Starting phenix.real_space_refine on Mon Apr 15 16:43:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwb_29500/04_2024/8fwb_29500.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwb_29500/04_2024/8fwb_29500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwb_29500/04_2024/8fwb_29500.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwb_29500/04_2024/8fwb_29500.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwb_29500/04_2024/8fwb_29500.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwb_29500/04_2024/8fwb_29500.pdb" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.042 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: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 22320 2.51 5 N 6048 2.21 5 O 6720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "U ARG 29": "NH1" <-> "NH2" Residue "U PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 53": "OE1" <-> "OE2" Residue "U ASP 86": "OD1" <-> "OD2" Residue "U TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 136": "OD1" <-> "OD2" Residue "U PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 168": "OE1" <-> "OE2" Residue "U PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 181": "OE1" <-> "OE2" Residue "U PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 233": "OD1" <-> "OD2" Residue "U ASP 250": "OD1" <-> "OD2" Residue "U ASP 252": "OD1" <-> "OD2" Residue "U GLU 258": "OE1" <-> "OE2" Residue "U GLU 265": "OE1" <-> "OE2" Residue "U ASP 271": "OD1" <-> "OD2" Residue "U GLU 275": "OE1" <-> "OE2" Residue "U PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 303": "OD1" <-> "OD2" Residue "U GLU 343": "OE1" <-> "OE2" Residue "U ASP 344": "OD1" <-> "OD2" Residue "U TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 355": "OE1" <-> "OE2" Residue "U ASP 356": "OD1" <-> "OD2" Residue "U PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 385": "OD1" <-> "OD2" Residue "U PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 29": "NH1" <-> "NH2" Residue "V PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 53": "OE1" <-> "OE2" Residue "V ASP 86": "OD1" <-> "OD2" Residue "V TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 136": "OD1" <-> "OD2" Residue "V PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 168": "OE1" <-> "OE2" Residue "V PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 181": "OE1" <-> "OE2" Residue "V PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 233": "OD1" <-> "OD2" Residue "V ASP 250": "OD1" <-> "OD2" Residue "V ASP 252": "OD1" <-> "OD2" Residue "V GLU 258": "OE1" <-> "OE2" Residue "V GLU 265": "OE1" <-> "OE2" Residue "V ASP 271": "OD1" <-> "OD2" Residue "V GLU 275": "OE1" <-> "OE2" Residue "V PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 303": "OD1" <-> "OD2" Residue "V GLU 343": "OE1" <-> "OE2" Residue "V ASP 344": "OD1" <-> "OD2" Residue "V TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 355": "OE1" <-> "OE2" Residue "V ASP 356": "OD1" <-> "OD2" Residue "V PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 385": "OD1" <-> "OD2" Residue "V PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 29": "NH1" <-> "NH2" Residue "W PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 53": "OE1" <-> "OE2" Residue "W ASP 86": "OD1" <-> "OD2" Residue "W TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 136": "OD1" <-> "OD2" Residue "W PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 168": "OE1" <-> "OE2" Residue "W PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 181": "OE1" <-> "OE2" Residue "W PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 233": "OD1" <-> "OD2" Residue "W ASP 250": "OD1" <-> "OD2" Residue "W ASP 252": "OD1" <-> "OD2" Residue "W GLU 258": "OE1" <-> "OE2" Residue "W GLU 265": "OE1" <-> "OE2" Residue "W ASP 271": "OD1" <-> "OD2" Residue "W GLU 275": "OE1" <-> "OE2" Residue "W PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 303": "OD1" <-> "OD2" Residue "W GLU 343": "OE1" <-> "OE2" Residue "W ASP 344": "OD1" <-> "OD2" Residue "W TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 355": "OE1" <-> "OE2" Residue "W ASP 356": "OD1" <-> "OD2" Residue "W ASP 385": "OD1" <-> "OD2" Residue "W PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 29": "NH1" <-> "NH2" Residue "X PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 53": "OE1" <-> "OE2" Residue "X ASP 86": "OD1" <-> "OD2" Residue "X TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 136": "OD1" <-> "OD2" Residue "X PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 168": "OE1" <-> "OE2" Residue "X PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 181": "OE1" <-> "OE2" Residue "X PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 233": "OD1" <-> "OD2" Residue "X ASP 250": "OD1" <-> "OD2" Residue "X ASP 252": "OD1" <-> "OD2" Residue "X GLU 258": "OE1" <-> "OE2" Residue "X GLU 265": "OE1" <-> "OE2" Residue "X ASP 271": "OD1" <-> "OD2" Residue "X GLU 275": "OE1" <-> "OE2" Residue "X PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 303": "OD1" <-> "OD2" Residue "X GLU 343": "OE1" <-> "OE2" Residue "X ASP 344": "OD1" <-> "OD2" Residue "X TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 355": "OE1" <-> "OE2" Residue "X ASP 356": "OD1" <-> "OD2" Residue "X PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 385": "OD1" <-> "OD2" Residue "X PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 53": "OE1" <-> "OE2" Residue "Y ASP 86": "OD1" <-> "OD2" Residue "Y TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 136": "OD1" <-> "OD2" Residue "Y PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 168": "OE1" <-> "OE2" Residue "Y PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 181": "OE1" <-> "OE2" Residue "Y PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 233": "OD1" <-> "OD2" Residue "Y ASP 250": "OD1" <-> "OD2" Residue "Y ASP 252": "OD1" <-> "OD2" Residue "Y GLU 258": "OE1" <-> "OE2" Residue "Y GLU 265": "OE1" <-> "OE2" Residue "Y ASP 271": "OD1" <-> "OD2" Residue "Y GLU 275": "OE1" <-> "OE2" Residue "Y PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 303": "OD1" <-> "OD2" Residue "Y GLU 343": "OE1" <-> "OE2" Residue "Y ASP 344": "OD1" <-> "OD2" Residue "Y TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 355": "OE1" <-> "OE2" Residue "Y ASP 356": "OD1" <-> "OD2" Residue "Y PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 385": "OD1" <-> "OD2" Residue "Y PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 53": "OE1" <-> "OE2" Residue "Z ASP 86": "OD1" <-> "OD2" Residue "Z TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 136": "OD1" <-> "OD2" Residue "Z PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 168": "OE1" <-> "OE2" Residue "Z PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 181": "OE1" <-> "OE2" Residue "Z PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 233": "OD1" <-> "OD2" Residue "Z ASP 250": "OD1" <-> "OD2" Residue "Z ASP 252": "OD1" <-> "OD2" Residue "Z GLU 258": "OE1" <-> "OE2" Residue "Z GLU 265": "OE1" <-> "OE2" Residue "Z ASP 271": "OD1" <-> "OD2" Residue "Z GLU 275": "OE1" <-> "OE2" Residue "Z PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 303": "OD1" <-> "OD2" Residue "Z GLU 343": "OE1" <-> "OE2" Residue "Z ASP 344": "OD1" <-> "OD2" Residue "Z TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 355": "OE1" <-> "OE2" Residue "Z ASP 356": "OD1" <-> "OD2" Residue "Z ASP 385": "OD1" <-> "OD2" Residue "Z PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 29": "NH1" <-> "NH2" Residue "a PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 53": "OE1" <-> "OE2" Residue "a ASP 86": "OD1" <-> "OD2" Residue "a TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 136": "OD1" <-> "OD2" Residue "a PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 168": "OE1" <-> "OE2" Residue "a PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 181": "OE1" <-> "OE2" Residue "a PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 233": "OD1" <-> "OD2" Residue "a ASP 250": "OD1" <-> "OD2" Residue "a ASP 252": "OD1" <-> "OD2" Residue "a GLU 258": "OE1" <-> "OE2" Residue "a GLU 265": "OE1" <-> "OE2" Residue "a ASP 271": "OD1" <-> "OD2" Residue "a GLU 275": "OE1" <-> "OE2" Residue "a PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 303": "OD1" <-> "OD2" Residue "a GLU 343": "OE1" <-> "OE2" Residue "a ASP 344": "OD1" <-> "OD2" Residue "a TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 355": "OE1" <-> "OE2" Residue "a ASP 356": "OD1" <-> "OD2" Residue "a PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 385": "OD1" <-> "OD2" Residue "a PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 29": "NH1" <-> "NH2" Residue "b PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 53": "OE1" <-> "OE2" Residue "b ASP 86": "OD1" <-> "OD2" Residue "b TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 136": "OD1" <-> "OD2" Residue "b PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 168": "OE1" <-> "OE2" Residue "b PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 181": "OE1" <-> "OE2" Residue "b PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 233": "OD1" <-> "OD2" Residue "b ASP 250": "OD1" <-> "OD2" Residue "b ASP 252": "OD1" <-> "OD2" Residue "b GLU 258": "OE1" <-> "OE2" Residue "b GLU 265": "OE1" <-> "OE2" Residue "b ASP 271": "OD1" <-> "OD2" Residue "b GLU 275": "OE1" <-> "OE2" Residue "b PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 303": "OD1" <-> "OD2" Residue "b GLU 343": "OE1" <-> "OE2" Residue "b ASP 344": "OD1" <-> "OD2" Residue "b TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 355": "OE1" <-> "OE2" Residue "b ASP 356": "OD1" <-> "OD2" Residue "b PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 385": "OD1" <-> "OD2" Residue "b PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 29": "NH1" <-> "NH2" Residue "c PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 53": "OE1" <-> "OE2" Residue "c ASP 86": "OD1" <-> "OD2" Residue "c TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 136": "OD1" <-> "OD2" Residue "c PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 168": "OE1" <-> "OE2" Residue "c PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 181": "OE1" <-> "OE2" Residue "c PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 233": "OD1" <-> "OD2" Residue "c ASP 250": "OD1" <-> "OD2" Residue "c ASP 252": "OD1" <-> "OD2" Residue "c GLU 258": "OE1" <-> "OE2" Residue "c GLU 265": "OE1" <-> "OE2" Residue "c ASP 271": "OD1" <-> "OD2" Residue "c GLU 275": "OE1" <-> "OE2" Residue "c PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 303": "OD1" <-> "OD2" Residue "c GLU 343": "OE1" <-> "OE2" Residue "c ASP 344": "OD1" <-> "OD2" Residue "c TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 355": "OE1" <-> "OE2" Residue "c ASP 356": "OD1" <-> "OD2" Residue "c ASP 385": "OD1" <-> "OD2" Residue "c PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 29": "NH1" <-> "NH2" Residue "d PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 53": "OE1" <-> "OE2" Residue "d ASP 86": "OD1" <-> "OD2" Residue "d TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 136": "OD1" <-> "OD2" Residue "d PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 168": "OE1" <-> "OE2" Residue "d PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 181": "OE1" <-> "OE2" Residue "d PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 233": "OD1" <-> "OD2" Residue "d ASP 250": "OD1" <-> "OD2" Residue "d ASP 252": "OD1" <-> "OD2" Residue "d GLU 258": "OE1" <-> "OE2" Residue "d GLU 265": "OE1" <-> "OE2" Residue "d ASP 271": "OD1" <-> "OD2" Residue "d GLU 275": "OE1" <-> "OE2" Residue "d PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 303": "OD1" <-> "OD2" Residue "d GLU 343": "OE1" <-> "OE2" Residue "d ASP 344": "OD1" <-> "OD2" Residue "d TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 355": "OE1" <-> "OE2" Residue "d ASP 356": "OD1" <-> "OD2" Residue "d PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 385": "OD1" <-> "OD2" Residue "d PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 29": "NH1" <-> "NH2" Residue "e PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 53": "OE1" <-> "OE2" Residue "e ASP 86": "OD1" <-> "OD2" Residue "e TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 136": "OD1" <-> "OD2" Residue "e PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 168": "OE1" <-> "OE2" Residue "e PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 181": "OE1" <-> "OE2" Residue "e PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 233": "OD1" <-> "OD2" Residue "e ASP 250": "OD1" <-> "OD2" Residue "e ASP 252": "OD1" <-> "OD2" Residue "e GLU 258": "OE1" <-> "OE2" Residue "e GLU 265": "OE1" <-> "OE2" Residue "e ASP 271": "OD1" <-> "OD2" Residue "e GLU 275": "OE1" <-> "OE2" Residue "e PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 303": "OD1" <-> "OD2" Residue "e GLU 343": "OE1" <-> "OE2" Residue "e ASP 344": "OD1" <-> "OD2" Residue "e TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 355": "OE1" <-> "OE2" Residue "e ASP 356": "OD1" <-> "OD2" Residue "e PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 385": "OD1" <-> "OD2" Residue "e PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 29": "NH1" <-> "NH2" Residue "f PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 53": "OE1" <-> "OE2" Residue "f ASP 86": "OD1" <-> "OD2" Residue "f TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 136": "OD1" <-> "OD2" Residue "f PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 168": "OE1" <-> "OE2" Residue "f PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 181": "OE1" <-> "OE2" Residue "f PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 233": "OD1" <-> "OD2" Residue "f ASP 250": "OD1" <-> "OD2" Residue "f ASP 252": "OD1" <-> "OD2" Residue "f GLU 258": "OE1" <-> "OE2" Residue "f GLU 265": "OE1" <-> "OE2" Residue "f ASP 271": "OD1" <-> "OD2" Residue "f GLU 275": "OE1" <-> "OE2" Residue "f PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 303": "OD1" <-> "OD2" Residue "f GLU 343": "OE1" <-> "OE2" Residue "f ASP 344": "OD1" <-> "OD2" Residue "f TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 355": "OE1" <-> "OE2" Residue "f ASP 356": "OD1" <-> "OD2" Residue "f ASP 385": "OD1" <-> "OD2" Residue "f PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 35256 Number of models: 1 Model: "" Number of chains: 12 Chain: "U" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "V" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "W" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "X" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "Y" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "Z" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "a" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "b" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "c" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "d" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "e" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "f" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Time building chain proxies: 18.72, per 1000 atoms: 0.53 Number of scatterers: 35256 At special positions: 0 Unit cell: (165.24, 165.24, 112.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 6720 8.00 N 6048 7.00 C 22320 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=0, symmetry=0 Time building additional restraints: 14.92 Conformation dependent library (CDL) restraints added in 6.3 seconds 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8400 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 60 sheets defined 46.7% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'U' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE U 27 " --> pdb=" O ALA U 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG U 28 " --> pdb=" O LYS U 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 23 through 28' Processing helix chain 'U' and resid 41 through 51 Processing helix chain 'U' and resid 54 through 70 Processing helix chain 'U' and resid 92 through 103 Processing helix chain 'U' and resid 109 through 125 Processing helix chain 'U' and resid 212 through 216 Processing helix chain 'U' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP U 236 " --> pdb=" O ILE U 232 " (cutoff:3.500A) Processing helix chain 'U' and resid 251 through 265 removed outlier: 4.264A pdb=" N GLN U 255 " --> pdb=" O LEU U 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA U 256 " --> pdb=" O ASP U 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS U 257 " --> pdb=" O ASP U 253 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU U 258 " --> pdb=" O GLY U 254 " (cutoff:3.500A) Processing helix chain 'U' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP U 304 " --> pdb=" O VAL U 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN U 305 " --> pdb=" O PRO U 301 " (cutoff:3.500A) Processing helix chain 'U' and resid 316 through 320 Processing helix chain 'U' and resid 335 through 345 removed outlier: 3.750A pdb=" N THR U 345 " --> pdb=" O PHE U 341 " (cutoff:3.500A) Processing helix chain 'U' and resid 346 through 361 removed outlier: 6.136A pdb=" N THR U 352 " --> pdb=" O PRO U 348 " (cutoff:3.500A) Proline residue: U 353 - end of helix removed outlier: 3.547A pdb=" N PHE U 361 " --> pdb=" O GLY U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 373 through 378 Proline residue: U 377 - end of helix Processing helix chain 'U' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL U 393 " --> pdb=" O THR U 389 " (cutoff:3.500A) Processing helix chain 'U' and resid 397 through 404 Processing helix chain 'V' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE V 27 " --> pdb=" O ALA V 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG V 28 " --> pdb=" O LYS V 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 23 through 28' Processing helix chain 'V' and resid 41 through 51 Processing helix chain 'V' and resid 54 through 70 Processing helix chain 'V' and resid 92 through 103 Processing helix chain 'V' and resid 109 through 125 Processing helix chain 'V' and resid 212 through 216 Processing helix chain 'V' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP V 236 " --> pdb=" O ILE V 232 " (cutoff:3.500A) Processing helix chain 'V' and resid 251 through 265 removed outlier: 4.265A pdb=" N GLN V 255 " --> pdb=" O LEU V 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA V 256 " --> pdb=" O ASP V 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS V 257 " --> pdb=" O ASP V 253 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU V 258 " --> pdb=" O GLY V 254 " (cutoff:3.500A) Processing helix chain 'V' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP V 304 " --> pdb=" O VAL V 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN V 305 " --> pdb=" O PRO V 301 " (cutoff:3.500A) Processing helix chain 'V' and resid 316 through 320 Processing helix chain 'V' and resid 335 through 345 removed outlier: 3.749A pdb=" N THR V 345 " --> pdb=" O PHE V 341 " (cutoff:3.500A) Processing helix chain 'V' and resid 346 through 361 removed outlier: 6.136A pdb=" N THR V 352 " --> pdb=" O PRO V 348 " (cutoff:3.500A) Proline residue: V 353 - end of helix removed outlier: 3.547A pdb=" N PHE V 361 " --> pdb=" O GLY V 357 " (cutoff:3.500A) Processing helix chain 'V' and resid 373 through 378 Proline residue: V 377 - end of helix Processing helix chain 'V' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL V 393 " --> pdb=" O THR V 389 " (cutoff:3.500A) Processing helix chain 'V' and resid 397 through 404 Processing helix chain 'W' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE W 27 " --> pdb=" O ALA W 23 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG W 28 " --> pdb=" O LYS W 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 23 through 28' Processing helix chain 'W' and resid 41 through 51 Processing helix chain 'W' and resid 54 through 70 Processing helix chain 'W' and resid 92 through 103 Processing helix chain 'W' and resid 109 through 125 Processing helix chain 'W' and resid 212 through 216 Processing helix chain 'W' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP W 236 " --> pdb=" O ILE W 232 " (cutoff:3.500A) Processing helix chain 'W' and resid 251 through 265 removed outlier: 4.265A pdb=" N GLN W 255 " --> pdb=" O LEU W 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA W 256 " --> pdb=" O ASP W 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS W 257 " --> pdb=" O ASP W 253 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU W 258 " --> pdb=" O GLY W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP W 304 " --> pdb=" O VAL W 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN W 305 " --> pdb=" O PRO W 301 " (cutoff:3.500A) Processing helix chain 'W' and resid 316 through 320 Processing helix chain 'W' and resid 335 through 345 removed outlier: 3.750A pdb=" N THR W 345 " --> pdb=" O PHE W 341 " (cutoff:3.500A) Processing helix chain 'W' and resid 346 through 361 removed outlier: 6.135A pdb=" N THR W 352 " --> pdb=" O PRO W 348 " (cutoff:3.500A) Proline residue: W 353 - end of helix removed outlier: 3.548A pdb=" N PHE W 361 " --> pdb=" O GLY W 357 " (cutoff:3.500A) Processing helix chain 'W' and resid 373 through 378 Proline residue: W 377 - end of helix Processing helix chain 'W' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL W 393 " --> pdb=" O THR W 389 " (cutoff:3.500A) Processing helix chain 'W' and resid 397 through 404 Processing helix chain 'X' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE X 27 " --> pdb=" O ALA X 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG X 28 " --> pdb=" O LYS X 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 23 through 28' Processing helix chain 'X' and resid 41 through 51 Processing helix chain 'X' and resid 54 through 70 Processing helix chain 'X' and resid 92 through 103 Processing helix chain 'X' and resid 109 through 125 Processing helix chain 'X' and resid 212 through 216 Processing helix chain 'X' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP X 236 " --> pdb=" O ILE X 232 " (cutoff:3.500A) Processing helix chain 'X' and resid 251 through 265 removed outlier: 4.264A pdb=" N GLN X 255 " --> pdb=" O LEU X 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA X 256 " --> pdb=" O ASP X 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS X 257 " --> pdb=" O ASP X 253 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU X 258 " --> pdb=" O GLY X 254 " (cutoff:3.500A) Processing helix chain 'X' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP X 304 " --> pdb=" O VAL X 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN X 305 " --> pdb=" O PRO X 301 " (cutoff:3.500A) Processing helix chain 'X' and resid 316 through 320 Processing helix chain 'X' and resid 335 through 345 removed outlier: 3.750A pdb=" N THR X 345 " --> pdb=" O PHE X 341 " (cutoff:3.500A) Processing helix chain 'X' and resid 346 through 361 removed outlier: 6.136A pdb=" N THR X 352 " --> pdb=" O PRO X 348 " (cutoff:3.500A) Proline residue: X 353 - end of helix removed outlier: 3.547A pdb=" N PHE X 361 " --> pdb=" O GLY X 357 " (cutoff:3.500A) Processing helix chain 'X' and resid 373 through 378 Proline residue: X 377 - end of helix Processing helix chain 'X' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL X 393 " --> pdb=" O THR X 389 " (cutoff:3.500A) Processing helix chain 'X' and resid 397 through 404 Processing helix chain 'Y' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE Y 27 " --> pdb=" O ALA Y 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG Y 28 " --> pdb=" O LYS Y 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 23 through 28' Processing helix chain 'Y' and resid 41 through 51 Processing helix chain 'Y' and resid 54 through 70 Processing helix chain 'Y' and resid 92 through 103 Processing helix chain 'Y' and resid 109 through 125 Processing helix chain 'Y' and resid 212 through 216 Processing helix chain 'Y' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP Y 236 " --> pdb=" O ILE Y 232 " (cutoff:3.500A) Processing helix chain 'Y' and resid 251 through 265 removed outlier: 4.265A pdb=" N GLN Y 255 " --> pdb=" O LEU Y 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA Y 256 " --> pdb=" O ASP Y 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS Y 257 " --> pdb=" O ASP Y 253 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU Y 258 " --> pdb=" O GLY Y 254 " (cutoff:3.500A) Processing helix chain 'Y' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP Y 304 " --> pdb=" O VAL Y 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN Y 305 " --> pdb=" O PRO Y 301 " (cutoff:3.500A) Processing helix chain 'Y' and resid 316 through 320 Processing helix chain 'Y' and resid 335 through 345 removed outlier: 3.749A pdb=" N THR Y 345 " --> pdb=" O PHE Y 341 " (cutoff:3.500A) Processing helix chain 'Y' and resid 346 through 361 removed outlier: 6.136A pdb=" N THR Y 352 " --> pdb=" O PRO Y 348 " (cutoff:3.500A) Proline residue: Y 353 - end of helix removed outlier: 3.547A pdb=" N PHE Y 361 " --> pdb=" O GLY Y 357 " (cutoff:3.500A) Processing helix chain 'Y' and resid 373 through 378 Proline residue: Y 377 - end of helix Processing helix chain 'Y' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL Y 393 " --> pdb=" O THR Y 389 " (cutoff:3.500A) Processing helix chain 'Y' and resid 397 through 404 Processing helix chain 'Z' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE Z 27 " --> pdb=" O ALA Z 23 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG Z 28 " --> pdb=" O LYS Z 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 23 through 28' Processing helix chain 'Z' and resid 41 through 51 Processing helix chain 'Z' and resid 54 through 70 Processing helix chain 'Z' and resid 92 through 103 Processing helix chain 'Z' and resid 109 through 125 Processing helix chain 'Z' and resid 212 through 216 Processing helix chain 'Z' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP Z 236 " --> pdb=" O ILE Z 232 " (cutoff:3.500A) Processing helix chain 'Z' and resid 251 through 265 removed outlier: 4.265A pdb=" N GLN Z 255 " --> pdb=" O LEU Z 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA Z 256 " --> pdb=" O ASP Z 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS Z 257 " --> pdb=" O ASP Z 253 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU Z 258 " --> pdb=" O GLY Z 254 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP Z 304 " --> pdb=" O VAL Z 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN Z 305 " --> pdb=" O PRO Z 301 " (cutoff:3.500A) Processing helix chain 'Z' and resid 316 through 320 Processing helix chain 'Z' and resid 335 through 345 removed outlier: 3.750A pdb=" N THR Z 345 " --> pdb=" O PHE Z 341 " (cutoff:3.500A) Processing helix chain 'Z' and resid 346 through 361 removed outlier: 6.135A pdb=" N THR Z 352 " --> pdb=" O PRO Z 348 " (cutoff:3.500A) Proline residue: Z 353 - end of helix removed outlier: 3.548A pdb=" N PHE Z 361 " --> pdb=" O GLY Z 357 " (cutoff:3.500A) Processing helix chain 'Z' and resid 373 through 378 Proline residue: Z 377 - end of helix Processing helix chain 'Z' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL Z 393 " --> pdb=" O THR Z 389 " (cutoff:3.500A) Processing helix chain 'Z' and resid 397 through 404 Processing helix chain 'a' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE a 27 " --> pdb=" O ALA a 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG a 28 " --> pdb=" O LYS a 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 23 through 28' Processing helix chain 'a' and resid 41 through 51 Processing helix chain 'a' and resid 54 through 70 Processing helix chain 'a' and resid 92 through 103 Processing helix chain 'a' and resid 109 through 125 Processing helix chain 'a' and resid 212 through 216 Processing helix chain 'a' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP a 236 " --> pdb=" O ILE a 232 " (cutoff:3.500A) Processing helix chain 'a' and resid 251 through 265 removed outlier: 4.264A pdb=" N GLN a 255 " --> pdb=" O LEU a 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA a 256 " --> pdb=" O ASP a 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS a 257 " --> pdb=" O ASP a 253 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU a 258 " --> pdb=" O GLY a 254 " (cutoff:3.500A) Processing helix chain 'a' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP a 304 " --> pdb=" O VAL a 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN a 305 " --> pdb=" O PRO a 301 " (cutoff:3.500A) Processing helix chain 'a' and resid 316 through 320 Processing helix chain 'a' and resid 335 through 345 removed outlier: 3.750A pdb=" N THR a 345 " --> pdb=" O PHE a 341 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 361 removed outlier: 6.136A pdb=" N THR a 352 " --> pdb=" O PRO a 348 " (cutoff:3.500A) Proline residue: a 353 - end of helix removed outlier: 3.547A pdb=" N PHE a 361 " --> pdb=" O GLY a 357 " (cutoff:3.500A) Processing helix chain 'a' and resid 373 through 378 Proline residue: a 377 - end of helix Processing helix chain 'a' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL a 393 " --> pdb=" O THR a 389 " (cutoff:3.500A) Processing helix chain 'a' and resid 397 through 404 Processing helix chain 'b' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE b 27 " --> pdb=" O ALA b 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG b 28 " --> pdb=" O LYS b 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 23 through 28' Processing helix chain 'b' and resid 41 through 51 Processing helix chain 'b' and resid 54 through 70 Processing helix chain 'b' and resid 92 through 103 Processing helix chain 'b' and resid 109 through 125 Processing helix chain 'b' and resid 212 through 216 Processing helix chain 'b' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP b 236 " --> pdb=" O ILE b 232 " (cutoff:3.500A) Processing helix chain 'b' and resid 251 through 265 removed outlier: 4.265A pdb=" N GLN b 255 " --> pdb=" O LEU b 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA b 256 " --> pdb=" O ASP b 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS b 257 " --> pdb=" O ASP b 253 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU b 258 " --> pdb=" O GLY b 254 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP b 304 " --> pdb=" O VAL b 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN b 305 " --> pdb=" O PRO b 301 " (cutoff:3.500A) Processing helix chain 'b' and resid 316 through 320 Processing helix chain 'b' and resid 335 through 345 removed outlier: 3.749A pdb=" N THR b 345 " --> pdb=" O PHE b 341 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 361 removed outlier: 6.136A pdb=" N THR b 352 " --> pdb=" O PRO b 348 " (cutoff:3.500A) Proline residue: b 353 - end of helix removed outlier: 3.547A pdb=" N PHE b 361 " --> pdb=" O GLY b 357 " (cutoff:3.500A) Processing helix chain 'b' and resid 373 through 378 Proline residue: b 377 - end of helix Processing helix chain 'b' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL b 393 " --> pdb=" O THR b 389 " (cutoff:3.500A) Processing helix chain 'b' and resid 397 through 404 Processing helix chain 'c' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE c 27 " --> pdb=" O ALA c 23 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG c 28 " --> pdb=" O LYS c 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 23 through 28' Processing helix chain 'c' and resid 41 through 51 Processing helix chain 'c' and resid 54 through 70 Processing helix chain 'c' and resid 92 through 103 Processing helix chain 'c' and resid 109 through 125 Processing helix chain 'c' and resid 212 through 216 Processing helix chain 'c' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP c 236 " --> pdb=" O ILE c 232 " (cutoff:3.500A) Processing helix chain 'c' and resid 251 through 265 removed outlier: 4.265A pdb=" N GLN c 255 " --> pdb=" O LEU c 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA c 256 " --> pdb=" O ASP c 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS c 257 " --> pdb=" O ASP c 253 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU c 258 " --> pdb=" O GLY c 254 " (cutoff:3.500A) Processing helix chain 'c' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP c 304 " --> pdb=" O VAL c 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN c 305 " --> pdb=" O PRO c 301 " (cutoff:3.500A) Processing helix chain 'c' and resid 316 through 320 Processing helix chain 'c' and resid 335 through 345 removed outlier: 3.750A pdb=" N THR c 345 " --> pdb=" O PHE c 341 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 361 removed outlier: 6.135A pdb=" N THR c 352 " --> pdb=" O PRO c 348 " (cutoff:3.500A) Proline residue: c 353 - end of helix removed outlier: 3.548A pdb=" N PHE c 361 " --> pdb=" O GLY c 357 " (cutoff:3.500A) Processing helix chain 'c' and resid 373 through 378 Proline residue: c 377 - end of helix Processing helix chain 'c' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL c 393 " --> pdb=" O THR c 389 " (cutoff:3.500A) Processing helix chain 'c' and resid 397 through 404 Processing helix chain 'd' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE d 27 " --> pdb=" O ALA d 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG d 28 " --> pdb=" O LYS d 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 23 through 28' Processing helix chain 'd' and resid 41 through 51 Processing helix chain 'd' and resid 54 through 70 Processing helix chain 'd' and resid 92 through 103 Processing helix chain 'd' and resid 109 through 125 Processing helix chain 'd' and resid 212 through 216 Processing helix chain 'd' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP d 236 " --> pdb=" O ILE d 232 " (cutoff:3.500A) Processing helix chain 'd' and resid 251 through 265 removed outlier: 4.264A pdb=" N GLN d 255 " --> pdb=" O LEU d 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA d 256 " --> pdb=" O ASP d 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS d 257 " --> pdb=" O ASP d 253 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU d 258 " --> pdb=" O GLY d 254 " (cutoff:3.500A) Processing helix chain 'd' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP d 304 " --> pdb=" O VAL d 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN d 305 " --> pdb=" O PRO d 301 " (cutoff:3.500A) Processing helix chain 'd' and resid 316 through 320 Processing helix chain 'd' and resid 335 through 345 removed outlier: 3.750A pdb=" N THR d 345 " --> pdb=" O PHE d 341 " (cutoff:3.500A) Processing helix chain 'd' and resid 346 through 361 removed outlier: 6.136A pdb=" N THR d 352 " --> pdb=" O PRO d 348 " (cutoff:3.500A) Proline residue: d 353 - end of helix removed outlier: 3.547A pdb=" N PHE d 361 " --> pdb=" O GLY d 357 " (cutoff:3.500A) Processing helix chain 'd' and resid 373 through 378 Proline residue: d 377 - end of helix Processing helix chain 'd' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL d 393 " --> pdb=" O THR d 389 " (cutoff:3.500A) Processing helix chain 'd' and resid 397 through 404 Processing helix chain 'e' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE e 27 " --> pdb=" O ALA e 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG e 28 " --> pdb=" O LYS e 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 23 through 28' Processing helix chain 'e' and resid 41 through 51 Processing helix chain 'e' and resid 54 through 70 Processing helix chain 'e' and resid 92 through 103 Processing helix chain 'e' and resid 109 through 125 Processing helix chain 'e' and resid 212 through 216 Processing helix chain 'e' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP e 236 " --> pdb=" O ILE e 232 " (cutoff:3.500A) Processing helix chain 'e' and resid 251 through 265 removed outlier: 4.265A pdb=" N GLN e 255 " --> pdb=" O LEU e 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA e 256 " --> pdb=" O ASP e 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS e 257 " --> pdb=" O ASP e 253 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU e 258 " --> pdb=" O GLY e 254 " (cutoff:3.500A) Processing helix chain 'e' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP e 304 " --> pdb=" O VAL e 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN e 305 " --> pdb=" O PRO e 301 " (cutoff:3.500A) Processing helix chain 'e' and resid 316 through 320 Processing helix chain 'e' and resid 335 through 345 removed outlier: 3.749A pdb=" N THR e 345 " --> pdb=" O PHE e 341 " (cutoff:3.500A) Processing helix chain 'e' and resid 346 through 361 removed outlier: 6.136A pdb=" N THR e 352 " --> pdb=" O PRO e 348 " (cutoff:3.500A) Proline residue: e 353 - end of helix removed outlier: 3.547A pdb=" N PHE e 361 " --> pdb=" O GLY e 357 " (cutoff:3.500A) Processing helix chain 'e' and resid 373 through 378 Proline residue: e 377 - end of helix Processing helix chain 'e' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL e 393 " --> pdb=" O THR e 389 " (cutoff:3.500A) Processing helix chain 'e' and resid 397 through 404 Processing helix chain 'f' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE f 27 " --> pdb=" O ALA f 23 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG f 28 " --> pdb=" O LYS f 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 23 through 28' Processing helix chain 'f' and resid 41 through 51 Processing helix chain 'f' and resid 54 through 70 Processing helix chain 'f' and resid 92 through 103 Processing helix chain 'f' and resid 109 through 125 Processing helix chain 'f' and resid 212 through 216 Processing helix chain 'f' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP f 236 " --> pdb=" O ILE f 232 " (cutoff:3.500A) Processing helix chain 'f' and resid 251 through 265 removed outlier: 4.265A pdb=" N GLN f 255 " --> pdb=" O LEU f 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA f 256 " --> pdb=" O ASP f 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS f 257 " --> pdb=" O ASP f 253 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU f 258 " --> pdb=" O GLY f 254 " (cutoff:3.500A) Processing helix chain 'f' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP f 304 " --> pdb=" O VAL f 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN f 305 " --> pdb=" O PRO f 301 " (cutoff:3.500A) Processing helix chain 'f' and resid 316 through 320 Processing helix chain 'f' and resid 335 through 345 removed outlier: 3.750A pdb=" N THR f 345 " --> pdb=" O PHE f 341 " (cutoff:3.500A) Processing helix chain 'f' and resid 346 through 361 removed outlier: 6.135A pdb=" N THR f 352 " --> pdb=" O PRO f 348 " (cutoff:3.500A) Proline residue: f 353 - end of helix removed outlier: 3.548A pdb=" N PHE f 361 " --> pdb=" O GLY f 357 " (cutoff:3.500A) Processing helix chain 'f' and resid 373 through 378 Proline residue: f 377 - end of helix Processing helix chain 'f' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL f 393 " --> pdb=" O THR f 389 " (cutoff:3.500A) Processing helix chain 'f' and resid 397 through 404 Processing sheet with id=AA1, first strand: chain 'U' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER U 162 " --> pdb=" O LYS U 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'U' and resid 73 through 77 Processing sheet with id=AA3, first strand: chain 'U' and resid 126 through 127 Processing sheet with id=AA4, first strand: chain 'U' and resid 142 through 144 removed outlier: 3.707A pdb=" N TYR U 192 " --> pdb=" O VAL U 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'U' and resid 285 through 287 removed outlier: 3.502A pdb=" N GLN U 287 " --> pdb=" O LEU U 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE V 277 " --> pdb=" O VAL U 245 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'U' and resid 277 through 279 removed outlier: 5.713A pdb=" N ILE U 277 " --> pdb=" O VAL f 245 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN f 287 " --> pdb=" O LEU f 244 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'V' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER V 162 " --> pdb=" O LYS V 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'V' and resid 73 through 77 Processing sheet with id=AA9, first strand: chain 'V' and resid 126 through 127 Processing sheet with id=AB1, first strand: chain 'V' and resid 142 through 144 removed outlier: 3.708A pdb=" N TYR V 192 " --> pdb=" O VAL V 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'V' and resid 285 through 287 removed outlier: 3.501A pdb=" N GLN V 287 " --> pdb=" O LEU V 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE W 277 " --> pdb=" O VAL V 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'W' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER W 162 " --> pdb=" O LYS W 153 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'W' and resid 73 through 77 Processing sheet with id=AB5, first strand: chain 'W' and resid 126 through 127 Processing sheet with id=AB6, first strand: chain 'W' and resid 142 through 144 removed outlier: 3.707A pdb=" N TYR W 192 " --> pdb=" O VAL W 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'W' and resid 285 through 287 removed outlier: 3.501A pdb=" N GLN W 287 " --> pdb=" O LEU W 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE X 277 " --> pdb=" O VAL W 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'X' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER X 162 " --> pdb=" O LYS X 153 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'X' and resid 73 through 77 Processing sheet with id=AC1, first strand: chain 'X' and resid 126 through 127 Processing sheet with id=AC2, first strand: chain 'X' and resid 142 through 144 removed outlier: 3.707A pdb=" N TYR X 192 " --> pdb=" O VAL X 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'X' and resid 285 through 287 removed outlier: 3.502A pdb=" N GLN X 287 " --> pdb=" O LEU X 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE Y 277 " --> pdb=" O VAL X 245 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Y' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER Y 162 " --> pdb=" O LYS Y 153 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Y' and resid 73 through 77 Processing sheet with id=AC6, first strand: chain 'Y' and resid 126 through 127 Processing sheet with id=AC7, first strand: chain 'Y' and resid 142 through 144 removed outlier: 3.708A pdb=" N TYR Y 192 " --> pdb=" O VAL Y 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Y' and resid 285 through 287 removed outlier: 3.501A pdb=" N GLN Y 287 " --> pdb=" O LEU Y 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE Z 277 " --> pdb=" O VAL Y 245 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Z' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER Z 162 " --> pdb=" O LYS Z 153 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 73 through 77 Processing sheet with id=AD2, first strand: chain 'Z' and resid 126 through 127 Processing sheet with id=AD3, first strand: chain 'Z' and resid 142 through 144 removed outlier: 3.707A pdb=" N TYR Z 192 " --> pdb=" O VAL Z 131 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Z' and resid 285 through 287 removed outlier: 3.501A pdb=" N GLN Z 287 " --> pdb=" O LEU Z 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE a 277 " --> pdb=" O VAL Z 245 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'a' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER a 162 " --> pdb=" O LYS a 153 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'a' and resid 73 through 77 Processing sheet with id=AD7, first strand: chain 'a' and resid 126 through 127 Processing sheet with id=AD8, first strand: chain 'a' and resid 142 through 144 removed outlier: 3.707A pdb=" N TYR a 192 " --> pdb=" O VAL a 131 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'a' and resid 285 through 287 removed outlier: 3.502A pdb=" N GLN a 287 " --> pdb=" O LEU a 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE b 277 " --> pdb=" O VAL a 245 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'b' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER b 162 " --> pdb=" O LYS b 153 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'b' and resid 73 through 77 Processing sheet with id=AE3, first strand: chain 'b' and resid 126 through 127 Processing sheet with id=AE4, first strand: chain 'b' and resid 142 through 144 removed outlier: 3.708A pdb=" N TYR b 192 " --> pdb=" O VAL b 131 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'b' and resid 285 through 287 removed outlier: 3.501A pdb=" N GLN b 287 " --> pdb=" O LEU b 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE c 277 " --> pdb=" O VAL b 245 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'c' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER c 162 " --> pdb=" O LYS c 153 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 73 through 77 Processing sheet with id=AE8, first strand: chain 'c' and resid 126 through 127 Processing sheet with id=AE9, first strand: chain 'c' and resid 142 through 144 removed outlier: 3.707A pdb=" N TYR c 192 " --> pdb=" O VAL c 131 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'c' and resid 285 through 287 removed outlier: 3.501A pdb=" N GLN c 287 " --> pdb=" O LEU c 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE d 277 " --> pdb=" O VAL c 245 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'd' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER d 162 " --> pdb=" O LYS d 153 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'd' and resid 73 through 77 Processing sheet with id=AF4, first strand: chain 'd' and resid 126 through 127 Processing sheet with id=AF5, first strand: chain 'd' and resid 142 through 144 removed outlier: 3.707A pdb=" N TYR d 192 " --> pdb=" O VAL d 131 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'd' and resid 285 through 287 removed outlier: 3.502A pdb=" N GLN d 287 " --> pdb=" O LEU d 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE e 277 " --> pdb=" O VAL d 245 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'e' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER e 162 " --> pdb=" O LYS e 153 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'e' and resid 73 through 77 Processing sheet with id=AF9, first strand: chain 'e' and resid 126 through 127 Processing sheet with id=AG1, first strand: chain 'e' and resid 142 through 144 removed outlier: 3.708A pdb=" N TYR e 192 " --> pdb=" O VAL e 131 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'e' and resid 285 through 287 removed outlier: 3.501A pdb=" N GLN e 287 " --> pdb=" O LEU e 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE f 277 " --> pdb=" O VAL e 245 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'f' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER f 162 " --> pdb=" O LYS f 153 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'f' and resid 73 through 77 Processing sheet with id=AG5, first strand: chain 'f' and resid 126 through 127 Processing sheet with id=AG6, first strand: chain 'f' and resid 142 through 144 removed outlier: 3.707A pdb=" N TYR f 192 " --> pdb=" O VAL f 131 " (cutoff:3.500A) 1464 hydrogen bonds defined for protein. 4068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.78 Time building geometry restraints manager: 15.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11736 1.34 - 1.46: 7968 1.46 - 1.59: 15996 1.59 - 1.71: 0 1.71 - 1.83: 300 Bond restraints: 36000 Sorted by residual: bond pdb=" C GLY V 349 " pdb=" N TYR V 350 " ideal model delta sigma weight residual 1.332 1.306 0.026 1.40e-02 5.10e+03 3.55e+00 bond pdb=" C GLY Y 349 " pdb=" N TYR Y 350 " ideal model delta sigma weight residual 1.332 1.306 0.026 1.40e-02 5.10e+03 3.55e+00 bond pdb=" C GLY b 349 " pdb=" N TYR b 350 " ideal model delta sigma weight residual 1.332 1.306 0.026 1.40e-02 5.10e+03 3.55e+00 bond pdb=" C GLY e 349 " pdb=" N TYR e 350 " ideal model delta sigma weight residual 1.332 1.306 0.026 1.40e-02 5.10e+03 3.55e+00 bond pdb=" C GLY d 349 " pdb=" N TYR d 350 " ideal model delta sigma weight residual 1.332 1.307 0.026 1.40e-02 5.10e+03 3.38e+00 ... (remaining 35995 not shown) Histogram of bond angle deviations from ideal: 98.78 - 105.82: 1052 105.82 - 112.87: 18532 112.87 - 119.91: 12406 119.91 - 126.96: 16250 126.96 - 134.00: 432 Bond angle restraints: 48672 Sorted by residual: angle pdb=" C ASP f 167 " pdb=" N GLU f 168 " pdb=" CA GLU f 168 " ideal model delta sigma weight residual 121.54 114.05 7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C ASP W 167 " pdb=" N GLU W 168 " pdb=" CA GLU W 168 " ideal model delta sigma weight residual 121.54 114.05 7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C ASP Z 167 " pdb=" N GLU Z 168 " pdb=" CA GLU Z 168 " ideal model delta sigma weight residual 121.54 114.05 7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C ASP c 167 " pdb=" N GLU c 168 " pdb=" CA GLU c 168 " ideal model delta sigma weight residual 121.54 114.05 7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C ASP U 167 " pdb=" N GLU U 168 " pdb=" CA GLU U 168 " ideal model delta sigma weight residual 121.54 114.05 7.49 1.91e+00 2.74e-01 1.54e+01 ... (remaining 48667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 19436 17.85 - 35.69: 1864 35.69 - 53.54: 408 53.54 - 71.39: 36 71.39 - 89.23: 60 Dihedral angle restraints: 21804 sinusoidal: 8736 harmonic: 13068 Sorted by residual: dihedral pdb=" CA PHE X 361 " pdb=" C PHE X 361 " pdb=" N LEU X 362 " pdb=" CA LEU X 362 " ideal model delta harmonic sigma weight residual 180.00 153.65 26.35 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA PHE a 361 " pdb=" C PHE a 361 " pdb=" N LEU a 362 " pdb=" CA LEU a 362 " ideal model delta harmonic sigma weight residual 180.00 153.65 26.35 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA PHE d 361 " pdb=" C PHE d 361 " pdb=" N LEU d 362 " pdb=" CA LEU d 362 " ideal model delta harmonic sigma weight residual 180.00 153.65 26.35 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 21801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2779 0.030 - 0.060: 1349 0.060 - 0.090: 738 0.090 - 0.119: 298 0.119 - 0.149: 104 Chirality restraints: 5268 Sorted by residual: chirality pdb=" CA ASP f 208 " pdb=" N ASP f 208 " pdb=" C ASP f 208 " pdb=" CB ASP f 208 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ASP W 208 " pdb=" N ASP W 208 " pdb=" C ASP W 208 " pdb=" CB ASP W 208 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ASP c 208 " pdb=" N ASP c 208 " pdb=" C ASP c 208 " pdb=" CB ASP c 208 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 5265 not shown) Planarity restraints: 6420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL Z 133 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C VAL Z 133 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL Z 133 " 0.009 2.00e-02 2.50e+03 pdb=" N MET Z 134 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL W 133 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C VAL W 133 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL W 133 " 0.009 2.00e-02 2.50e+03 pdb=" N MET W 134 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL c 133 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C VAL c 133 " 0.025 2.00e-02 2.50e+03 pdb=" O VAL c 133 " -0.009 2.00e-02 2.50e+03 pdb=" N MET c 134 " -0.008 2.00e-02 2.50e+03 ... (remaining 6417 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 7576 2.77 - 3.30: 35256 3.30 - 3.83: 57400 3.83 - 4.37: 67052 4.37 - 4.90: 114906 Nonbonded interactions: 282190 Sorted by model distance: nonbonded pdb=" N ASN f 183 " pdb=" O ARG f 187 " model vdw 2.237 2.520 nonbonded pdb=" N ASN c 183 " pdb=" O ARG c 187 " model vdw 2.237 2.520 nonbonded pdb=" N ASN W 183 " pdb=" O ARG W 187 " model vdw 2.237 2.520 nonbonded pdb=" N ASN Z 183 " pdb=" O ARG Z 187 " model vdw 2.237 2.520 nonbonded pdb=" N ASN d 183 " pdb=" O ARG d 187 " model vdw 2.237 2.520 ... (remaining 282185 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 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 20.060 Check model and map are aligned: 0.520 Set scattering table: 0.310 Process input model: 93.000 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.250 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:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.005 0.049 36000 Z= 0.346 Angle : 0.827 11.446 48672 Z= 0.438 Chirality : 0.048 0.149 5268 Planarity : 0.005 0.035 6420 Dihedral : 14.996 89.231 13404 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.82 % Favored : 87.18 % Rotamer: Outliers : 2.57 % Allowed : 9.00 % Favored : 88.42 % 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: -3.49 (0.11), residues: 4524 helix: -1.10 (0.10), residues: 1968 sheet: -1.79 (0.24), residues: 504 loop : -3.78 (0.11), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 143 HIS 0.014 0.005 HIS e 297 PHE 0.021 0.002 PHE Z 361 TYR 0.012 0.001 TYR c 192 ARG 0.005 0.001 ARG X 373 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 992 time to evaluate : 4.382 Fit side-chains REVERT: U 49 GLN cc_start: 0.8821 (tp40) cc_final: 0.8447 (tp40) REVERT: U 153 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8302 (ttmt) REVERT: U 201 ILE cc_start: 0.8213 (mt) cc_final: 0.7981 (tp) REVERT: U 249 ARG cc_start: 0.5831 (tpt170) cc_final: 0.4484 (ttt90) REVERT: U 285 LYS cc_start: 0.8762 (ttpp) cc_final: 0.8492 (tttp) REVERT: U 386 ILE cc_start: 0.9048 (mm) cc_final: 0.8809 (mt) REVERT: V 37 LYS cc_start: 0.8598 (tttt) cc_final: 0.8335 (tttt) REVERT: V 49 GLN cc_start: 0.8803 (tp40) cc_final: 0.8592 (mm-40) REVERT: V 201 ILE cc_start: 0.8196 (mt) cc_final: 0.7955 (tp) REVERT: V 209 VAL cc_start: 0.8957 (t) cc_final: 0.8741 (m) REVERT: V 249 ARG cc_start: 0.6309 (tpt170) cc_final: 0.4988 (ttt90) REVERT: W 49 GLN cc_start: 0.8782 (tp40) cc_final: 0.8427 (mm-40) REVERT: W 99 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8708 (mm-40) REVERT: W 164 GLN cc_start: 0.8175 (tt0) cc_final: 0.7960 (tt0) REVERT: W 183 ASN cc_start: 0.6904 (m-40) cc_final: 0.6629 (m-40) REVERT: W 209 VAL cc_start: 0.8925 (t) cc_final: 0.8611 (t) REVERT: W 249 ARG cc_start: 0.5983 (tpt170) cc_final: 0.4562 (ttt90) REVERT: W 285 LYS cc_start: 0.8780 (ttpp) cc_final: 0.8467 (tttp) REVERT: W 290 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8429 (tptp) REVERT: X 49 GLN cc_start: 0.8821 (tp40) cc_final: 0.8445 (tp40) REVERT: X 153 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8301 (ttmt) REVERT: X 201 ILE cc_start: 0.8211 (mt) cc_final: 0.7978 (tp) REVERT: X 249 ARG cc_start: 0.5830 (tpt170) cc_final: 0.4485 (ttt90) REVERT: X 285 LYS cc_start: 0.8759 (ttpp) cc_final: 0.8493 (tttp) REVERT: X 386 ILE cc_start: 0.9042 (mm) cc_final: 0.8802 (mt) REVERT: Y 37 LYS cc_start: 0.8596 (tttt) cc_final: 0.8335 (tttt) REVERT: Y 49 GLN cc_start: 0.8801 (tp40) cc_final: 0.8590 (mm-40) REVERT: Y 201 ILE cc_start: 0.8194 (mt) cc_final: 0.7950 (tp) REVERT: Y 209 VAL cc_start: 0.8960 (t) cc_final: 0.8743 (m) REVERT: Y 249 ARG cc_start: 0.6316 (tpt170) cc_final: 0.4992 (ttt90) REVERT: Z 49 GLN cc_start: 0.8775 (tp40) cc_final: 0.8421 (mm-40) REVERT: Z 99 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8709 (mm-40) REVERT: Z 164 GLN cc_start: 0.8173 (tt0) cc_final: 0.7959 (tt0) REVERT: Z 183 ASN cc_start: 0.6902 (m-40) cc_final: 0.6632 (m-40) REVERT: Z 209 VAL cc_start: 0.8932 (t) cc_final: 0.8620 (t) REVERT: Z 249 ARG cc_start: 0.5981 (tpt170) cc_final: 0.4567 (ttt90) REVERT: Z 285 LYS cc_start: 0.8777 (ttpp) cc_final: 0.8465 (tttp) REVERT: Z 290 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8428 (tptp) REVERT: a 49 GLN cc_start: 0.8819 (tp40) cc_final: 0.8447 (tp40) REVERT: a 153 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8303 (ttmt) REVERT: a 201 ILE cc_start: 0.8213 (mt) cc_final: 0.7987 (tp) REVERT: a 249 ARG cc_start: 0.5830 (tpt170) cc_final: 0.4481 (ttt90) REVERT: a 285 LYS cc_start: 0.8757 (ttpp) cc_final: 0.8492 (tttp) REVERT: a 386 ILE cc_start: 0.9040 (mm) cc_final: 0.8802 (mt) REVERT: b 37 LYS cc_start: 0.8598 (tttt) cc_final: 0.8336 (tttt) REVERT: b 49 GLN cc_start: 0.8799 (tp40) cc_final: 0.8591 (mm-40) REVERT: b 201 ILE cc_start: 0.8191 (mt) cc_final: 0.7946 (tp) REVERT: b 209 VAL cc_start: 0.8963 (t) cc_final: 0.8748 (m) REVERT: b 249 ARG cc_start: 0.6319 (tpt170) cc_final: 0.4994 (ttt90) REVERT: c 49 GLN cc_start: 0.8774 (tp40) cc_final: 0.8419 (mm-40) REVERT: c 99 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8709 (mm-40) REVERT: c 164 GLN cc_start: 0.8171 (tt0) cc_final: 0.7957 (tt0) REVERT: c 183 ASN cc_start: 0.6900 (m-40) cc_final: 0.6633 (m-40) REVERT: c 209 VAL cc_start: 0.8928 (t) cc_final: 0.8614 (t) REVERT: c 249 ARG cc_start: 0.5982 (tpt170) cc_final: 0.4569 (ttt90) REVERT: c 285 LYS cc_start: 0.8778 (ttpp) cc_final: 0.8466 (tttp) REVERT: c 290 LYS cc_start: 0.8735 (mmmt) cc_final: 0.8429 (tptp) REVERT: d 49 GLN cc_start: 0.8820 (tp40) cc_final: 0.8448 (tp40) REVERT: d 153 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8303 (ttmt) REVERT: d 201 ILE cc_start: 0.8215 (mt) cc_final: 0.7990 (tp) REVERT: d 249 ARG cc_start: 0.5828 (tpt170) cc_final: 0.4478 (ttt90) REVERT: d 285 LYS cc_start: 0.8759 (ttpp) cc_final: 0.8493 (tttp) REVERT: d 386 ILE cc_start: 0.9046 (mm) cc_final: 0.8807 (mt) REVERT: e 37 LYS cc_start: 0.8599 (tttt) cc_final: 0.8338 (tttt) REVERT: e 49 GLN cc_start: 0.8801 (tp40) cc_final: 0.8592 (mm-40) REVERT: e 201 ILE cc_start: 0.8196 (mt) cc_final: 0.7954 (tp) REVERT: e 209 VAL cc_start: 0.8965 (t) cc_final: 0.8748 (m) REVERT: e 249 ARG cc_start: 0.6311 (tpt170) cc_final: 0.4988 (ttt90) REVERT: f 49 GLN cc_start: 0.8780 (tp40) cc_final: 0.8423 (mm-40) REVERT: f 99 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8708 (mm-40) REVERT: f 164 GLN cc_start: 0.8171 (tt0) cc_final: 0.7959 (tt0) REVERT: f 183 ASN cc_start: 0.6903 (m-40) cc_final: 0.6628 (m-40) REVERT: f 209 VAL cc_start: 0.8925 (t) cc_final: 0.8613 (t) REVERT: f 249 ARG cc_start: 0.5979 (tpt170) cc_final: 0.4561 (ttt90) REVERT: f 285 LYS cc_start: 0.8779 (ttpp) cc_final: 0.8468 (tttp) REVERT: f 290 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8429 (tptp) outliers start: 96 outliers final: 28 residues processed: 1064 average time/residue: 0.5953 time to fit residues: 970.7363 Evaluate side-chains 684 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 656 time to evaluate : 4.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 41 SER Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain W residue 41 SER Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain W residue 391 ASP Chi-restraints excluded: chain X residue 41 SER Chi-restraints excluded: chain X residue 168 GLU Chi-restraints excluded: chain Y residue 41 SER Chi-restraints excluded: chain Y residue 168 GLU Chi-restraints excluded: chain Z residue 41 SER Chi-restraints excluded: chain Z residue 168 GLU Chi-restraints excluded: chain Z residue 391 ASP Chi-restraints excluded: chain a residue 41 SER Chi-restraints excluded: chain a residue 168 GLU Chi-restraints excluded: chain b residue 41 SER Chi-restraints excluded: chain b residue 168 GLU Chi-restraints excluded: chain c residue 41 SER Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 391 ASP Chi-restraints excluded: chain d residue 41 SER Chi-restraints excluded: chain d residue 168 GLU Chi-restraints excluded: chain e residue 41 SER Chi-restraints excluded: chain e residue 168 GLU Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 168 GLU Chi-restraints excluded: chain f residue 391 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 385 optimal weight: 2.9990 chunk 345 optimal weight: 8.9990 chunk 191 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 233 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 357 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 chunk 217 optimal weight: 0.9980 chunk 266 optimal weight: 9.9990 chunk 414 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: