Starting phenix.real_space_refine on Mon Apr 8 01:25:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqh_23486/04_2024/7lqh_23486_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqh_23486/04_2024/7lqh_23486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqh_23486/04_2024/7lqh_23486.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqh_23486/04_2024/7lqh_23486.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqh_23486/04_2024/7lqh_23486_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqh_23486/04_2024/7lqh_23486_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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 8640 2.51 5 N 1584 2.21 5 O 1872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 204": "OE1" <-> "OE2" Residue "K PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 304": "OE1" <-> "OE2" Residue "L PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 1204": "OE1" <-> "OE2" Residue "O PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 1304": "OE1" <-> "OE2" Residue "P PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 304": "OE1" <-> "OE2" Residue "S PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 1204": "OE1" <-> "OE2" Residue "V PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 1304": "OE1" <-> "OE2" Residue "W PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 204": "OE1" <-> "OE2" Residue "Y PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 304": "OE1" <-> "OE2" Residue "Z PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 1204": "OE1" <-> "OE2" Residue "l PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 1304": "OE1" <-> "OE2" Residue "m PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 204": "OE1" <-> "OE2" Residue "o PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 304": "OE1" <-> "OE2" Residue "p PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 1204": "OE1" <-> "OE2" Residue "s PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 1304": "OE1" <-> "OE2" Residue "t PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 204": "OE1" <-> "OE2" Residue "v PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 304": "OE1" <-> "OE2" Residue "w PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 1204": "OE1" <-> "OE2" Residue "z PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 1304": "OE1" <-> "OE2" Residue "0 PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 204": "OE1" <-> "OE2" Residue "2 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 304": "OE1" <-> "OE2" Residue "3 PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 1204": "OE1" <-> "OE2" Residue "6 PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 1304": "OE1" <-> "OE2" Residue "7 PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 204": "OE1" <-> "OE2" Residue "9 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA GLU 304": "OE1" <-> "OE2" Residue "AA PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA GLU 1204": "OE1" <-> "OE2" Residue "DA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EA PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EA GLU 1304": "OE1" <-> "OE2" Residue "EA PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GA GLU 204": "OE1" <-> "OE2" Residue "GA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HA PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HA GLU 304": "OE1" <-> "OE2" Residue "HA PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JA PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JA PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KA GLU 1204": "OE1" <-> "OE2" Residue "KA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA GLU 1304": "OE1" <-> "OE2" Residue "LA PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MA PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MA PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA GLU 204": "OE1" <-> "OE2" Residue "NA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OA PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OA GLU 304": "OE1" <-> "OE2" Residue "OA PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "QA PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "QA PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RA GLU 1204": "OE1" <-> "OE2" Residue "RA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA GLU 1304": "OE1" <-> "OE2" Residue "SA PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "UA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "UA GLU 204": "OE1" <-> "OE2" Residue "UA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "UA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VA GLU 304": "OE1" <-> "OE2" Residue "WA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "WA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YA GLU 1204": "OE1" <-> "OE2" Residue "YA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ZA GLU 1304": "OE1" <-> "OE2" Residue "b PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bA GLU 204": "OE1" <-> "OE2" Residue "bA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "cA GLU 304": "OE1" <-> "OE2" Residue "dA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "dA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "fA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "fA GLU 1204": "OE1" <-> "OE2" Residue "fA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "fA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "gA GLU 1304": "OE1" <-> "OE2" Residue "c PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "iA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "iA GLU 204": "OE1" <-> "OE2" Residue "iA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "iA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "jA GLU 304": "OE1" <-> "OE2" Residue "kA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "kA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "mA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "mA GLU 1204": "OE1" <-> "OE2" Residue "mA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "mA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "nA GLU 1304": "OE1" <-> "OE2" Residue "d PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "pA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "pA GLU 204": "OE1" <-> "OE2" Residue "pA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "pA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "qA GLU 304": "OE1" <-> "OE2" Residue "rA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "rA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "tA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "tA GLU 1204": "OE1" <-> "OE2" Residue "tA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "tA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "uA GLU 1304": "OE1" <-> "OE2" Residue "e PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "wA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "wA GLU 204": "OE1" <-> "OE2" Residue "wA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "wA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "xA GLU 304": "OE1" <-> "OE2" Residue "yA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "yA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0A PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0A GLU 1204": "OE1" <-> "OE2" Residue "0A PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0A PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A GLU 1304": "OE1" <-> "OE2" Residue "f PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A GLU 204": "OE1" <-> "OE2" Residue "3A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A GLU 304": "OE1" <-> "OE2" Residue "5A PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7A PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7A GLU 1204": "OE1" <-> "OE2" Residue "7A PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7A PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8A GLU 1304": "OE1" <-> "OE2" Residue "g PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB GLU 204": "OE1" <-> "OE2" Residue "AB PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BB GLU 304": "OE1" <-> "OE2" Residue "CB PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EB PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EB GLU 1204": "OE1" <-> "OE2" Residue "EB PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EB PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FB GLU 1304": "OE1" <-> "OE2" Residue "h PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HB PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HB GLU 204": "OE1" <-> "OE2" Residue "HB PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HB PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IB GLU 304": "OE1" <-> "OE2" Residue "JB PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JB PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB GLU 1204": "OE1" <-> "OE2" Residue "LB PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MB GLU 1304": "OE1" <-> "OE2" Residue "i PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OB PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OB GLU 204": "OE1" <-> "OE2" Residue "OB PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OB PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PB GLU 304": "OE1" <-> "OE2" Residue "QB PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "QB PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB GLU 1204": "OE1" <-> "OE2" Residue "SB PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TB GLU 1304": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 5.49, per 1000 atoms: 0.45 Number of scatterers: 12096 At special positions: 0 Unit cell: (89.64, 89.64, 111.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1872 8.00 N 1584 7.00 C 8640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=35, symmetry=0 Number of additional bonds: simple=35, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.73 Conformation dependent library (CDL) restraints added in 1.1 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: 1.25 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: 0.00 Time building geometry restraints manager: 5.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 1489 1.26 - 1.33: 1391 1.33 - 1.41: 3600 1.41 - 1.48: 1308 1.48 - 1.56: 4740 Bond restraints: 12528 Sorted by residual: bond pdb=" N 5CR d 1 " pdb=" CAL 5CR d 1 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" N 5CR e 1 " pdb=" CAL 5CR e 1 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" N 5CRrA1001 " pdb=" CAL 5CRrA1001 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" N 5CRyA1001 " pdb=" CAL 5CRyA1001 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" N 5CR i 1 " pdb=" CAL 5CR i 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+01 ... (remaining 12523 not shown) Histogram of bond angle deviations from ideal: 105.41 - 109.75: 1131 109.75 - 114.08: 4107 114.08 - 118.42: 2126 118.42 - 122.76: 7479 122.76 - 127.10: 1429 Bond angle restraints: 16272 Sorted by residual: angle pdb=" N 5CR b 1 " pdb=" CAL 5CR b 1 " pdb=" CAA 5CR b 1 " ideal model delta sigma weight residual 114.91 124.81 -9.90 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " pdb=" CAA 5CR f 1 " ideal model delta sigma weight residual 114.91 124.80 -9.89 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR5A1001 " pdb=" CAL 5CR5A1001 " pdb=" CAA 5CR5A1001 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR a 1 " pdb=" CAL 5CR a 1 " pdb=" CAA 5CR a 1 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CRWA1001 " pdb=" CAL 5CRWA1001 " pdb=" CAA 5CRWA1001 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.08e+01 ... (remaining 16267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 4844 15.26 - 30.52: 790 30.52 - 45.79: 342 45.79 - 61.05: 198 61.05 - 76.31: 18 Dihedral angle restraints: 6192 sinusoidal: 2880 harmonic: 3312 Sorted by residual: dihedral pdb=" CA LYSMA 106 " pdb=" CB LYSMA 106 " pdb=" CG LYSMA 106 " pdb=" CD LYSMA 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.26 58.74 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYSQA1106 " pdb=" CB LYSQA1106 " pdb=" CG LYSQA1106 " pdb=" CD LYSQA1106 " ideal model delta sinusoidal sigma weight residual 60.00 1.29 58.71 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYS 1 106 " pdb=" CB LYS 1 106 " pdb=" CG LYS 1 106 " pdb=" CD LYS 1 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.29 58.71 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 6189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.018: 407 0.018 - 0.036: 334 0.036 - 0.054: 299 0.054 - 0.073: 89 0.073 - 0.091: 23 Chirality restraints: 1152 Sorted by residual: chirality pdb=" CA LYS R 202 " pdb=" N LYS R 202 " pdb=" C LYS R 202 " pdb=" CB LYS R 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.06e-01 chirality pdb=" CA LYS V1202 " pdb=" N LYS V1202 " pdb=" C LYS V1202 " pdb=" CB LYS V1202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.02e-01 chirality pdb=" CA LYS Y 202 " pdb=" N LYS Y 202 " pdb=" C LYS Y 202 " pdb=" CB LYS Y 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.86e-01 ... (remaining 1149 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHEUA 205 " -0.008 2.00e-02 2.50e+03 7.00e-03 8.57e-01 pdb=" CG PHEUA 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEUA 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHEUA 205 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHEUA 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEUA 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHEUA 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEYA1205 " -0.009 2.00e-02 2.50e+03 6.98e-03 8.53e-01 pdb=" CG PHEYA1205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEYA1205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHEYA1205 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHEYA1205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEYA1205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHEYA1205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEAB 205 " -0.009 2.00e-02 2.50e+03 6.97e-03 8.51e-01 pdb=" CG PHEAB 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEAB 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHEAB 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHEAB 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEAB 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHEAB 205 " -0.003 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 281 2.66 - 3.22: 10252 3.22 - 3.78: 19307 3.78 - 4.34: 28745 4.34 - 4.90: 46337 Nonbonded interactions: 104922 Sorted by model distance: nonbonded pdb=" CD LYS N1102 " pdb=" OE2 GMA 9 208 " model vdw 2.098 2.752 nonbonded pdb=" OE2 GMA Y 208 " pdb=" CD LYS r1102 " model vdw 2.116 2.752 nonbonded pdb=" CD LYS U1102 " pdb=" OE2 GMA v 208 " model vdw 2.116 2.752 nonbonded pdb=" CD LYS k1102 " pdb=" OE2 GMANA 208 " model vdw 2.117 2.752 nonbonded pdb=" CD LYS Q 102 " pdb=" OE2 GMADA1208 " model vdw 2.118 2.752 ... (remaining 104917 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: 1.350 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: 7.100 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 28.070 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.410 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.118 12528 Z= 0.763 Angle : 1.417 9.902 16272 Z= 0.592 Chirality : 0.035 0.091 1152 Planarity : 0.002 0.009 2160 Dihedral : 20.718 76.311 3888 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 31.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 14.58 % Allowed : 14.58 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.94 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHEUA 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 472 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7369 (mp0) cc_final: 0.6755 (pm20) REVERT: B 4 GLU cc_start: 0.7493 (mp0) cc_final: 0.6748 (pm20) REVERT: S 306 LYS cc_start: 0.8629 (tttt) cc_final: 0.8357 (mttt) REVERT: Y 206 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8180 (ttmm) REVERT: Z 306 LYS cc_start: 0.8563 (tttt) cc_final: 0.8262 (tttt) REVERT: j 1006 LYS cc_start: 0.8500 (mtmt) cc_final: 0.8034 (mtmt) REVERT: m 1306 LYS cc_start: 0.8633 (tttt) cc_final: 0.8339 (mttt) REVERT: o 204 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7064 (mt-10) REVERT: s 1206 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8228 (ttmm) REVERT: t 1306 LYS cc_start: 0.8695 (tttt) cc_final: 0.8441 (mttt) REVERT: v 206 LYS cc_start: 0.8477 (ttmm) cc_final: 0.8231 (ttmm) REVERT: w 304 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7091 (mm-30) REVERT: w 306 LYS cc_start: 0.8689 (tttt) cc_final: 0.8339 (mttt) REVERT: x 1004 GLU cc_start: 0.7152 (mp0) cc_final: 0.6745 (mp0) REVERT: 0 1304 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7144 (mm-30) REVERT: 0 1306 LYS cc_start: 0.8594 (tttt) cc_final: 0.8264 (tttt) REVERT: F 4 GLU cc_start: 0.7397 (mp0) cc_final: 0.6657 (pm20) REVERT: 3 304 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7148 (mm-30) REVERT: 6 1204 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6808 (mt-10) REVERT: 6 1206 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8366 (ttmm) REVERT: 7 1306 LYS cc_start: 0.8772 (tttt) cc_final: 0.8420 (mttt) REVERT: G 4 GLU cc_start: 0.7313 (mp0) cc_final: 0.6485 (pm20) REVERT: 9 204 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6532 (mt-10) REVERT: AA 306 LYS cc_start: 0.8673 (tttt) cc_final: 0.8387 (mttt) REVERT: DA 1204 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7037 (mt-10) REVERT: EA 1306 LYS cc_start: 0.8705 (tttt) cc_final: 0.8431 (mttt) REVERT: HA 306 LYS cc_start: 0.8699 (tttt) cc_final: 0.8363 (mttt) REVERT: LA 1306 LYS cc_start: 0.8705 (tttt) cc_final: 0.8323 (mttt) REVERT: OA 306 LYS cc_start: 0.8570 (tttt) cc_final: 0.8318 (mttt) REVERT: SA 1306 LYS cc_start: 0.8648 (tttt) cc_final: 0.8295 (tttt) REVERT: a 2 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8344 (ttpt) REVERT: TA 104 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: TA 105 PHE cc_start: 0.9072 (t80) cc_final: 0.8761 (t80) REVERT: UA 202 LYS cc_start: 0.8784 (tttm) cc_final: 0.8340 (ttmm) REVERT: VA 305 PHE cc_start: 0.8549 (t80) cc_final: 0.8266 (t80) REVERT: WA 1003 PHE cc_start: 0.9115 (t80) cc_final: 0.8755 (t80) REVERT: WA 1005 PHE cc_start: 0.8951 (t80) cc_final: 0.8609 (t80) REVERT: WA 1007 PHE cc_start: 0.9301 (t80) cc_final: 0.8997 (t80) REVERT: XA 1103 PHE cc_start: 0.8930 (t80) cc_final: 0.8678 (t80) REVERT: XA 1107 PHE cc_start: 0.8921 (t80) cc_final: 0.8714 (t80) REVERT: YA 1202 LYS cc_start: 0.8788 (tttm) cc_final: 0.8391 (tttm) REVERT: ZA 1304 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8190 (tm-30) REVERT: aA 103 PHE cc_start: 0.9101 (t80) cc_final: 0.8425 (t80) REVERT: aA 106 LYS cc_start: 0.8822 (tttp) cc_final: 0.8564 (tttp) REVERT: bA 202 LYS cc_start: 0.8841 (tttm) cc_final: 0.8397 (ttmm) REVERT: cA 303 PHE cc_start: 0.9015 (t80) cc_final: 0.8654 (t80) REVERT: cA 304 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8429 (tm-30) REVERT: fA 1202 LYS cc_start: 0.8656 (tttm) cc_final: 0.8373 (tttm) REVERT: c 5 PHE cc_start: 0.8932 (t80) cc_final: 0.8452 (t80) REVERT: c 7 PHE cc_start: 0.9209 (t80) cc_final: 0.8995 (t80) REVERT: hA 106 LYS cc_start: 0.8870 (tttp) cc_final: 0.8657 (tttp) REVERT: iA 202 LYS cc_start: 0.8878 (tttm) cc_final: 0.8562 (ttmm) REVERT: jA 306 LYS cc_start: 0.8334 (tptp) cc_final: 0.8046 (tptp) REVERT: kA 1005 PHE cc_start: 0.9077 (t80) cc_final: 0.8703 (t80) REVERT: lA 1103 PHE cc_start: 0.8901 (t80) cc_final: 0.8521 (t80) REVERT: mA 1206 LYS cc_start: 0.8797 (tttt) cc_final: 0.8582 (tttt) REVERT: nA 1305 PHE cc_start: 0.8662 (t80) cc_final: 0.8453 (t80) REVERT: d 3 PHE cc_start: 0.9295 (t80) cc_final: 0.8996 (t80) REVERT: d 5 PHE cc_start: 0.9090 (t80) cc_final: 0.8869 (t80) REVERT: d 7 PHE cc_start: 0.9253 (t80) cc_final: 0.8845 (t80) REVERT: oA 107 PHE cc_start: 0.8813 (t80) cc_final: 0.8347 (t80) REVERT: pA 202 LYS cc_start: 0.8916 (tttm) cc_final: 0.8524 (mmmm) REVERT: pA 206 LYS cc_start: 0.8826 (tttt) cc_final: 0.8593 (tttt) REVERT: qA 305 PHE cc_start: 0.8722 (t80) cc_final: 0.8402 (t80) REVERT: rA 1005 PHE cc_start: 0.8915 (t80) cc_final: 0.8588 (t80) REVERT: sA 1103 PHE cc_start: 0.9020 (t80) cc_final: 0.8784 (t80) REVERT: tA 1206 LYS cc_start: 0.8812 (tttt) cc_final: 0.8431 (tttt) REVERT: vA 106 LYS cc_start: 0.8825 (tttp) cc_final: 0.8561 (tttp) REVERT: wA 202 LYS cc_start: 0.8733 (tttm) cc_final: 0.8401 (mmmm) REVERT: wA 206 LYS cc_start: 0.8797 (tttt) cc_final: 0.8503 (tttt) REVERT: xA 303 PHE cc_start: 0.8927 (t80) cc_final: 0.8677 (t80) REVERT: zA 1106 LYS cc_start: 0.8767 (tttp) cc_final: 0.8557 (tttp) REVERT: 1A 1303 PHE cc_start: 0.8829 (t80) cc_final: 0.8602 (t80) REVERT: 1A 1305 PHE cc_start: 0.8465 (t80) cc_final: 0.8239 (t80) REVERT: 3A 202 LYS cc_start: 0.8922 (tttm) cc_final: 0.8551 (mmmm) REVERT: 3A 206 LYS cc_start: 0.8739 (tttt) cc_final: 0.8527 (tttt) REVERT: 4A 306 LYS cc_start: 0.8459 (tptp) cc_final: 0.8229 (tptp) REVERT: 4A 307 PHE cc_start: 0.8508 (t80) cc_final: 0.8127 (t80) REVERT: 5A 1003 PHE cc_start: 0.9169 (t80) cc_final: 0.8731 (t80) REVERT: 5A 1005 PHE cc_start: 0.9041 (t80) cc_final: 0.8732 (t80) REVERT: 5A 1007 PHE cc_start: 0.9152 (t80) cc_final: 0.8671 (t80) REVERT: 6A 1106 LYS cc_start: 0.8863 (tttp) cc_final: 0.8585 (tttp) REVERT: 7A 1205 PHE cc_start: 0.8502 (t80) cc_final: 0.8271 (t80) REVERT: 7A 1206 LYS cc_start: 0.8695 (tttt) cc_final: 0.8343 (tttm) REVERT: 9A 104 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: 9A 106 LYS cc_start: 0.8906 (tttp) cc_final: 0.8655 (tttm) REVERT: BB 305 PHE cc_start: 0.8766 (t80) cc_final: 0.8355 (t80) REVERT: BB 307 PHE cc_start: 0.8514 (t80) cc_final: 0.8208 (t80) REVERT: CB 1003 PHE cc_start: 0.9123 (t80) cc_final: 0.8740 (t80) REVERT: CB 1005 PHE cc_start: 0.9008 (t80) cc_final: 0.8652 (t80) REVERT: CB 1007 PHE cc_start: 0.9161 (t80) cc_final: 0.8929 (t80) REVERT: DB 1106 LYS cc_start: 0.8792 (tttp) cc_final: 0.8527 (tttp) REVERT: EB 1202 LYS cc_start: 0.8867 (tttm) cc_final: 0.8491 (tttm) REVERT: EB 1206 LYS cc_start: 0.8740 (tttt) cc_final: 0.8538 (tttm) REVERT: FB 1304 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8667 (tm-30) REVERT: GB 103 PHE cc_start: 0.9078 (t80) cc_final: 0.8876 (t80) REVERT: GB 106 LYS cc_start: 0.8643 (tttp) cc_final: 0.8431 (tttm) REVERT: HB 206 LYS cc_start: 0.8809 (tttt) cc_final: 0.8555 (tttm) REVERT: IB 303 PHE cc_start: 0.8906 (t80) cc_final: 0.8678 (t80) REVERT: IB 304 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8429 (tm-30) REVERT: KB 1105 PHE cc_start: 0.8731 (t80) cc_final: 0.8308 (t80) REVERT: KB 1106 LYS cc_start: 0.8655 (tttp) cc_final: 0.8378 (tttp) REVERT: MB 1303 PHE cc_start: 0.8794 (t80) cc_final: 0.8553 (t80) REVERT: i 6 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8467 (ttpt) REVERT: NB 104 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: OB 206 LYS cc_start: 0.8866 (tttt) cc_final: 0.8654 (tttt) REVERT: PB 304 GLU cc_start: 0.8840 (tm-30) cc_final: 0.6113 (pm20) REVERT: PB 305 PHE cc_start: 0.8434 (t80) cc_final: 0.7272 (t80) REVERT: TB 1305 PHE cc_start: 0.8317 (t80) cc_final: 0.8019 (t80) REVERT: TB 1307 PHE cc_start: 0.8067 (t80) cc_final: 0.7620 (t80) outliers start: 126 outliers final: 85 residues processed: 495 average time/residue: 0.4733 time to fit residues: 286.5788 Evaluate side-chains 550 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 460 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain N residue 1102 LYS Chi-restraints excluded: chain N residue 1106 LYS Chi-restraints excluded: chain Q residue 106 LYS Chi-restraints excluded: chain U residue 1102 LYS Chi-restraints excluded: chain U residue 1106 LYS Chi-restraints excluded: chain W residue 1302 LYS Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 106 LYS Chi-restraints excluded: chain k residue 1102 LYS Chi-restraints excluded: chain k residue 1106 LYS Chi-restraints excluded: chain n residue 102 LYS Chi-restraints excluded: chain n residue 106 LYS Chi-restraints excluded: chain p residue 302 LYS Chi-restraints excluded: chain r residue 1102 LYS Chi-restraints excluded: chain r residue 1106 LYS Chi-restraints excluded: chain t residue 1302 LYS Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain y residue 1102 LYS Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain 1 residue 102 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 3 residue 302 LYS Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain CA residue 1102 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain FA residue 102 LYS Chi-restraints excluded: chain FA residue 106 LYS Chi-restraints excluded: chain JA residue 1102 LYS Chi-restraints excluded: chain JA residue 1106 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain QA residue 1102 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 104 GLU Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain dA residue 1002 LYS Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain kA residue 1004 GLU Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain rA residue 1004 GLU Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain yA residue 1006 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 5A residue 1006 LYS Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain 9A residue 104 GLU Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain CB residue 1006 LYS Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain JB residue 1006 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.7980 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: 0.8523 moved from start: 0.6801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.111 0.346 12528 Z= 6.173 Angle : 3.942 32.453 16272 Z= 1.769 Chirality : 0.303 1.020 1152 Planarity : 0.016 0.080 2160 Dihedral : 22.232 97.642 1779 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 101.50 Ramachandran Plot: Outliers : 1.22 % Allowed : 23.26 % Favored : 75.52 % Rotamer: Outliers : 12.50 % Allowed : 18.75 % Favored : 68.75 % Cbeta Deviations : 11.89 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.79 % 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: -7.20 (0.19), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.49 (0.15), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.113 0.017 PHE 2 205 *********************** 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 567 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 459 time to evaluate : 1.198 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: A 6 LYS cc_start: 0.9023 (mtmt) cc_final: 0.8465 (mtmt) REVERT: J 106 LYS cc_start: 0.8982 (mmmm) cc_final: 0.8577 (mmmm) REVERT: M 1006 LYS cc_start: 0.9028 (mtmt) cc_final: 0.8601 (mtmt) REVERT: N 1104 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7683 (mm-30) REVERT: N 1106 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8512 (mmmm) REVERT: B 4 GLU cc_start: 0.8228 (mp0) cc_final: 0.7423 (mp0) REVERT: Q 104 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7387 (mm-30) REVERT: Q 106 LYS cc_start: 0.9092 (mmmm) cc_final: 0.8783 (mmmm) REVERT: T 1006 LYS cc_start: 0.9041 (mtmt) cc_final: 0.8647 (mtmt) REVERT: U 1106 LYS cc_start: 0.8616 (mmmm) cc_final: 0.8307 (mmmm) REVERT: W 1302 LYS cc_start: 0.9168 (ttpt) cc_final: 0.8938 (mtpt) REVERT: C 6 LYS cc_start: 0.8975 (mtmt) cc_final: 0.8487 (mtmt) REVERT: X 104 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7705 (mm-30) REVERT: X 106 LYS cc_start: 0.9020 (mmmm) cc_final: 0.8700 (mmmm) REVERT: Y 206 LYS cc_start: 0.9096 (ttmm) cc_final: 0.8816 (mtpp) REVERT: j 1004 GLU cc_start: 0.8132 (mp0) cc_final: 0.7285 (mp0) REVERT: k 1102 LYS cc_start: 0.7997 (ttpt) cc_final: 0.7324 (ttpt) REVERT: k 1104 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7718 (mm-30) REVERT: k 1106 LYS cc_start: 0.8869 (mmmm) cc_final: 0.8567 (mmmm) REVERT: l 1206 LYS cc_start: 0.8930 (ttmm) cc_final: 0.8686 (ttmm) REVERT: n 106 LYS cc_start: 0.8880 (mmmm) cc_final: 0.8406 (mmmm) REVERT: o 204 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7547 (mt-10) REVERT: q 1004 GLU cc_start: 0.8425 (mp0) cc_final: 0.8128 (mp0) REVERT: r 1106 LYS cc_start: 0.9062 (mmmm) cc_final: 0.8787 (mmmm) REVERT: s 1204 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7465 (mt-10) REVERT: t 1304 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7513 (mm-30) REVERT: u 102 LYS cc_start: 0.9044 (ttpt) cc_final: 0.8651 (ttpt) REVERT: u 104 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7693 (mm-30) REVERT: u 106 LYS cc_start: 0.8928 (mmmm) cc_final: 0.8545 (mmmm) REVERT: v 202 LYS cc_start: 0.9190 (mtpt) cc_final: 0.8874 (mmmm) REVERT: y 1102 LYS cc_start: 0.9073 (ttpt) cc_final: 0.8699 (ttpt) REVERT: y 1106 LYS cc_start: 0.8845 (mmmm) cc_final: 0.8414 (mmmm) REVERT: 1 106 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8602 (mmmm) REVERT: 3 304 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7706 (mm-30) REVERT: 4 1004 GLU cc_start: 0.7785 (mp0) cc_final: 0.7427 (mp0) REVERT: 5 1104 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7763 (mm-30) REVERT: 6 1202 LYS cc_start: 0.9293 (mtpt) cc_final: 0.8946 (mmmm) REVERT: 6 1204 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7270 (mt-10) REVERT: 7 1304 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7362 (mm-30) REVERT: G 4 GLU cc_start: 0.8055 (mp0) cc_final: 0.7150 (mp0) REVERT: G 6 LYS cc_start: 0.9084 (mtmt) cc_final: 0.8707 (mtmt) REVERT: 8 102 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8760 (ttpt) REVERT: 8 104 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7683 (mm-30) REVERT: 8 106 LYS cc_start: 0.8896 (mmmm) cc_final: 0.8310 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8064 (mp0) cc_final: 0.7417 (mp0) REVERT: BA 1006 LYS cc_start: 0.8943 (mtmt) cc_final: 0.8729 (mtmt) REVERT: CA 1104 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7483 (mm-30) REVERT: CA 1106 LYS cc_start: 0.8977 (mmmm) cc_final: 0.8649 (mmmm) REVERT: DA 1206 LYS cc_start: 0.9016 (ttmm) cc_final: 0.8781 (ttmm) REVERT: EA 1304 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7771 (mm-30) REVERT: EA 1306 LYS cc_start: 0.9019 (tttt) cc_final: 0.8762 (mttt) REVERT: FA 104 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7468 (mm-30) REVERT: FA 106 LYS cc_start: 0.8845 (mmmm) cc_final: 0.8442 (mmmm) REVERT: JA 1106 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8710 (mmmm) REVERT: LA 1304 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7132 (mm-30) REVERT: I 6 LYS cc_start: 0.8945 (mtmt) cc_final: 0.8518 (mtmt) REVERT: PA 1004 GLU cc_start: 0.7925 (mp0) cc_final: 0.7020 (mp0) REVERT: QA 1102 LYS cc_start: 0.8993 (mtmt) cc_final: 0.8689 (mmmt) REVERT: RA 1202 LYS cc_start: 0.9178 (mtpt) cc_final: 0.8763 (mtpp) REVERT: RA 1204 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7749 (mt-10) REVERT: SA 1304 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8097 (mm-30) REVERT: SA 1306 LYS cc_start: 0.8990 (tttt) cc_final: 0.8743 (tttt) REVERT: a 2 LYS cc_start: 0.9101 (tppt) cc_final: 0.8600 (tppt) REVERT: a 4 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8261 (tp30) REVERT: VA 306 LYS cc_start: 0.9044 (tptp) cc_final: 0.8828 (tptp) REVERT: WA 1002 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8872 (tppt) REVERT: XA 1102 LYS cc_start: 0.9177 (tptm) cc_final: 0.8892 (tptm) REVERT: XA 1105 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8862 (p90) REVERT: YA 1202 LYS cc_start: 0.9222 (tttm) cc_final: 0.8969 (tttm) REVERT: b 6 LYS cc_start: 0.9200 (ttpt) cc_final: 0.8928 (ttpt) REVERT: aA 104 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8231 (tm-30) REVERT: aA 105 PHE cc_start: 0.9161 (t80) cc_final: 0.8960 (t80) REVERT: bA 202 LYS cc_start: 0.9397 (tttm) cc_final: 0.9011 (tppp) REVERT: dA 1002 LYS cc_start: 0.9112 (ttmt) cc_final: 0.8874 (ttmt) REVERT: iA 202 LYS cc_start: 0.9355 (tttm) cc_final: 0.8955 (tppp) REVERT: jA 302 LYS cc_start: 0.8955 (tptp) cc_final: 0.8655 (tptp) REVERT: nA 1306 LYS cc_start: 0.9001 (tptp) cc_final: 0.8770 (tptp) REVERT: d 2 LYS cc_start: 0.8999 (tppt) cc_final: 0.8477 (tppt) REVERT: pA 202 LYS cc_start: 0.9381 (tttm) cc_final: 0.9002 (ttmm) REVERT: qA 306 LYS cc_start: 0.8989 (tptp) cc_final: 0.8684 (tptp) REVERT: rA 1002 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8910 (ttpt) REVERT: uA 1302 LYS cc_start: 0.9029 (tptp) cc_final: 0.8804 (tptp) REVERT: uA 1303 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8650 (t80) REVERT: vA 102 LYS cc_start: 0.9194 (tptm) cc_final: 0.8970 (tptm) REVERT: wA 202 LYS cc_start: 0.9414 (tttm) cc_final: 0.9141 (tppp) REVERT: yA 1002 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8850 (tppt) REVERT: zA 1104 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7880 (tm-30) REVERT: zA 1105 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8856 (t80) REVERT: f 2 LYS cc_start: 0.9068 (ttmt) cc_final: 0.8812 (ttmt) REVERT: 3A 202 LYS cc_start: 0.9321 (tttm) cc_final: 0.9031 (tppp) REVERT: 3A 204 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7410 (tm-30) REVERT: 4A 302 LYS cc_start: 0.8651 (tptp) cc_final: 0.8219 (tptp) REVERT: 4A 306 LYS cc_start: 0.8923 (tptp) cc_final: 0.8630 (tptp) REVERT: 5A 1002 LYS cc_start: 0.9161 (ptpt) cc_final: 0.8926 (ptpt) REVERT: 8A 1305 PHE cc_start: 0.9138 (t80) cc_final: 0.8856 (t80) REVERT: 8A 1306 LYS cc_start: 0.8816 (tptp) cc_final: 0.8537 (tptp) REVERT: g 2 LYS cc_start: 0.9055 (tppt) cc_final: 0.8530 (tppt) REVERT: AB 202 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8927 (ttmm) REVERT: BB 302 LYS cc_start: 0.9027 (tptp) cc_final: 0.8799 (tptp) REVERT: BB 307 PHE cc_start: 0.9421 (t80) cc_final: 0.9115 (t80) REVERT: FB 1306 LYS cc_start: 0.9014 (tptp) cc_final: 0.8781 (tptp) REVERT: HB 202 LYS cc_start: 0.9260 (tttm) cc_final: 0.8908 (pttm) REVERT: JB 1002 LYS cc_start: 0.9179 (ttmt) cc_final: 0.8845 (ttmt) REVERT: KB 1105 PHE cc_start: 0.9178 (t80) cc_final: 0.8801 (t80) REVERT: KB 1106 LYS cc_start: 0.9132 (tttp) cc_final: 0.8894 (tttm) REVERT: LB 1202 LYS cc_start: 0.9213 (tttm) cc_final: 0.8995 (pptt) REVERT: LB 1204 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: i 4 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8376 (tp30) REVERT: i 6 LYS cc_start: 0.9249 (ttpt) cc_final: 0.9018 (ttpt) REVERT: NB 104 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7896 (pm20) REVERT: NB 105 PHE cc_start: 0.9127 (t80) cc_final: 0.8777 (t80) REVERT: OB 202 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.9168 (mmmm) REVERT: OB 206 LYS cc_start: 0.9231 (tttt) cc_final: 0.8990 (tttm) REVERT: PB 306 LYS cc_start: 0.8858 (tptp) cc_final: 0.8654 (tptp) REVERT: SB 1202 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9111 (ttmm) REVERT: TB 1306 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8647 (tptp) outliers start: 108 outliers final: 63 residues processed: 483 average time/residue: 0.4777 time to fit residues: 279.6151 Evaluate side-chains 539 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 459 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 104 GLU Chi-restraints excluded: chain VA residue 307 PHE 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 ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain bA residue 204 GLU Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain c residue 4 GLU 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 kA residue 1004 GLU Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain rA residue 1004 GLU Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1204 GLU Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain wA residue 204 GLU Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain 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 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 104 GLU Chi-restraints excluded: chain AB residue 202 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 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 QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain TB residue 1306 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: 0.8458 moved from start: 0.7483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.111 0.332 12528 Z= 6.196 Angle : 4.073 62.158 16272 Z= 1.822 Chirality : 0.301 0.910 1152 Planarity : 0.016 0.076 2160 Dihedral : 22.071 103.256 1536 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 106.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 31.25 % Favored : 68.58 % Rotamer: Outliers : 17.59 % Allowed : 23.50 % Favored : 58.91 % Cbeta Deviations : 13.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.39 % 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: -7.35 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.60 (0.16), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.126 0.016 PHE 2 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 443 time to evaluate : 1.328 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: A 6 LYS cc_start: 0.8990 (mtmt) cc_final: 0.8545 (mtmt) REVERT: J 106 LYS cc_start: 0.8955 (mmmm) cc_final: 0.8505 (mmmm) REVERT: K 206 LYS cc_start: 0.9022 (ttmm) cc_final: 0.8804 (ttmm) REVERT: M 1004 GLU cc_start: 0.8056 (mp0) cc_final: 0.7568 (mp0) REVERT: M 1006 LYS cc_start: 0.8996 (mtmt) cc_final: 0.8693 (mtmt) REVERT: N 1104 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8084 (mm-30) REVERT: N 1106 LYS cc_start: 0.8941 (mmmm) cc_final: 0.8541 (mmmm) REVERT: B 4 GLU cc_start: 0.8390 (mp0) cc_final: 0.7962 (mp0) REVERT: Q 104 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7535 (mm-30) REVERT: Q 106 LYS cc_start: 0.9091 (mmmm) cc_final: 0.8688 (mmmm) REVERT: R 206 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8722 (ttmm) REVERT: T 1006 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8793 (mtmt) REVERT: U 1104 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7867 (mm-30) REVERT: U 1106 LYS cc_start: 0.8677 (mmmm) cc_final: 0.8391 (mmmm) REVERT: C 4 GLU cc_start: 0.8018 (mp0) cc_final: 0.7340 (mp0) REVERT: X 104 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7792 (mm-30) REVERT: X 106 LYS cc_start: 0.9051 (mmmm) cc_final: 0.8713 (mmmm) REVERT: Z 304 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8370 (mm-30) REVERT: j 1004 GLU cc_start: 0.8199 (mp0) cc_final: 0.7518 (mp0) REVERT: k 1102 LYS cc_start: 0.7641 (ttpt) cc_final: 0.7106 (ttpt) REVERT: k 1106 LYS cc_start: 0.8910 (mmmm) cc_final: 0.8535 (mmmm) REVERT: l 1202 LYS cc_start: 0.9200 (mtpt) cc_final: 0.8875 (mtpp) REVERT: D 4 GLU cc_start: 0.8044 (mp0) cc_final: 0.7137 (mp0) REVERT: D 6 LYS cc_start: 0.8975 (mtmt) cc_final: 0.8447 (mtmt) REVERT: D 7 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.8683 (t80) REVERT: n 106 LYS cc_start: 0.8922 (mmmm) cc_final: 0.8435 (mmmm) REVERT: o 202 LYS cc_start: 0.9197 (ttpt) cc_final: 0.8928 (ttpt) REVERT: o 204 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7772 (mt-10) REVERT: q 1004 GLU cc_start: 0.8347 (mp0) cc_final: 0.8065 (mp0) REVERT: r 1106 LYS cc_start: 0.9006 (mmmm) cc_final: 0.8742 (mmmm) REVERT: s 1204 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7830 (mt-10) REVERT: E 6 LYS cc_start: 0.8972 (mtmt) cc_final: 0.8728 (mtmt) REVERT: u 106 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8576 (mmmm) REVERT: x 1003 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8188 (m-80) REVERT: y 1102 LYS cc_start: 0.9036 (ttpt) cc_final: 0.8624 (ttpt) REVERT: y 1106 LYS cc_start: 0.8781 (mmmm) cc_final: 0.8354 (mmmm) REVERT: 1 104 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7299 (mm-30) REVERT: 1 106 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8357 (mmmm) REVERT: 3 304 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8100 (mm-30) REVERT: 4 1006 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8567 (ttmt) REVERT: 6 1202 LYS cc_start: 0.9262 (mtpt) cc_final: 0.8789 (mtpp) REVERT: 7 1304 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7907 (mm-30) REVERT: G 4 GLU cc_start: 0.8169 (mp0) cc_final: 0.7407 (mp0) REVERT: G 6 LYS cc_start: 0.9077 (mtmt) cc_final: 0.8803 (mtmt) REVERT: 8 106 LYS cc_start: 0.8810 (mmmm) cc_final: 0.8262 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8060 (mp0) cc_final: 0.7562 (mp0) REVERT: CA 1104 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7352 (mm-30) REVERT: CA 1106 LYS cc_start: 0.8999 (mmmm) cc_final: 0.8793 (mmmm) REVERT: DA 1206 LYS cc_start: 0.9054 (ttmm) cc_final: 0.8795 (ttmm) REVERT: EA 1306 LYS cc_start: 0.9073 (mttt) cc_final: 0.8672 (mttt) REVERT: FA 104 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7390 (mm-30) REVERT: FA 106 LYS cc_start: 0.8979 (mmmm) cc_final: 0.8624 (mmmm) REVERT: HA 302 LYS cc_start: 0.9103 (mtpt) cc_final: 0.8705 (mmmm) REVERT: JA 1106 LYS cc_start: 0.9092 (mmmm) cc_final: 0.8654 (mmmm) REVERT: KA 1207 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8899 (t80) REVERT: LA 1306 LYS cc_start: 0.9007 (tttt) cc_final: 0.8775 (ttpt) REVERT: PA 1004 GLU cc_start: 0.7807 (mp0) cc_final: 0.6946 (mp0) REVERT: RA 1202 LYS cc_start: 0.9131 (mtpt) cc_final: 0.8811 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8252 (mm-30) REVERT: SA 1307 PHE cc_start: 0.9296 (OUTLIER) cc_final: 0.8218 (m-80) REVERT: a 2 LYS cc_start: 0.9133 (tppt) cc_final: 0.8763 (tppt) REVERT: a 4 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8368 (tp30) REVERT: WA 1002 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8887 (tppt) REVERT: XA 1105 PHE cc_start: 0.9319 (OUTLIER) cc_final: 0.8686 (p90) REVERT: YA 1204 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7904 (tm-30) REVERT: ZA 1306 LYS cc_start: 0.8877 (tptp) cc_final: 0.8620 (tptp) REVERT: b 6 LYS cc_start: 0.9223 (ttpt) cc_final: 0.8947 (ttpt) REVERT: aA 104 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8395 (tm-30) REVERT: bA 202 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9038 (tppp) REVERT: dA 1002 LYS cc_start: 0.9067 (ttmt) cc_final: 0.8804 (ttmt) REVERT: c 2 LYS cc_start: 0.9220 (tppt) cc_final: 0.8971 (tppt) REVERT: hA 104 GLU cc_start: 0.8558 (tm-30) cc_final: 0.7660 (tm-30) REVERT: d 2 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8749 (tppt) REVERT: qA 306 LYS cc_start: 0.8903 (tptp) cc_final: 0.8648 (tptp) REVERT: sA 1103 PHE cc_start: 0.9315 (OUTLIER) cc_final: 0.9021 (t80) REVERT: vA 104 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8330 (tm-30) REVERT: wA 202 LYS cc_start: 0.9470 (OUTLIER) cc_final: 0.9007 (tppp) REVERT: zA 1104 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7910 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9404 (t80) cc_final: 0.9122 (t80) REVERT: f 2 LYS cc_start: 0.9093 (ttmt) cc_final: 0.8799 (ttmt) REVERT: f 4 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8411 (tp30) REVERT: 3A 202 LYS cc_start: 0.9329 (tttm) cc_final: 0.8920 (tppp) REVERT: 4A 302 LYS cc_start: 0.8661 (tptp) cc_final: 0.8373 (tptp) REVERT: 8A 1306 LYS cc_start: 0.8982 (tptp) cc_final: 0.8713 (tptp) REVERT: g 2 LYS cc_start: 0.9028 (tppt) cc_final: 0.8579 (tppt) REVERT: AB 202 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.8959 (ttmm) REVERT: BB 302 LYS cc_start: 0.9047 (tptp) cc_final: 0.8747 (tptp) REVERT: BB 304 GLU cc_start: 0.9315 (tm-30) cc_final: 0.8773 (tm-30) REVERT: EB 1204 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7793 (tm-30) REVERT: HB 202 LYS cc_start: 0.9269 (tttm) cc_final: 0.8897 (pttm) REVERT: IB 306 LYS cc_start: 0.8946 (tptp) cc_final: 0.8635 (tptp) REVERT: IB 307 PHE cc_start: 0.9401 (OUTLIER) cc_final: 0.8538 (t80) REVERT: i 6 LYS cc_start: 0.9282 (ttpt) cc_final: 0.9052 (ttpt) REVERT: NB 104 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8052 (pm20) REVERT: OB 202 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9154 (mmmm) REVERT: PB 306 LYS cc_start: 0.8760 (tptp) cc_final: 0.8544 (tptp) REVERT: SB 1202 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.9131 (ttmm) REVERT: TB 1302 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8573 (tptp) outliers start: 152 outliers final: 109 residues processed: 484 average time/residue: 0.4898 time to fit residues: 287.5475 Evaluate side-chains 571 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 443 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 304 GLU Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 104 GLU Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain bA residue 202 LYS Chi-restraints excluded: chain bA residue 204 GLU Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain dA residue 1006 LYS Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 6 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain hA residue 106 LYS Chi-restraints excluded: chain iA residue 204 GLU Chi-restraints excluded: chain jA residue 306 LYS 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 nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE 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 oA residue 102 LYS Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain sA residue 1106 LYS Chi-restraints excluded: chain tA residue 1204 GLU Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain wA residue 202 LYS Chi-restraints excluded: chain wA residue 204 GLU Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 7A residue 1204 GLU Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 104 GLU Chi-restraints excluded: chain AB residue 202 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain 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 QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain TB residue 1302 LYS Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.7815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.111 0.364 12528 Z= 6.204 Angle : 4.090 55.727 16272 Z= 1.835 Chirality : 0.301 0.888 1152 Planarity : 0.016 0.071 2160 Dihedral : 21.289 87.219 1502 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 106.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 33.51 % Favored : 66.32 % Rotamer: Outliers : 20.14 % Allowed : 24.19 % Favored : 55.67 % Cbeta Deviations : 14.76 % 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: -7.47 (0.21), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.69 (0.16), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.129 0.016 PHE 2 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 440 time to evaluate : 1.291 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: A 6 LYS cc_start: 0.9070 (mtmt) cc_final: 0.8616 (mtmt) REVERT: J 106 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8532 (mmmm) REVERT: K 206 LYS cc_start: 0.9000 (ttmm) cc_final: 0.8797 (ttmm) REVERT: M 1004 GLU cc_start: 0.8128 (mp0) cc_final: 0.7560 (mp0) REVERT: M 1006 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8766 (mtmt) REVERT: N 1104 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8062 (mm-30) REVERT: N 1106 LYS cc_start: 0.8987 (mmmm) cc_final: 0.8574 (mmmm) REVERT: O 1206 LYS cc_start: 0.8902 (ttmm) cc_final: 0.8662 (ttmm) REVERT: B 4 GLU cc_start: 0.8356 (mp0) cc_final: 0.7800 (mp0) REVERT: Q 104 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7385 (mm-30) REVERT: Q 106 LYS cc_start: 0.9115 (mmmm) cc_final: 0.8720 (mmmm) REVERT: S 307 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.9035 (m-80) REVERT: T 1006 LYS cc_start: 0.9044 (mtmt) cc_final: 0.8809 (mtmt) REVERT: U 1104 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7809 (mm-30) REVERT: U 1106 LYS cc_start: 0.8724 (mmmm) cc_final: 0.8420 (mmmm) REVERT: W 1302 LYS cc_start: 0.9242 (mtpt) cc_final: 0.8809 (mtpp) REVERT: C 4 GLU cc_start: 0.8004 (mp0) cc_final: 0.7393 (mp0) REVERT: X 106 LYS cc_start: 0.9036 (mmmm) cc_final: 0.8641 (mmmm) REVERT: Z 304 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8279 (mm-30) REVERT: j 1004 GLU cc_start: 0.8112 (mp0) cc_final: 0.7457 (mp0) REVERT: k 1106 LYS cc_start: 0.8937 (mmmm) cc_final: 0.8455 (mmmm) REVERT: l 1202 LYS cc_start: 0.9192 (mtpt) cc_final: 0.8788 (mtpp) REVERT: l 1206 LYS cc_start: 0.8998 (ttmm) cc_final: 0.8773 (ttmm) REVERT: D 4 GLU cc_start: 0.7994 (mp0) cc_final: 0.7079 (mp0) REVERT: D 6 LYS cc_start: 0.8909 (mtmt) cc_final: 0.8380 (mtmt) REVERT: D 7 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.8490 (t80) REVERT: n 104 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7873 (mm-30) REVERT: n 106 LYS cc_start: 0.8933 (mmmm) cc_final: 0.8433 (mmmm) REVERT: o 202 LYS cc_start: 0.9226 (ttpt) cc_final: 0.8903 (ttpt) REVERT: o 206 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8891 (ttmm) REVERT: q 1004 GLU cc_start: 0.8374 (mp0) cc_final: 0.8056 (mp0) REVERT: r 1106 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8701 (mmmm) REVERT: s 1204 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7819 (mt-10) REVERT: E 6 LYS cc_start: 0.8961 (mtmt) cc_final: 0.8748 (mtmt) REVERT: u 106 LYS cc_start: 0.8953 (mmmm) cc_final: 0.8577 (mmmm) REVERT: x 1003 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8476 (m-80) REVERT: x 1006 LYS cc_start: 0.8854 (mtmt) cc_final: 0.8130 (mtmt) REVERT: y 1102 LYS cc_start: 0.9056 (ttpt) cc_final: 0.8661 (ttpt) REVERT: y 1104 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7933 (mm-30) REVERT: y 1106 LYS cc_start: 0.8752 (mmmm) cc_final: 0.8378 (mmmm) REVERT: F 6 LYS cc_start: 0.9029 (mtmt) cc_final: 0.8717 (mtmt) REVERT: 1 104 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7323 (mm-30) REVERT: 1 106 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8368 (mmmm) REVERT: 3 302 LYS cc_start: 0.9252 (ttpt) cc_final: 0.8791 (ttmm) REVERT: 3 304 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8160 (mm-30) REVERT: 4 1006 LYS cc_start: 0.8982 (ttmt) cc_final: 0.8551 (ttmt) REVERT: 5 1104 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8040 (mm-30) REVERT: 5 1106 LYS cc_start: 0.8881 (mmmm) cc_final: 0.8519 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9253 (mtpt) cc_final: 0.8769 (mtpp) REVERT: 7 1304 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7811 (mm-30) REVERT: G 3 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: G 4 GLU cc_start: 0.8185 (mp0) cc_final: 0.7464 (mp0) REVERT: G 6 LYS cc_start: 0.9062 (mtmt) cc_final: 0.8825 (mtmt) REVERT: 8 106 LYS cc_start: 0.8789 (mmmm) cc_final: 0.8268 (mmmm) REVERT: AA 306 LYS cc_start: 0.9054 (mttt) cc_final: 0.8710 (mttm) REVERT: BA 1004 GLU cc_start: 0.8096 (mp0) cc_final: 0.7131 (mp0) REVERT: CA 1104 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7419 (mm-30) REVERT: DA 1206 LYS cc_start: 0.9149 (ttmm) cc_final: 0.8905 (ttmm) REVERT: EA 1306 LYS cc_start: 0.9106 (mttt) cc_final: 0.8695 (mttt) REVERT: H 4 GLU cc_start: 0.3246 (OUTLIER) cc_final: 0.2342 (pm20) REVERT: FA 106 LYS cc_start: 0.8977 (mmmm) cc_final: 0.8674 (mmmm) REVERT: HA 302 LYS cc_start: 0.9098 (mtpt) cc_final: 0.8723 (mtpp) REVERT: JA 1106 LYS cc_start: 0.9060 (mmmm) cc_final: 0.8616 (mmmm) REVERT: I 4 GLU cc_start: 0.7786 (mp0) cc_final: 0.7147 (mp0) REVERT: PA 1004 GLU cc_start: 0.7783 (mp0) cc_final: 0.7040 (mp0) REVERT: RA 1202 LYS cc_start: 0.9167 (mtpt) cc_final: 0.8834 (mtpp) REVERT: SA 1307 PHE cc_start: 0.9361 (OUTLIER) cc_final: 0.8617 (m-80) REVERT: a 2 LYS cc_start: 0.9143 (tppt) cc_final: 0.8818 (tppt) REVERT: a 4 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8305 (tp30) REVERT: VA 306 LYS cc_start: 0.8974 (tptp) cc_final: 0.8706 (tptp) REVERT: WA 1002 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8817 (tppt) REVERT: XA 1105 PHE cc_start: 0.9354 (OUTLIER) cc_final: 0.8717 (p90) REVERT: YA 1204 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: ZA 1306 LYS cc_start: 0.8891 (tptp) cc_final: 0.8590 (tptp) REVERT: b 6 LYS cc_start: 0.9221 (ttpt) cc_final: 0.8955 (ttpt) REVERT: aA 104 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8191 (tm-30) REVERT: bA 202 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9088 (tppp) REVERT: dA 1002 LYS cc_start: 0.9058 (ttmt) cc_final: 0.8787 (ttmt) REVERT: eA 1104 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8001 (tm-30) REVERT: eA 1105 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8744 (t80) REVERT: c 2 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.9043 (tppt) REVERT: hA 104 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8049 (tm-30) REVERT: iA 202 LYS cc_start: 0.9394 (tttm) cc_final: 0.9052 (tppp) REVERT: jA 302 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8754 (tptp) REVERT: lA 1105 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.7742 (t80) REVERT: nA 1306 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8880 (tptp) REVERT: d 2 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8792 (tppt) REVERT: oA 103 PHE cc_start: 0.9282 (t80) cc_final: 0.8932 (t80) REVERT: qA 306 LYS cc_start: 0.8906 (tptp) cc_final: 0.8599 (tptp) REVERT: sA 1103 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.9039 (t80) REVERT: vA 104 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8339 (tm-30) REVERT: wA 202 LYS cc_start: 0.9467 (tttm) cc_final: 0.8996 (tppp) REVERT: zA 1104 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7917 (tm-30) REVERT: f 2 LYS cc_start: 0.9092 (ttmt) cc_final: 0.8795 (ttmt) REVERT: 4A 302 LYS cc_start: 0.8679 (tptp) cc_final: 0.8370 (tptp) REVERT: 4A 305 PHE cc_start: 0.9362 (t80) cc_final: 0.9129 (t80) REVERT: g 2 LYS cc_start: 0.9019 (tppt) cc_final: 0.8618 (tppt) REVERT: AB 202 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.8972 (ttmm) REVERT: BB 304 GLU cc_start: 0.9327 (tm-30) cc_final: 0.8752 (tm-30) REVERT: EB 1204 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7869 (tm-30) REVERT: FB 1306 LYS cc_start: 0.8982 (tptp) cc_final: 0.8769 (tptp) REVERT: HB 202 LYS cc_start: 0.9301 (tttm) cc_final: 0.8951 (pttt) REVERT: IB 306 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8660 (tptp) REVERT: i 6 LYS cc_start: 0.9281 (ttpt) cc_final: 0.9050 (ttpt) REVERT: NB 104 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8118 (pm20) REVERT: OB 202 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9156 (mmmm) REVERT: PB 307 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8883 (t80) REVERT: SB 1202 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.9133 (ttmm) REVERT: TB 1302 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8536 (tptp) outliers start: 174 outliers final: 121 residues processed: 487 average time/residue: 0.5031 time to fit residues: 298.8581 Evaluate side-chains 589 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 441 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain M residue 1007 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain l residue 1204 GLU Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 4 residue 1002 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain AA residue 304 GLU Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain QA residue 1104 GLU Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 104 GLU Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1204 GLU Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain bA residue 202 LYS Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain dA residue 1006 LYS Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 6 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain iA residue 204 GLU Chi-restraints excluded: chain jA residue 302 LYS 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 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 d residue 4 GLU Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain sA residue 1106 LYS Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1204 GLU Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain wA residue 204 GLU Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 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 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 104 GLU Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 202 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 302 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain 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 QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain SB residue 1204 GLU Chi-restraints excluded: chain TB residue 1302 LYS Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.7916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.111 0.346 12528 Z= 6.191 Angle : 4.086 58.632 16272 Z= 1.834 Chirality : 0.301 0.884 1152 Planarity : 0.016 0.074 2160 Dihedral : 21.123 84.705 1495 Min Nonbonded Distance : 1.619 Molprobity Statistics. All-atom Clashscore : 107.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 34.03 % Favored : 65.80 % Rotamer: Outliers : 21.30 % Allowed : 26.16 % Favored : 52.55 % Cbeta Deviations : 14.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.39 % 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: -7.54 (0.21), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.74 (0.16), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.128 0.016 PHE 2 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 441 time to evaluate : 1.714 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: A 6 LYS cc_start: 0.9070 (mtmt) cc_final: 0.8642 (mtmt) REVERT: J 106 LYS cc_start: 0.8995 (mmmm) cc_final: 0.8536 (mmmm) REVERT: M 1004 GLU cc_start: 0.8180 (mp0) cc_final: 0.7735 (mp0) REVERT: M 1006 LYS cc_start: 0.9017 (mtmt) cc_final: 0.8785 (mtmt) REVERT: N 1106 LYS cc_start: 0.8935 (mmmm) cc_final: 0.8538 (mmmm) REVERT: O 1206 LYS cc_start: 0.8888 (ttmm) cc_final: 0.8642 (ttmm) REVERT: B 4 GLU cc_start: 0.8337 (mp0) cc_final: 0.7795 (mp0) REVERT: B 5 PHE cc_start: 0.9248 (OUTLIER) cc_final: 0.9028 (m-80) REVERT: Q 104 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7453 (mm-30) REVERT: Q 106 LYS cc_start: 0.9065 (mmmm) cc_final: 0.8689 (mmmm) REVERT: S 307 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.8994 (m-80) REVERT: T 1006 LYS cc_start: 0.9029 (mtmt) cc_final: 0.8702 (mtmt) REVERT: U 1104 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7865 (mm-30) REVERT: U 1106 LYS cc_start: 0.8731 (mmmm) cc_final: 0.8435 (mmmm) REVERT: W 1302 LYS cc_start: 0.9227 (mtpt) cc_final: 0.8791 (mtpp) REVERT: C 4 GLU cc_start: 0.7979 (mp0) cc_final: 0.7395 (mp0) REVERT: X 104 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7920 (mm-30) REVERT: X 106 LYS cc_start: 0.9058 (mmmm) cc_final: 0.8657 (mmmm) REVERT: j 1004 GLU cc_start: 0.8099 (mp0) cc_final: 0.7734 (mp0) REVERT: k 1106 LYS cc_start: 0.8927 (mmmm) cc_final: 0.8573 (mmmm) REVERT: l 1202 LYS cc_start: 0.9165 (mtpt) cc_final: 0.8787 (mtpp) REVERT: l 1206 LYS cc_start: 0.9014 (ttmm) cc_final: 0.8803 (ttmm) REVERT: D 4 GLU cc_start: 0.7998 (mp0) cc_final: 0.7042 (mp0) REVERT: D 6 LYS cc_start: 0.8925 (mtmt) cc_final: 0.8380 (mtmt) REVERT: D 7 PHE cc_start: 0.9319 (OUTLIER) cc_final: 0.8473 (t80) REVERT: n 104 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7934 (mm-30) REVERT: n 106 LYS cc_start: 0.8946 (mmmm) cc_final: 0.8439 (mmmm) REVERT: o 202 LYS cc_start: 0.9232 (ttpt) cc_final: 0.9020 (ttpt) REVERT: o 206 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8828 (ttmm) REVERT: q 1004 GLU cc_start: 0.8332 (mp0) cc_final: 0.8079 (mp0) REVERT: r 1106 LYS cc_start: 0.9052 (mmmm) cc_final: 0.8666 (mmmm) REVERT: u 106 LYS cc_start: 0.8983 (mmmm) cc_final: 0.8588 (mmmm) REVERT: w 307 PHE cc_start: 0.9468 (OUTLIER) cc_final: 0.8752 (m-80) REVERT: x 1003 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8538 (m-80) REVERT: x 1006 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8115 (mtmt) REVERT: y 1102 LYS cc_start: 0.9067 (ttpt) cc_final: 0.8667 (ttpt) REVERT: y 1106 LYS cc_start: 0.8762 (mmmm) cc_final: 0.8381 (mmmm) REVERT: F 6 LYS cc_start: 0.9058 (mtmt) cc_final: 0.8716 (mtmt) REVERT: 1 104 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7387 (mm-30) REVERT: 1 106 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8396 (mmmm) REVERT: 4 1006 LYS cc_start: 0.9001 (ttmt) cc_final: 0.8534 (ttmt) REVERT: 5 1106 LYS cc_start: 0.8877 (mmmm) cc_final: 0.8519 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9222 (mtpt) cc_final: 0.8770 (mtpp) REVERT: 7 1304 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8014 (mm-30) REVERT: G 3 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: G 4 GLU cc_start: 0.8164 (mp0) cc_final: 0.7432 (mp0) REVERT: G 6 LYS cc_start: 0.9080 (mtmt) cc_final: 0.8808 (mtmt) REVERT: 8 106 LYS cc_start: 0.8778 (mmmm) cc_final: 0.8268 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8030 (mp0) cc_final: 0.7623 (mp0) REVERT: CA 1104 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7271 (mm-30) REVERT: DA 1206 LYS cc_start: 0.9252 (ttmm) cc_final: 0.9047 (ttmm) REVERT: EA 1306 LYS cc_start: 0.9090 (mttt) cc_final: 0.8732 (mttt) REVERT: H 4 GLU cc_start: 0.2932 (OUTLIER) cc_final: 0.2062 (pm20) REVERT: FA 106 LYS cc_start: 0.8980 (mmmm) cc_final: 0.8682 (mmmm) REVERT: HA 302 LYS cc_start: 0.9082 (mtpt) cc_final: 0.8664 (mmmm) REVERT: JA 1104 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7852 (tm-30) REVERT: JA 1106 LYS cc_start: 0.9055 (mmmm) cc_final: 0.8588 (mmmm) REVERT: I 4 GLU cc_start: 0.7805 (mp0) cc_final: 0.7211 (mp0) REVERT: PA 1004 GLU cc_start: 0.7782 (mp0) cc_final: 0.7062 (mp0) REVERT: PA 1007 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.8827 (m-80) REVERT: RA 1202 LYS cc_start: 0.9139 (mtpt) cc_final: 0.8822 (mtpp) REVERT: SA 1307 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.8540 (m-80) REVERT: a 2 LYS cc_start: 0.9167 (tppt) cc_final: 0.8830 (tppt) REVERT: a 4 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8355 (tp30) REVERT: VA 306 LYS cc_start: 0.8967 (tptp) cc_final: 0.8724 (tptp) REVERT: WA 1002 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8910 (tppt) REVERT: XA 1105 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8713 (p90) REVERT: YA 1204 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8143 (tm-30) REVERT: ZA 1306 LYS cc_start: 0.8870 (tptp) cc_final: 0.8567 (tptp) REVERT: b 6 LYS cc_start: 0.9230 (ttpt) cc_final: 0.8968 (ttpt) REVERT: aA 104 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8174 (tm-30) REVERT: bA 202 LYS cc_start: 0.9386 (tttm) cc_final: 0.9051 (tppp) REVERT: dA 1002 LYS cc_start: 0.9057 (ttmt) cc_final: 0.8782 (ttmt) REVERT: eA 1105 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8749 (t80) REVERT: c 2 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.9028 (tppt) REVERT: hA 104 GLU cc_start: 0.8664 (tm-30) cc_final: 0.7922 (tm-30) REVERT: lA 1105 PHE cc_start: 0.9183 (OUTLIER) cc_final: 0.7973 (t80) REVERT: d 2 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8811 (tppt) REVERT: qA 306 LYS cc_start: 0.8872 (tptp) cc_final: 0.8581 (tptp) REVERT: sA 1103 PHE cc_start: 0.9333 (OUTLIER) cc_final: 0.8972 (t80) REVERT: uA 1303 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8797 (t80) REVERT: uA 1307 PHE cc_start: 0.9410 (OUTLIER) cc_final: 0.9209 (t80) REVERT: vA 104 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8307 (tm-30) REVERT: wA 202 LYS cc_start: 0.9466 (OUTLIER) cc_final: 0.9117 (tppp) REVERT: zA 1104 GLU cc_start: 0.8456 (tm-30) cc_final: 0.7928 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9332 (t80) cc_final: 0.9085 (t80) REVERT: f 2 LYS cc_start: 0.9078 (ttmt) cc_final: 0.8779 (ttmt) REVERT: 3A 202 LYS cc_start: 0.9345 (tttm) cc_final: 0.8941 (tppp) REVERT: 3A 204 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7538 (tm-30) REVERT: 4A 302 LYS cc_start: 0.8762 (tptp) cc_final: 0.8447 (tptp) REVERT: 8A 1302 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8471 (tptp) REVERT: g 2 LYS cc_start: 0.9018 (tppt) cc_final: 0.8611 (tppt) REVERT: AB 202 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.8972 (ttmm) REVERT: BB 304 GLU cc_start: 0.9309 (tm-30) cc_final: 0.8755 (tm-30) REVERT: EB 1204 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7975 (tm-30) REVERT: FB 1306 LYS cc_start: 0.8931 (tptp) cc_final: 0.8690 (tptp) REVERT: GB 103 PHE cc_start: 0.9485 (OUTLIER) cc_final: 0.9260 (t80) REVERT: HB 202 LYS cc_start: 0.9298 (tttm) cc_final: 0.8927 (pttt) REVERT: IB 306 LYS cc_start: 0.9032 (tptp) cc_final: 0.8667 (tptp) REVERT: i 6 LYS cc_start: 0.9283 (ttpt) cc_final: 0.9062 (ttpt) REVERT: NB 104 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8113 (pm20) REVERT: OB 202 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.9153 (mmmm) REVERT: PB 306 LYS cc_start: 0.8752 (tptp) cc_final: 0.8460 (tptp) REVERT: PB 307 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8882 (t80) REVERT: QB 1005 PHE cc_start: 0.9403 (t80) cc_final: 0.9202 (t80) REVERT: RB 1104 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8081 (pm20) REVERT: SB 1202 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.9127 (ttmm) REVERT: TB 1302 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8541 (tptp) outliers start: 184 outliers final: 139 residues processed: 501 average time/residue: 0.4776 time to fit residues: 292.7508 Evaluate side-chains 612 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 441 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain M residue 1007 PHE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1002 LYS Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1204 GLU Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 4 residue 1002 LYS Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 304 GLU Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1007 PHE Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 104 GLU Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 304 GLU Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1204 GLU Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain cA residue 302 LYS Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1105 PHE 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 c residue 4 GLU Chi-restraints excluded: chain c residue 6 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain iA residue 204 GLU Chi-restraints excluded: chain jA residue 302 LYS 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 nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE 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 oA residue 102 LYS Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain sA residue 1106 LYS Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1204 GLU Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain wA residue 202 LYS Chi-restraints excluded: chain wA residue 204 GLU Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 3A residue 204 GLU 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 1204 GLU Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 104 GLU Chi-restraints excluded: chain AB residue 202 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 302 LYS Chi-restraints excluded: chain IB residue 305 PHE 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 LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain SB residue 1204 GLU Chi-restraints excluded: chain TB residue 1302 LYS Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.7986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.111 0.337 12528 Z= 6.192 Angle : 4.109 62.599 16272 Z= 1.841 Chirality : 0.301 0.889 1152 Planarity : 0.016 0.068 2160 Dihedral : 21.144 85.340 1495 Min Nonbonded Distance : 1.505 Molprobity Statistics. All-atom Clashscore : 108.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 34.55 % Favored : 65.28 % Rotamer: Outliers : 22.11 % Allowed : 29.28 % Favored : 48.61 % Cbeta Deviations : 15.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.39 % 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: -7.52 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.73 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.129 0.016 PHE 2 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 442 time to evaluate : 1.788 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: A 6 LYS cc_start: 0.9091 (mtmt) cc_final: 0.8652 (mtmt) REVERT: J 106 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8533 (mmmm) REVERT: M 1004 GLU cc_start: 0.8227 (mp0) cc_final: 0.7745 (mp0) REVERT: M 1006 LYS cc_start: 0.9035 (mtmt) cc_final: 0.8798 (mtmt) REVERT: N 1106 LYS cc_start: 0.8931 (mmmm) cc_final: 0.8586 (mmmm) REVERT: O 1206 LYS cc_start: 0.8888 (ttmm) cc_final: 0.8651 (ttmm) REVERT: B 4 GLU cc_start: 0.8349 (mp0) cc_final: 0.7714 (mp0) REVERT: B 5 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8989 (m-80) REVERT: Q 104 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7448 (mm-30) REVERT: Q 106 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8687 (mmmm) REVERT: S 307 PHE cc_start: 0.9325 (OUTLIER) cc_final: 0.8990 (m-80) REVERT: T 1006 LYS cc_start: 0.9023 (mtmt) cc_final: 0.8643 (mtmt) REVERT: U 1104 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7584 (mm-30) REVERT: U 1106 LYS cc_start: 0.8743 (mmmm) cc_final: 0.8423 (mmmm) REVERT: W 1302 LYS cc_start: 0.9211 (mtpt) cc_final: 0.8790 (mtpp) REVERT: C 4 GLU cc_start: 0.8013 (mp0) cc_final: 0.7434 (mp0) REVERT: X 104 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7743 (mm-30) REVERT: X 106 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8647 (mmmm) REVERT: Y 202 LYS cc_start: 0.9045 (ttpt) cc_final: 0.8836 (ttpt) REVERT: j 1004 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: k 1106 LYS cc_start: 0.8954 (mmmm) cc_final: 0.8611 (mmmm) REVERT: l 1202 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8813 (mtpp) REVERT: l 1204 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.8012 (mm-30) REVERT: D 4 GLU cc_start: 0.8005 (mp0) cc_final: 0.7065 (mp0) REVERT: D 6 LYS cc_start: 0.8924 (mtmt) cc_final: 0.8406 (mtmt) REVERT: D 7 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8442 (t80) REVERT: n 104 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7935 (mm-30) REVERT: n 106 LYS cc_start: 0.8953 (mmmm) cc_final: 0.8466 (mmmm) REVERT: o 202 LYS cc_start: 0.9245 (ttpt) cc_final: 0.9029 (ttpt) REVERT: o 206 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8909 (ttmm) REVERT: q 1004 GLU cc_start: 0.8331 (mp0) cc_final: 0.8033 (mp0) REVERT: r 1106 LYS cc_start: 0.9062 (mmmm) cc_final: 0.8637 (mmmm) REVERT: E 4 GLU cc_start: 0.7861 (mp0) cc_final: 0.7466 (mp0) REVERT: u 106 LYS cc_start: 0.8952 (mmmm) cc_final: 0.8614 (mmmm) REVERT: x 1003 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8589 (m-80) REVERT: x 1006 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8305 (mtmt) REVERT: y 1106 LYS cc_start: 0.8768 (mmmm) cc_final: 0.8399 (mmmm) REVERT: F 6 LYS cc_start: 0.9070 (mtmt) cc_final: 0.8744 (mtmt) REVERT: 1 104 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7426 (mm-30) REVERT: 1 106 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8457 (mmmm) REVERT: 4 1004 GLU cc_start: 0.8247 (mp0) cc_final: 0.7959 (mp0) REVERT: 5 1106 LYS cc_start: 0.8893 (mmmm) cc_final: 0.8547 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9212 (mtpt) cc_final: 0.8744 (mtpp) REVERT: G 3 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.8257 (m-80) REVERT: G 4 GLU cc_start: 0.8202 (mp0) cc_final: 0.7515 (mp0) REVERT: G 6 LYS cc_start: 0.9063 (mtmt) cc_final: 0.8796 (mtmt) REVERT: 8 106 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8289 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8034 (mp0) cc_final: 0.7623 (mp0) REVERT: CA 1104 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7238 (mm-30) REVERT: CA 1106 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8817 (mmmm) REVERT: DA 1206 LYS cc_start: 0.9259 (ttmm) cc_final: 0.9003 (ttmm) REVERT: EA 1306 LYS cc_start: 0.9089 (mttt) cc_final: 0.8723 (mttt) REVERT: H 4 GLU cc_start: 0.2910 (OUTLIER) cc_final: 0.2025 (pm20) REVERT: FA 106 LYS cc_start: 0.8973 (mmmm) cc_final: 0.8676 (mmmm) REVERT: HA 302 LYS cc_start: 0.9095 (mtpt) cc_final: 0.8703 (mmmm) REVERT: JA 1106 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8592 (mmmm) REVERT: I 4 GLU cc_start: 0.7806 (mp0) cc_final: 0.7244 (mp0) REVERT: PA 1004 GLU cc_start: 0.7776 (mp0) cc_final: 0.7029 (mp0) REVERT: PA 1007 PHE cc_start: 0.9381 (OUTLIER) cc_final: 0.9053 (m-80) REVERT: RA 1202 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8828 (mtpp) REVERT: SA 1307 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.8551 (m-80) REVERT: a 2 LYS cc_start: 0.9178 (tppt) cc_final: 0.8839 (tppt) REVERT: WA 1002 LYS cc_start: 0.9217 (tptt) cc_final: 0.8911 (tppt) REVERT: XA 1105 PHE cc_start: 0.9355 (OUTLIER) cc_final: 0.8703 (p90) REVERT: ZA 1306 LYS cc_start: 0.8869 (tptp) cc_final: 0.8545 (tptp) REVERT: b 6 LYS cc_start: 0.9243 (ttpt) cc_final: 0.8965 (ttpt) REVERT: aA 104 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8148 (tm-30) REVERT: bA 202 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.9085 (tppp) REVERT: cA 302 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8667 (tptp) REVERT: dA 1002 LYS cc_start: 0.9056 (ttmt) cc_final: 0.8779 (ttmt) REVERT: eA 1104 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8035 (tm-30) REVERT: eA 1105 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8747 (t80) REVERT: c 2 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.9069 (tppt) REVERT: hA 104 GLU cc_start: 0.8660 (tm-30) cc_final: 0.7700 (tm-30) REVERT: lA 1105 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8125 (t80) REVERT: nA 1306 LYS cc_start: 0.9055 (tptp) cc_final: 0.8818 (tptp) REVERT: oA 104 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8233 (tm-30) REVERT: qA 306 LYS cc_start: 0.8858 (tptp) cc_final: 0.8563 (tptp) REVERT: sA 1103 PHE cc_start: 0.9319 (OUTLIER) cc_final: 0.9006 (t80) REVERT: uA 1303 PHE cc_start: 0.9097 (t80) cc_final: 0.8856 (t80) REVERT: uA 1307 PHE cc_start: 0.9404 (OUTLIER) cc_final: 0.9148 (t80) REVERT: vA 104 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8303 (tm-30) REVERT: wA 202 LYS cc_start: 0.9467 (tttm) cc_final: 0.8996 (tppp) REVERT: zA 1104 GLU cc_start: 0.8449 (tm-30) cc_final: 0.7963 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9360 (t80) cc_final: 0.9064 (t80) REVERT: f 2 LYS cc_start: 0.9081 (ttmt) cc_final: 0.8781 (ttmt) REVERT: 3A 202 LYS cc_start: 0.9332 (tttm) cc_final: 0.8911 (tppp) REVERT: 4A 302 LYS cc_start: 0.8819 (tptp) cc_final: 0.8478 (tptp) REVERT: 4A 306 LYS cc_start: 0.8598 (tptp) cc_final: 0.8295 (tptp) REVERT: 8A 1305 PHE cc_start: 0.9113 (t80) cc_final: 0.8861 (t80) REVERT: g 2 LYS cc_start: 0.9015 (tppt) cc_final: 0.8600 (tppt) REVERT: AB 202 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.8968 (ttmm) REVERT: BB 304 GLU cc_start: 0.9314 (tm-30) cc_final: 0.8753 (tm-30) REVERT: FB 1306 LYS cc_start: 0.8904 (tptp) cc_final: 0.8625 (tptp) REVERT: HB 202 LYS cc_start: 0.9302 (tttm) cc_final: 0.8925 (pttt) REVERT: IB 306 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8654 (tptp) REVERT: i 6 LYS cc_start: 0.9291 (ttpt) cc_final: 0.9056 (ttpt) REVERT: NB 104 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8120 (pm20) REVERT: NB 106 LYS cc_start: 0.9205 (tttp) cc_final: 0.8688 (pptt) REVERT: OB 202 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9150 (mmmm) REVERT: RB 1104 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8085 (pm20) REVERT: SB 1202 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.9133 (ttmm) REVERT: TB 1302 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8541 (tptp) outliers start: 191 outliers final: 154 residues processed: 505 average time/residue: 0.4832 time to fit residues: 299.5246 Evaluate side-chains 622 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 442 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain M residue 1007 PHE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1204 GLU Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 304 GLU Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain LA residue 1304 GLU Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1007 PHE Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 104 GLU Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 304 GLU Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1204 GLU Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain bA residue 202 LYS Chi-restraints excluded: chain cA residue 302 LYS Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain dA residue 1006 LYS Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 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 c residue 4 GLU Chi-restraints excluded: chain c residue 6 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain iA residue 204 GLU Chi-restraints excluded: chain jA residue 302 LYS 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 nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE 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 qA residue 307 PHE Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain sA residue 1106 LYS Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1204 GLU Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain wA residue 204 GLU Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 0A residue 1206 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 3A residue 204 GLU Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 5A residue 1006 LYS Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 7A residue 1204 GLU Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 104 GLU Chi-restraints excluded: chain AB residue 202 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 302 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain 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 QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain SB residue 1204 GLU Chi-restraints excluded: chain TB residue 1302 LYS Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.8031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.111 0.338 12528 Z= 6.188 Angle : 4.095 55.573 16272 Z= 1.837 Chirality : 0.302 0.885 1152 Planarity : 0.016 0.069 2160 Dihedral : 21.034 86.354 1488 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 108.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 34.90 % Favored : 64.93 % Rotamer: Outliers : 22.45 % Allowed : 29.51 % Favored : 48.03 % Cbeta Deviations : 15.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.49 % 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: -7.52 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.72 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.128 0.016 PHE 2 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 441 time to evaluate : 1.266 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: A 6 LYS cc_start: 0.9111 (mtmt) cc_final: 0.8661 (mtmt) REVERT: J 106 LYS cc_start: 0.9001 (mmmm) cc_final: 0.8529 (mmmm) REVERT: M 1004 GLU cc_start: 0.8247 (mp0) cc_final: 0.7669 (mp0) REVERT: M 1006 LYS cc_start: 0.9039 (mtmt) cc_final: 0.8804 (mtmt) REVERT: N 1106 LYS cc_start: 0.8931 (mmmm) cc_final: 0.8585 (mmmm) REVERT: O 1206 LYS cc_start: 0.8881 (ttmm) cc_final: 0.8643 (ttmm) REVERT: B 4 GLU cc_start: 0.8351 (mp0) cc_final: 0.7704 (mp0) REVERT: B 5 PHE cc_start: 0.9245 (OUTLIER) cc_final: 0.8982 (m-80) REVERT: Q 104 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7253 (mm-30) REVERT: Q 106 LYS cc_start: 0.9070 (mmmm) cc_final: 0.8688 (mmmm) REVERT: T 1006 LYS cc_start: 0.9011 (mtmt) cc_final: 0.8604 (mtmt) REVERT: U 1104 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7826 (mm-30) REVERT: U 1106 LYS cc_start: 0.8742 (mmmm) cc_final: 0.8428 (mmmm) REVERT: W 1302 LYS cc_start: 0.9207 (mtpt) cc_final: 0.8787 (mtpp) REVERT: C 4 GLU cc_start: 0.8034 (mp0) cc_final: 0.7467 (mp0) REVERT: X 104 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7894 (mm-30) REVERT: X 106 LYS cc_start: 0.9055 (mmmm) cc_final: 0.8668 (mmmm) REVERT: Y 202 LYS cc_start: 0.9076 (ttpt) cc_final: 0.8832 (ttpt) REVERT: j 1004 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: k 1106 LYS cc_start: 0.8944 (mmmm) cc_final: 0.8599 (mmmm) REVERT: l 1202 LYS cc_start: 0.9129 (mtpt) cc_final: 0.8796 (mtpp) REVERT: D 4 GLU cc_start: 0.8001 (mp0) cc_final: 0.7111 (mp0) REVERT: D 6 LYS cc_start: 0.8934 (mtmt) cc_final: 0.8410 (mtmt) REVERT: D 7 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8381 (t80) REVERT: n 104 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7922 (mm-30) REVERT: n 106 LYS cc_start: 0.8957 (mmmm) cc_final: 0.8467 (mmmm) REVERT: o 202 LYS cc_start: 0.9246 (ttpt) cc_final: 0.9037 (ttpt) REVERT: r 1106 LYS cc_start: 0.9055 (mmmm) cc_final: 0.8608 (mmmm) REVERT: u 106 LYS cc_start: 0.8951 (mmmm) cc_final: 0.8623 (mmmm) REVERT: w 302 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8781 (mmmm) REVERT: w 304 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8071 (mm-30) REVERT: x 1006 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8236 (mtmt) REVERT: y 1106 LYS cc_start: 0.8749 (mmmm) cc_final: 0.8406 (mmmm) REVERT: F 6 LYS cc_start: 0.9053 (mtmt) cc_final: 0.8806 (mtmt) REVERT: 1 104 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7460 (mm-30) REVERT: 1 106 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8491 (mmmm) REVERT: 3 304 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8031 (mm-30) REVERT: 4 1004 GLU cc_start: 0.8326 (mp0) cc_final: 0.7893 (mp0) REVERT: 5 1106 LYS cc_start: 0.8882 (mmmm) cc_final: 0.8547 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9197 (mtpt) cc_final: 0.8727 (mtpp) REVERT: G 3 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8246 (m-80) REVERT: G 4 GLU cc_start: 0.8215 (mp0) cc_final: 0.7528 (mp0) REVERT: 8 106 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8289 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8026 (mp0) cc_final: 0.7100 (mp0) REVERT: CA 1104 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7262 (mm-30) REVERT: CA 1106 LYS cc_start: 0.9021 (mmmm) cc_final: 0.8776 (mmmm) REVERT: DA 1206 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.9060 (ttmm) REVERT: EA 1306 LYS cc_start: 0.9104 (mttt) cc_final: 0.8791 (mttt) REVERT: H 4 GLU cc_start: 0.2921 (OUTLIER) cc_final: 0.2027 (pm20) REVERT: FA 106 LYS cc_start: 0.8983 (mmmm) cc_final: 0.8679 (mmmm) REVERT: HA 302 LYS cc_start: 0.9085 (mtpt) cc_final: 0.8670 (mmmm) REVERT: JA 1106 LYS cc_start: 0.9021 (mmmm) cc_final: 0.8567 (mmmm) REVERT: I 4 GLU cc_start: 0.7801 (mp0) cc_final: 0.7230 (mp0) REVERT: I 6 LYS cc_start: 0.9017 (mtmt) cc_final: 0.8718 (ttmt) REVERT: PA 1004 GLU cc_start: 0.7788 (mp0) cc_final: 0.7072 (mp0) REVERT: PA 1007 PHE cc_start: 0.9399 (OUTLIER) cc_final: 0.8876 (m-80) REVERT: RA 1202 LYS cc_start: 0.9153 (mtpt) cc_final: 0.8837 (mtpp) REVERT: SA 1307 PHE cc_start: 0.9373 (OUTLIER) cc_final: 0.8553 (m-80) REVERT: a 2 LYS cc_start: 0.9179 (tppt) cc_final: 0.8833 (tppt) REVERT: VA 306 LYS cc_start: 0.8968 (tptp) cc_final: 0.8732 (tptp) REVERT: WA 1002 LYS cc_start: 0.9198 (tptt) cc_final: 0.8922 (tppt) REVERT: XA 1105 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.8709 (p90) REVERT: ZA 1306 LYS cc_start: 0.8868 (tptp) cc_final: 0.8547 (tptp) REVERT: b 6 LYS cc_start: 0.9242 (ttpt) cc_final: 0.8969 (ttpt) REVERT: aA 104 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8151 (tm-30) REVERT: bA 202 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9085 (tppp) REVERT: cA 302 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8647 (tptp) REVERT: dA 1002 LYS cc_start: 0.9057 (ttmt) cc_final: 0.8779 (ttmt) REVERT: eA 1105 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8726 (t80) REVERT: c 2 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.9043 (tppt) REVERT: hA 104 GLU cc_start: 0.8681 (tm-30) cc_final: 0.7720 (tm-30) REVERT: mA 1206 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8938 (pptt) REVERT: nA 1306 LYS cc_start: 0.9069 (tptp) cc_final: 0.8819 (tptp) REVERT: qA 306 LYS cc_start: 0.8864 (tptp) cc_final: 0.8594 (tptp) REVERT: sA 1103 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.9000 (t80) REVERT: vA 104 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8308 (tm-30) REVERT: wA 202 LYS cc_start: 0.9471 (OUTLIER) cc_final: 0.9127 (tppp) REVERT: zA 1104 GLU cc_start: 0.8449 (tm-30) cc_final: 0.7961 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9377 (t80) cc_final: 0.9120 (t80) REVERT: f 2 LYS cc_start: 0.9082 (ttmt) cc_final: 0.8780 (ttmt) REVERT: 4A 305 PHE cc_start: 0.9277 (t80) cc_final: 0.9076 (t80) REVERT: 4A 306 LYS cc_start: 0.8600 (tptp) cc_final: 0.8277 (tptp) REVERT: g 2 LYS cc_start: 0.9012 (tppt) cc_final: 0.8604 (tppt) REVERT: AB 202 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.8972 (ttmm) REVERT: BB 304 GLU cc_start: 0.9311 (tm-30) cc_final: 0.8756 (tm-30) REVERT: DB 1104 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8174 (tm-30) REVERT: FB 1306 LYS cc_start: 0.8890 (tptp) cc_final: 0.8580 (tptp) REVERT: HB 202 LYS cc_start: 0.9309 (tttm) cc_final: 0.8935 (pttt) REVERT: IB 306 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8688 (tptp) REVERT: i 6 LYS cc_start: 0.9295 (ttpt) cc_final: 0.9061 (ttpt) REVERT: NB 104 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8194 (pm20) REVERT: NB 106 LYS cc_start: 0.9209 (tttp) cc_final: 0.8690 (pptt) REVERT: OB 202 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9148 (mmmm) REVERT: RB 1104 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8085 (pm20) REVERT: SB 1202 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.9126 (ttmm) REVERT: TB 1302 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8539 (tptp) outliers start: 194 outliers final: 154 residues processed: 505 average time/residue: 0.4898 time to fit residues: 303.7366 Evaluate side-chains 621 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 442 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain M residue 1007 PHE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 304 GLU Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain DA residue 1206 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1007 PHE Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 104 GLU Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 304 GLU Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain bA residue 202 LYS Chi-restraints excluded: chain cA residue 302 LYS Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1105 PHE 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 c residue 4 GLU Chi-restraints excluded: chain c residue 6 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain iA residue 204 GLU Chi-restraints excluded: chain jA residue 302 LYS 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 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 d residue 4 GLU Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain sA residue 1106 LYS Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1204 GLU Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain wA residue 202 LYS Chi-restraints excluded: chain wA residue 204 GLU Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 0A residue 1206 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 3A residue 204 GLU Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 5A residue 1006 LYS 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 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 104 GLU Chi-restraints excluded: chain AB residue 202 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 302 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain 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 QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain SB residue 1204 GLU Chi-restraints excluded: chain TB residue 1302 LYS Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 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: 0.8433 moved from start: 0.8065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.111 0.337 12528 Z= 6.196 Angle : 4.129 59.490 16272 Z= 1.848 Chirality : 0.302 0.899 1152 Planarity : 0.016 0.069 2160 Dihedral : 21.057 86.514 1488 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 108.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 35.07 % Favored : 64.93 % Rotamer: Outliers : 23.15 % Allowed : 29.40 % Favored : 47.45 % Cbeta Deviations : 14.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.39 % 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: -7.56 (0.21), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.75 (0.16), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.128 0.016 PHE 2 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 437 time to evaluate : 1.327 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: A 6 LYS cc_start: 0.9120 (mtmt) cc_final: 0.8509 (mtmt) REVERT: J 106 LYS cc_start: 0.8992 (mmmm) cc_final: 0.8531 (mmmm) REVERT: M 1004 GLU cc_start: 0.8241 (mp0) cc_final: 0.7524 (mp0) REVERT: M 1006 LYS cc_start: 0.9038 (mtmt) cc_final: 0.8805 (mtmt) REVERT: N 1106 LYS cc_start: 0.8935 (mmmm) cc_final: 0.8590 (mmmm) REVERT: O 1206 LYS cc_start: 0.8882 (ttmm) cc_final: 0.8640 (ttmm) REVERT: B 4 GLU cc_start: 0.8332 (mp0) cc_final: 0.7700 (mp0) REVERT: B 5 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.8988 (m-80) REVERT: Q 104 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7344 (mm-30) REVERT: Q 106 LYS cc_start: 0.9060 (mmmm) cc_final: 0.8659 (mmmm) REVERT: T 1006 LYS cc_start: 0.9006 (mtmt) cc_final: 0.8588 (mtmt) REVERT: U 1104 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7834 (mm-30) REVERT: U 1106 LYS cc_start: 0.8757 (mmmm) cc_final: 0.8435 (mmmm) REVERT: C 4 GLU cc_start: 0.8048 (mp0) cc_final: 0.7475 (mp0) REVERT: X 106 LYS cc_start: 0.9040 (mmmm) cc_final: 0.8636 (mmmm) REVERT: Y 202 LYS cc_start: 0.9092 (ttpt) cc_final: 0.8835 (ttpt) REVERT: j 1004 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: k 1106 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8597 (mmmm) REVERT: l 1202 LYS cc_start: 0.9138 (mtpt) cc_final: 0.8805 (mtpp) REVERT: D 4 GLU cc_start: 0.7999 (mp0) cc_final: 0.7143 (mp0) REVERT: D 6 LYS cc_start: 0.8925 (mtmt) cc_final: 0.8421 (mtmt) REVERT: D 7 PHE cc_start: 0.9297 (OUTLIER) cc_final: 0.8443 (t80) REVERT: n 104 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7906 (mm-30) REVERT: n 106 LYS cc_start: 0.8953 (mmmm) cc_final: 0.8472 (mmmm) REVERT: o 202 LYS cc_start: 0.9256 (ttpt) cc_final: 0.9034 (ttpt) REVERT: r 1106 LYS cc_start: 0.9040 (mmmm) cc_final: 0.8591 (mmmm) REVERT: u 106 LYS cc_start: 0.8941 (mmmm) cc_final: 0.8675 (mmmm) REVERT: w 302 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8780 (mmmm) REVERT: w 304 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8062 (mm-30) REVERT: w 307 PHE cc_start: 0.9461 (OUTLIER) cc_final: 0.8869 (m-80) REVERT: x 1006 LYS cc_start: 0.8835 (mtmt) cc_final: 0.8247 (mtmt) REVERT: y 1106 LYS cc_start: 0.8752 (mmmm) cc_final: 0.8415 (mmmm) REVERT: F 6 LYS cc_start: 0.9058 (mtmt) cc_final: 0.8803 (mtmt) REVERT: 1 104 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7475 (mm-30) REVERT: 1 106 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8468 (mmmm) REVERT: 3 304 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8126 (mm-30) REVERT: 4 1004 GLU cc_start: 0.8355 (mp0) cc_final: 0.7977 (mp0) REVERT: 5 1106 LYS cc_start: 0.8867 (mmmm) cc_final: 0.8556 (mmmm) REVERT: G 3 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8231 (m-80) REVERT: G 4 GLU cc_start: 0.8213 (mp0) cc_final: 0.7575 (mp0) REVERT: 8 106 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8298 (mmmm) REVERT: AA 306 LYS cc_start: 0.9064 (mttt) cc_final: 0.8717 (mttm) REVERT: BA 1004 GLU cc_start: 0.8069 (mp0) cc_final: 0.7527 (mp0) REVERT: CA 1104 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7271 (mm-30) REVERT: CA 1106 LYS cc_start: 0.9035 (mmmm) cc_final: 0.8767 (mmmm) REVERT: EA 1306 LYS cc_start: 0.9113 (mttt) cc_final: 0.8898 (mttt) REVERT: H 4 GLU cc_start: 0.2908 (OUTLIER) cc_final: 0.2021 (pm20) REVERT: FA 106 LYS cc_start: 0.8981 (mmmm) cc_final: 0.8677 (mmmm) REVERT: HA 302 LYS cc_start: 0.9087 (mtpt) cc_final: 0.8677 (mmmm) REVERT: JA 1106 LYS cc_start: 0.9025 (mmmm) cc_final: 0.8570 (mmmm) REVERT: I 4 GLU cc_start: 0.7794 (mp0) cc_final: 0.7247 (mp0) REVERT: I 6 LYS cc_start: 0.9022 (mtmt) cc_final: 0.8731 (ttmt) REVERT: PA 1004 GLU cc_start: 0.7783 (mp0) cc_final: 0.7077 (mp0) REVERT: PA 1007 PHE cc_start: 0.9411 (OUTLIER) cc_final: 0.9023 (m-80) REVERT: RA 1202 LYS cc_start: 0.9157 (mtpt) cc_final: 0.8839 (mtpp) REVERT: SA 1307 PHE cc_start: 0.9372 (OUTLIER) cc_final: 0.8556 (m-80) REVERT: a 2 LYS cc_start: 0.9188 (tppt) cc_final: 0.8852 (tppt) REVERT: VA 306 LYS cc_start: 0.8972 (tptp) cc_final: 0.8732 (tptp) REVERT: WA 1002 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8939 (tppt) REVERT: XA 1105 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8709 (p90) REVERT: ZA 1306 LYS cc_start: 0.8877 (tptp) cc_final: 0.8555 (tptp) REVERT: b 6 LYS cc_start: 0.9245 (ttpt) cc_final: 0.8967 (ttpt) REVERT: aA 104 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8149 (tm-30) REVERT: bA 202 LYS cc_start: 0.9417 (OUTLIER) cc_final: 0.9107 (tppp) REVERT: cA 302 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8632 (tptp) REVERT: dA 1002 LYS cc_start: 0.9055 (ttmt) cc_final: 0.8778 (ttmt) REVERT: eA 1104 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8022 (tm-30) REVERT: eA 1105 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8730 (t80) REVERT: c 2 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.9037 (tppt) REVERT: hA 104 GLU cc_start: 0.8689 (tm-30) cc_final: 0.7950 (tm-30) REVERT: nA 1306 LYS cc_start: 0.9028 (tptp) cc_final: 0.8794 (tptp) REVERT: pA 202 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.8939 (mptm) REVERT: qA 306 LYS cc_start: 0.8880 (tptp) cc_final: 0.8593 (tptp) REVERT: sA 1103 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.9006 (t80) REVERT: uA 1307 PHE cc_start: 0.9426 (OUTLIER) cc_final: 0.9138 (t80) REVERT: vA 104 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8305 (tm-30) REVERT: wA 202 LYS cc_start: 0.9467 (OUTLIER) cc_final: 0.9125 (tppp) REVERT: zA 1104 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8022 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9370 (t80) cc_final: 0.9103 (t80) REVERT: f 2 LYS cc_start: 0.9086 (ttmt) cc_final: 0.8783 (ttmt) REVERT: 4A 306 LYS cc_start: 0.8659 (tptp) cc_final: 0.8314 (tptp) REVERT: 8A 1305 PHE cc_start: 0.9049 (t80) cc_final: 0.8834 (t80) REVERT: g 2 LYS cc_start: 0.9026 (tppt) cc_final: 0.8599 (tppt) REVERT: AB 202 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.8971 (ttmm) REVERT: BB 304 GLU cc_start: 0.9310 (tm-30) cc_final: 0.8755 (tm-30) REVERT: DB 1104 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8203 (tm-30) REVERT: FB 1306 LYS cc_start: 0.8881 (tptp) cc_final: 0.8561 (tptp) REVERT: HB 202 LYS cc_start: 0.9336 (tttm) cc_final: 0.8970 (pttt) REVERT: IB 306 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8688 (tptp) REVERT: i 6 LYS cc_start: 0.9296 (ttpt) cc_final: 0.9067 (ttpt) REVERT: NB 104 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8197 (pm20) REVERT: NB 106 LYS cc_start: 0.9210 (tttp) cc_final: 0.8691 (pptt) REVERT: OB 202 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.9147 (mmmm) REVERT: RB 1104 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8061 (pm20) REVERT: SB 1202 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.9132 (ttmm) REVERT: TB 1302 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8538 (tptp) outliers start: 200 outliers final: 159 residues processed: 505 average time/residue: 0.4818 time to fit residues: 295.6977 Evaluate side-chains 624 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 438 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain M residue 1007 PHE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 304 GLU Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1007 PHE Chi-restraints excluded: chain RA residue 1205 PHE Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 104 GLU Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 304 GLU Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain bA residue 202 LYS Chi-restraints excluded: chain cA residue 302 LYS Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 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 c residue 4 GLU Chi-restraints excluded: chain c residue 6 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain iA residue 204 GLU Chi-restraints excluded: chain jA residue 302 LYS 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 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 d residue 4 GLU Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain sA residue 1106 LYS Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1204 GLU Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain wA residue 202 LYS Chi-restraints excluded: chain wA residue 204 GLU Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 0A residue 1206 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 3A residue 204 GLU Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 5A residue 1006 LYS 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 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 104 GLU Chi-restraints excluded: chain AB residue 202 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 302 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain 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 QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain SB residue 1204 GLU Chi-restraints excluded: chain TB residue 1302 LYS Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 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: 0.8432 moved from start: 0.8095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.111 0.347 12528 Z= 6.195 Angle : 4.129 48.577 16272 Z= 1.848 Chirality : 0.302 0.911 1152 Planarity : 0.016 0.068 2160 Dihedral : 21.095 86.564 1488 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 108.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 35.07 % Favored : 64.93 % Rotamer: Outliers : 22.57 % Allowed : 30.44 % Favored : 46.99 % Cbeta Deviations : 15.19 % 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: -7.61 (0.21), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.79 (0.16), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.128 0.016 PHE g 7 *********************** 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 633 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 438 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.9111 (mtmt) cc_final: 0.8514 (mtmt) REVERT: J 106 LYS cc_start: 0.8987 (mmmm) cc_final: 0.8530 (mmmm) REVERT: M 1004 GLU cc_start: 0.8217 (mp0) cc_final: 0.7544 (mp0) REVERT: N 1106 LYS cc_start: 0.8927 (mmmm) cc_final: 0.8581 (mmmm) REVERT: O 1206 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8647 (ttmm) REVERT: B 4 GLU cc_start: 0.8319 (mp0) cc_final: 0.7647 (mp0) REVERT: B 5 PHE cc_start: 0.9248 (OUTLIER) cc_final: 0.8986 (m-80) REVERT: Q 104 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7311 (mm-30) REVERT: Q 106 LYS cc_start: 0.9058 (mmmm) cc_final: 0.8664 (mmmm) REVERT: T 1006 LYS cc_start: 0.9018 (mtmt) cc_final: 0.8604 (mtmt) REVERT: U 1104 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7761 (mm-30) REVERT: U 1106 LYS cc_start: 0.8774 (mmmm) cc_final: 0.8438 (mmmm) REVERT: W 1302 LYS cc_start: 0.9207 (mtpt) cc_final: 0.8687 (mtpp) REVERT: C 4 GLU cc_start: 0.8051 (mp0) cc_final: 0.7493 (mp0) REVERT: X 106 LYS cc_start: 0.9034 (mmmm) cc_final: 0.8627 (mmmm) REVERT: Y 202 LYS cc_start: 0.9076 (ttpt) cc_final: 0.8838 (ttpt) REVERT: j 1004 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7810 (mp0) REVERT: k 1106 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8604 (mmmm) REVERT: l 1202 LYS cc_start: 0.9135 (mtpt) cc_final: 0.8859 (mtpp) REVERT: l 1204 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8004 (mm-30) REVERT: D 4 GLU cc_start: 0.8004 (mp0) cc_final: 0.6940 (mp0) REVERT: D 6 LYS cc_start: 0.8931 (mtmt) cc_final: 0.8452 (mtmt) REVERT: D 7 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.8449 (t80) REVERT: n 104 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7943 (mm-30) REVERT: n 106 LYS cc_start: 0.8935 (mmmm) cc_final: 0.8467 (mmmm) REVERT: o 202 LYS cc_start: 0.9259 (ttpt) cc_final: 0.9043 (ttpt) REVERT: q 1004 GLU cc_start: 0.8142 (mp0) cc_final: 0.7915 (mp0) REVERT: r 1106 LYS cc_start: 0.9036 (mmmm) cc_final: 0.8574 (mmmm) REVERT: u 106 LYS cc_start: 0.8945 (mmmm) cc_final: 0.8598 (mmmm) REVERT: w 302 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8784 (mmmm) REVERT: w 304 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8073 (mm-30) REVERT: x 1006 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8268 (mtmt) REVERT: y 1106 LYS cc_start: 0.8757 (mmmm) cc_final: 0.8419 (mmmm) REVERT: F 6 LYS cc_start: 0.9046 (mtmt) cc_final: 0.8791 (mtmt) REVERT: 1 104 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7346 (mm-30) REVERT: 1 106 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8471 (mmmm) REVERT: 3 304 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8141 (mm-30) REVERT: 4 1004 GLU cc_start: 0.8326 (mp0) cc_final: 0.8029 (mp0) REVERT: 5 1106 LYS cc_start: 0.8871 (mmmm) cc_final: 0.8552 (mmmm) REVERT: G 3 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8231 (m-80) REVERT: G 4 GLU cc_start: 0.8219 (mp0) cc_final: 0.7582 (mp0) REVERT: G 6 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8833 (ttmt) REVERT: 8 106 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8303 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8067 (mp0) cc_final: 0.7672 (mp0) REVERT: CA 1104 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7255 (mm-30) REVERT: CA 1106 LYS cc_start: 0.9025 (mmmm) cc_final: 0.8772 (mmmm) REVERT: EA 1306 LYS cc_start: 0.9100 (mttt) cc_final: 0.8733 (mttt) REVERT: H 4 GLU cc_start: 0.2910 (OUTLIER) cc_final: 0.2024 (pm20) REVERT: FA 106 LYS cc_start: 0.8975 (mmmm) cc_final: 0.8670 (mmmm) REVERT: HA 302 LYS cc_start: 0.9089 (mtpt) cc_final: 0.8678 (mmmm) REVERT: JA 1106 LYS cc_start: 0.9021 (mmmm) cc_final: 0.8560 (mmmm) REVERT: I 4 GLU cc_start: 0.7789 (mp0) cc_final: 0.7241 (mp0) REVERT: I 6 LYS cc_start: 0.9029 (mtmt) cc_final: 0.8755 (ttmt) REVERT: OA 304 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7962 (mm-30) REVERT: PA 1004 GLU cc_start: 0.7781 (mp0) cc_final: 0.7038 (mp0) REVERT: PA 1007 PHE cc_start: 0.9410 (OUTLIER) cc_final: 0.8999 (m-80) REVERT: RA 1202 LYS cc_start: 0.9156 (mtpt) cc_final: 0.8837 (mtpp) REVERT: SA 1307 PHE cc_start: 0.9372 (OUTLIER) cc_final: 0.8557 (m-80) REVERT: a 2 LYS cc_start: 0.9143 (tppt) cc_final: 0.8804 (tppt) REVERT: VA 306 LYS cc_start: 0.8974 (tptp) cc_final: 0.8727 (tptp) REVERT: WA 1002 LYS cc_start: 0.9202 (tptt) cc_final: 0.8951 (tppt) REVERT: XA 1105 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8710 (p90) REVERT: ZA 1306 LYS cc_start: 0.8876 (tptp) cc_final: 0.8551 (tptp) REVERT: b 6 LYS cc_start: 0.9241 (ttpt) cc_final: 0.8963 (ttpt) REVERT: aA 104 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8464 (tm-30) REVERT: bA 202 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.9106 (tppp) REVERT: dA 1002 LYS cc_start: 0.9055 (ttmt) cc_final: 0.8776 (ttmt) REVERT: eA 1105 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8717 (t80) REVERT: c 2 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.9030 (tppt) REVERT: hA 104 GLU cc_start: 0.8702 (tm-30) cc_final: 0.7983 (tm-30) REVERT: nA 1306 LYS cc_start: 0.9027 (tptp) cc_final: 0.8798 (tptp) REVERT: qA 306 LYS cc_start: 0.8867 (tptp) cc_final: 0.8563 (tptp) REVERT: sA 1103 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.9016 (t80) REVERT: uA 1303 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8673 (t80) REVERT: uA 1307 PHE cc_start: 0.9391 (OUTLIER) cc_final: 0.9158 (t80) REVERT: vA 104 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8302 (tm-30) REVERT: wA 202 LYS cc_start: 0.9468 (OUTLIER) cc_final: 0.9127 (tppp) REVERT: zA 1104 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8020 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9377 (t80) cc_final: 0.9121 (t80) REVERT: f 2 LYS cc_start: 0.9085 (ttmt) cc_final: 0.8783 (ttmt) REVERT: 4A 305 PHE cc_start: 0.9283 (t80) cc_final: 0.9055 (t80) REVERT: 4A 306 LYS cc_start: 0.8613 (tptp) cc_final: 0.8270 (tptp) REVERT: 8A 1305 PHE cc_start: 0.9026 (t80) cc_final: 0.8814 (t80) REVERT: g 2 LYS cc_start: 0.9026 (tppt) cc_final: 0.8594 (tppt) REVERT: AB 202 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.8971 (ttmm) REVERT: BB 304 GLU cc_start: 0.9307 (tm-30) cc_final: 0.8752 (tm-30) REVERT: FB 1306 LYS cc_start: 0.8876 (tptp) cc_final: 0.8557 (tptp) REVERT: HB 202 LYS cc_start: 0.9336 (tttm) cc_final: 0.8969 (pttt) REVERT: IB 306 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8677 (tptp) REVERT: i 6 LYS cc_start: 0.9298 (ttpt) cc_final: 0.9070 (ttpt) REVERT: NB 104 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8124 (pm20) REVERT: NB 106 LYS cc_start: 0.9213 (tttp) cc_final: 0.8706 (pptt) REVERT: OB 202 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9147 (mmmm) REVERT: QB 1005 PHE cc_start: 0.9345 (t80) cc_final: 0.9067 (t80) REVERT: RB 1104 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8060 (pm20) REVERT: SB 1202 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9128 (ttmm) REVERT: TB 1302 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8539 (tptp) outliers start: 195 outliers final: 159 residues processed: 505 average time/residue: 0.4705 time to fit residues: 288.9790 Evaluate side-chains 623 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 438 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain M residue 1007 PHE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain t residue 1304 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 304 GLU Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain 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 105 PHE Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 304 GLU Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1007 PHE Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 104 GLU Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 304 GLU Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain bA residue 202 LYS Chi-restraints excluded: chain cA residue 302 LYS Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1105 PHE 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 c residue 4 GLU Chi-restraints excluded: chain c residue 6 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain iA residue 204 GLU Chi-restraints excluded: chain jA residue 302 LYS 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 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 d residue 4 GLU Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain sA residue 1106 LYS Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1204 GLU Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain wA residue 202 LYS Chi-restraints excluded: chain wA residue 204 GLU Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 0A residue 1206 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 3A residue 204 GLU Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 5A residue 1006 LYS 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 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 104 GLU Chi-restraints excluded: chain AB residue 202 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 302 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain 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 QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain SB residue 1204 GLU Chi-restraints excluded: chain TB residue 1302 LYS Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.8110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.111 0.336 12528 Z= 6.200 Angle : 4.115 32.959 16272 Z= 1.847 Chirality : 0.302 0.904 1152 Planarity : 0.016 0.069 2160 Dihedral : 21.093 86.236 1488 Min Nonbonded Distance : 1.636 Molprobity Statistics. All-atom Clashscore : 108.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 35.24 % Favored : 64.76 % Rotamer: Outliers : 22.57 % Allowed : 30.67 % Favored : 46.76 % Cbeta Deviations : 15.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.49 % 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: -7.62 (0.21), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.80 (0.16), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.129 0.016 PHE g 7 ********************** 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 633 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 438 time to evaluate : 1.421 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: A 4 GLU cc_start: 0.7719 (mp0) cc_final: 0.6849 (mp0) REVERT: A 6 LYS cc_start: 0.9113 (mtmt) cc_final: 0.8495 (mtmt) REVERT: J 106 LYS cc_start: 0.8993 (mmmm) cc_final: 0.8544 (mmmm) REVERT: M 1004 GLU cc_start: 0.8207 (mp0) cc_final: 0.7517 (mp0) REVERT: N 1106 LYS cc_start: 0.8925 (mmmm) cc_final: 0.8594 (mmmm) REVERT: O 1206 LYS cc_start: 0.8889 (ttmm) cc_final: 0.8643 (ttmm) REVERT: B 4 GLU cc_start: 0.8304 (mp0) cc_final: 0.7637 (mp0) REVERT: B 5 PHE cc_start: 0.9251 (OUTLIER) cc_final: 0.8987 (m-80) REVERT: Q 106 LYS cc_start: 0.9066 (mmmm) cc_final: 0.8656 (mmmm) REVERT: T 1006 LYS cc_start: 0.8998 (mtmt) cc_final: 0.8598 (mtmt) REVERT: U 1104 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7940 (mm-30) REVERT: U 1106 LYS cc_start: 0.8774 (mmmm) cc_final: 0.8438 (mmmm) REVERT: W 1302 LYS cc_start: 0.9195 (mtpt) cc_final: 0.8670 (mtpp) REVERT: C 4 GLU cc_start: 0.8053 (mp0) cc_final: 0.7497 (mp0) REVERT: X 106 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8626 (mmmm) REVERT: Y 202 LYS cc_start: 0.9110 (ttpt) cc_final: 0.8870 (ttpt) REVERT: j 1004 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: k 1106 LYS cc_start: 0.8957 (mmmm) cc_final: 0.8606 (mmmm) REVERT: l 1202 LYS cc_start: 0.9132 (mtpt) cc_final: 0.8862 (mtpp) REVERT: l 1204 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7997 (mm-30) REVERT: D 4 GLU cc_start: 0.7994 (mp0) cc_final: 0.6924 (mp0) REVERT: D 6 LYS cc_start: 0.8933 (mtmt) cc_final: 0.8446 (mtmt) REVERT: D 7 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.8446 (t80) REVERT: n 106 LYS cc_start: 0.8937 (mmmm) cc_final: 0.8471 (mmmm) REVERT: o 202 LYS cc_start: 0.9257 (ttpt) cc_final: 0.9041 (ttpt) REVERT: r 1106 LYS cc_start: 0.9033 (mmmm) cc_final: 0.8570 (mmmm) REVERT: u 106 LYS cc_start: 0.8951 (mmmm) cc_final: 0.8579 (mmmm) REVERT: w 302 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8783 (mmmm) REVERT: w 304 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8060 (mm-30) REVERT: x 1006 LYS cc_start: 0.8821 (mtmt) cc_final: 0.8269 (mtmt) REVERT: y 1106 LYS cc_start: 0.8762 (mmmm) cc_final: 0.8418 (mmmm) REVERT: F 6 LYS cc_start: 0.9049 (mtmt) cc_final: 0.8792 (mtmt) REVERT: 1 104 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7348 (mm-30) REVERT: 1 106 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8467 (mmmm) REVERT: 4 1004 GLU cc_start: 0.8324 (mp0) cc_final: 0.8040 (mp0) REVERT: 5 1106 LYS cc_start: 0.8874 (mmmm) cc_final: 0.8552 (mmmm) REVERT: G 3 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8231 (m-80) REVERT: G 4 GLU cc_start: 0.8221 (mp0) cc_final: 0.7589 (mp0) REVERT: G 6 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8845 (ttmt) REVERT: 8 106 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8314 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8089 (mp0) cc_final: 0.7767 (mp0) REVERT: CA 1104 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7257 (mm-30) REVERT: CA 1106 LYS cc_start: 0.9031 (mmmm) cc_final: 0.8773 (mmmm) REVERT: H 4 GLU cc_start: 0.2910 (OUTLIER) cc_final: 0.2020 (pm20) REVERT: FA 106 LYS cc_start: 0.8972 (mmmm) cc_final: 0.8667 (mmmm) REVERT: HA 302 LYS cc_start: 0.9096 (mtpt) cc_final: 0.8720 (mmmm) REVERT: JA 1106 LYS cc_start: 0.9019 (mmmm) cc_final: 0.8559 (mmmm) REVERT: I 4 GLU cc_start: 0.7788 (mp0) cc_final: 0.7243 (mp0) REVERT: I 6 LYS cc_start: 0.9028 (mtmt) cc_final: 0.8752 (ttmt) REVERT: PA 1004 GLU cc_start: 0.7778 (mp0) cc_final: 0.7049 (mp0) REVERT: PA 1007 PHE cc_start: 0.9413 (OUTLIER) cc_final: 0.9008 (m-80) REVERT: RA 1202 LYS cc_start: 0.9158 (mtpt) cc_final: 0.8839 (mtpp) REVERT: SA 1307 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.8543 (m-80) REVERT: a 2 LYS cc_start: 0.9190 (tppt) cc_final: 0.8861 (tppt) REVERT: VA 306 LYS cc_start: 0.8976 (tptp) cc_final: 0.8730 (tptp) REVERT: WA 1002 LYS cc_start: 0.9200 (tptt) cc_final: 0.8950 (tppt) REVERT: XA 1105 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.8710 (p90) REVERT: ZA 1306 LYS cc_start: 0.8876 (tptp) cc_final: 0.8554 (tptp) REVERT: b 6 LYS cc_start: 0.9241 (ttpt) cc_final: 0.8967 (ttpt) REVERT: aA 104 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8462 (tm-30) REVERT: bA 202 LYS cc_start: 0.9417 (OUTLIER) cc_final: 0.9106 (tppp) REVERT: dA 1002 LYS cc_start: 0.9055 (ttmt) cc_final: 0.8779 (ttmt) REVERT: eA 1105 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8729 (t80) REVERT: c 2 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.9015 (tppt) REVERT: hA 104 GLU cc_start: 0.8700 (tm-30) cc_final: 0.7982 (tm-30) REVERT: nA 1306 LYS cc_start: 0.9020 (tptp) cc_final: 0.8794 (tptp) REVERT: qA 306 LYS cc_start: 0.8861 (tptp) cc_final: 0.8560 (tptp) REVERT: sA 1103 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.9039 (t80) REVERT: uA 1303 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8782 (t80) REVERT: uA 1307 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.9139 (t80) REVERT: vA 104 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8305 (tm-30) REVERT: wA 202 LYS cc_start: 0.9468 (OUTLIER) cc_final: 0.9128 (tppp) REVERT: zA 1104 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8021 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9381 (t80) cc_final: 0.9121 (t80) REVERT: f 2 LYS cc_start: 0.9084 (ttmt) cc_final: 0.8782 (ttmt) REVERT: 4A 306 LYS cc_start: 0.8631 (tptp) cc_final: 0.8286 (tptp) REVERT: 8A 1305 PHE cc_start: 0.9036 (t80) cc_final: 0.8798 (t80) REVERT: g 2 LYS cc_start: 0.9027 (tppt) cc_final: 0.8603 (tppt) REVERT: AB 202 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.8970 (ttmm) REVERT: BB 304 GLU cc_start: 0.9309 (tm-30) cc_final: 0.8751 (tm-30) REVERT: DB 1104 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8236 (tm-30) REVERT: FB 1306 LYS cc_start: 0.8875 (tptp) cc_final: 0.8554 (tptp) REVERT: HB 202 LYS cc_start: 0.9336 (tttm) cc_final: 0.8969 (pttt) REVERT: IB 306 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8677 (tptp) REVERT: i 6 LYS cc_start: 0.9296 (ttpt) cc_final: 0.9054 (ttpt) REVERT: NB 104 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8116 (pm20) REVERT: NB 106 LYS cc_start: 0.9214 (tttp) cc_final: 0.8707 (pptt) REVERT: OB 202 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.9148 (mmmm) REVERT: QB 1005 PHE cc_start: 0.9353 (t80) cc_final: 0.9070 (t80) REVERT: RB 1104 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8059 (pm20) REVERT: SB 1202 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9127 (ttmm) REVERT: TB 1302 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8538 (tptp) outliers start: 195 outliers final: 165 residues processed: 505 average time/residue: 0.4835 time to fit residues: 298.2196 Evaluate side-chains 628 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 438 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain M residue 1002 LYS Chi-restraints excluded: chain M residue 1007 PHE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain U residue 1102 LYS Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 304 GLU Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain t residue 1304 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 304 GLU Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain DA residue 1206 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain 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 105 PHE Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 304 GLU Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1007 PHE Chi-restraints excluded: chain RA residue 1205 PHE Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 104 GLU Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 304 GLU Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain bA residue 202 LYS Chi-restraints excluded: chain cA residue 302 LYS Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1105 PHE 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 c residue 4 GLU Chi-restraints excluded: chain c residue 6 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain iA residue 204 GLU Chi-restraints excluded: chain jA residue 302 LYS 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 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 d residue 4 GLU Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain sA residue 1106 LYS Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1204 GLU Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain wA residue 202 LYS Chi-restraints excluded: chain wA residue 204 GLU Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 0A residue 1206 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 3A residue 204 GLU Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 5A residue 1006 LYS 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 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 104 GLU Chi-restraints excluded: chain AB residue 202 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 302 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain 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 QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain SB residue 1204 GLU Chi-restraints excluded: chain TB residue 1302 LYS Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.073055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.061949 restraints weight = 33429.577| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.18 r_work: 0.2687 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.8124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.111 0.336 12528 Z= 6.199 Angle : 4.110 31.038 16272 Z= 1.845 Chirality : 0.302 0.903 1152 Planarity : 0.016 0.069 2160 Dihedral : 21.096 85.467 1488 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 108.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 35.42 % Favored : 64.58 % Rotamer: Outliers : 22.80 % Allowed : 31.13 % Favored : 46.06 % Cbeta Deviations : 15.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.69 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.62 (0.21), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.81 (0.16), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.128 0.016 PHE 2 205 =============================================================================== Job complete usr+sys time: 3990.67 seconds wall clock time: 72 minutes 59.08 seconds (4379.08 seconds total)