: 184 outliers final: 136 residues processed: 489 average time/residue: 0.4589 time to fit residues: 272.5765 Evaluate side-chains 613 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 446 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain U residue 1104 GLU Chi-restraints excluded: chain U residue 1107 PHE Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain X residue 104 GLU Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 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 m residue 1306 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain s residue 1207 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS 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 z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain 7 residue 1307 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain BA residue 1006 LYS Chi-restraints excluded: chain DA residue 1204 GLU Chi-restraints excluded: chain H residue 4 GLU 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 304 GLU Chi-restraints excluded: chain IA residue 1002 LYS Chi-restraints excluded: chain IA residue 1004 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 NA residue 207 PHE Chi-restraints excluded: chain OA residue 306 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain QA residue 1107 PHE Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain TA residue 107 PHE Chi-restraints excluded: chain UA residue 202 LYS Chi-restraints excluded: chain UA residue 204 GLU Chi-restraints excluded: chain UA residue 206 LYS 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 1204 GLU Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 104 GLU Chi-restraints excluded: chain bA residue 204 GLU Chi-restraints excluded: chain cA residue 302 LYS Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain hA residue 107 PHE Chi-restraints excluded: chain iA residue 204 GLU Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain lA residue 1107 PHE Chi-restraints excluded: chain mA residue 1202 LYS Chi-restraints excluded: chain mA residue 1204 GLU Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS 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 2 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 204 GLU Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1204 GLU Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain wA residue 204 GLU Chi-restraints excluded: chain wA residue 206 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 0A residue 1204 GLU Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 3A residue 204 GLU Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 7A residue 1204 GLU Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 306 LYS Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS 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 1202 LYS Chi-restraints excluded: chain EB residue 1204 GLU 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 103 PHE Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain IB residue 302 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 1206 LYS Chi-restraints excluded: chain MB residue 1302 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain NB residue 106 LYS Chi-restraints excluded: chain OB residue 204 GLU Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain RB residue 1102 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1204 GLU Chi-restraints excluded: chain TB residue 1302 LYS Chi-restraints excluded: chain TB residue 1306 LYS 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: 0.8469 moved from start: 0.7779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.349 12528 Z= 6.110 Angle : 4.275 61.192 16272 Z= 1.873 Chirality : 0.298 0.788 1152 Planarity : 0.016 0.058 2160 Dihedral : 21.421 87.960 1492 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 114.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 34.20 % Favored : 65.80 % Rotamer: Outliers : 21.53 % Allowed : 30.09 % Favored : 48.38 % Cbeta Deviations : 13.89 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.48 % 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: -7.95 (0.19), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.05 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.136 0.016 PHEgA1307 *********************** 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 631 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 445 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8999 (mtmt) cc_final: 0.8771 (mmmt) REVERT: J 106 LYS cc_start: 0.9010 (mmmm) cc_final: 0.8535 (mmmm) REVERT: M 1006 LYS cc_start: 0.8984 (mtmt) cc_final: 0.8777 (mmmt) REVERT: N 1104 GLU cc_start: 0.7842 (mm-30) cc_final: 0.6808 (mm-30) REVERT: N 1106 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8537 (mmmm) REVERT: P 1304 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8214 (mm-30) REVERT: B 4 GLU cc_start: 0.8420 (mp0) cc_final: 0.7582 (mp0) REVERT: B 6 LYS cc_start: 0.9092 (mtmt) cc_final: 0.8700 (mtmt) REVERT: Q 106 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8485 (mmmm) REVERT: R 202 LYS cc_start: 0.9152 (mtpt) cc_final: 0.8839 (mtpt) REVERT: S 302 LYS cc_start: 0.9222 (ttpt) cc_final: 0.8891 (mtpp) REVERT: T 1004 GLU cc_start: 0.8406 (mp0) cc_final: 0.7593 (mp0) REVERT: T 1006 LYS cc_start: 0.9051 (mtmt) cc_final: 0.8651 (mtmt) REVERT: U 1106 LYS cc_start: 0.8871 (mmmm) cc_final: 0.8522 (mmmm) REVERT: V 1202 LYS cc_start: 0.9096 (mtpt) cc_final: 0.8863 (mtpt) REVERT: V 1206 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8827 (ttmm) REVERT: W 1302 LYS cc_start: 0.9305 (ttpt) cc_final: 0.8949 (ttmm) REVERT: C 4 GLU cc_start: 0.7383 (mp0) cc_final: 0.7022 (mp0) REVERT: C 6 LYS cc_start: 0.8994 (mtmt) cc_final: 0.8675 (mtmt) REVERT: X 106 LYS cc_start: 0.9047 (mmmm) cc_final: 0.8676 (mmmm) REVERT: Y 206 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8798 (ttmm) REVERT: Z 302 LYS cc_start: 0.9356 (ttpt) cc_final: 0.9047 (ttpp) REVERT: j 1004 GLU cc_start: 0.7262 (mp0) cc_final: 0.6300 (mp0) REVERT: j 1006 LYS cc_start: 0.8992 (mtmt) cc_final: 0.8642 (mtmt) REVERT: k 1106 LYS cc_start: 0.8978 (mmmm) cc_final: 0.8658 (mmmm) REVERT: l 1202 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8728 (mtpp) REVERT: m 1302 LYS cc_start: 0.9381 (ttpt) cc_final: 0.8904 (ttpp) REVERT: m 1306 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.8954 (mttt) REVERT: D 4 GLU cc_start: 0.8397 (mp0) cc_final: 0.7937 (mp0) REVERT: n 104 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7314 (mm-30) REVERT: n 106 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8645 (mmmm) REVERT: o 202 LYS cc_start: 0.9149 (mtpt) cc_final: 0.8840 (mmmm) REVERT: o 206 LYS cc_start: 0.8941 (ttmm) cc_final: 0.8709 (ttmm) REVERT: q 1002 LYS cc_start: 0.7819 (tttt) cc_final: 0.7595 (tptm) REVERT: q 1004 GLU cc_start: 0.8456 (mp0) cc_final: 0.7991 (mp0) REVERT: r 1104 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7107 (mm-30) REVERT: r 1106 LYS cc_start: 0.9058 (mmmm) cc_final: 0.8654 (mmmm) REVERT: s 1202 LYS cc_start: 0.9101 (mtpt) cc_final: 0.8732 (mtpp) REVERT: E 6 LYS cc_start: 0.8863 (mtmt) cc_final: 0.8471 (mtmt) REVERT: u 104 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7685 (mm-30) REVERT: u 106 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8908 (mmmm) REVERT: w 302 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8859 (ttmm) REVERT: x 1002 LYS cc_start: 0.6742 (OUTLIER) cc_final: 0.6464 (mmtp) REVERT: y 1104 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7685 (mm-30) REVERT: y 1106 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8297 (mmmm) REVERT: 0 1302 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8905 (ttmm) REVERT: F 4 GLU cc_start: 0.8112 (mp0) cc_final: 0.7013 (mp0) REVERT: F 6 LYS cc_start: 0.8934 (mtmt) cc_final: 0.8673 (mtmt) REVERT: 1 104 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7944 (mm-30) REVERT: 1 106 LYS cc_start: 0.9003 (mmmm) cc_final: 0.8696 (mmmm) REVERT: 2 206 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8667 (ptmm) REVERT: 4 1004 GLU cc_start: 0.8225 (mp0) cc_final: 0.7179 (mp0) REVERT: 4 1006 LYS cc_start: 0.8971 (mtmt) cc_final: 0.8712 (mtmt) REVERT: 5 1104 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7889 (mm-30) REVERT: 5 1106 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8621 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9144 (mtpt) cc_final: 0.8811 (mtpt) REVERT: 6 1206 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8668 (ptmm) REVERT: G 4 GLU cc_start: 0.8028 (mp0) cc_final: 0.6949 (mp0) REVERT: G 6 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8615 (mtmt) REVERT: 8 106 LYS cc_start: 0.8950 (mmmm) cc_final: 0.8680 (mmmm) REVERT: AA 302 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8975 (ttpt) REVERT: BA 1004 GLU cc_start: 0.8001 (mp0) cc_final: 0.6947 (mp0) REVERT: BA 1006 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8486 (mtmt) REVERT: CA 1106 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8632 (mmmm) REVERT: FA 104 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7584 (mm-30) REVERT: FA 106 LYS cc_start: 0.8996 (mmmm) cc_final: 0.8728 (mmmm) REVERT: GA 202 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8702 (mtpt) REVERT: HA 304 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8431 (mm-30) REVERT: HA 306 LYS cc_start: 0.9181 (tttt) cc_final: 0.8882 (ttpt) REVERT: JA 1104 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7587 (mm-30) REVERT: JA 1106 LYS cc_start: 0.8989 (mmmm) cc_final: 0.8746 (mmmm) REVERT: I 6 LYS cc_start: 0.8956 (mtmt) cc_final: 0.8538 (mtmt) REVERT: OA 302 LYS cc_start: 0.9287 (ttpt) cc_final: 0.8788 (tptt) REVERT: OA 306 LYS cc_start: 0.3521 (OUTLIER) cc_final: 0.2941 (mmmt) REVERT: PA 1006 LYS cc_start: 0.8940 (mtmt) cc_final: 0.8687 (mtmt) REVERT: QA 1107 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.7888 (t80) REVERT: RA 1202 LYS cc_start: 0.9049 (ttpt) cc_final: 0.8645 (ttmm) REVERT: SA 1302 LYS cc_start: 0.9323 (ttpt) cc_final: 0.8805 (tptt) REVERT: SA 1306 LYS cc_start: 0.3370 (OUTLIER) cc_final: 0.2640 (mmmt) REVERT: a 2 LYS cc_start: 0.9302 (ptpt) cc_final: 0.9018 (ptpt) REVERT: TA 105 PHE cc_start: 0.9373 (OUTLIER) cc_final: 0.8839 (p90) REVERT: XA 1105 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.8837 (p90) REVERT: b 2 LYS cc_start: 0.9017 (ttmt) cc_final: 0.8775 (ttmt) REVERT: gA 1306 LYS cc_start: 0.9074 (tptp) cc_final: 0.8807 (tptp) REVERT: c 2 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8633 (ptpt) REVERT: hA 103 PHE cc_start: 0.9443 (OUTLIER) cc_final: 0.9164 (t80) REVERT: hA 107 PHE cc_start: 0.9419 (OUTLIER) cc_final: 0.8967 (t80) REVERT: iA 202 LYS cc_start: 0.9387 (tttm) cc_final: 0.9019 (ttmm) REVERT: iA 204 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8294 (tm-30) REVERT: jA 306 LYS cc_start: 0.9197 (tptp) cc_final: 0.8887 (ttpp) REVERT: lA 1107 PHE cc_start: 0.9428 (OUTLIER) cc_final: 0.8974 (t80) REVERT: mA 1204 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8254 (tm-30) REVERT: nA 1306 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8868 (ttpp) REVERT: e 2 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8806 (tppt) REVERT: wA 202 LYS cc_start: 0.9314 (tttm) cc_final: 0.8797 (ttmm) REVERT: yA 1002 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8760 (tppt) REVERT: zA 1105 PHE cc_start: 0.9206 (t80) cc_final: 0.8935 (t80) REVERT: 0A 1202 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8830 (ttmm) REVERT: 3A 202 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.8768 (tppp) REVERT: 4A 306 LYS cc_start: 0.9045 (tptp) cc_final: 0.8736 (tptp) REVERT: 8A 1306 LYS cc_start: 0.8905 (tptp) cc_final: 0.8613 (tptp) REVERT: BB 302 LYS cc_start: 0.8890 (tptp) cc_final: 0.8507 (tptp) REVERT: BB 305 PHE cc_start: 0.9341 (t80) cc_final: 0.9067 (t80) REVERT: BB 306 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8936 (tptp) REVERT: EB 1202 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.8847 (tppp) REVERT: FB 1305 PHE cc_start: 0.9319 (t80) cc_final: 0.9014 (t80) REVERT: NB 106 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8973 (ptmm) REVERT: OB 202 LYS cc_start: 0.9352 (tttm) cc_final: 0.9027 (tppp) REVERT: PB 302 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8745 (tptp) REVERT: PB 304 GLU cc_start: 0.8795 (tm-30) cc_final: 0.7893 (pm20) REVERT: TB 1302 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8696 (tptp) REVERT: TB 1304 GLU cc_start: 0.8822 (tm-30) cc_final: 0.7858 (pm20) outliers start: 186 outliers final: 134 residues processed: 489 average time/residue: 0.4690 time to fit residues: 277.8881 Evaluate side-chains 615 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 445 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain P residue 1304 GLU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain U residue 1104 GLU Chi-restraints excluded: chain U residue 1107 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain X residue 104 GLU Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 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 m residue 1306 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain s residue 1207 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain 7 residue 1307 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain AA residue 302 LYS Chi-restraints excluded: chain BA residue 1006 LYS Chi-restraints excluded: chain DA residue 1204 GLU Chi-restraints excluded: chain H residue 4 GLU 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 304 GLU Chi-restraints excluded: chain IA residue 1002 LYS Chi-restraints excluded: chain IA residue 1004 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 NA residue 207 PHE Chi-restraints excluded: chain OA residue 306 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain QA residue 1107 PHE Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain TA residue 107 PHE Chi-restraints excluded: chain UA residue 204 GLU Chi-restraints excluded: chain UA residue 206 LYS 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 1202 LYS Chi-restraints excluded: chain YA residue 1204 GLU Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 104 GLU Chi-restraints excluded: chain bA residue 204 GLU Chi-restraints excluded: chain cA residue 302 LYS Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain hA residue 107 PHE Chi-restraints excluded: chain iA residue 204 GLU Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain lA residue 1107 PHE Chi-restraints excluded: chain mA residue 1202 LYS Chi-restraints excluded: chain mA residue 1204 GLU Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS 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 2 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 204 GLU Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1204 GLU Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain wA residue 204 GLU Chi-restraints excluded: chain wA residue 206 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 0A residue 1204 GLU Chi-restraints excluded: chain 0A residue 1206 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 3A residue 204 GLU Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 7A residue 1204 GLU Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 306 LYS Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS 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 1202 LYS Chi-restraints excluded: chain EB residue 1204 GLU 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 HB residue 206 LYS Chi-restraints excluded: chain IB residue 302 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 1206 LYS Chi-restraints excluded: chain MB residue 1302 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain NB residue 106 LYS Chi-restraints excluded: chain OB residue 204 GLU Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 306 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain RB residue 1102 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1204 GLU Chi-restraints excluded: chain TB residue 1302 LYS Chi-restraints excluded: chain TB residue 1306 LYS 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: 0.8470 moved from start: 0.7800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.330 12528 Z= 6.114 Angle : 4.291 64.839 16272 Z= 1.878 Chirality : 0.297 0.789 1152 Planarity : 0.016 0.069 2160 Dihedral : 21.481 87.956 1492 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 114.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 34.55 % Favored : 65.45 % Rotamer: Outliers : 20.60 % Allowed : 31.25 % Favored : 48.15 % Cbeta Deviations : 14.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.28 % 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: -7.98 (0.19), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.08 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.160 0.016 PHEgA1307 ********************** 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 625 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 447 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8996 (mtmt) cc_final: 0.8774 (mmmt) REVERT: J 106 LYS cc_start: 0.9011 (mmmm) cc_final: 0.8542 (mmmm) REVERT: M 1006 LYS cc_start: 0.8993 (mtmt) cc_final: 0.8781 (mmmt) REVERT: N 1104 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7028 (mm-30) REVERT: N 1106 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8542 (mmmm) REVERT: B 6 LYS cc_start: 0.9092 (mtmt) cc_final: 0.8693 (mtmt) REVERT: Q 106 LYS cc_start: 0.8942 (mmmm) cc_final: 0.8482 (mmmm) REVERT: R 202 LYS cc_start: 0.9157 (mtpt) cc_final: 0.8846 (mtpt) REVERT: S 302 LYS cc_start: 0.9218 (ttpt) cc_final: 0.8888 (mtpp) REVERT: T 1006 LYS cc_start: 0.9052 (mtmt) cc_final: 0.8640 (mtmt) REVERT: U 1106 LYS cc_start: 0.8867 (mmmm) cc_final: 0.8521 (mmmm) REVERT: V 1202 LYS cc_start: 0.9105 (mtpt) cc_final: 0.8862 (mtpt) REVERT: V 1206 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8838 (ttmm) REVERT: W 1302 LYS cc_start: 0.9305 (ttpt) cc_final: 0.8945 (ttmm) REVERT: C 4 GLU cc_start: 0.7474 (mp0) cc_final: 0.7144 (mp0) REVERT: C 6 LYS cc_start: 0.8987 (mtmt) cc_final: 0.8667 (mtmt) REVERT: X 106 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8672 (mmmm) REVERT: Y 206 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8794 (ttmm) REVERT: Z 302 LYS cc_start: 0.9354 (ttpt) cc_final: 0.9046 (ttpp) REVERT: j 1004 GLU cc_start: 0.7313 (mp0) cc_final: 0.6446 (mp0) REVERT: j 1006 LYS cc_start: 0.8991 (mtmt) cc_final: 0.8646 (mtmt) REVERT: k 1106 LYS cc_start: 0.8981 (mmmm) cc_final: 0.8657 (mmmm) REVERT: l 1202 LYS cc_start: 0.9040 (mtpt) cc_final: 0.8727 (mtpp) REVERT: m 1302 LYS cc_start: 0.9376 (ttpt) cc_final: 0.8903 (ttpp) REVERT: m 1306 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8952 (mttt) REVERT: D 4 GLU cc_start: 0.8396 (mp0) cc_final: 0.7933 (mp0) REVERT: n 106 LYS cc_start: 0.9061 (mmmm) cc_final: 0.8656 (mmmm) REVERT: o 202 LYS cc_start: 0.9144 (mtpt) cc_final: 0.8837 (mmmm) REVERT: o 206 LYS cc_start: 0.8936 (ttmm) cc_final: 0.8711 (ttmm) REVERT: q 1002 LYS cc_start: 0.7832 (tttt) cc_final: 0.7611 (tptm) REVERT: q 1004 GLU cc_start: 0.8458 (mp0) cc_final: 0.7997 (mp0) REVERT: r 1106 LYS cc_start: 0.9061 (mmmm) cc_final: 0.8649 (mmmm) REVERT: s 1202 LYS cc_start: 0.9096 (mtpt) cc_final: 0.8727 (mtpp) REVERT: u 104 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7680 (mm-30) REVERT: u 106 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.8941 (mmmm) REVERT: w 302 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8858 (ttmm) REVERT: x 1002 LYS cc_start: 0.6730 (OUTLIER) cc_final: 0.6452 (mmtp) REVERT: y 1104 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7686 (mm-30) REVERT: y 1106 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8328 (mmmm) REVERT: 0 1302 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8904 (ttmm) REVERT: F 4 GLU cc_start: 0.8191 (mp0) cc_final: 0.7208 (mp0) REVERT: F 6 LYS cc_start: 0.8934 (mtmt) cc_final: 0.8673 (mtmt) REVERT: 1 104 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7945 (mm-30) REVERT: 1 106 LYS cc_start: 0.9007 (mmmm) cc_final: 0.8687 (mmmm) REVERT: 2 206 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8671 (ptmm) REVERT: 4 1004 GLU cc_start: 0.8228 (mp0) cc_final: 0.7194 (mp0) REVERT: 4 1006 LYS cc_start: 0.8971 (mtmt) cc_final: 0.8716 (mtmt) REVERT: 5 1104 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7894 (mm-30) REVERT: 5 1106 LYS cc_start: 0.9007 (mmmm) cc_final: 0.8670 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9144 (mtpt) cc_final: 0.8809 (mtpt) REVERT: 6 1206 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8671 (ptmm) REVERT: G 4 GLU cc_start: 0.8041 (mp0) cc_final: 0.6956 (mp0) REVERT: G 6 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8622 (mtmt) REVERT: 8 106 LYS cc_start: 0.8952 (mmmm) cc_final: 0.8687 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8002 (mp0) cc_final: 0.6954 (mp0) REVERT: BA 1006 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8495 (mtmt) REVERT: CA 1106 LYS cc_start: 0.8928 (mmmm) cc_final: 0.8626 (mmmm) REVERT: FA 104 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7610 (mm-30) REVERT: FA 106 LYS cc_start: 0.8995 (mmmm) cc_final: 0.8727 (mmmm) REVERT: GA 202 LYS cc_start: 0.8917 (mtpt) cc_final: 0.8707 (mtpt) REVERT: HA 304 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8435 (mm-30) REVERT: HA 306 LYS cc_start: 0.9191 (tttt) cc_final: 0.8904 (ttpt) REVERT: JA 1104 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7594 (mm-30) REVERT: JA 1106 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8748 (mmmm) REVERT: I 6 LYS cc_start: 0.8965 (mtmt) cc_final: 0.8554 (mtmt) REVERT: OA 302 LYS cc_start: 0.9277 (ttpt) cc_final: 0.8779 (tptt) REVERT: OA 306 LYS cc_start: 0.3633 (OUTLIER) cc_final: 0.2651 (mmmt) REVERT: PA 1006 LYS cc_start: 0.8935 (mtmt) cc_final: 0.8691 (mtmt) REVERT: QA 1107 PHE cc_start: 0.9322 (OUTLIER) cc_final: 0.7751 (t80) REVERT: RA 1202 LYS cc_start: 0.9049 (ttpt) cc_final: 0.8644 (ttmm) REVERT: SA 1302 LYS cc_start: 0.9300 (ttpt) cc_final: 0.8800 (tptt) REVERT: a 2 LYS cc_start: 0.9301 (ptpt) cc_final: 0.9013 (ptpt) REVERT: TA 105 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8842 (p90) REVERT: XA 1105 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8836 (p90) REVERT: b 2 LYS cc_start: 0.9017 (ttmt) cc_final: 0.8774 (ttmt) REVERT: gA 1306 LYS cc_start: 0.9063 (tptp) cc_final: 0.8812 (tptp) REVERT: c 2 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8631 (ptpt) REVERT: hA 103 PHE cc_start: 0.9442 (OUTLIER) cc_final: 0.9159 (t80) REVERT: hA 107 PHE cc_start: 0.9419 (OUTLIER) cc_final: 0.8968 (t80) REVERT: iA 202 LYS cc_start: 0.9388 (tttm) cc_final: 0.9019 (ttmm) REVERT: iA 204 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8294 (tm-30) REVERT: jA 306 LYS cc_start: 0.9196 (tptp) cc_final: 0.8897 (ttpp) REVERT: lA 1107 PHE cc_start: 0.9429 (OUTLIER) cc_final: 0.8975 (t80) REVERT: mA 1204 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8251 (tm-30) REVERT: nA 1306 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8873 (ttpp) REVERT: e 2 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8803 (tppt) REVERT: wA 202 LYS cc_start: 0.9311 (tttm) cc_final: 0.8798 (ttmm) REVERT: yA 1002 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8758 (tppt) REVERT: zA 1105 PHE cc_start: 0.9205 (t80) cc_final: 0.8937 (t80) REVERT: 0A 1202 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8830 (ttmm) REVERT: 3A 202 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8769 (tppp) REVERT: 4A 306 LYS cc_start: 0.9049 (tptp) cc_final: 0.8742 (tptp) REVERT: 8A 1306 LYS cc_start: 0.8870 (tptp) cc_final: 0.8561 (tptp) REVERT: BB 305 PHE cc_start: 0.9340 (t80) cc_final: 0.9071 (t80) REVERT: BB 306 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8932 (tptp) REVERT: EB 1202 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.8851 (tppp) REVERT: FB 1305 PHE cc_start: 0.9316 (t80) cc_final: 0.9012 (t80) REVERT: NB 106 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8973 (ptmm) REVERT: OB 202 LYS cc_start: 0.9346 (tttm) cc_final: 0.8875 (tppp) REVERT: PB 302 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8746 (tptp) REVERT: PB 304 GLU cc_start: 0.8795 (tm-30) cc_final: 0.7899 (pm20) REVERT: TB 1302 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8695 (tptp) REVERT: TB 1304 GLU cc_start: 0.8821 (tm-30) cc_final: 0.7861 (pm20) outliers start: 178 outliers final: 138 residues processed: 490 average time/residue: 0.4711 time to fit residues: 279.9846 Evaluate side-chains 617 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 446 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain M residue 1002 LYS Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain U residue 1104 GLU Chi-restraints excluded: chain U residue 1107 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain X residue 104 GLU Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 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 m residue 1306 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain s residue 1207 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS 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 z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain 7 residue 1307 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain BA residue 1006 LYS Chi-restraints excluded: chain DA residue 1204 GLU Chi-restraints excluded: chain H residue 4 GLU 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 304 GLU Chi-restraints excluded: chain IA residue 1002 LYS Chi-restraints excluded: chain IA residue 1004 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 NA residue 207 PHE Chi-restraints excluded: chain OA residue 306 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain QA residue 1107 PHE Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain TA residue 107 PHE Chi-restraints excluded: chain UA residue 204 GLU Chi-restraints excluded: chain UA residue 206 LYS 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 1202 LYS Chi-restraints excluded: chain YA residue 1204 GLU Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 104 GLU Chi-restraints excluded: chain bA residue 204 GLU Chi-restraints excluded: chain cA residue 302 LYS Chi-restraints excluded: chain dA residue 1006 LYS Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain hA residue 107 PHE Chi-restraints excluded: chain iA residue 204 GLU Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain lA residue 1107 PHE Chi-restraints excluded: chain mA residue 1202 LYS Chi-restraints excluded: chain mA residue 1204 GLU Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS 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 2 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 204 GLU Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1204 GLU Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain wA residue 204 GLU Chi-restraints excluded: chain wA residue 206 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 0A residue 1204 GLU 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 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 3A residue 204 GLU Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 7A residue 1204 GLU Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 306 LYS Chi-restraints excluded: chain BB residue 307 PHE 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 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 1204 GLU Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain IB residue 302 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 1206 LYS Chi-restraints excluded: chain MB residue 1302 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain NB residue 106 LYS Chi-restraints excluded: chain OB residue 204 GLU Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 306 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain RB residue 1102 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1204 GLU Chi-restraints excluded: chain TB residue 1302 LYS Chi-restraints excluded: chain TB residue 1306 LYS 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 = 0.3142 r_free = 0.3142 target = 0.071596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.061588 restraints weight = 32960.113| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.05 r_work: 0.2696 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.7813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.340 12528 Z= 6.111 Angle : 4.288 64.475 16272 Z= 1.876 Chirality : 0.298 0.785 1152 Planarity : 0.016 0.056 2160 Dihedral : 21.493 88.085 1492 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 115.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 35.24 % Favored : 64.76 % Rotamer: Outliers : 20.60 % Allowed : 31.48 % Favored : 47.92 % Cbeta Deviations : 14.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.38 % 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: -8.00 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.09 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.127 0.016 PHEcA 307 =============================================================================== Job complete usr+sys time: 3895.69 seconds wall clock time: 70 minutes 35.76 seconds (4235.76 seconds total)