Starting phenix.real_space_refine on Sat Dec 9 19:43:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqg_23485/12_2023/7lqg_23485_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqg_23485/12_2023/7lqg_23485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqg_23485/12_2023/7lqg_23485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqg_23485/12_2023/7lqg_23485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqg_23485/12_2023/7lqg_23485_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqg_23485/12_2023/7lqg_23485_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 8640 2.51 5 N 1584 2.21 5 O 1872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 204": "OE1" <-> "OE2" Residue "K PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 304": "OE1" <-> "OE2" Residue "L PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 1204": "OE1" <-> "OE2" Residue "O PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 1304": "OE1" <-> "OE2" Residue "P PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 304": "OE1" <-> "OE2" Residue "S PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 1204": "OE1" <-> "OE2" Residue "V PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 1304": "OE1" <-> "OE2" Residue "W PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 204": "OE1" <-> "OE2" Residue "Y PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 304": "OE1" <-> "OE2" Residue "Z PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 1204": "OE1" <-> "OE2" Residue "l PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 1304": "OE1" <-> "OE2" Residue "m PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 204": "OE1" <-> "OE2" Residue "o PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 304": "OE1" <-> "OE2" Residue "p PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 1204": "OE1" <-> "OE2" Residue "s PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 1304": "OE1" <-> "OE2" Residue "t PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 204": "OE1" <-> "OE2" Residue "v PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 304": "OE1" <-> "OE2" Residue "w PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 1204": "OE1" <-> "OE2" Residue "z PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 1304": "OE1" <-> "OE2" Residue "0 PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 204": "OE1" <-> "OE2" Residue "2 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 304": "OE1" <-> "OE2" Residue "3 PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 1204": "OE1" <-> "OE2" Residue "6 PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 1304": "OE1" <-> "OE2" Residue "7 PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 204": "OE1" <-> "OE2" Residue "9 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA GLU 304": "OE1" <-> "OE2" Residue "AA PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA GLU 1204": "OE1" <-> "OE2" Residue "DA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EA PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EA GLU 1304": "OE1" <-> "OE2" Residue "EA PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GA GLU 204": "OE1" <-> "OE2" Residue "GA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HA PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HA GLU 304": "OE1" <-> "OE2" Residue "HA PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JA PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JA PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KA GLU 1204": "OE1" <-> "OE2" Residue "KA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA GLU 1304": "OE1" <-> "OE2" Residue "LA PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MA PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MA PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA GLU 204": "OE1" <-> "OE2" Residue "NA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OA PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OA GLU 304": "OE1" <-> "OE2" Residue "OA PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "QA PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "QA PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RA GLU 1204": "OE1" <-> "OE2" Residue "RA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA GLU 1304": "OE1" <-> "OE2" Residue "SA PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "UA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "UA GLU 204": "OE1" <-> "OE2" Residue "UA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "UA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VA GLU 304": "OE1" <-> "OE2" Residue "WA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "WA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YA GLU 1204": "OE1" <-> "OE2" Residue "YA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ZA GLU 1304": "OE1" <-> "OE2" Residue "b PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bA GLU 204": "OE1" <-> "OE2" Residue "bA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "cA GLU 304": "OE1" <-> "OE2" Residue "dA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "dA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "fA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "fA GLU 1204": "OE1" <-> "OE2" Residue "fA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "fA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "gA GLU 1304": "OE1" <-> "OE2" Residue "c PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "iA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "iA GLU 204": "OE1" <-> "OE2" Residue "iA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "iA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "jA GLU 304": "OE1" <-> "OE2" Residue "kA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "kA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "mA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "mA GLU 1204": "OE1" <-> "OE2" Residue "mA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "mA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "nA GLU 1304": "OE1" <-> "OE2" Residue "d PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "pA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "pA GLU 204": "OE1" <-> "OE2" Residue "pA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "pA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "qA GLU 304": "OE1" <-> "OE2" Residue "rA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "rA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "tA PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "tA GLU 1204": "OE1" <-> "OE2" Residue "tA PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "tA PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "uA GLU 1304": "OE1" <-> "OE2" Residue "e PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "wA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "wA GLU 204": "OE1" <-> "OE2" Residue "wA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "wA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "xA GLU 304": "OE1" <-> "OE2" Residue "yA PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "yA PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0A PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0A GLU 1204": "OE1" <-> "OE2" Residue "0A PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0A PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A GLU 1304": "OE1" <-> "OE2" Residue "f PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A GLU 204": "OE1" <-> "OE2" Residue "3A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A GLU 304": "OE1" <-> "OE2" Residue "5A PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7A PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7A GLU 1204": "OE1" <-> "OE2" Residue "7A PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7A PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8A GLU 1304": "OE1" <-> "OE2" Residue "g PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB GLU 204": "OE1" <-> "OE2" Residue "AB PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BB GLU 304": "OE1" <-> "OE2" Residue "CB PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EB PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EB GLU 1204": "OE1" <-> "OE2" Residue "EB PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EB PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FB GLU 1304": "OE1" <-> "OE2" Residue "h PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HB PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HB GLU 204": "OE1" <-> "OE2" Residue "HB PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HB PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IB GLU 304": "OE1" <-> "OE2" Residue "JB PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JB PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB GLU 1204": "OE1" <-> "OE2" Residue "LB PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MB GLU 1304": "OE1" <-> "OE2" Residue "i PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OB PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OB GLU 204": "OE1" <-> "OE2" Residue "OB PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OB PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PB GLU 304": "OE1" <-> "OE2" Residue "QB PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "QB PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB GLU 1204": "OE1" <-> "OE2" Residue "SB PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TB GLU 1304": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.52, per 1000 atoms: 0.46 Number of scatterers: 12096 At special positions: 0 Unit cell: (89.64, 89.64, 108, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1872 8.00 N 1584 7.00 C 8640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=36, symmetry=0 Number of additional bonds: simple=36, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.62 Conformation dependent library (CDL) restraints added in 858.8 milliseconds 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... 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: 1.48 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.01 Time building geometry restraints manager: 5.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 1530 1.26 - 1.33: 1350 1.33 - 1.41: 3600 1.41 - 1.48: 1300 1.48 - 1.56: 4748 Bond restraints: 12528 Sorted by residual: bond pdb=" N 5CRrA1001 " pdb=" CAL 5CRrA1001 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" N 5CR d 1 " pdb=" CAL 5CR d 1 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" N 5CR e 1 " pdb=" CAL 5CR e 1 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" N 5CRyA1001 " pdb=" CAL 5CRyA1001 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" N 5CRQB1001 " pdb=" CAL 5CRQB1001 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+01 ... (remaining 12523 not shown) Histogram of bond angle deviations from ideal: 105.44 - 109.77: 1156 109.77 - 114.09: 4084 114.09 - 118.42: 2116 118.42 - 122.74: 7470 122.74 - 127.06: 1446 Bond angle restraints: 16272 Sorted by residual: angle pdb=" N 5CR5A1001 " pdb=" CAL 5CR5A1001 " pdb=" CAA 5CR5A1001 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " pdb=" CAA 5CR f 1 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR a 1 " pdb=" CAL 5CR a 1 " pdb=" CAA 5CR a 1 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N 5CRWA1001 " pdb=" CAL 5CRWA1001 " pdb=" CAA 5CRWA1001 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N 5CR i 1 " pdb=" CAL 5CR i 1 " pdb=" CAA 5CR i 1 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.08e+01 ... (remaining 16267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 4840 15.26 - 30.52: 794 30.52 - 45.78: 342 45.78 - 61.04: 198 61.04 - 76.30: 18 Dihedral angle restraints: 6192 sinusoidal: 2880 harmonic: 3312 Sorted by residual: dihedral pdb=" CA LYSMA 106 " pdb=" CB LYSMA 106 " pdb=" CG LYSMA 106 " pdb=" CD LYSMA 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.29 58.71 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYSQA1106 " pdb=" CB LYSQA1106 " pdb=" CG LYSQA1106 " pdb=" CD LYSQA1106 " ideal model delta sinusoidal sigma weight residual 60.00 1.29 58.71 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYS 8 106 " pdb=" CB LYS 8 106 " pdb=" CG LYS 8 106 " pdb=" CD LYS 8 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.30 58.70 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 6189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.018: 404 0.018 - 0.036: 326 0.036 - 0.054: 308 0.054 - 0.072: 88 0.072 - 0.090: 26 Chirality restraints: 1152 Sorted by residual: chirality pdb=" CA LYS R 202 " pdb=" N LYS R 202 " pdb=" C LYS R 202 " pdb=" CB LYS R 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.02e-01 chirality pdb=" CA LYS V1202 " pdb=" N LYS V1202 " pdb=" C LYS V1202 " pdb=" CB LYS V1202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.02e-01 chirality pdb=" CA LYS l1202 " pdb=" N LYS l1202 " pdb=" C LYS l1202 " pdb=" CB LYS l1202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.86e-01 ... (remaining 1149 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHEYA1205 " -0.009 2.00e-02 2.50e+03 6.98e-03 8.53e-01 pdb=" CG PHEYA1205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEYA1205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHEYA1205 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHEYA1205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEYA1205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHEYA1205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEUA 205 " -0.009 2.00e-02 2.50e+03 6.98e-03 8.53e-01 pdb=" CG PHEUA 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEUA 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHEUA 205 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHEUA 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEUA 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHEUA 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHESB1205 " -0.008 2.00e-02 2.50e+03 6.92e-03 8.39e-01 pdb=" CG PHESB1205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHESB1205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHESB1205 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHESB1205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHESB1205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHESB1205 " -0.002 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 48 2.45 - 3.07: 6948 3.07 - 3.68: 18344 3.68 - 4.29: 30140 4.29 - 4.90: 49410 Nonbonded interactions: 104890 Sorted by model distance: nonbonded pdb=" CD LYS A 2 " pdb=" OE2 GMADA1208 " model vdw 1.842 2.752 nonbonded pdb=" CD LYS M1002 " pdb=" OE2 GMA 9 208 " model vdw 1.842 2.752 nonbonded pdb=" OE2 GMA V1208 " pdb=" CD LYS H 2 " model vdw 1.868 2.752 nonbonded pdb=" OE2 GMA R 208 " pdb=" CD LYSIA1002 " model vdw 1.868 2.752 nonbonded pdb=" OE2 GMA l1208 " pdb=" NZ LYS D 2 " model vdw 1.870 2.496 ... (remaining 104885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '0A' selection = chain '1' selection = chain '1A' selection = chain '2' selection = chain '2A' selection = chain '3' selection = chain '3A' selection = chain '4' selection = chain '4A' selection = chain '5' selection = chain '5A' selection = chain '6' selection = chain '6A' selection = chain '7' selection = chain '7A' selection = chain '8' selection = chain '8A' selection = chain '9' selection = chain '9A' selection = chain 'A' selection = chain 'AA' selection = chain 'AB' selection = chain 'B' selection = chain 'BA' selection = chain 'BB' selection = chain 'C' selection = chain 'CA' selection = chain 'CB' selection = chain 'D' selection = chain 'DA' selection = chain 'DB' selection = chain 'E' selection = chain 'EA' selection = chain 'EB' selection = chain 'F' selection = chain 'FA' selection = chain 'FB' selection = chain 'G' selection = chain 'GA' selection = chain 'GB' selection = chain 'H' selection = chain 'HA' selection = chain 'HB' selection = chain 'I' selection = chain 'IA' selection = chain 'IB' selection = chain 'J' selection = chain 'JA' selection = chain 'JB' selection = chain 'K' selection = chain 'KA' selection = chain 'KB' selection = chain 'L' selection = chain 'LA' selection = chain 'LB' selection = chain 'M' selection = chain 'MA' selection = chain 'MB' selection = chain 'N' selection = chain 'NA' selection = chain 'NB' selection = chain 'O' selection = chain 'OA' selection = chain 'OB' selection = chain 'P' selection = chain 'PA' selection = chain 'PB' selection = chain 'Q' selection = chain 'QA' selection = chain 'QB' selection = chain 'R' selection = chain 'RA' selection = chain 'RB' selection = chain 'S' selection = chain 'SA' selection = chain 'SB' selection = chain 'T' selection = chain 'TA' selection = chain 'TB' selection = chain 'U' selection = chain 'UA' selection = chain 'V' selection = chain 'VA' selection = chain 'W' selection = chain 'WA' selection = chain 'X' selection = chain 'XA' selection = chain 'Y' selection = chain 'YA' selection = chain 'Z' selection = chain 'ZA' selection = chain 'a' selection = chain 'aA' selection = chain 'b' selection = chain 'bA' selection = chain 'c' selection = chain 'cA' selection = chain 'd' selection = chain 'dA' selection = chain 'e' selection = chain 'eA' selection = chain 'f' selection = chain 'fA' selection = chain 'g' selection = chain 'gA' selection = chain 'h' selection = chain 'hA' selection = chain 'i' selection = chain 'iA' selection = chain 'j' selection = chain 'jA' selection = chain 'k' selection = chain 'kA' selection = chain 'l' selection = chain 'lA' selection = chain 'm' selection = chain 'mA' selection = chain 'n' selection = chain 'nA' selection = chain 'o' selection = chain 'oA' selection = chain 'p' selection = chain 'pA' selection = chain 'q' selection = chain 'qA' selection = chain 'r' selection = chain 'rA' selection = chain 's' selection = chain 'sA' selection = chain 't' selection = chain 'tA' selection = chain 'u' selection = chain 'uA' selection = chain 'v' selection = chain 'vA' selection = chain 'w' selection = chain 'wA' selection = chain 'x' selection = chain 'xA' selection = chain 'y' selection = chain 'yA' selection = chain 'z' selection = chain 'zA' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.840 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 28.110 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.430 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.118 12528 Z= 0.844 Angle : 1.417 9.883 16272 Z= 0.592 Chirality : 0.035 0.090 1152 Planarity : 0.002 0.009 2160 Dihedral : 20.718 76.303 3888 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 31.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 14.58 % Allowed : 14.58 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.94 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHEUA 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 502 time to evaluate : 1.315 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 outliers start: 126 outliers final: 85 residues processed: 528 average time/residue: 0.4655 time to fit residues: 299.5695 Evaluate side-chains 574 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 489 time to evaluate : 1.345 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 10 residues processed: 85 average time/residue: 0.3814 time to fit residues: 42.7128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.6980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.6705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.109 0.314 12528 Z= 6.050 Angle : 3.904 31.690 16272 Z= 1.728 Chirality : 0.297 0.797 1152 Planarity : 0.017 0.062 2160 Dihedral : 19.650 80.487 1440 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 104.96 Ramachandran Plot: Outliers : 0.35 % Allowed : 20.49 % Favored : 79.17 % Rotamer: Outliers : 11.92 % Allowed : 19.68 % Favored : 68.40 % Cbeta Deviations : 11.89 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.69 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.37 (0.16), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.61 (0.12), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.117 0.018 PHE G 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 458 time to evaluate : 1.287 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 outliers start: 103 outliers final: 60 residues processed: 473 average time/residue: 0.4941 time to fit residues: 281.9822 Evaluate side-chains 520 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 460 time to evaluate : 1.386 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 4 residues processed: 60 average time/residue: 0.2767 time to fit residues: 24.0739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8454 moved from start: 0.7571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.308 12528 Z= 6.084 Angle : 4.144 47.616 16272 Z= 1.820 Chirality : 0.296 0.852 1152 Planarity : 0.017 0.062 2160 Dihedral : 19.992 83.423 1440 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 114.15 Ramachandran Plot: Outliers : 0.52 % Allowed : 30.03 % Favored : 69.44 % Rotamer: Outliers : 12.27 % Allowed : 26.85 % Favored : 60.88 % Cbeta Deviations : 14.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.67 (0.19), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.84 (0.15), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.107 0.017 PHE k1105 *********************** 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 556 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 450 time to evaluate : 1.361 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 outliers start: 106 outliers final: 67 residues processed: 472 average time/residue: 0.4864 time to fit residues: 277.0121 Evaluate side-chains 521 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 454 time to evaluate : 1.292 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 8 residues processed: 67 average time/residue: 0.2681 time to fit residues: 25.9395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8437 moved from start: 0.7929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.311 12528 Z= 6.104 Angle : 4.171 47.633 16272 Z= 1.839 Chirality : 0.296 0.818 1152 Planarity : 0.017 0.059 2160 Dihedral : 20.549 87.078 1440 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 114.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 31.94 % Favored : 68.06 % Rotamer: Outliers : 8.80 % Allowed : 31.83 % Favored : 59.38 % Cbeta Deviations : 14.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.79 (0.19), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.93 (0.15), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.108 0.016 PHETB1303 *********************** 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 521 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 445 time to evaluate : 1.302 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 outliers start: 76 outliers final: 50 residues processed: 471 average time/residue: 0.5180 time to fit residues: 294.0471 Evaluate side-chains 497 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 447 time to evaluate : 1.331 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 8 residues processed: 50 average time/residue: 0.2788 time to fit residues: 20.4411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8408 moved from start: 0.8109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.374 12528 Z= 6.107 Angle : 4.191 42.456 16272 Z= 1.850 Chirality : 0.296 0.812 1152 Planarity : 0.017 0.058 2160 Dihedral : 20.502 88.827 1440 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 116.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 35.59 % Favored : 64.41 % Rotamer: Outliers : 9.84 % Allowed : 35.42 % Favored : 54.75 % Cbeta Deviations : 15.54 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.68 % 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: -7.78 (0.20), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.93 (0.15), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.112 0.016 PHE V1207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 441 time to evaluate : 1.446 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 outliers start: 85 outliers final: 54 residues processed: 463 average time/residue: 0.5009 time to fit residues: 279.6754 Evaluate side-chains 496 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 442 time to evaluate : 1.311 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 9 residues processed: 54 average time/residue: 0.2849 time to fit residues: 22.3143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8401 moved from start: 0.8195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.325 12528 Z= 6.104 Angle : 4.237 55.761 16272 Z= 1.864 Chirality : 0.295 0.824 1152 Planarity : 0.017 0.059 2160 Dihedral : 20.554 88.746 1440 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 117.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 35.59 % Favored : 64.41 % Rotamer: Outliers : 8.33 % Allowed : 40.51 % Favored : 51.16 % Cbeta Deviations : 15.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.68 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.87 (0.20), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.99 (0.15), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.120 0.016 PHEMB1305 *********************** 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 513 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 441 time to evaluate : 1.316 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 outliers start: 72 outliers final: 48 residues processed: 466 average time/residue: 0.4969 time to fit residues: 279.4432 Evaluate side-chains 489 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 441 time to evaluate : 1.384 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 7 residues processed: 48 average time/residue: 0.2765 time to fit residues: 19.6098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8396 moved from start: 0.8251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.325 12528 Z= 6.113 Angle : 4.266 60.391 16272 Z= 1.876 Chirality : 0.295 0.824 1152 Planarity : 0.017 0.068 2160 Dihedral : 20.567 89.335 1440 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 118.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 36.11 % Favored : 63.89 % Rotamer: Outliers : 8.33 % Allowed : 41.44 % Favored : 50.23 % Cbeta Deviations : 15.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.58 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.92 (0.20), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.03 (0.15), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.121 0.016 PHEIB 305 *********************** 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 508 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 436 time to evaluate : 1.346 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 outliers start: 72 outliers final: 46 residues processed: 455 average time/residue: 0.5058 time to fit residues: 278.1486 Evaluate side-chains 482 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 436 time to evaluate : 1.330 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 6 residues processed: 46 average time/residue: 0.3086 time to fit residues: 20.4923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.8309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.323 12528 Z= 6.115 Angle : 4.279 61.546 16272 Z= 1.883 Chirality : 0.296 0.846 1152 Planarity : 0.017 0.060 2160 Dihedral : 20.728 88.943 1440 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 119.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 36.81 % Favored : 63.19 % Rotamer: Outliers : 6.60 % Allowed : 44.79 % Favored : 48.61 % Cbeta Deviations : 15.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.78 % 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: -7.99 (0.19), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.08 (0.15), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.120 0.016 PHEgA1307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 437 time to evaluate : 1.346 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 outliers start: 57 outliers final: 28 residues processed: 450 average time/residue: 0.5121 time to fit residues: 278.2813 Evaluate side-chains 465 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 437 time to evaluate : 1.373 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 3 residues processed: 28 average time/residue: 0.2864 time to fit residues: 12.4488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.8343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.320 12528 Z= 6.109 Angle : 4.320 63.692 16272 Z= 1.899 Chirality : 0.296 0.871 1152 Planarity : 0.017 0.062 2160 Dihedral : 20.635 89.197 1440 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 118.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 34.72 % Favored : 65.28 % Rotamer: Outliers : 5.67 % Allowed : 46.06 % Favored : 48.26 % Cbeta Deviations : 14.93 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.58 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -8.03 (0.19), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.11 (0.15), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.128 0.016 PHEcA 307 *********************** 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 487 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 438 time to evaluate : 1.361 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 outliers start: 49 outliers final: 30 residues processed: 451 average time/residue: 0.5189 time to fit residues: 282.1742 Evaluate side-chains 469 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 439 time to evaluate : 1.330 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 3 residues processed: 30 average time/residue: 0.2945 time to fit residues: 13.3720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 0.8391 moved from start: 0.8387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.320 12528 Z= 6.112 Angle : 4.338 62.423 16272 Z= 1.907 Chirality : 0.297 0.913 1152 Planarity : 0.017 0.078 2160 Dihedral : 20.672 89.528 1440 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 120.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 36.28 % Favored : 63.72 % Rotamer: Outliers : 4.05 % Allowed : 47.92 % Favored : 48.03 % Cbeta Deviations : 15.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.68 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -8.04 (0.19), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.12 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.162 0.016 PHEOA 305 ********************** 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 469 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 434 time to evaluate : 1.381 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 outliers start: 35 outliers final: 24 residues processed: 437 average time/residue: 0.5046 time to fit residues: 266.2357 Evaluate side-chains 458 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 434 time to evaluate : 1.372 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 4 residues processed: 24 average time/residue: 0.3538 time to fit residues: 12.6982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 = 0.3229 r_free = 0.3229 target = 0.075632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.065142 restraints weight = 32788.781| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.03 r_work: 0.2771 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.8406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.313 12528 Z= 6.103 Angle : 4.338 59.947 16272 Z= 1.909 Chirality : 0.297 0.871 1152 Planarity : 0.017 0.069 2160 Dihedral : 20.696 88.486 1440 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 119.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 35.59 % Favored : 64.41 % Rotamer: Outliers : 3.24 % Allowed : 47.80 % Favored : 48.96 % Cbeta Deviations : 15.97 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.78 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -8.04 (0.19), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.12 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.158 0.016 PHEOA 305 =============================================================================== Job complete usr+sys time: 4109.37 seconds wall clock time: 74 minutes 39.89 seconds (4479.89 seconds total)