Starting phenix.real_space_refine on Thu Feb 22 20:56:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwb_29500/02_2024/8fwb_29500.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwb_29500/02_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_29500/02_2024/8fwb_29500.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwb_29500/02_2024/8fwb_29500.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwb_29500/02_2024/8fwb_29500.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwb_29500/02_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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 17.99, per 1000 atoms: 0.51 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: 15.12 Conformation dependent library (CDL) restraints added in 6.7 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: 3.77 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: 12.30 Time building geometry restraints manager: 16.07 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: 4.530 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: 0.040 Extract box with map and model: 20.260 Check model and map are aligned: 0.510 Set scattering table: 0.320 Process input model: 90.530 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.210 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.500 ------------------------------------------------------------------------------- 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 : 4.530 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: 0.5896 time to fit residues: 959.7094 Evaluate side-chains 684 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 656 time to evaluate : 4.286 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: U 112 GLN U 164 GLN U 191 ASN U 202 ASN U 291 ASN V 80 GLN V 191 ASN V 202 ASN ** V 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 291 ASN W 80 GLN ** W 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 112 GLN W 191 ASN W 202 ASN ** W 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 291 ASN W 305 GLN X 112 GLN X 164 GLN X 191 ASN X 202 ASN X 291 ASN Y 80 GLN Y 191 ASN Y 202 ASN ** Y 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 291 ASN Y 305 GLN Z 80 GLN ** Z 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 112 GLN Z 191 ASN Z 202 ASN ** Z 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 291 ASN Z 305 GLN a 112 GLN a 164 GLN a 191 ASN a 202 ASN a 291 ASN a 305 GLN b 80 GLN b 191 ASN b 202 ASN ** b 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 291 ASN b 305 GLN c 80 GLN ** c 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 112 GLN c 191 ASN c 202 ASN ** c 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 291 ASN c 305 GLN d 112 GLN d 164 GLN d 191 ASN d 202 ASN d 291 ASN e 80 GLN e 191 ASN e 202 ASN ** e 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 291 ASN e 305 GLN ** f 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 112 GLN f 191 ASN f 202 ASN ** f 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 291 ASN f 305 GLN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 36000 Z= 0.231 Angle : 0.665 7.754 48672 Z= 0.341 Chirality : 0.045 0.153 5268 Planarity : 0.005 0.032 6420 Dihedral : 6.095 51.163 4952 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 3.32 % Allowed : 15.86 % Favored : 80.81 % 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: -2.13 (0.12), residues: 4524 helix: 0.27 (0.12), residues: 1944 sheet: -0.84 (0.31), residues: 360 loop : -3.23 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP c 143 HIS 0.009 0.003 HIS b 297 PHE 0.011 0.001 PHE Y 26 TYR 0.009 0.001 TYR c 367 ARG 0.004 0.001 ARG f 383 *********************** REFINEMENT MACRO_CYCLE 2 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 876 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 752 time to evaluate : 4.489 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: U 49 GLN cc_start: 0.8790 (tp40) cc_final: 0.8479 (tp40) REVERT: U 89 MET cc_start: 0.6050 (mmm) cc_final: 0.5700 (mmm) REVERT: U 154 PHE cc_start: 0.8446 (m-80) cc_final: 0.8187 (m-80) REVERT: U 157 TYR cc_start: 0.7749 (m-80) cc_final: 0.7399 (m-80) REVERT: U 205 MET cc_start: 0.7926 (mtm) cc_final: 0.7607 (mtt) REVERT: U 249 ARG cc_start: 0.5932 (tpt170) cc_final: 0.4719 (ttt90) REVERT: U 285 LYS cc_start: 0.8449 (ttpp) cc_final: 0.8028 (tttp) REVERT: U 350 TYR cc_start: 0.9434 (m-80) cc_final: 0.8996 (m-80) REVERT: U 386 ILE cc_start: 0.9024 (mm) cc_final: 0.8809 (mt) REVERT: U 405 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8413 (p) REVERT: V 99 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8358 (mp10) REVERT: V 153 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8228 (ttmp) REVERT: V 183 ASN cc_start: 0.6636 (m-40) cc_final: 0.6373 (m-40) REVERT: V 205 MET cc_start: 0.7971 (mtt) cc_final: 0.7770 (mmt) REVERT: V 249 ARG cc_start: 0.6085 (tpt170) cc_final: 0.4830 (ttt90) REVERT: V 355 GLU cc_start: 0.7769 (pt0) cc_final: 0.7560 (pt0) REVERT: V 405 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8484 (p) REVERT: W 49 GLN cc_start: 0.8772 (tp40) cc_final: 0.8357 (mm-40) REVERT: W 66 LEU cc_start: 0.9084 (mt) cc_final: 0.8749 (mt) REVERT: W 89 MET cc_start: 0.5480 (mmm) cc_final: 0.5213 (mmm) REVERT: W 99 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8712 (mm-40) REVERT: W 153 LYS cc_start: 0.8752 (ttmt) cc_final: 0.8517 (ttmt) REVERT: W 183 ASN cc_start: 0.7118 (m-40) cc_final: 0.6870 (m-40) REVERT: W 249 ARG cc_start: 0.6109 (tpt170) cc_final: 0.4612 (ttt90) REVERT: W 285 LYS cc_start: 0.8438 (ttpp) cc_final: 0.8213 (tttp) REVERT: W 290 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8511 (tptp) REVERT: X 49 GLN cc_start: 0.8789 (tp40) cc_final: 0.8477 (tp40) REVERT: X 89 MET cc_start: 0.6065 (mmm) cc_final: 0.5714 (mmm) REVERT: X 154 PHE cc_start: 0.8443 (m-80) cc_final: 0.8185 (m-80) REVERT: X 157 TYR cc_start: 0.7747 (m-80) cc_final: 0.7396 (m-80) REVERT: X 205 MET cc_start: 0.7900 (mtm) cc_final: 0.7623 (mtt) REVERT: X 249 ARG cc_start: 0.5933 (tpt170) cc_final: 0.4724 (ttt90) REVERT: X 285 LYS cc_start: 0.8445 (ttpp) cc_final: 0.8027 (tttp) REVERT: X 350 TYR cc_start: 0.9430 (m-80) cc_final: 0.8995 (m-80) REVERT: X 386 ILE cc_start: 0.9021 (mm) cc_final: 0.8806 (mt) REVERT: X 405 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8410 (p) REVERT: Y 99 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8361 (mp10) REVERT: Y 153 LYS cc_start: 0.8565 (ttmt) cc_final: 0.8230 (ttmp) REVERT: Y 183 ASN cc_start: 0.6644 (m-40) cc_final: 0.6379 (m-40) REVERT: Y 205 MET cc_start: 0.7971 (mtt) cc_final: 0.7771 (mmt) REVERT: Y 249 ARG cc_start: 0.6090 (tpt170) cc_final: 0.4836 (ttt90) REVERT: Y 355 GLU cc_start: 0.7771 (pt0) cc_final: 0.7562 (pt0) REVERT: Y 405 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8460 (p) REVERT: Z 49 GLN cc_start: 0.8770 (tp40) cc_final: 0.8353 (mm-40) REVERT: Z 66 LEU cc_start: 0.9076 (mt) cc_final: 0.8741 (mt) REVERT: Z 89 MET cc_start: 0.5476 (mmm) cc_final: 0.5208 (mmm) REVERT: Z 99 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8713 (mm-40) REVERT: Z 153 LYS cc_start: 0.8750 (ttmt) cc_final: 0.8517 (ttmt) REVERT: Z 183 ASN cc_start: 0.7117 (m-40) cc_final: 0.6871 (m-40) REVERT: Z 249 ARG cc_start: 0.6107 (tpt170) cc_final: 0.4617 (ttt90) REVERT: Z 285 LYS cc_start: 0.8435 (ttpp) cc_final: 0.8211 (tttp) REVERT: Z 290 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8506 (tptp) REVERT: a 49 GLN cc_start: 0.8786 (tp40) cc_final: 0.8479 (tp40) REVERT: a 89 MET cc_start: 0.6053 (mmm) cc_final: 0.5704 (mmm) REVERT: a 154 PHE cc_start: 0.8445 (m-80) cc_final: 0.8188 (m-80) REVERT: a 157 TYR cc_start: 0.7749 (m-80) cc_final: 0.7398 (m-80) REVERT: a 205 MET cc_start: 0.7900 (mtm) cc_final: 0.7623 (mtt) REVERT: a 249 ARG cc_start: 0.5931 (tpt170) cc_final: 0.4719 (ttt90) REVERT: a 285 LYS cc_start: 0.8446 (ttpp) cc_final: 0.8027 (tttp) REVERT: a 350 TYR cc_start: 0.9429 (m-80) cc_final: 0.8994 (m-80) REVERT: a 386 ILE cc_start: 0.9017 (mm) cc_final: 0.8803 (mt) REVERT: a 405 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8413 (p) REVERT: b 99 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8360 (mp10) REVERT: b 153 LYS cc_start: 0.8566 (ttmt) cc_final: 0.8231 (ttmp) REVERT: b 183 ASN cc_start: 0.6643 (m-40) cc_final: 0.6378 (m-40) REVERT: b 205 MET cc_start: 0.7971 (mtt) cc_final: 0.7768 (mmt) REVERT: b 249 ARG cc_start: 0.6092 (tpt170) cc_final: 0.4837 (ttt90) REVERT: b 355 GLU cc_start: 0.7775 (pt0) cc_final: 0.7563 (pt0) REVERT: b 405 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8463 (p) REVERT: c 49 GLN cc_start: 0.8765 (tp40) cc_final: 0.8351 (mm-40) REVERT: c 66 LEU cc_start: 0.9079 (mt) cc_final: 0.8744 (mt) REVERT: c 89 MET cc_start: 0.5481 (mmm) cc_final: 0.5216 (mmm) REVERT: c 99 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8712 (mm-40) REVERT: c 153 LYS cc_start: 0.8751 (ttmt) cc_final: 0.8519 (ttmt) REVERT: c 183 ASN cc_start: 0.7115 (m-40) cc_final: 0.6869 (m-40) REVERT: c 249 ARG cc_start: 0.6107 (tpt170) cc_final: 0.4617 (ttt90) REVERT: c 285 LYS cc_start: 0.8438 (ttpp) cc_final: 0.8215 (tttp) REVERT: c 290 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8507 (tptp) REVERT: d 49 GLN cc_start: 0.8788 (tp40) cc_final: 0.8479 (tp40) REVERT: d 89 MET cc_start: 0.6034 (mmm) cc_final: 0.5687 (mmm) REVERT: d 154 PHE cc_start: 0.8445 (m-80) cc_final: 0.8188 (m-80) REVERT: d 157 TYR cc_start: 0.7746 (m-80) cc_final: 0.7399 (m-80) REVERT: d 205 MET cc_start: 0.7898 (mtm) cc_final: 0.7622 (mtt) REVERT: d 249 ARG cc_start: 0.5926 (tpt170) cc_final: 0.4712 (ttt90) REVERT: d 285 LYS cc_start: 0.8447 (ttpp) cc_final: 0.8030 (tttp) REVERT: d 350 TYR cc_start: 0.9433 (m-80) cc_final: 0.8997 (m-80) REVERT: d 386 ILE cc_start: 0.9023 (mm) cc_final: 0.8807 (mt) REVERT: d 405 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8410 (p) REVERT: e 99 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8358 (mp10) REVERT: e 153 LYS cc_start: 0.8567 (ttmt) cc_final: 0.8231 (ttmp) REVERT: e 183 ASN cc_start: 0.6638 (m-40) cc_final: 0.6375 (m-40) REVERT: e 205 MET cc_start: 0.7971 (mtt) cc_final: 0.7768 (mmt) REVERT: e 249 ARG cc_start: 0.6086 (tpt170) cc_final: 0.4832 (ttt90) REVERT: e 355 GLU cc_start: 0.7774 (pt0) cc_final: 0.7563 (pt0) REVERT: e 405 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8485 (p) REVERT: f 49 GLN cc_start: 0.8772 (tp40) cc_final: 0.8357 (mm-40) REVERT: f 66 LEU cc_start: 0.9079 (mt) cc_final: 0.8744 (mt) REVERT: f 89 MET cc_start: 0.5480 (mmm) cc_final: 0.5213 (mmm) REVERT: f 99 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8712 (mm-40) REVERT: f 153 LYS cc_start: 0.8752 (ttmt) cc_final: 0.8518 (ttmt) REVERT: f 183 ASN cc_start: 0.7118 (m-40) cc_final: 0.6869 (m-40) REVERT: f 249 ARG cc_start: 0.6107 (tpt170) cc_final: 0.4612 (ttt90) REVERT: f 285 LYS cc_start: 0.8438 (ttpp) cc_final: 0.8216 (tttp) REVERT: f 290 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8510 (tptp) outliers start: 124 outliers final: 84 residues processed: 836 average time/residue: 0.4727 time to fit residues: 633.1297 Evaluate side-chains 740 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 648 time to evaluate : 4.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 74 ASP Chi-restraints excluded: chain U residue 120 SER Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 232 ILE Chi-restraints excluded: chain U residue 245 VAL Chi-restraints excluded: chain U residue 371 PHE Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain V residue 93 GLN Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain V residue 232 ILE Chi-restraints excluded: chain V residue 241 SER Chi-restraints excluded: chain V residue 245 VAL Chi-restraints excluded: chain V residue 371 PHE Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 93 GLN Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain W residue 236 ASP Chi-restraints excluded: chain W residue 258 GLU Chi-restraints excluded: chain W residue 371 PHE Chi-restraints excluded: chain W residue 391 ASP Chi-restraints excluded: chain X residue 74 ASP Chi-restraints excluded: chain X residue 120 SER Chi-restraints excluded: chain X residue 168 GLU Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 232 ILE Chi-restraints excluded: chain X residue 245 VAL Chi-restraints excluded: chain X residue 371 PHE Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain Y residue 74 ASP Chi-restraints excluded: chain Y residue 93 GLN Chi-restraints excluded: chain Y residue 168 GLU Chi-restraints excluded: chain Y residue 232 ILE Chi-restraints excluded: chain Y residue 241 SER Chi-restraints excluded: chain Y residue 245 VAL Chi-restraints excluded: chain Y residue 371 PHE Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Z residue 93 GLN Chi-restraints excluded: chain Z residue 102 GLN Chi-restraints excluded: chain Z residue 168 GLU Chi-restraints excluded: chain Z residue 236 ASP Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 371 PHE Chi-restraints excluded: chain Z residue 391 ASP Chi-restraints excluded: chain a residue 74 ASP Chi-restraints excluded: chain a residue 120 SER Chi-restraints excluded: chain a residue 168 GLU Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 232 ILE Chi-restraints excluded: chain a residue 245 VAL Chi-restraints excluded: chain a residue 371 PHE Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain b residue 74 ASP Chi-restraints excluded: chain b residue 93 GLN Chi-restraints excluded: chain b residue 168 GLU Chi-restraints excluded: chain b residue 232 ILE Chi-restraints excluded: chain b residue 241 SER Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 371 PHE Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain c residue 93 GLN Chi-restraints excluded: chain c residue 102 GLN Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 258 GLU Chi-restraints excluded: chain c residue 371 PHE Chi-restraints excluded: chain c residue 391 ASP Chi-restraints excluded: chain d residue 74 ASP Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain d residue 168 GLU Chi-restraints excluded: chain d residue 209 VAL Chi-restraints excluded: chain d residue 232 ILE Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 371 PHE Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain e residue 74 ASP Chi-restraints excluded: chain e residue 93 GLN Chi-restraints excluded: chain e residue 168 GLU Chi-restraints excluded: chain e residue 232 ILE Chi-restraints excluded: chain e residue 241 SER Chi-restraints excluded: chain e residue 245 VAL Chi-restraints excluded: chain e residue 371 PHE Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain f residue 93 GLN Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 168 GLU Chi-restraints excluded: chain f residue 236 ASP Chi-restraints excluded: chain f residue 258 GLU Chi-restraints excluded: chain f residue 371 PHE Chi-restraints excluded: chain f residue 391 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 230 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 344 optimal weight: 7.9990 chunk 281 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 414 optimal weight: 6.9990 chunk 448 optimal weight: 8.9990 chunk 369 optimal weight: 5.9990 chunk 411 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 332 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 112 GLN V 69 GLN ** V 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 305 GLN W 69 GLN W 80 GLN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 112 GLN W 215 GLN X 112 GLN Y 69 GLN ** Y 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 69 GLN Z 80 GLN ** Z 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 112 GLN Z 215 GLN b 69 GLN ** b 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 69 GLN c 80 GLN ** c 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 112 GLN c 215 GLN d 112 GLN e 69 GLN ** e 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 69 GLN ** f 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 112 GLN f 215 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 36000 Z= 0.366 Angle : 0.704 9.035 48672 Z= 0.360 Chirality : 0.047 0.204 5268 Planarity : 0.005 0.032 6420 Dihedral : 6.070 54.909 4940 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer: Outliers : 4.93 % Allowed : 20.42 % Favored : 74.65 % 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: -1.81 (0.13), residues: 4524 helix: 0.56 (0.12), residues: 1956 sheet: -0.77 (0.28), residues: 480 loop : -3.19 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP c 143 HIS 0.014 0.005 HIS Y 297 PHE 0.014 0.002 PHE X 371 TYR 0.008 0.002 TYR c 367 ARG 0.005 0.001 ARG Y 50 *********************** REFINEMENT MACRO_CYCLE 3 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 837 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 653 time to evaluate : 4.358 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: U 49 GLN cc_start: 0.8787 (tp40) cc_final: 0.8554 (tp40) REVERT: U 149 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.6958 (p90) REVERT: U 205 MET cc_start: 0.7849 (mtm) cc_final: 0.7533 (mtt) REVERT: U 249 ARG cc_start: 0.6171 (tpt170) cc_final: 0.4655 (ttt90) REVERT: U 386 ILE cc_start: 0.9078 (mm) cc_final: 0.8866 (mt) REVERT: U 405 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8555 (p) REVERT: V 149 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.6807 (p90) REVERT: V 153 LYS cc_start: 0.8687 (ttmt) cc_final: 0.8374 (ttmm) REVERT: V 249 ARG cc_start: 0.5899 (tpt170) cc_final: 0.4681 (ttt90) REVERT: V 355 GLU cc_start: 0.7810 (pt0) cc_final: 0.7573 (pt0) REVERT: V 405 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8538 (p) REVERT: W 153 LYS cc_start: 0.8782 (ttmt) cc_final: 0.8449 (ttmt) REVERT: W 157 TYR cc_start: 0.7714 (m-80) cc_final: 0.7379 (m-80) REVERT: W 183 ASN cc_start: 0.7131 (m-40) cc_final: 0.6850 (m-40) REVERT: W 249 ARG cc_start: 0.6136 (tpt170) cc_final: 0.4472 (ttt90) REVERT: W 285 LYS cc_start: 0.8477 (ttpp) cc_final: 0.8178 (tttp) REVERT: W 290 LYS cc_start: 0.8855 (mmmt) cc_final: 0.8507 (tptp) REVERT: X 49 GLN cc_start: 0.8786 (tp40) cc_final: 0.8551 (tp40) REVERT: X 149 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.6954 (p90) REVERT: X 205 MET cc_start: 0.7906 (mtm) cc_final: 0.7521 (mtt) REVERT: X 249 ARG cc_start: 0.6175 (tpt170) cc_final: 0.4660 (ttt90) REVERT: X 386 ILE cc_start: 0.9073 (mm) cc_final: 0.8862 (mt) REVERT: X 405 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8551 (p) REVERT: Y 149 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.6807 (p90) REVERT: Y 153 LYS cc_start: 0.8690 (ttmt) cc_final: 0.8377 (ttmm) REVERT: Y 249 ARG cc_start: 0.5907 (tpt170) cc_final: 0.4684 (ttt90) REVERT: Y 355 GLU cc_start: 0.7811 (pt0) cc_final: 0.7577 (pt0) REVERT: Y 405 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8537 (p) REVERT: Z 153 LYS cc_start: 0.8781 (ttmt) cc_final: 0.8452 (ttmt) REVERT: Z 157 TYR cc_start: 0.7715 (m-80) cc_final: 0.7382 (m-80) REVERT: Z 183 ASN cc_start: 0.7130 (m-40) cc_final: 0.6850 (m-40) REVERT: Z 249 ARG cc_start: 0.6132 (tpt170) cc_final: 0.4477 (ttt90) REVERT: Z 285 LYS cc_start: 0.8477 (ttpp) cc_final: 0.8175 (tttp) REVERT: Z 290 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8506 (tptp) REVERT: a 49 GLN cc_start: 0.8782 (tp40) cc_final: 0.8547 (tp40) REVERT: a 99 GLN cc_start: 0.8931 (mm-40) cc_final: 0.8655 (mm-40) REVERT: a 149 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.6959 (p90) REVERT: a 205 MET cc_start: 0.7906 (mtm) cc_final: 0.7523 (mtt) REVERT: a 249 ARG cc_start: 0.6172 (tpt170) cc_final: 0.4655 (ttt90) REVERT: a 386 ILE cc_start: 0.9072 (mm) cc_final: 0.8861 (mt) REVERT: a 405 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8556 (p) REVERT: b 149 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.6811 (p90) REVERT: b 153 LYS cc_start: 0.8689 (ttmt) cc_final: 0.8376 (ttmm) REVERT: b 249 ARG cc_start: 0.5909 (tpt170) cc_final: 0.4688 (ttt90) REVERT: b 355 GLU cc_start: 0.7811 (pt0) cc_final: 0.7577 (pt0) REVERT: b 405 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8542 (p) REVERT: c 153 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8456 (ttmt) REVERT: c 157 TYR cc_start: 0.7711 (m-80) cc_final: 0.7383 (m-80) REVERT: c 183 ASN cc_start: 0.7131 (m-40) cc_final: 0.6850 (m-40) REVERT: c 249 ARG cc_start: 0.6132 (tpt170) cc_final: 0.4477 (ttt90) REVERT: c 285 LYS cc_start: 0.8478 (ttpp) cc_final: 0.8176 (tttp) REVERT: c 290 LYS cc_start: 0.8857 (mmmt) cc_final: 0.8508 (tptp) REVERT: d 49 GLN cc_start: 0.8786 (tp40) cc_final: 0.8551 (tp40) REVERT: d 149 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.6960 (p90) REVERT: d 205 MET cc_start: 0.7902 (mtm) cc_final: 0.7522 (mtt) REVERT: d 249 ARG cc_start: 0.6166 (tpt170) cc_final: 0.4649 (ttt90) REVERT: d 386 ILE cc_start: 0.9077 (mm) cc_final: 0.8864 (mt) REVERT: d 405 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8554 (p) REVERT: e 149 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.6808 (p90) REVERT: e 153 LYS cc_start: 0.8691 (ttmt) cc_final: 0.8378 (ttmm) REVERT: e 249 ARG cc_start: 0.5901 (tpt170) cc_final: 0.4682 (ttt90) REVERT: e 355 GLU cc_start: 0.7813 (pt0) cc_final: 0.7579 (pt0) REVERT: e 405 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8543 (p) REVERT: f 153 LYS cc_start: 0.8782 (ttmt) cc_final: 0.8452 (ttmt) REVERT: f 157 TYR cc_start: 0.7716 (m-80) cc_final: 0.7382 (m-80) REVERT: f 183 ASN cc_start: 0.7128 (m-40) cc_final: 0.6845 (m-40) REVERT: f 249 ARG cc_start: 0.6129 (tpt170) cc_final: 0.4473 (ttt90) REVERT: f 285 LYS cc_start: 0.8480 (ttpp) cc_final: 0.8180 (tttp) REVERT: f 290 LYS cc_start: 0.8856 (mmmt) cc_final: 0.8508 (tptp) outliers start: 184 outliers final: 112 residues processed: 797 average time/residue: 0.4992 time to fit residues: 634.8178 Evaluate side-chains 757 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 629 time to evaluate : 4.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 74 ASP Chi-restraints excluded: chain U residue 120 SER Chi-restraints excluded: chain U residue 149 PHE Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 232 ILE Chi-restraints excluded: chain U residue 236 ASP Chi-restraints excluded: chain U residue 245 VAL Chi-restraints excluded: chain U residue 246 THR Chi-restraints excluded: chain U residue 371 PHE Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 38 ASN Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain V residue 93 GLN Chi-restraints excluded: chain V residue 149 PHE Chi-restraints excluded: chain V residue 232 ILE Chi-restraints excluded: chain V residue 241 SER Chi-restraints excluded: chain V residue 245 VAL Chi-restraints excluded: chain V residue 246 THR Chi-restraints excluded: chain V residue 293 LEU Chi-restraints excluded: chain V residue 371 PHE Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 75 VAL Chi-restraints excluded: chain W residue 93 GLN Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 209 VAL Chi-restraints excluded: chain W residue 236 ASP Chi-restraints excluded: chain W residue 246 THR Chi-restraints excluded: chain W residue 258 GLU Chi-restraints excluded: chain W residue 267 LYS Chi-restraints excluded: chain W residue 371 PHE Chi-restraints excluded: chain W residue 391 ASP Chi-restraints excluded: chain X residue 74 ASP Chi-restraints excluded: chain X residue 120 SER Chi-restraints excluded: chain X residue 149 PHE Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 232 ILE Chi-restraints excluded: chain X residue 236 ASP Chi-restraints excluded: chain X residue 245 VAL Chi-restraints excluded: chain X residue 246 THR Chi-restraints excluded: chain X residue 371 PHE Chi-restraints excluded: chain X residue 397 THR Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain Y residue 38 ASN Chi-restraints excluded: chain Y residue 74 ASP Chi-restraints excluded: chain Y residue 93 GLN Chi-restraints excluded: chain Y residue 149 PHE Chi-restraints excluded: chain Y residue 232 ILE Chi-restraints excluded: chain Y residue 241 SER Chi-restraints excluded: chain Y residue 245 VAL Chi-restraints excluded: chain Y residue 246 THR Chi-restraints excluded: chain Y residue 293 LEU Chi-restraints excluded: chain Y residue 371 PHE Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 93 GLN Chi-restraints excluded: chain Z residue 102 GLN Chi-restraints excluded: chain Z residue 209 VAL Chi-restraints excluded: chain Z residue 236 ASP Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 267 LYS Chi-restraints excluded: chain Z residue 371 PHE Chi-restraints excluded: chain Z residue 391 ASP Chi-restraints excluded: chain a residue 74 ASP Chi-restraints excluded: chain a residue 120 SER Chi-restraints excluded: chain a residue 149 PHE Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 232 ILE Chi-restraints excluded: chain a residue 236 ASP Chi-restraints excluded: chain a residue 245 VAL Chi-restraints excluded: chain a residue 246 THR Chi-restraints excluded: chain a residue 371 PHE Chi-restraints excluded: chain a residue 397 THR Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain b residue 38 ASN Chi-restraints excluded: chain b residue 74 ASP Chi-restraints excluded: chain b residue 93 GLN Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 232 ILE Chi-restraints excluded: chain b residue 241 SER Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 246 THR Chi-restraints excluded: chain b residue 293 LEU Chi-restraints excluded: chain b residue 371 PHE Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 93 GLN Chi-restraints excluded: chain c residue 102 GLN Chi-restraints excluded: chain c residue 209 VAL Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 246 THR Chi-restraints excluded: chain c residue 258 GLU Chi-restraints excluded: chain c residue 267 LYS Chi-restraints excluded: chain c residue 371 PHE Chi-restraints excluded: chain c residue 391 ASP Chi-restraints excluded: chain d residue 74 ASP Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain d residue 149 PHE Chi-restraints excluded: chain d residue 209 VAL Chi-restraints excluded: chain d residue 232 ILE Chi-restraints excluded: chain d residue 236 ASP Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 246 THR Chi-restraints excluded: chain d residue 371 PHE Chi-restraints excluded: chain d residue 397 THR Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain e residue 38 ASN Chi-restraints excluded: chain e residue 74 ASP Chi-restraints excluded: chain e residue 93 GLN Chi-restraints excluded: chain e residue 149 PHE Chi-restraints excluded: chain e residue 232 ILE Chi-restraints excluded: chain e residue 241 SER Chi-restraints excluded: chain e residue 245 VAL Chi-restraints excluded: chain e residue 246 THR Chi-restraints excluded: chain e residue 293 LEU Chi-restraints excluded: chain e residue 371 PHE Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain f residue 75 VAL Chi-restraints excluded: chain f residue 93 GLN Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 209 VAL Chi-restraints excluded: chain f residue 236 ASP Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 258 GLU Chi-restraints excluded: chain f residue 267 LYS Chi-restraints excluded: chain f residue 371 PHE Chi-restraints excluded: chain f residue 391 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 409 optimal weight: 0.9980 chunk 311 optimal weight: 9.9990 chunk 215 optimal weight: 0.0670 chunk 45 optimal weight: 0.5980 chunk 197 optimal weight: 7.9990 chunk 278 optimal weight: 4.9990 chunk 416 optimal weight: 0.9990 chunk 440 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 chunk 394 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 305 GLN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 305 GLN ** Z 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 112 GLN ** c 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN d 305 GLN ** f 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36000 Z= 0.166 Angle : 0.603 7.149 48672 Z= 0.307 Chirality : 0.043 0.202 5268 Planarity : 0.004 0.034 6420 Dihedral : 4.979 27.475 4904 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 3.64 % Allowed : 22.43 % Favored : 73.93 % 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: -1.41 (0.13), residues: 4524 helix: 0.97 (0.12), residues: 1968 sheet: -0.56 (0.28), residues: 480 loop : -3.09 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 121 HIS 0.003 0.001 HIS Y 297 PHE 0.009 0.001 PHE a 30 TYR 0.010 0.001 TYR f 367 ARG 0.003 0.000 ARG Y 103 *********************** REFINEMENT MACRO_CYCLE 4 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 857 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 721 time to evaluate : 4.530 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: U 157 TYR cc_start: 0.7830 (m-80) cc_final: 0.7487 (m-80) REVERT: U 208 ASP cc_start: 0.8050 (t0) cc_final: 0.7832 (m-30) REVERT: U 249 ARG cc_start: 0.6125 (tpt170) cc_final: 0.4362 (ttm-80) REVERT: U 386 ILE cc_start: 0.9049 (mm) cc_final: 0.8830 (mt) REVERT: V 153 LYS cc_start: 0.8667 (ttmt) cc_final: 0.8319 (ttmt) REVERT: V 157 TYR cc_start: 0.7689 (m-80) cc_final: 0.7435 (m-80) REVERT: V 183 ASN cc_start: 0.6854 (m-40) cc_final: 0.6595 (m-40) REVERT: V 249 ARG cc_start: 0.5823 (tpt170) cc_final: 0.4046 (ttm-80) REVERT: V 355 GLU cc_start: 0.7812 (pt0) cc_final: 0.7523 (pt0) REVERT: V 367 TYR cc_start: 0.8125 (m-80) cc_final: 0.7776 (m-80) REVERT: W 49 GLN cc_start: 0.8691 (tp40) cc_final: 0.8328 (tp40) REVERT: W 99 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8441 (mp10) REVERT: W 149 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7803 (p90) REVERT: W 153 LYS cc_start: 0.8724 (ttmt) cc_final: 0.8424 (ttmt) REVERT: W 157 TYR cc_start: 0.7490 (m-80) cc_final: 0.7033 (m-80) REVERT: W 205 MET cc_start: 0.7529 (mtm) cc_final: 0.7221 (mtt) REVERT: W 249 ARG cc_start: 0.6107 (tpt170) cc_final: 0.3654 (ttm170) REVERT: W 290 LYS cc_start: 0.8867 (mmmt) cc_final: 0.8525 (tptp) REVERT: W 391 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8566 (t70) REVERT: X 157 TYR cc_start: 0.7829 (m-80) cc_final: 0.7486 (m-80) REVERT: X 205 MET cc_start: 0.7593 (mtm) cc_final: 0.7334 (mtt) REVERT: X 208 ASP cc_start: 0.8033 (t0) cc_final: 0.7819 (m-30) REVERT: X 249 ARG cc_start: 0.6125 (tpt170) cc_final: 0.4364 (ttm-80) REVERT: X 386 ILE cc_start: 0.9045 (mm) cc_final: 0.8827 (mt) REVERT: Y 153 LYS cc_start: 0.8669 (ttmt) cc_final: 0.8322 (ttmt) REVERT: Y 157 TYR cc_start: 0.7690 (m-80) cc_final: 0.7435 (m-80) REVERT: Y 183 ASN cc_start: 0.6855 (m-40) cc_final: 0.6597 (m-40) REVERT: Y 249 ARG cc_start: 0.5827 (tpt170) cc_final: 0.4050 (ttm-80) REVERT: Y 355 GLU cc_start: 0.7816 (pt0) cc_final: 0.7526 (pt0) REVERT: Y 367 TYR cc_start: 0.8124 (m-80) cc_final: 0.7777 (m-80) REVERT: Z 49 GLN cc_start: 0.8685 (tp40) cc_final: 0.8318 (tp40) REVERT: Z 99 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8441 (mp10) REVERT: Z 149 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7804 (p90) REVERT: Z 153 LYS cc_start: 0.8724 (ttmt) cc_final: 0.8427 (ttmt) REVERT: Z 157 TYR cc_start: 0.7489 (m-80) cc_final: 0.7033 (m-80) REVERT: Z 205 MET cc_start: 0.7522 (mtm) cc_final: 0.7214 (mtt) REVERT: Z 249 ARG cc_start: 0.6105 (tpt170) cc_final: 0.3655 (ttm170) REVERT: Z 290 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8520 (tptp) REVERT: Z 391 ASP cc_start: 0.8888 (OUTLIER) cc_final: 0.8570 (t70) REVERT: a 157 TYR cc_start: 0.7827 (m-80) cc_final: 0.7484 (m-80) REVERT: a 205 MET cc_start: 0.7592 (mtm) cc_final: 0.7333 (mtt) REVERT: a 208 ASP cc_start: 0.8041 (t0) cc_final: 0.7825 (m-30) REVERT: a 249 ARG cc_start: 0.6123 (tpt170) cc_final: 0.4361 (ttm-80) REVERT: a 386 ILE cc_start: 0.9044 (mm) cc_final: 0.8825 (mt) REVERT: b 153 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8320 (ttmt) REVERT: b 157 TYR cc_start: 0.7687 (m-80) cc_final: 0.7434 (m-80) REVERT: b 183 ASN cc_start: 0.6853 (m-40) cc_final: 0.6596 (m-40) REVERT: b 249 ARG cc_start: 0.5832 (tpt170) cc_final: 0.4051 (ttm-80) REVERT: b 355 GLU cc_start: 0.7813 (pt0) cc_final: 0.7527 (pt0) REVERT: b 367 TYR cc_start: 0.8126 (m-80) cc_final: 0.7778 (m-80) REVERT: c 49 GLN cc_start: 0.8683 (tp40) cc_final: 0.8317 (tp40) REVERT: c 99 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8439 (mp10) REVERT: c 149 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7802 (p90) REVERT: c 153 LYS cc_start: 0.8726 (ttmt) cc_final: 0.8430 (ttmt) REVERT: c 157 TYR cc_start: 0.7488 (m-80) cc_final: 0.7034 (m-80) REVERT: c 249 ARG cc_start: 0.6103 (tpt170) cc_final: 0.3657 (ttm170) REVERT: c 290 LYS cc_start: 0.8868 (mmmt) cc_final: 0.8521 (tptp) REVERT: c 391 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8564 (t70) REVERT: d 157 TYR cc_start: 0.7826 (m-80) cc_final: 0.7484 (m-80) REVERT: d 205 MET cc_start: 0.7589 (mtm) cc_final: 0.7327 (mtt) REVERT: d 208 ASP cc_start: 0.8037 (t0) cc_final: 0.7825 (m-30) REVERT: d 249 ARG cc_start: 0.6118 (tpt170) cc_final: 0.4358 (ttm-80) REVERT: d 386 ILE cc_start: 0.9049 (mm) cc_final: 0.8830 (mt) REVERT: e 153 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8323 (ttmt) REVERT: e 157 TYR cc_start: 0.7689 (m-80) cc_final: 0.7436 (m-80) REVERT: e 183 ASN cc_start: 0.6854 (m-40) cc_final: 0.6597 (m-40) REVERT: e 249 ARG cc_start: 0.5823 (tpt170) cc_final: 0.4046 (ttm-80) REVERT: e 355 GLU cc_start: 0.7816 (pt0) cc_final: 0.7528 (pt0) REVERT: e 367 TYR cc_start: 0.8130 (m-80) cc_final: 0.7780 (m-80) REVERT: f 49 GLN cc_start: 0.8688 (tp40) cc_final: 0.8326 (tp40) REVERT: f 99 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8439 (mp10) REVERT: f 149 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7803 (p90) REVERT: f 153 LYS cc_start: 0.8725 (ttmt) cc_final: 0.8425 (ttmt) REVERT: f 157 TYR cc_start: 0.7493 (m-80) cc_final: 0.7036 (m-80) REVERT: f 249 ARG cc_start: 0.6105 (tpt170) cc_final: 0.3653 (ttm170) REVERT: f 290 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8524 (tptp) REVERT: f 391 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8564 (t70) outliers start: 136 outliers final: 76 residues processed: 805 average time/residue: 0.5076 time to fit residues: 667.8225 Evaluate side-chains 739 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 655 time to evaluate : 4.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 232 ILE Chi-restraints excluded: chain U residue 245 VAL Chi-restraints excluded: chain U residue 252 ASP Chi-restraints excluded: chain U residue 371 PHE Chi-restraints excluded: chain V residue 241 SER Chi-restraints excluded: chain V residue 245 VAL Chi-restraints excluded: chain V residue 371 PHE Chi-restraints excluded: chain V residue 397 THR Chi-restraints excluded: chain W residue 38 ASN Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 149 PHE Chi-restraints excluded: chain W residue 209 VAL Chi-restraints excluded: chain W residue 236 ASP Chi-restraints excluded: chain W residue 258 GLU Chi-restraints excluded: chain W residue 267 LYS Chi-restraints excluded: chain W residue 371 PHE Chi-restraints excluded: chain W residue 391 ASP Chi-restraints excluded: chain W residue 397 THR Chi-restraints excluded: chain X residue 38 ASN Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 232 ILE Chi-restraints excluded: chain X residue 245 VAL Chi-restraints excluded: chain X residue 252 ASP Chi-restraints excluded: chain X residue 371 PHE Chi-restraints excluded: chain Y residue 241 SER Chi-restraints excluded: chain Y residue 245 VAL Chi-restraints excluded: chain Y residue 371 PHE Chi-restraints excluded: chain Y residue 397 THR Chi-restraints excluded: chain Z residue 38 ASN Chi-restraints excluded: chain Z residue 102 GLN Chi-restraints excluded: chain Z residue 131 VAL Chi-restraints excluded: chain Z residue 149 PHE Chi-restraints excluded: chain Z residue 209 VAL Chi-restraints excluded: chain Z residue 236 ASP Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 267 LYS Chi-restraints excluded: chain Z residue 371 PHE Chi-restraints excluded: chain Z residue 391 ASP Chi-restraints excluded: chain Z residue 397 THR Chi-restraints excluded: chain a residue 38 ASN Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 232 ILE Chi-restraints excluded: chain a residue 245 VAL Chi-restraints excluded: chain a residue 252 ASP Chi-restraints excluded: chain a residue 371 PHE Chi-restraints excluded: chain b residue 241 SER Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 371 PHE Chi-restraints excluded: chain b residue 397 THR Chi-restraints excluded: chain c residue 38 ASN Chi-restraints excluded: chain c residue 102 GLN Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 149 PHE Chi-restraints excluded: chain c residue 209 VAL Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 258 GLU Chi-restraints excluded: chain c residue 267 LYS Chi-restraints excluded: chain c residue 371 PHE Chi-restraints excluded: chain c residue 391 ASP Chi-restraints excluded: chain c residue 397 THR Chi-restraints excluded: chain d residue 38 ASN Chi-restraints excluded: chain d residue 209 VAL Chi-restraints excluded: chain d residue 232 ILE Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 252 ASP Chi-restraints excluded: chain d residue 371 PHE Chi-restraints excluded: chain e residue 241 SER Chi-restraints excluded: chain e residue 245 VAL Chi-restraints excluded: chain e residue 371 PHE Chi-restraints excluded: chain e residue 397 THR Chi-restraints excluded: chain f residue 38 ASN Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 149 PHE Chi-restraints excluded: chain f residue 209 VAL Chi-restraints excluded: chain f residue 236 ASP Chi-restraints excluded: chain f residue 258 GLU Chi-restraints excluded: chain f residue 267 LYS Chi-restraints excluded: chain f residue 371 PHE Chi-restraints excluded: chain f residue 391 ASP Chi-restraints excluded: chain f residue 397 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 367 optimal weight: 4.9990 chunk 250 optimal weight: 5.9990 chunk 6 optimal weight: 0.3980 chunk 328 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 376 optimal weight: 9.9990 chunk 304 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 225 optimal weight: 10.0000 chunk 395 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 112 GLN ** V 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 112 GLN ** Z 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN ** f 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 36000 Z= 0.329 Angle : 0.670 7.959 48672 Z= 0.337 Chirality : 0.045 0.211 5268 Planarity : 0.004 0.031 6420 Dihedral : 5.059 28.326 4904 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 5.20 % Allowed : 22.64 % Favored : 72.16 % 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: -1.41 (0.13), residues: 4524 helix: 0.89 (0.12), residues: 1968 sheet: -0.46 (0.28), residues: 480 loop : -3.03 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 121 HIS 0.004 0.002 HIS Y 297 PHE 0.018 0.002 PHE d 371 TYR 0.012 0.002 TYR d 350 ARG 0.005 0.000 ARG U 103 *********************** REFINEMENT MACRO_CYCLE 5 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 826 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 632 time to evaluate : 4.403 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: U 149 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.6992 (p90) REVERT: U 249 ARG cc_start: 0.6088 (tpt170) cc_final: 0.4208 (ttm-80) REVERT: U 258 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: U 265 GLU cc_start: 0.7552 (tt0) cc_final: 0.7284 (tt0) REVERT: V 149 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.6847 (p90) REVERT: V 153 LYS cc_start: 0.8714 (ttmt) cc_final: 0.8326 (ttmt) REVERT: V 249 ARG cc_start: 0.5848 (tpt170) cc_final: 0.4440 (ttt90) REVERT: V 355 GLU cc_start: 0.7868 (pt0) cc_final: 0.7589 (pt0) REVERT: V 391 ASP cc_start: 0.8997 (OUTLIER) cc_final: 0.8601 (t0) REVERT: W 49 GLN cc_start: 0.8702 (tp40) cc_final: 0.8309 (tp40) REVERT: W 99 GLN cc_start: 0.8952 (mm-40) cc_final: 0.8501 (mp10) REVERT: W 149 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8039 (p90) REVERT: W 153 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8458 (ttmt) REVERT: W 157 TYR cc_start: 0.7671 (m-80) cc_final: 0.7234 (m-80) REVERT: W 205 MET cc_start: 0.7648 (mtm) cc_final: 0.7363 (mtt) REVERT: W 249 ARG cc_start: 0.5912 (tpt170) cc_final: 0.3753 (ttm170) REVERT: W 285 LYS cc_start: 0.8396 (ttpp) cc_final: 0.8182 (tttp) REVERT: W 290 LYS cc_start: 0.8861 (mmmt) cc_final: 0.8514 (tptp) REVERT: W 391 ASP cc_start: 0.8981 (OUTLIER) cc_final: 0.8605 (t70) REVERT: X 149 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.6991 (p90) REVERT: X 205 MET cc_start: 0.7728 (mtm) cc_final: 0.7487 (mtt) REVERT: X 249 ARG cc_start: 0.6090 (tpt170) cc_final: 0.4211 (ttm-80) REVERT: X 258 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7937 (tt0) REVERT: X 265 GLU cc_start: 0.7552 (tt0) cc_final: 0.7283 (tt0) REVERT: Y 149 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.6844 (p90) REVERT: Y 153 LYS cc_start: 0.8715 (ttmt) cc_final: 0.8328 (ttmt) REVERT: Y 249 ARG cc_start: 0.5855 (tpt170) cc_final: 0.4442 (ttt90) REVERT: Y 355 GLU cc_start: 0.7870 (pt0) cc_final: 0.7592 (pt0) REVERT: Y 391 ASP cc_start: 0.8996 (OUTLIER) cc_final: 0.8601 (t0) REVERT: Z 49 GLN cc_start: 0.8699 (tp40) cc_final: 0.8302 (tp40) REVERT: Z 99 GLN cc_start: 0.8952 (mm-40) cc_final: 0.8503 (mp10) REVERT: Z 149 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8041 (p90) REVERT: Z 153 LYS cc_start: 0.8785 (ttmt) cc_final: 0.8458 (ttmt) REVERT: Z 157 TYR cc_start: 0.7671 (m-80) cc_final: 0.7236 (m-80) REVERT: Z 205 MET cc_start: 0.7641 (mtm) cc_final: 0.7353 (mtt) REVERT: Z 249 ARG cc_start: 0.5910 (tpt170) cc_final: 0.3753 (ttm170) REVERT: Z 290 LYS cc_start: 0.8863 (mmmt) cc_final: 0.8512 (tptp) REVERT: Z 391 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8605 (t70) REVERT: a 149 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.6993 (p90) REVERT: a 205 MET cc_start: 0.7726 (mtm) cc_final: 0.7486 (mtt) REVERT: a 249 ARG cc_start: 0.6087 (tpt170) cc_final: 0.4208 (ttm-80) REVERT: a 258 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: a 265 GLU cc_start: 0.7551 (tt0) cc_final: 0.7287 (tt0) REVERT: b 149 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.6846 (p90) REVERT: b 153 LYS cc_start: 0.8716 (ttmt) cc_final: 0.8327 (ttmt) REVERT: b 249 ARG cc_start: 0.5856 (tpt170) cc_final: 0.4444 (ttt90) REVERT: b 355 GLU cc_start: 0.7870 (pt0) cc_final: 0.7595 (pt0) REVERT: b 391 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8599 (t0) REVERT: c 49 GLN cc_start: 0.8694 (tp40) cc_final: 0.8300 (tp40) REVERT: c 99 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8502 (mp10) REVERT: c 149 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8039 (p90) REVERT: c 153 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8460 (ttmt) REVERT: c 157 TYR cc_start: 0.7668 (m-80) cc_final: 0.7232 (m-80) REVERT: c 249 ARG cc_start: 0.5907 (tpt170) cc_final: 0.3754 (ttm170) REVERT: c 285 LYS cc_start: 0.8390 (ttpp) cc_final: 0.8181 (tttp) REVERT: c 290 LYS cc_start: 0.8862 (mmmt) cc_final: 0.8514 (tptp) REVERT: c 391 ASP cc_start: 0.8983 (OUTLIER) cc_final: 0.8603 (t70) REVERT: d 149 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.6997 (p90) REVERT: d 205 MET cc_start: 0.7722 (mtm) cc_final: 0.7482 (mtt) REVERT: d 249 ARG cc_start: 0.6082 (tpt170) cc_final: 0.4206 (ttm-80) REVERT: d 258 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7940 (tt0) REVERT: d 265 GLU cc_start: 0.7552 (tt0) cc_final: 0.7287 (tt0) REVERT: e 149 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.6845 (p90) REVERT: e 153 LYS cc_start: 0.8713 (ttmt) cc_final: 0.8324 (ttmt) REVERT: e 249 ARG cc_start: 0.5847 (tpt170) cc_final: 0.4440 (ttt90) REVERT: e 355 GLU cc_start: 0.7870 (pt0) cc_final: 0.7594 (pt0) REVERT: e 391 ASP cc_start: 0.8998 (OUTLIER) cc_final: 0.8600 (t0) REVERT: f 49 GLN cc_start: 0.8701 (tp40) cc_final: 0.8308 (tp40) REVERT: f 99 GLN cc_start: 0.8952 (mm-40) cc_final: 0.8501 (mp10) REVERT: f 149 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8040 (p90) REVERT: f 153 LYS cc_start: 0.8786 (ttmt) cc_final: 0.8457 (ttmt) REVERT: f 157 TYR cc_start: 0.7673 (m-80) cc_final: 0.7238 (m-80) REVERT: f 249 ARG cc_start: 0.5907 (tpt170) cc_final: 0.3750 (ttm170) REVERT: f 290 LYS cc_start: 0.8861 (mmmt) cc_final: 0.8514 (tptp) REVERT: f 391 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8601 (t70) outliers start: 194 outliers final: 122 residues processed: 784 average time/residue: 0.4777 time to fit residues: 608.7513 Evaluate side-chains 775 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 629 time to evaluate : 4.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 120 SER Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 149 PHE Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 232 ILE Chi-restraints excluded: chain U residue 245 VAL Chi-restraints excluded: chain U residue 246 THR Chi-restraints excluded: chain U residue 258 GLU Chi-restraints excluded: chain U residue 345 THR Chi-restraints excluded: chain U residue 371 PHE Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain V residue 149 PHE Chi-restraints excluded: chain V residue 241 SER Chi-restraints excluded: chain V residue 245 VAL Chi-restraints excluded: chain V residue 246 THR Chi-restraints excluded: chain V residue 258 GLU Chi-restraints excluded: chain V residue 293 LEU Chi-restraints excluded: chain V residue 371 PHE Chi-restraints excluded: chain V residue 372 ASP Chi-restraints excluded: chain V residue 391 ASP Chi-restraints excluded: chain V residue 397 THR Chi-restraints excluded: chain W residue 38 ASN Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 149 PHE Chi-restraints excluded: chain W residue 184 ASP Chi-restraints excluded: chain W residue 201 ILE Chi-restraints excluded: chain W residue 209 VAL Chi-restraints excluded: chain W residue 236 ASP Chi-restraints excluded: chain W residue 246 THR Chi-restraints excluded: chain W residue 258 GLU Chi-restraints excluded: chain W residue 267 LYS Chi-restraints excluded: chain W residue 345 THR Chi-restraints excluded: chain W residue 371 PHE Chi-restraints excluded: chain W residue 391 ASP Chi-restraints excluded: chain W residue 397 THR Chi-restraints excluded: chain X residue 38 ASN Chi-restraints excluded: chain X residue 120 SER Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain X residue 149 PHE Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 232 ILE Chi-restraints excluded: chain X residue 245 VAL Chi-restraints excluded: chain X residue 246 THR Chi-restraints excluded: chain X residue 258 GLU Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 371 PHE Chi-restraints excluded: chain Y residue 69 GLN Chi-restraints excluded: chain Y residue 149 PHE Chi-restraints excluded: chain Y residue 241 SER Chi-restraints excluded: chain Y residue 245 VAL Chi-restraints excluded: chain Y residue 246 THR Chi-restraints excluded: chain Y residue 258 GLU Chi-restraints excluded: chain Y residue 293 LEU Chi-restraints excluded: chain Y residue 371 PHE Chi-restraints excluded: chain Y residue 372 ASP Chi-restraints excluded: chain Y residue 391 ASP Chi-restraints excluded: chain Y residue 397 THR Chi-restraints excluded: chain Z residue 38 ASN Chi-restraints excluded: chain Z residue 102 GLN Chi-restraints excluded: chain Z residue 131 VAL Chi-restraints excluded: chain Z residue 149 PHE Chi-restraints excluded: chain Z residue 184 ASP Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 209 VAL Chi-restraints excluded: chain Z residue 236 ASP Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 267 LYS Chi-restraints excluded: chain Z residue 345 THR Chi-restraints excluded: chain Z residue 371 PHE Chi-restraints excluded: chain Z residue 391 ASP Chi-restraints excluded: chain Z residue 397 THR Chi-restraints excluded: chain a residue 38 ASN Chi-restraints excluded: chain a residue 120 SER Chi-restraints excluded: chain a residue 131 VAL Chi-restraints excluded: chain a residue 149 PHE Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 232 ILE Chi-restraints excluded: chain a residue 245 VAL Chi-restraints excluded: chain a residue 246 THR Chi-restraints excluded: chain a residue 258 GLU Chi-restraints excluded: chain a residue 345 THR Chi-restraints excluded: chain a residue 371 PHE Chi-restraints excluded: chain b residue 69 GLN Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 241 SER Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 246 THR Chi-restraints excluded: chain b residue 293 LEU Chi-restraints excluded: chain b residue 371 PHE Chi-restraints excluded: chain b residue 372 ASP Chi-restraints excluded: chain b residue 391 ASP Chi-restraints excluded: chain b residue 397 THR Chi-restraints excluded: chain c residue 38 ASN Chi-restraints excluded: chain c residue 102 GLN Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 149 PHE Chi-restraints excluded: chain c residue 184 ASP Chi-restraints excluded: chain c residue 201 ILE Chi-restraints excluded: chain c residue 209 VAL Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 246 THR Chi-restraints excluded: chain c residue 258 GLU Chi-restraints excluded: chain c residue 267 LYS Chi-restraints excluded: chain c residue 345 THR Chi-restraints excluded: chain c residue 371 PHE Chi-restraints excluded: chain c residue 391 ASP Chi-restraints excluded: chain c residue 397 THR Chi-restraints excluded: chain d residue 38 ASN Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain d residue 131 VAL Chi-restraints excluded: chain d residue 149 PHE Chi-restraints excluded: chain d residue 209 VAL Chi-restraints excluded: chain d residue 232 ILE Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 246 THR Chi-restraints excluded: chain d residue 258 GLU Chi-restraints excluded: chain d residue 345 THR Chi-restraints excluded: chain d residue 371 PHE Chi-restraints excluded: chain e residue 69 GLN Chi-restraints excluded: chain e residue 149 PHE Chi-restraints excluded: chain e residue 241 SER Chi-restraints excluded: chain e residue 245 VAL Chi-restraints excluded: chain e residue 246 THR Chi-restraints excluded: chain e residue 293 LEU Chi-restraints excluded: chain e residue 371 PHE Chi-restraints excluded: chain e residue 372 ASP Chi-restraints excluded: chain e residue 391 ASP Chi-restraints excluded: chain e residue 397 THR Chi-restraints excluded: chain f residue 38 ASN Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 149 PHE Chi-restraints excluded: chain f residue 184 ASP Chi-restraints excluded: chain f residue 201 ILE Chi-restraints excluded: chain f residue 209 VAL Chi-restraints excluded: chain f residue 236 ASP Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 258 GLU Chi-restraints excluded: chain f residue 267 LYS Chi-restraints excluded: chain f residue 345 THR Chi-restraints excluded: chain f residue 371 PHE Chi-restraints excluded: chain f residue 391 ASP Chi-restraints excluded: chain f residue 397 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 148 optimal weight: 4.9990 chunk 396 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 441 optimal weight: 0.9980 chunk 366 optimal weight: 0.9990 chunk 204 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 231 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 105 ASN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 105 ASN X 112 GLN ** Z 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 105 ASN ** c 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 105 ASN ** d 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN ** f 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 105 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36000 Z= 0.197 Angle : 0.608 7.097 48672 Z= 0.307 Chirality : 0.043 0.191 5268 Planarity : 0.004 0.032 6420 Dihedral : 4.933 26.631 4904 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.45 % Favored : 88.55 % Rotamer: Outliers : 4.80 % Allowed : 23.63 % Favored : 71.57 % 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: -1.25 (0.13), residues: 4524 helix: 1.03 (0.12), residues: 1968 sheet: -0.46 (0.28), residues: 480 loop : -2.93 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP V 143 HIS 0.002 0.001 HIS c 297 PHE 0.011 0.001 PHE c 30 TYR 0.009 0.001 TYR f 367 ARG 0.004 0.000 ARG U 103 *********************** REFINEMENT MACRO_CYCLE 6 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 873 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 694 time to evaluate : 3.972 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: U 99 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8444 (mp10) REVERT: U 149 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.6948 (p90) REVERT: U 208 ASP cc_start: 0.8010 (t0) cc_final: 0.7798 (m-30) REVERT: U 249 ARG cc_start: 0.5975 (tpt170) cc_final: 0.3676 (ttm170) REVERT: U 258 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: U 265 GLU cc_start: 0.7570 (tt0) cc_final: 0.7344 (tt0) REVERT: U 350 TYR cc_start: 0.9475 (m-80) cc_final: 0.8913 (m-80) REVERT: U 361 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7028 (p90) REVERT: V 149 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.6809 (p90) REVERT: V 153 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8286 (ttmt) REVERT: V 157 TYR cc_start: 0.7747 (m-80) cc_final: 0.7483 (m-80) REVERT: V 249 ARG cc_start: 0.5918 (tpt170) cc_final: 0.4088 (ttm-80) REVERT: W 37 LYS cc_start: 0.8613 (ptmt) cc_final: 0.8353 (pttt) REVERT: W 49 GLN cc_start: 0.8649 (tp40) cc_final: 0.8283 (tp40) REVERT: W 99 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8468 (mp10) REVERT: W 149 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.7907 (p90) REVERT: W 153 LYS cc_start: 0.8781 (ttmt) cc_final: 0.8505 (ttmt) REVERT: W 157 TYR cc_start: 0.7542 (m-80) cc_final: 0.7053 (m-80) REVERT: W 205 MET cc_start: 0.7493 (mtm) cc_final: 0.7217 (mtt) REVERT: W 249 ARG cc_start: 0.5791 (tpt170) cc_final: 0.3712 (ttm170) REVERT: W 290 LYS cc_start: 0.8902 (mmmt) cc_final: 0.8519 (tptp) REVERT: W 381 LYS cc_start: 0.8150 (tppt) cc_final: 0.7909 (tppt) REVERT: W 391 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8546 (t70) REVERT: X 149 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.6938 (p90) REVERT: X 205 MET cc_start: 0.7477 (mtm) cc_final: 0.7189 (mtt) REVERT: X 249 ARG cc_start: 0.5976 (tpt170) cc_final: 0.3680 (ttm170) REVERT: X 258 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: X 265 GLU cc_start: 0.7570 (tt0) cc_final: 0.7344 (tt0) REVERT: X 350 TYR cc_start: 0.9472 (m-80) cc_final: 0.8912 (m-80) REVERT: X 361 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7035 (p90) REVERT: Y 149 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.6800 (p90) REVERT: Y 153 LYS cc_start: 0.8684 (ttmt) cc_final: 0.8289 (ttmt) REVERT: Y 157 TYR cc_start: 0.7748 (m-80) cc_final: 0.7407 (m-80) REVERT: Y 249 ARG cc_start: 0.5924 (tpt170) cc_final: 0.4092 (ttm-80) REVERT: Z 37 LYS cc_start: 0.8614 (ptmt) cc_final: 0.8355 (pttt) REVERT: Z 49 GLN cc_start: 0.8645 (tp40) cc_final: 0.8278 (tp40) REVERT: Z 99 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8469 (mp10) REVERT: Z 149 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7907 (p90) REVERT: Z 153 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8507 (ttmt) REVERT: Z 157 TYR cc_start: 0.7544 (m-80) cc_final: 0.7054 (m-80) REVERT: Z 205 MET cc_start: 0.7486 (mtm) cc_final: 0.7211 (mtt) REVERT: Z 249 ARG cc_start: 0.5788 (tpt170) cc_final: 0.3713 (ttm170) REVERT: Z 290 LYS cc_start: 0.8902 (mmmt) cc_final: 0.8519 (tptp) REVERT: Z 381 LYS cc_start: 0.8146 (tppt) cc_final: 0.7906 (tppt) REVERT: Z 391 ASP cc_start: 0.8898 (OUTLIER) cc_final: 0.8551 (t70) REVERT: a 149 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.6942 (p90) REVERT: a 205 MET cc_start: 0.7472 (mtm) cc_final: 0.7186 (mtt) REVERT: a 249 ARG cc_start: 0.5972 (tpt170) cc_final: 0.3674 (ttm170) REVERT: a 258 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: a 265 GLU cc_start: 0.7568 (tt0) cc_final: 0.7347 (tt0) REVERT: a 350 TYR cc_start: 0.9472 (m-80) cc_final: 0.8912 (m-80) REVERT: a 361 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7036 (p90) REVERT: b 149 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.6805 (p90) REVERT: b 153 LYS cc_start: 0.8683 (ttmt) cc_final: 0.8286 (ttmt) REVERT: b 157 TYR cc_start: 0.7745 (m-80) cc_final: 0.7401 (m-80) REVERT: b 249 ARG cc_start: 0.5926 (tpt170) cc_final: 0.4093 (ttm-80) REVERT: c 37 LYS cc_start: 0.8614 (ptmt) cc_final: 0.8353 (pttt) REVERT: c 49 GLN cc_start: 0.8640 (tp40) cc_final: 0.8275 (tp40) REVERT: c 99 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8467 (mp10) REVERT: c 149 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7906 (p90) REVERT: c 153 LYS cc_start: 0.8782 (ttmt) cc_final: 0.8510 (ttmt) REVERT: c 157 TYR cc_start: 0.7542 (m-80) cc_final: 0.7052 (m-80) REVERT: c 205 MET cc_start: 0.8503 (mmm) cc_final: 0.8294 (mmt) REVERT: c 249 ARG cc_start: 0.5785 (tpt170) cc_final: 0.3713 (ttm170) REVERT: c 290 LYS cc_start: 0.8902 (mmmt) cc_final: 0.8521 (tptp) REVERT: c 381 LYS cc_start: 0.8147 (tppt) cc_final: 0.7908 (tppt) REVERT: c 391 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8548 (t70) REVERT: d 99 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8457 (mp10) REVERT: d 149 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.6948 (p90) REVERT: d 205 MET cc_start: 0.7470 (mtm) cc_final: 0.7183 (mtt) REVERT: d 249 ARG cc_start: 0.5966 (tpt170) cc_final: 0.3662 (ttm170) REVERT: d 258 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: d 265 GLU cc_start: 0.7572 (tt0) cc_final: 0.7348 (tt0) REVERT: d 350 TYR cc_start: 0.9475 (m-80) cc_final: 0.8916 (m-80) REVERT: d 361 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7036 (p90) REVERT: e 149 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.6802 (p90) REVERT: e 153 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8286 (ttmt) REVERT: e 157 TYR cc_start: 0.7750 (m-80) cc_final: 0.7402 (m-80) REVERT: e 249 ARG cc_start: 0.5916 (tpt170) cc_final: 0.4088 (ttm-80) REVERT: f 37 LYS cc_start: 0.8610 (ptmt) cc_final: 0.8352 (pttt) REVERT: f 49 GLN cc_start: 0.8646 (tp40) cc_final: 0.8281 (tp40) REVERT: f 99 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8467 (mp10) REVERT: f 149 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7908 (p90) REVERT: f 153 LYS cc_start: 0.8781 (ttmt) cc_final: 0.8507 (ttmt) REVERT: f 157 TYR cc_start: 0.7549 (m-80) cc_final: 0.7055 (m-80) REVERT: f 249 ARG cc_start: 0.5787 (tpt170) cc_final: 0.3709 (ttm170) REVERT: f 290 LYS cc_start: 0.8902 (mmmt) cc_final: 0.8519 (tptp) REVERT: f 361 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7815 (p90) REVERT: f 381 LYS cc_start: 0.8153 (tppt) cc_final: 0.7916 (tppt) REVERT: f 391 ASP cc_start: 0.8891 (OUTLIER) cc_final: 0.8545 (t70) outliers start: 179 outliers final: 123 residues processed: 812 average time/residue: 0.4628 time to fit residues: 608.1371 Evaluate side-chains 816 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 668 time to evaluate : 3.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 120 SER Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 149 PHE Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 245 VAL Chi-restraints excluded: chain U residue 252 ASP Chi-restraints excluded: chain U residue 258 GLU Chi-restraints excluded: chain U residue 272 ASN Chi-restraints excluded: chain U residue 345 THR Chi-restraints excluded: chain U residue 361 PHE Chi-restraints excluded: chain U residue 371 PHE Chi-restraints excluded: chain U residue 372 ASP Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain V residue 38 ASN Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain V residue 149 PHE Chi-restraints excluded: chain V residue 241 SER Chi-restraints excluded: chain V residue 245 VAL Chi-restraints excluded: chain V residue 258 GLU Chi-restraints excluded: chain V residue 371 PHE Chi-restraints excluded: chain V residue 397 THR Chi-restraints excluded: chain W residue 38 ASN Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 149 PHE Chi-restraints excluded: chain W residue 184 ASP Chi-restraints excluded: chain W residue 201 ILE Chi-restraints excluded: chain W residue 209 VAL Chi-restraints excluded: chain W residue 236 ASP Chi-restraints excluded: chain W residue 246 THR Chi-restraints excluded: chain W residue 258 GLU Chi-restraints excluded: chain W residue 267 LYS Chi-restraints excluded: chain W residue 272 ASN Chi-restraints excluded: chain W residue 345 THR Chi-restraints excluded: chain W residue 371 PHE Chi-restraints excluded: chain W residue 391 ASP Chi-restraints excluded: chain W residue 397 THR Chi-restraints excluded: chain X residue 120 SER Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain X residue 149 PHE Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 245 VAL Chi-restraints excluded: chain X residue 252 ASP Chi-restraints excluded: chain X residue 258 GLU Chi-restraints excluded: chain X residue 272 ASN Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 361 PHE Chi-restraints excluded: chain X residue 371 PHE Chi-restraints excluded: chain X residue 372 ASP Chi-restraints excluded: chain X residue 397 THR Chi-restraints excluded: chain Y residue 38 ASN Chi-restraints excluded: chain Y residue 69 GLN Chi-restraints excluded: chain Y residue 149 PHE Chi-restraints excluded: chain Y residue 241 SER Chi-restraints excluded: chain Y residue 245 VAL Chi-restraints excluded: chain Y residue 258 GLU Chi-restraints excluded: chain Y residue 371 PHE Chi-restraints excluded: chain Y residue 397 THR Chi-restraints excluded: chain Z residue 38 ASN Chi-restraints excluded: chain Z residue 102 GLN Chi-restraints excluded: chain Z residue 131 VAL Chi-restraints excluded: chain Z residue 149 PHE Chi-restraints excluded: chain Z residue 184 ASP Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 209 VAL Chi-restraints excluded: chain Z residue 236 ASP Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 267 LYS Chi-restraints excluded: chain Z residue 272 ASN Chi-restraints excluded: chain Z residue 345 THR Chi-restraints excluded: chain Z residue 371 PHE Chi-restraints excluded: chain Z residue 391 ASP Chi-restraints excluded: chain Z residue 397 THR Chi-restraints excluded: chain a residue 120 SER Chi-restraints excluded: chain a residue 131 VAL Chi-restraints excluded: chain a residue 149 PHE Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 245 VAL Chi-restraints excluded: chain a residue 252 ASP Chi-restraints excluded: chain a residue 258 GLU Chi-restraints excluded: chain a residue 272 ASN Chi-restraints excluded: chain a residue 345 THR Chi-restraints excluded: chain a residue 361 PHE Chi-restraints excluded: chain a residue 371 PHE Chi-restraints excluded: chain a residue 372 ASP Chi-restraints excluded: chain a residue 397 THR Chi-restraints excluded: chain b residue 38 ASN Chi-restraints excluded: chain b residue 69 GLN Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 241 SER Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 258 GLU Chi-restraints excluded: chain b residue 371 PHE Chi-restraints excluded: chain b residue 397 THR Chi-restraints excluded: chain c residue 38 ASN Chi-restraints excluded: chain c residue 102 GLN Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 149 PHE Chi-restraints excluded: chain c residue 184 ASP Chi-restraints excluded: chain c residue 201 ILE Chi-restraints excluded: chain c residue 209 VAL Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 246 THR Chi-restraints excluded: chain c residue 258 GLU Chi-restraints excluded: chain c residue 267 LYS Chi-restraints excluded: chain c residue 272 ASN Chi-restraints excluded: chain c residue 345 THR Chi-restraints excluded: chain c residue 371 PHE Chi-restraints excluded: chain c residue 391 ASP Chi-restraints excluded: chain c residue 397 THR Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain d residue 131 VAL Chi-restraints excluded: chain d residue 149 PHE Chi-restraints excluded: chain d residue 209 VAL Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 252 ASP Chi-restraints excluded: chain d residue 258 GLU Chi-restraints excluded: chain d residue 272 ASN Chi-restraints excluded: chain d residue 345 THR Chi-restraints excluded: chain d residue 361 PHE Chi-restraints excluded: chain d residue 371 PHE Chi-restraints excluded: chain d residue 372 ASP Chi-restraints excluded: chain d residue 397 THR Chi-restraints excluded: chain e residue 38 ASN Chi-restraints excluded: chain e residue 69 GLN Chi-restraints excluded: chain e residue 149 PHE Chi-restraints excluded: chain e residue 241 SER Chi-restraints excluded: chain e residue 245 VAL Chi-restraints excluded: chain e residue 258 GLU Chi-restraints excluded: chain e residue 371 PHE Chi-restraints excluded: chain e residue 397 THR Chi-restraints excluded: chain f residue 38 ASN Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 149 PHE Chi-restraints excluded: chain f residue 184 ASP Chi-restraints excluded: chain f residue 201 ILE Chi-restraints excluded: chain f residue 209 VAL Chi-restraints excluded: chain f residue 236 ASP Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 258 GLU Chi-restraints excluded: chain f residue 267 LYS Chi-restraints excluded: chain f residue 345 THR Chi-restraints excluded: chain f residue 361 PHE Chi-restraints excluded: chain f residue 371 PHE Chi-restraints excluded: chain f residue 391 ASP Chi-restraints excluded: chain f residue 397 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 425 optimal weight: 0.0270 chunk 49 optimal weight: 6.9990 chunk 251 optimal weight: 4.9990 chunk 322 optimal weight: 0.0050 chunk 249 optimal weight: 6.9990 chunk 371 optimal weight: 6.9990 chunk 246 optimal weight: 0.0270 chunk 439 optimal weight: 5.9990 chunk 275 optimal weight: 6.9990 chunk 267 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 overall best weight: 1.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 105 ASN ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 105 ASN ** a 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 105 ASN ** d 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36000 Z= 0.190 Angle : 0.605 7.169 48672 Z= 0.303 Chirality : 0.043 0.193 5268 Planarity : 0.004 0.073 6420 Dihedral : 4.827 26.663 4904 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 4.80 % Allowed : 24.01 % Favored : 71.20 % 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: -1.25 (0.13), residues: 4524 helix: 1.03 (0.12), residues: 1968 sheet: -0.78 (0.26), residues: 504 loop : -2.87 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP V 121 HIS 0.002 0.001 HIS W 297 PHE 0.010 0.001 PHE W 361 TYR 0.009 0.001 TYR Z 367 ARG 0.004 0.000 ARG W 50 *********************** REFINEMENT MACRO_CYCLE 7 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 875 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 696 time to evaluate : 4.118 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: U 99 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8439 (mp10) REVERT: U 149 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.6922 (p90) REVERT: U 249 ARG cc_start: 0.5879 (tpt170) cc_final: 0.3632 (ttm170) REVERT: U 265 GLU cc_start: 0.7715 (tt0) cc_final: 0.7448 (tt0) REVERT: U 361 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.6988 (p90) REVERT: V 149 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.6820 (p90) REVERT: V 157 TYR cc_start: 0.7683 (m-80) cc_final: 0.7452 (m-80) REVERT: V 249 ARG cc_start: 0.5829 (tpt170) cc_final: 0.3570 (ttm170) REVERT: V 371 PHE cc_start: 0.6103 (OUTLIER) cc_final: 0.5295 (p90) REVERT: W 37 LYS cc_start: 0.8624 (ptmt) cc_final: 0.8360 (pttt) REVERT: W 99 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8473 (mp10) REVERT: W 149 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.7981 (p90) REVERT: W 153 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8500 (ttmt) REVERT: W 205 MET cc_start: 0.7395 (mtm) cc_final: 0.7120 (mtt) REVERT: W 249 ARG cc_start: 0.5802 (tpt170) cc_final: 0.3745 (ttm170) REVERT: W 290 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8475 (tptp) REVERT: W 361 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7622 (p90) REVERT: W 391 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8558 (t70) REVERT: X 149 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.6917 (p90) REVERT: X 205 MET cc_start: 0.7423 (mtm) cc_final: 0.7127 (mtt) REVERT: X 249 ARG cc_start: 0.5880 (tpt170) cc_final: 0.3634 (ttm170) REVERT: X 265 GLU cc_start: 0.7716 (tt0) cc_final: 0.7450 (tt0) REVERT: X 361 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7040 (p90) REVERT: Y 149 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.6815 (p90) REVERT: Y 157 TYR cc_start: 0.7694 (m-80) cc_final: 0.7417 (m-80) REVERT: Y 249 ARG cc_start: 0.5834 (tpt170) cc_final: 0.3579 (ttm170) REVERT: Y 371 PHE cc_start: 0.6101 (OUTLIER) cc_final: 0.5288 (p90) REVERT: Z 37 LYS cc_start: 0.8625 (ptmt) cc_final: 0.8361 (pttt) REVERT: Z 99 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8475 (mp10) REVERT: Z 149 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.7983 (p90) REVERT: Z 153 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8502 (ttmt) REVERT: Z 205 MET cc_start: 0.7393 (mtm) cc_final: 0.7118 (mtt) REVERT: Z 249 ARG cc_start: 0.5800 (tpt170) cc_final: 0.3746 (ttm170) REVERT: Z 290 LYS cc_start: 0.8822 (mmmt) cc_final: 0.8474 (tptp) REVERT: Z 361 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7624 (p90) REVERT: Z 391 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8560 (t70) REVERT: a 149 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.6921 (p90) REVERT: a 205 MET cc_start: 0.7422 (mtm) cc_final: 0.7125 (mtt) REVERT: a 249 ARG cc_start: 0.5876 (tpt170) cc_final: 0.3628 (ttm170) REVERT: a 265 GLU cc_start: 0.7713 (tt0) cc_final: 0.7449 (tt0) REVERT: a 361 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7041 (p90) REVERT: b 149 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.6816 (p90) REVERT: b 157 TYR cc_start: 0.7691 (m-80) cc_final: 0.7417 (m-80) REVERT: b 249 ARG cc_start: 0.5837 (tpt170) cc_final: 0.3586 (ttm170) REVERT: b 371 PHE cc_start: 0.6101 (OUTLIER) cc_final: 0.5288 (p90) REVERT: c 37 LYS cc_start: 0.8619 (ptmt) cc_final: 0.8361 (pttt) REVERT: c 99 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8472 (mp10) REVERT: c 149 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.7984 (p90) REVERT: c 153 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8503 (ttmt) REVERT: c 205 MET cc_start: 0.8520 (mmm) cc_final: 0.8110 (mmp) REVERT: c 249 ARG cc_start: 0.5798 (tpt170) cc_final: 0.3748 (ttm170) REVERT: c 290 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8475 (tptp) REVERT: c 361 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7628 (p90) REVERT: c 391 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8557 (t70) REVERT: d 149 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.6922 (p90) REVERT: d 205 MET cc_start: 0.7415 (mtm) cc_final: 0.7120 (mtt) REVERT: d 249 ARG cc_start: 0.5870 (tpt170) cc_final: 0.3618 (ttm170) REVERT: d 265 GLU cc_start: 0.7715 (tt0) cc_final: 0.7451 (tt0) REVERT: d 361 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7043 (p90) REVERT: e 149 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.6815 (p90) REVERT: e 157 TYR cc_start: 0.7693 (m-80) cc_final: 0.7420 (m-80) REVERT: e 249 ARG cc_start: 0.5829 (tpt170) cc_final: 0.3573 (ttm170) REVERT: e 371 PHE cc_start: 0.6101 (OUTLIER) cc_final: 0.5290 (p90) REVERT: f 37 LYS cc_start: 0.8617 (ptmt) cc_final: 0.8360 (pttt) REVERT: f 99 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8472 (mp10) REVERT: f 149 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.7983 (p90) REVERT: f 153 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8502 (ttmt) REVERT: f 249 ARG cc_start: 0.5799 (tpt170) cc_final: 0.3743 (ttm170) REVERT: f 265 GLU cc_start: 0.7718 (tt0) cc_final: 0.7374 (tt0) REVERT: f 290 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8474 (tptp) REVERT: f 361 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7603 (p90) REVERT: f 391 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8554 (t70) outliers start: 179 outliers final: 111 residues processed: 821 average time/residue: 0.4489 time to fit residues: 600.1911 Evaluate side-chains 806 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 667 time to evaluate : 3.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 149 PHE Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 245 VAL Chi-restraints excluded: chain U residue 258 GLU Chi-restraints excluded: chain U residue 345 THR Chi-restraints excluded: chain U residue 361 PHE Chi-restraints excluded: chain U residue 371 PHE Chi-restraints excluded: chain U residue 372 ASP Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain V residue 38 ASN Chi-restraints excluded: chain V residue 149 PHE Chi-restraints excluded: chain V residue 241 SER Chi-restraints excluded: chain V residue 245 VAL Chi-restraints excluded: chain V residue 258 GLU Chi-restraints excluded: chain V residue 371 PHE Chi-restraints excluded: chain V residue 397 THR Chi-restraints excluded: chain W residue 38 ASN Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 149 PHE Chi-restraints excluded: chain W residue 184 ASP Chi-restraints excluded: chain W residue 201 ILE Chi-restraints excluded: chain W residue 209 VAL Chi-restraints excluded: chain W residue 236 ASP Chi-restraints excluded: chain W residue 246 THR Chi-restraints excluded: chain W residue 258 GLU Chi-restraints excluded: chain W residue 267 LYS Chi-restraints excluded: chain W residue 272 ASN Chi-restraints excluded: chain W residue 345 THR Chi-restraints excluded: chain W residue 361 PHE Chi-restraints excluded: chain W residue 371 PHE Chi-restraints excluded: chain W residue 391 ASP Chi-restraints excluded: chain W residue 397 THR Chi-restraints excluded: chain X residue 38 ASN Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain X residue 149 PHE Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 245 VAL Chi-restraints excluded: chain X residue 258 GLU Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 361 PHE Chi-restraints excluded: chain X residue 371 PHE Chi-restraints excluded: chain X residue 372 ASP Chi-restraints excluded: chain X residue 397 THR Chi-restraints excluded: chain Y residue 38 ASN Chi-restraints excluded: chain Y residue 149 PHE Chi-restraints excluded: chain Y residue 241 SER Chi-restraints excluded: chain Y residue 245 VAL Chi-restraints excluded: chain Y residue 258 GLU Chi-restraints excluded: chain Y residue 371 PHE Chi-restraints excluded: chain Y residue 397 THR Chi-restraints excluded: chain Z residue 38 ASN Chi-restraints excluded: chain Z residue 102 GLN Chi-restraints excluded: chain Z residue 131 VAL Chi-restraints excluded: chain Z residue 149 PHE Chi-restraints excluded: chain Z residue 184 ASP Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 209 VAL Chi-restraints excluded: chain Z residue 236 ASP Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 267 LYS Chi-restraints excluded: chain Z residue 272 ASN Chi-restraints excluded: chain Z residue 345 THR Chi-restraints excluded: chain Z residue 361 PHE Chi-restraints excluded: chain Z residue 371 PHE Chi-restraints excluded: chain Z residue 391 ASP Chi-restraints excluded: chain Z residue 397 THR Chi-restraints excluded: chain a residue 38 ASN Chi-restraints excluded: chain a residue 131 VAL Chi-restraints excluded: chain a residue 149 PHE Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 245 VAL Chi-restraints excluded: chain a residue 258 GLU Chi-restraints excluded: chain a residue 345 THR Chi-restraints excluded: chain a residue 361 PHE Chi-restraints excluded: chain a residue 371 PHE Chi-restraints excluded: chain a residue 372 ASP Chi-restraints excluded: chain a residue 397 THR Chi-restraints excluded: chain b residue 38 ASN Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 241 SER Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 258 GLU Chi-restraints excluded: chain b residue 371 PHE Chi-restraints excluded: chain b residue 397 THR Chi-restraints excluded: chain c residue 38 ASN Chi-restraints excluded: chain c residue 102 GLN Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 149 PHE Chi-restraints excluded: chain c residue 184 ASP Chi-restraints excluded: chain c residue 201 ILE Chi-restraints excluded: chain c residue 209 VAL Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 246 THR Chi-restraints excluded: chain c residue 258 GLU Chi-restraints excluded: chain c residue 267 LYS Chi-restraints excluded: chain c residue 272 ASN Chi-restraints excluded: chain c residue 345 THR Chi-restraints excluded: chain c residue 361 PHE Chi-restraints excluded: chain c residue 371 PHE Chi-restraints excluded: chain c residue 391 ASP Chi-restraints excluded: chain c residue 397 THR Chi-restraints excluded: chain d residue 38 ASN Chi-restraints excluded: chain d residue 131 VAL Chi-restraints excluded: chain d residue 149 PHE Chi-restraints excluded: chain d residue 209 VAL Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 258 GLU Chi-restraints excluded: chain d residue 345 THR Chi-restraints excluded: chain d residue 361 PHE Chi-restraints excluded: chain d residue 371 PHE Chi-restraints excluded: chain d residue 372 ASP Chi-restraints excluded: chain d residue 397 THR Chi-restraints excluded: chain e residue 38 ASN Chi-restraints excluded: chain e residue 149 PHE Chi-restraints excluded: chain e residue 241 SER Chi-restraints excluded: chain e residue 245 VAL Chi-restraints excluded: chain e residue 258 GLU Chi-restraints excluded: chain e residue 371 PHE Chi-restraints excluded: chain e residue 397 THR Chi-restraints excluded: chain f residue 38 ASN Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 149 PHE Chi-restraints excluded: chain f residue 184 ASP Chi-restraints excluded: chain f residue 201 ILE Chi-restraints excluded: chain f residue 209 VAL Chi-restraints excluded: chain f residue 236 ASP Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 258 GLU Chi-restraints excluded: chain f residue 267 LYS Chi-restraints excluded: chain f residue 345 THR Chi-restraints excluded: chain f residue 361 PHE Chi-restraints excluded: chain f residue 371 PHE Chi-restraints excluded: chain f residue 391 ASP Chi-restraints excluded: chain f residue 397 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 271 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 262 optimal weight: 7.9990 chunk 132 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 279 optimal weight: 7.9990 chunk 299 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 345 optimal weight: 8.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 112 GLN ** Z 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 112 GLN ** c 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 36000 Z= 0.421 Angle : 0.730 9.263 48672 Z= 0.368 Chirality : 0.048 0.200 5268 Planarity : 0.005 0.041 6420 Dihedral : 5.262 29.480 4904 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.96 % Favored : 88.04 % Rotamer: Outliers : 5.31 % Allowed : 24.09 % Favored : 70.61 % 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: -1.39 (0.13), residues: 4524 helix: 0.77 (0.12), residues: 1980 sheet: -0.44 (0.27), residues: 480 loop : -2.89 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP W 143 HIS 0.005 0.002 HIS e 297 PHE 0.027 0.002 PHE V 30 TYR 0.011 0.002 TYR Y 42 ARG 0.014 0.001 ARG d 103 *********************** REFINEMENT MACRO_CYCLE 8 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 848 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 650 time to evaluate : 4.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 99 GLN cc_start: 0.9037 (mm-40) cc_final: 0.8533 (mp10) REVERT: U 149 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.6988 (p90) REVERT: U 205 MET cc_start: 0.8874 (mmm) cc_final: 0.8386 (mmt) REVERT: U 249 ARG cc_start: 0.6135 (tpt170) cc_final: 0.3643 (ttm170) REVERT: U 265 GLU cc_start: 0.7792 (tt0) cc_final: 0.7486 (tt0) REVERT: U 361 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7392 (p90) REVERT: V 73 TRP cc_start: 0.8449 (OUTLIER) cc_final: 0.8165 (m-10) REVERT: V 149 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.6966 (p90) REVERT: V 249 ARG cc_start: 0.5859 (tpt170) cc_final: 0.3708 (ttm-80) REVERT: V 391 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8650 (t0) REVERT: V 403 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8495 (pp20) REVERT: W 37 LYS cc_start: 0.8631 (ptmt) cc_final: 0.8360 (pttt) REVERT: W 99 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8541 (mp10) REVERT: W 149 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8031 (p90) REVERT: W 153 LYS cc_start: 0.8845 (ttmt) cc_final: 0.8562 (ttmt) REVERT: W 205 MET cc_start: 0.7670 (mtm) cc_final: 0.7390 (mtt) REVERT: W 249 ARG cc_start: 0.5843 (tpt170) cc_final: 0.3700 (ttm170) REVERT: W 285 LYS cc_start: 0.8324 (ttpp) cc_final: 0.8037 (ttpp) REVERT: W 290 LYS cc_start: 0.8871 (mmmt) cc_final: 0.8520 (tptp) REVERT: W 360 MET cc_start: 0.9029 (ttm) cc_final: 0.8826 (ttm) REVERT: W 361 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7835 (p90) REVERT: W 391 ASP cc_start: 0.9076 (OUTLIER) cc_final: 0.8694 (t0) REVERT: X 149 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.6981 (p90) REVERT: X 205 MET cc_start: 0.7726 (mtm) cc_final: 0.7435 (mtt) REVERT: X 249 ARG cc_start: 0.6138 (tpt170) cc_final: 0.3648 (ttm170) REVERT: X 265 GLU cc_start: 0.7791 (tt0) cc_final: 0.7485 (tt0) REVERT: X 361 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7401 (p90) REVERT: Y 73 TRP cc_start: 0.8439 (OUTLIER) cc_final: 0.8158 (m-10) REVERT: Y 149 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.6950 (p90) REVERT: Y 157 TYR cc_start: 0.7853 (m-80) cc_final: 0.7615 (m-80) REVERT: Y 249 ARG cc_start: 0.5864 (tpt170) cc_final: 0.3707 (ttm-80) REVERT: Y 391 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8651 (t0) REVERT: Y 403 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8495 (pp20) REVERT: Z 37 LYS cc_start: 0.8634 (ptmt) cc_final: 0.8362 (pttt) REVERT: Z 99 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8543 (mp10) REVERT: Z 149 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8097 (p90) REVERT: Z 153 LYS cc_start: 0.8843 (ttmt) cc_final: 0.8563 (ttmt) REVERT: Z 205 MET cc_start: 0.7701 (mtm) cc_final: 0.7409 (mtt) REVERT: Z 249 ARG cc_start: 0.5853 (tpt170) cc_final: 0.3689 (ttm170) REVERT: Z 285 LYS cc_start: 0.8323 (ttpp) cc_final: 0.8039 (ttpp) REVERT: Z 290 LYS cc_start: 0.8871 (mmmt) cc_final: 0.8521 (tptp) REVERT: Z 361 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7824 (p90) REVERT: Z 391 ASP cc_start: 0.9078 (OUTLIER) cc_final: 0.8702 (t0) REVERT: a 99 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8442 (mp10) REVERT: a 149 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.6986 (p90) REVERT: a 205 MET cc_start: 0.7724 (mtm) cc_final: 0.7434 (mtt) REVERT: a 249 ARG cc_start: 0.6134 (tpt170) cc_final: 0.3640 (ttm170) REVERT: a 265 GLU cc_start: 0.7788 (tt0) cc_final: 0.7485 (tt0) REVERT: a 361 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7403 (p90) REVERT: b 73 TRP cc_start: 0.8438 (OUTLIER) cc_final: 0.8158 (m-10) REVERT: b 149 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.6953 (p90) REVERT: b 157 TYR cc_start: 0.7848 (m-80) cc_final: 0.7613 (m-80) REVERT: b 249 ARG cc_start: 0.5870 (tpt170) cc_final: 0.3716 (ttm-80) REVERT: b 391 ASP cc_start: 0.9030 (OUTLIER) cc_final: 0.8647 (t0) REVERT: b 403 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8492 (pp20) REVERT: c 37 LYS cc_start: 0.8645 (ptmt) cc_final: 0.8373 (pttt) REVERT: c 99 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8541 (mp10) REVERT: c 149 PHE cc_start: 0.8780 (OUTLIER) cc_final: 0.8095 (p90) REVERT: c 153 LYS cc_start: 0.8844 (ttmt) cc_final: 0.8566 (ttmt) REVERT: c 249 ARG cc_start: 0.5853 (tpt170) cc_final: 0.3692 (ttm170) REVERT: c 285 LYS cc_start: 0.8322 (ttpp) cc_final: 0.8037 (ttpp) REVERT: c 290 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8522 (tptp) REVERT: c 361 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7826 (p90) REVERT: c 391 ASP cc_start: 0.9075 (OUTLIER) cc_final: 0.8699 (t0) REVERT: d 149 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.6985 (p90) REVERT: d 205 MET cc_start: 0.7722 (mtm) cc_final: 0.7427 (mtt) REVERT: d 249 ARG cc_start: 0.6132 (tpt170) cc_final: 0.3631 (ttm170) REVERT: d 265 GLU cc_start: 0.7791 (tt0) cc_final: 0.7486 (tt0) REVERT: d 361 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7404 (p90) REVERT: e 73 TRP cc_start: 0.8436 (OUTLIER) cc_final: 0.8155 (m-10) REVERT: e 149 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.6952 (p90) REVERT: e 157 TYR cc_start: 0.7851 (m-80) cc_final: 0.7616 (m-80) REVERT: e 249 ARG cc_start: 0.5864 (tpt170) cc_final: 0.3712 (ttm-80) REVERT: e 391 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8650 (t0) REVERT: e 403 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8495 (pp20) REVERT: f 37 LYS cc_start: 0.8623 (ptmt) cc_final: 0.8351 (pttt) REVERT: f 99 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8541 (mp10) REVERT: f 149 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8099 (p90) REVERT: f 153 LYS cc_start: 0.8844 (ttmt) cc_final: 0.8563 (ttmt) REVERT: f 249 ARG cc_start: 0.5848 (tpt170) cc_final: 0.3685 (ttm170) REVERT: f 265 GLU cc_start: 0.7774 (tt0) cc_final: 0.7349 (tt0) REVERT: f 285 LYS cc_start: 0.8327 (ttpp) cc_final: 0.8041 (ttpp) REVERT: f 290 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8520 (tptp) REVERT: f 361 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7810 (p90) REVERT: f 391 ASP cc_start: 0.9073 (OUTLIER) cc_final: 0.8691 (t0) outliers start: 198 outliers final: 131 residues processed: 802 average time/residue: 0.4666 time to fit residues: 610.6331 Evaluate side-chains 815 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 648 time to evaluate : 4.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 49 GLN Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 149 PHE Chi-restraints excluded: chain U residue 208 ASP Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 245 VAL Chi-restraints excluded: chain U residue 246 THR Chi-restraints excluded: chain U residue 345 THR Chi-restraints excluded: chain U residue 361 PHE Chi-restraints excluded: chain U residue 371 PHE Chi-restraints excluded: chain U residue 372 ASP Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain V residue 38 ASN Chi-restraints excluded: chain V residue 73 TRP Chi-restraints excluded: chain V residue 149 PHE Chi-restraints excluded: chain V residue 241 SER Chi-restraints excluded: chain V residue 245 VAL Chi-restraints excluded: chain V residue 246 THR Chi-restraints excluded: chain V residue 258 GLU Chi-restraints excluded: chain V residue 371 PHE Chi-restraints excluded: chain V residue 391 ASP Chi-restraints excluded: chain V residue 397 THR Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 38 ASN Chi-restraints excluded: chain W residue 74 ASP Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 149 PHE Chi-restraints excluded: chain W residue 184 ASP Chi-restraints excluded: chain W residue 201 ILE Chi-restraints excluded: chain W residue 209 VAL Chi-restraints excluded: chain W residue 236 ASP Chi-restraints excluded: chain W residue 246 THR Chi-restraints excluded: chain W residue 258 GLU Chi-restraints excluded: chain W residue 267 LYS Chi-restraints excluded: chain W residue 272 ASN Chi-restraints excluded: chain W residue 345 THR Chi-restraints excluded: chain W residue 361 PHE Chi-restraints excluded: chain W residue 371 PHE Chi-restraints excluded: chain W residue 391 ASP Chi-restraints excluded: chain W residue 396 ILE Chi-restraints excluded: chain W residue 397 THR Chi-restraints excluded: chain X residue 38 ASN Chi-restraints excluded: chain X residue 49 GLN Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain X residue 149 PHE Chi-restraints excluded: chain X residue 208 ASP Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 245 VAL Chi-restraints excluded: chain X residue 246 THR Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 361 PHE Chi-restraints excluded: chain X residue 371 PHE Chi-restraints excluded: chain X residue 372 ASP Chi-restraints excluded: chain X residue 397 THR Chi-restraints excluded: chain Y residue 38 ASN Chi-restraints excluded: chain Y residue 73 TRP Chi-restraints excluded: chain Y residue 149 PHE Chi-restraints excluded: chain Y residue 241 SER Chi-restraints excluded: chain Y residue 245 VAL Chi-restraints excluded: chain Y residue 246 THR Chi-restraints excluded: chain Y residue 258 GLU Chi-restraints excluded: chain Y residue 371 PHE Chi-restraints excluded: chain Y residue 391 ASP Chi-restraints excluded: chain Y residue 397 THR Chi-restraints excluded: chain Y residue 403 GLU Chi-restraints excluded: chain Z residue 38 ASN Chi-restraints excluded: chain Z residue 74 ASP Chi-restraints excluded: chain Z residue 102 GLN Chi-restraints excluded: chain Z residue 149 PHE Chi-restraints excluded: chain Z residue 184 ASP Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 209 VAL Chi-restraints excluded: chain Z residue 236 ASP Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 267 LYS Chi-restraints excluded: chain Z residue 272 ASN Chi-restraints excluded: chain Z residue 345 THR Chi-restraints excluded: chain Z residue 361 PHE Chi-restraints excluded: chain Z residue 371 PHE Chi-restraints excluded: chain Z residue 391 ASP Chi-restraints excluded: chain Z residue 396 ILE Chi-restraints excluded: chain Z residue 397 THR Chi-restraints excluded: chain a residue 38 ASN Chi-restraints excluded: chain a residue 49 GLN Chi-restraints excluded: chain a residue 131 VAL Chi-restraints excluded: chain a residue 149 PHE Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 245 VAL Chi-restraints excluded: chain a residue 246 THR Chi-restraints excluded: chain a residue 345 THR Chi-restraints excluded: chain a residue 361 PHE Chi-restraints excluded: chain a residue 371 PHE Chi-restraints excluded: chain a residue 372 ASP Chi-restraints excluded: chain a residue 397 THR Chi-restraints excluded: chain b residue 38 ASN Chi-restraints excluded: chain b residue 73 TRP Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 241 SER Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 246 THR Chi-restraints excluded: chain b residue 258 GLU Chi-restraints excluded: chain b residue 371 PHE Chi-restraints excluded: chain b residue 391 ASP Chi-restraints excluded: chain b residue 397 THR Chi-restraints excluded: chain b residue 403 GLU Chi-restraints excluded: chain c residue 38 ASN Chi-restraints excluded: chain c residue 74 ASP Chi-restraints excluded: chain c residue 102 GLN Chi-restraints excluded: chain c residue 149 PHE Chi-restraints excluded: chain c residue 184 ASP Chi-restraints excluded: chain c residue 201 ILE Chi-restraints excluded: chain c residue 209 VAL Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 246 THR Chi-restraints excluded: chain c residue 258 GLU Chi-restraints excluded: chain c residue 267 LYS Chi-restraints excluded: chain c residue 272 ASN Chi-restraints excluded: chain c residue 345 THR Chi-restraints excluded: chain c residue 361 PHE Chi-restraints excluded: chain c residue 371 PHE Chi-restraints excluded: chain c residue 391 ASP Chi-restraints excluded: chain c residue 396 ILE Chi-restraints excluded: chain c residue 397 THR Chi-restraints excluded: chain d residue 38 ASN Chi-restraints excluded: chain d residue 49 GLN Chi-restraints excluded: chain d residue 131 VAL Chi-restraints excluded: chain d residue 149 PHE Chi-restraints excluded: chain d residue 208 ASP Chi-restraints excluded: chain d residue 209 VAL Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 246 THR Chi-restraints excluded: chain d residue 345 THR Chi-restraints excluded: chain d residue 361 PHE Chi-restraints excluded: chain d residue 371 PHE Chi-restraints excluded: chain d residue 372 ASP Chi-restraints excluded: chain d residue 397 THR Chi-restraints excluded: chain e residue 38 ASN Chi-restraints excluded: chain e residue 73 TRP Chi-restraints excluded: chain e residue 149 PHE Chi-restraints excluded: chain e residue 241 SER Chi-restraints excluded: chain e residue 245 VAL Chi-restraints excluded: chain e residue 246 THR Chi-restraints excluded: chain e residue 258 GLU Chi-restraints excluded: chain e residue 371 PHE Chi-restraints excluded: chain e residue 391 ASP Chi-restraints excluded: chain e residue 397 THR Chi-restraints excluded: chain e residue 403 GLU Chi-restraints excluded: chain f residue 38 ASN Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 149 PHE Chi-restraints excluded: chain f residue 184 ASP Chi-restraints excluded: chain f residue 201 ILE Chi-restraints excluded: chain f residue 209 VAL Chi-restraints excluded: chain f residue 236 ASP Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 258 GLU Chi-restraints excluded: chain f residue 267 LYS Chi-restraints excluded: chain f residue 345 THR Chi-restraints excluded: chain f residue 361 PHE Chi-restraints excluded: chain f residue 371 PHE Chi-restraints excluded: chain f residue 391 ASP Chi-restraints excluded: chain f residue 396 ILE Chi-restraints excluded: chain f residue 397 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 399 optimal weight: 0.0470 chunk 421 optimal weight: 4.9990 chunk 384 optimal weight: 2.9990 chunk 409 optimal weight: 0.8980 chunk 420 optimal weight: 7.9990 chunk 246 optimal weight: 0.1980 chunk 178 optimal weight: 0.9990 chunk 321 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 370 optimal weight: 0.8980 chunk 387 optimal weight: 20.0000 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 105 ASN ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 112 GLN ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 112 GLN ** a 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36000 Z= 0.170 Angle : 0.612 7.441 48672 Z= 0.307 Chirality : 0.042 0.197 5268 Planarity : 0.004 0.065 6420 Dihedral : 4.928 29.332 4904 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 4.23 % Allowed : 25.11 % Favored : 70.66 % 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: -1.21 (0.13), residues: 4524 helix: 1.03 (0.12), residues: 1980 sheet: -0.83 (0.26), residues: 504 loop : -2.79 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 121 HIS 0.000 0.000 HIS V 297 PHE 0.024 0.001 PHE Y 371 TYR 0.008 0.001 TYR e 165 ARG 0.011 0.000 ARG d 103 *********************** REFINEMENT MACRO_CYCLE 9 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 844 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 686 time to evaluate : 4.058 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: U 149 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.6934 (p90) REVERT: U 249 ARG cc_start: 0.5819 (tpt170) cc_final: 0.3590 (ttm170) REVERT: U 265 GLU cc_start: 0.7695 (tt0) cc_final: 0.7440 (tt0) REVERT: U 350 TYR cc_start: 0.9478 (m-80) cc_final: 0.8965 (m-80) REVERT: U 361 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7277 (p90) REVERT: U 403 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8404 (pp20) REVERT: V 149 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.6774 (p90) REVERT: V 157 TYR cc_start: 0.7682 (m-80) cc_final: 0.7445 (m-80) REVERT: V 249 ARG cc_start: 0.5785 (tpt170) cc_final: 0.3553 (ttm170) REVERT: V 371 PHE cc_start: 0.6566 (OUTLIER) cc_final: 0.5739 (p90) REVERT: V 403 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8503 (pp20) REVERT: W 37 LYS cc_start: 0.8605 (ptmt) cc_final: 0.8362 (pttt) REVERT: W 99 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8464 (mp10) REVERT: W 149 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7872 (p90) REVERT: W 153 LYS cc_start: 0.8777 (ttmt) cc_final: 0.8368 (ttmt) REVERT: W 205 MET cc_start: 0.7388 (mtm) cc_final: 0.7121 (mtt) REVERT: W 249 ARG cc_start: 0.5789 (tpt170) cc_final: 0.3727 (ttm170) REVERT: W 290 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8424 (tptp) REVERT: W 360 MET cc_start: 0.8947 (ttm) cc_final: 0.8735 (ttm) REVERT: W 361 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7730 (p90) REVERT: W 391 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8625 (t70) REVERT: W 403 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8508 (pp20) REVERT: X 149 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.6930 (p90) REVERT: X 205 MET cc_start: 0.7381 (mtm) cc_final: 0.7082 (mtt) REVERT: X 249 ARG cc_start: 0.5819 (tpt170) cc_final: 0.3594 (ttm170) REVERT: X 265 GLU cc_start: 0.7696 (tt0) cc_final: 0.7441 (tt0) REVERT: X 350 TYR cc_start: 0.9476 (m-80) cc_final: 0.8964 (m-80) REVERT: X 361 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7160 (p90) REVERT: X 403 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8406 (pp20) REVERT: Y 149 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.6766 (p90) REVERT: Y 157 TYR cc_start: 0.7617 (m-80) cc_final: 0.7365 (m-80) REVERT: Y 249 ARG cc_start: 0.5793 (tpt170) cc_final: 0.3563 (ttm170) REVERT: Y 371 PHE cc_start: 0.6565 (OUTLIER) cc_final: 0.5741 (p90) REVERT: Y 403 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8502 (pp20) REVERT: Z 37 LYS cc_start: 0.8607 (ptmt) cc_final: 0.8364 (pttt) REVERT: Z 99 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8465 (mp10) REVERT: Z 149 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.7861 (p90) REVERT: Z 153 LYS cc_start: 0.8776 (ttmt) cc_final: 0.8369 (ttmt) REVERT: Z 205 MET cc_start: 0.7425 (mtm) cc_final: 0.7150 (mtt) REVERT: Z 249 ARG cc_start: 0.5788 (tpt170) cc_final: 0.3726 (ttm170) REVERT: Z 290 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8422 (tptp) REVERT: Z 361 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7587 (p90) REVERT: Z 391 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8627 (t70) REVERT: Z 403 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8505 (pp20) REVERT: a 149 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.6931 (p90) REVERT: a 205 MET cc_start: 0.7382 (mtm) cc_final: 0.7079 (mtt) REVERT: a 249 ARG cc_start: 0.5814 (tpt170) cc_final: 0.3584 (ttm170) REVERT: a 265 GLU cc_start: 0.7692 (tt0) cc_final: 0.7441 (tt0) REVERT: a 350 TYR cc_start: 0.9475 (m-80) cc_final: 0.8964 (m-80) REVERT: a 361 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7157 (p90) REVERT: a 403 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8404 (pp20) REVERT: b 149 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.6769 (p90) REVERT: b 157 TYR cc_start: 0.7613 (m-80) cc_final: 0.7362 (m-80) REVERT: b 249 ARG cc_start: 0.5794 (tpt170) cc_final: 0.3569 (ttm170) REVERT: b 371 PHE cc_start: 0.6561 (OUTLIER) cc_final: 0.5739 (p90) REVERT: b 403 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8497 (pp20) REVERT: c 37 LYS cc_start: 0.8622 (ptmt) cc_final: 0.8384 (pttt) REVERT: c 99 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8463 (mp10) REVERT: c 149 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.7859 (p90) REVERT: c 153 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8372 (ttmt) REVERT: c 249 ARG cc_start: 0.5787 (tpt170) cc_final: 0.3730 (ttm170) REVERT: c 290 LYS cc_start: 0.8735 (mmmt) cc_final: 0.8428 (tptp) REVERT: c 361 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7442 (p90) REVERT: c 391 ASP cc_start: 0.8937 (OUTLIER) cc_final: 0.8625 (t70) REVERT: c 403 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8504 (pp20) REVERT: d 149 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.6920 (p90) REVERT: d 205 MET cc_start: 0.7371 (mtm) cc_final: 0.7068 (mtt) REVERT: d 249 ARG cc_start: 0.5813 (tpt170) cc_final: 0.3577 (ttm170) REVERT: d 265 GLU cc_start: 0.7692 (tt0) cc_final: 0.7439 (tt0) REVERT: d 350 TYR cc_start: 0.9477 (m-80) cc_final: 0.8966 (m-80) REVERT: d 361 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7157 (p90) REVERT: d 403 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8406 (pp20) REVERT: e 149 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.6769 (p90) REVERT: e 157 TYR cc_start: 0.7614 (m-80) cc_final: 0.7367 (m-80) REVERT: e 249 ARG cc_start: 0.5785 (tpt170) cc_final: 0.3554 (ttm170) REVERT: e 371 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.5742 (p90) REVERT: e 403 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8500 (pp20) REVERT: f 37 LYS cc_start: 0.8621 (ptmt) cc_final: 0.8381 (pttt) REVERT: f 99 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8464 (mp10) REVERT: f 149 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.7860 (p90) REVERT: f 153 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8369 (ttmt) REVERT: f 249 ARG cc_start: 0.5789 (tpt170) cc_final: 0.3724 (ttm170) REVERT: f 265 GLU cc_start: 0.7798 (tt0) cc_final: 0.7388 (tt0) REVERT: f 272 ASN cc_start: 0.8660 (p0) cc_final: 0.8363 (p0) REVERT: f 290 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8428 (tptp) REVERT: f 361 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7454 (p90) REVERT: f 391 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8621 (t70) REVERT: f 403 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8505 (pp20) outliers start: 158 outliers final: 115 residues processed: 806 average time/residue: 0.4612 time to fit residues: 604.1843 Evaluate side-chains 819 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 664 time to evaluate : 3.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 149 PHE Chi-restraints excluded: chain U residue 208 ASP Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 245 VAL Chi-restraints excluded: chain U residue 246 THR Chi-restraints excluded: chain U residue 252 ASP Chi-restraints excluded: chain U residue 345 THR Chi-restraints excluded: chain U residue 361 PHE Chi-restraints excluded: chain U residue 371 PHE Chi-restraints excluded: chain U residue 372 ASP Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 403 GLU Chi-restraints excluded: chain V residue 149 PHE Chi-restraints excluded: chain V residue 241 SER Chi-restraints excluded: chain V residue 245 VAL Chi-restraints excluded: chain V residue 246 THR Chi-restraints excluded: chain V residue 258 GLU Chi-restraints excluded: chain V residue 293 LEU Chi-restraints excluded: chain V residue 371 PHE Chi-restraints excluded: chain V residue 397 THR Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 38 ASN Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 149 PHE Chi-restraints excluded: chain W residue 201 ILE Chi-restraints excluded: chain W residue 209 VAL Chi-restraints excluded: chain W residue 236 ASP Chi-restraints excluded: chain W residue 258 GLU Chi-restraints excluded: chain W residue 267 LYS Chi-restraints excluded: chain W residue 272 ASN Chi-restraints excluded: chain W residue 345 THR Chi-restraints excluded: chain W residue 361 PHE Chi-restraints excluded: chain W residue 371 PHE Chi-restraints excluded: chain W residue 391 ASP Chi-restraints excluded: chain W residue 397 THR Chi-restraints excluded: chain W residue 403 GLU Chi-restraints excluded: chain X residue 38 ASN Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain X residue 149 PHE Chi-restraints excluded: chain X residue 208 ASP Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 245 VAL Chi-restraints excluded: chain X residue 246 THR Chi-restraints excluded: chain X residue 252 ASP Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 361 PHE Chi-restraints excluded: chain X residue 371 PHE Chi-restraints excluded: chain X residue 372 ASP Chi-restraints excluded: chain X residue 397 THR Chi-restraints excluded: chain X residue 403 GLU Chi-restraints excluded: chain Y residue 149 PHE Chi-restraints excluded: chain Y residue 241 SER Chi-restraints excluded: chain Y residue 245 VAL Chi-restraints excluded: chain Y residue 246 THR Chi-restraints excluded: chain Y residue 258 GLU Chi-restraints excluded: chain Y residue 293 LEU Chi-restraints excluded: chain Y residue 371 PHE Chi-restraints excluded: chain Y residue 397 THR Chi-restraints excluded: chain Y residue 403 GLU Chi-restraints excluded: chain Z residue 38 ASN Chi-restraints excluded: chain Z residue 102 GLN Chi-restraints excluded: chain Z residue 131 VAL Chi-restraints excluded: chain Z residue 149 PHE Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 209 VAL Chi-restraints excluded: chain Z residue 236 ASP Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 267 LYS Chi-restraints excluded: chain Z residue 272 ASN Chi-restraints excluded: chain Z residue 345 THR Chi-restraints excluded: chain Z residue 361 PHE Chi-restraints excluded: chain Z residue 371 PHE Chi-restraints excluded: chain Z residue 391 ASP Chi-restraints excluded: chain Z residue 397 THR Chi-restraints excluded: chain Z residue 403 GLU Chi-restraints excluded: chain a residue 38 ASN Chi-restraints excluded: chain a residue 131 VAL Chi-restraints excluded: chain a residue 149 PHE Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 245 VAL Chi-restraints excluded: chain a residue 246 THR Chi-restraints excluded: chain a residue 252 ASP Chi-restraints excluded: chain a residue 345 THR Chi-restraints excluded: chain a residue 361 PHE Chi-restraints excluded: chain a residue 371 PHE Chi-restraints excluded: chain a residue 372 ASP Chi-restraints excluded: chain a residue 397 THR Chi-restraints excluded: chain a residue 403 GLU Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 241 SER Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 246 THR Chi-restraints excluded: chain b residue 258 GLU Chi-restraints excluded: chain b residue 293 LEU Chi-restraints excluded: chain b residue 371 PHE Chi-restraints excluded: chain b residue 397 THR Chi-restraints excluded: chain b residue 403 GLU Chi-restraints excluded: chain c residue 38 ASN Chi-restraints excluded: chain c residue 102 GLN Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 149 PHE Chi-restraints excluded: chain c residue 201 ILE Chi-restraints excluded: chain c residue 209 VAL Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 258 GLU Chi-restraints excluded: chain c residue 267 LYS Chi-restraints excluded: chain c residue 272 ASN Chi-restraints excluded: chain c residue 345 THR Chi-restraints excluded: chain c residue 361 PHE Chi-restraints excluded: chain c residue 371 PHE Chi-restraints excluded: chain c residue 391 ASP Chi-restraints excluded: chain c residue 397 THR Chi-restraints excluded: chain c residue 403 GLU Chi-restraints excluded: chain d residue 38 ASN Chi-restraints excluded: chain d residue 131 VAL Chi-restraints excluded: chain d residue 149 PHE Chi-restraints excluded: chain d residue 208 ASP Chi-restraints excluded: chain d residue 209 VAL Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 246 THR Chi-restraints excluded: chain d residue 252 ASP Chi-restraints excluded: chain d residue 345 THR Chi-restraints excluded: chain d residue 361 PHE Chi-restraints excluded: chain d residue 371 PHE Chi-restraints excluded: chain d residue 372 ASP Chi-restraints excluded: chain d residue 397 THR Chi-restraints excluded: chain d residue 403 GLU Chi-restraints excluded: chain e residue 149 PHE Chi-restraints excluded: chain e residue 241 SER Chi-restraints excluded: chain e residue 245 VAL Chi-restraints excluded: chain e residue 246 THR Chi-restraints excluded: chain e residue 258 GLU Chi-restraints excluded: chain e residue 293 LEU Chi-restraints excluded: chain e residue 371 PHE Chi-restraints excluded: chain e residue 397 THR Chi-restraints excluded: chain e residue 403 GLU Chi-restraints excluded: chain f residue 38 ASN Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 149 PHE Chi-restraints excluded: chain f residue 201 ILE Chi-restraints excluded: chain f residue 209 VAL Chi-restraints excluded: chain f residue 236 ASP Chi-restraints excluded: chain f residue 258 GLU Chi-restraints excluded: chain f residue 267 LYS Chi-restraints excluded: chain f residue 345 THR Chi-restraints excluded: chain f residue 361 PHE Chi-restraints excluded: chain f residue 371 PHE Chi-restraints excluded: chain f residue 391 ASP Chi-restraints excluded: chain f residue 397 THR Chi-restraints excluded: chain f residue 403 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 408 optimal weight: 5.9990 chunk 268 optimal weight: 7.9990 chunk 433 optimal weight: 10.0000 chunk 264 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 chunk 301 optimal weight: 1.9990 chunk 454 optimal weight: 9.9990 chunk 418 optimal weight: 30.0000 chunk 361 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 279 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 36000 Z= 0.273 Angle : 0.655 8.149 48672 Z= 0.325 Chirality : 0.044 0.191 5268 Planarity : 0.005 0.083 6420 Dihedral : 4.966 28.815 4904 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 4.29 % Allowed : 24.95 % Favored : 70.77 % 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: -1.14 (0.13), residues: 4524 helix: 1.00 (0.12), residues: 1980 sheet: -0.46 (0.26), residues: 480 loop : -2.74 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 143 HIS 0.003 0.001 HIS W 297 PHE 0.019 0.001 PHE Y 371 TYR 0.016 0.001 TYR Y 350 ARG 0.012 0.000 ARG d 103 ********************** REFINEMENT MACRO_CYCLE 10 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 813 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 653 time to evaluate : 4.335 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: U 99 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8494 (mp10) REVERT: U 149 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.6926 (p90) REVERT: U 249 ARG cc_start: 0.5921 (tpt170) cc_final: 0.3650 (ttm170) REVERT: U 265 GLU cc_start: 0.7774 (tt0) cc_final: 0.7493 (tt0) REVERT: U 350 TYR cc_start: 0.9523 (m-80) cc_final: 0.8987 (m-80) REVERT: U 361 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7392 (p90) REVERT: U 403 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8411 (pp20) REVERT: V 149 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.6809 (p90) REVERT: V 157 TYR cc_start: 0.7728 (m-80) cc_final: 0.7527 (m-80) REVERT: V 195 MET cc_start: 0.9090 (tpt) cc_final: 0.8771 (tpt) REVERT: V 249 ARG cc_start: 0.5801 (tpt170) cc_final: 0.3525 (ttm170) REVERT: V 403 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8513 (pp20) REVERT: W 37 LYS cc_start: 0.8633 (ptmt) cc_final: 0.8380 (pttt) REVERT: W 99 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8496 (mp10) REVERT: W 149 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.7939 (p90) REVERT: W 153 LYS cc_start: 0.8800 (ttmt) cc_final: 0.8388 (ttmt) REVERT: W 249 ARG cc_start: 0.5770 (tpt170) cc_final: 0.3692 (ttm170) REVERT: W 290 LYS cc_start: 0.8684 (mmmt) cc_final: 0.8429 (tptp) REVERT: W 361 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7852 (p90) REVERT: W 391 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8529 (t70) REVERT: W 403 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8529 (pp20) REVERT: X 149 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.6928 (p90) REVERT: X 205 MET cc_start: 0.7523 (mtm) cc_final: 0.7212 (mtt) REVERT: X 249 ARG cc_start: 0.5923 (tpt170) cc_final: 0.3655 (ttm170) REVERT: X 265 GLU cc_start: 0.7774 (tt0) cc_final: 0.7493 (tt0) REVERT: X 350 TYR cc_start: 0.9522 (m-80) cc_final: 0.8988 (m-80) REVERT: X 361 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7323 (p90) REVERT: X 403 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8415 (pp20) REVERT: Y 149 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.6801 (p90) REVERT: Y 157 TYR cc_start: 0.7684 (m-80) cc_final: 0.7456 (m-80) REVERT: Y 195 MET cc_start: 0.9084 (tpt) cc_final: 0.8766 (tpt) REVERT: Y 249 ARG cc_start: 0.5807 (tpt170) cc_final: 0.3535 (ttm170) REVERT: Y 403 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8511 (pp20) REVERT: Z 37 LYS cc_start: 0.8634 (ptmt) cc_final: 0.8381 (pttt) REVERT: Z 99 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8484 (mp10) REVERT: Z 149 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.7973 (p90) REVERT: Z 153 LYS cc_start: 0.8798 (ttmt) cc_final: 0.8391 (ttmt) REVERT: Z 249 ARG cc_start: 0.5771 (tpt170) cc_final: 0.3692 (ttm170) REVERT: Z 290 LYS cc_start: 0.8684 (mmmt) cc_final: 0.8426 (tptp) REVERT: Z 361 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7668 (p90) REVERT: Z 391 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8535 (t70) REVERT: Z 403 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8526 (pp20) REVERT: a 149 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.6931 (p90) REVERT: a 205 MET cc_start: 0.7521 (mtm) cc_final: 0.7211 (mtt) REVERT: a 249 ARG cc_start: 0.5920 (tpt170) cc_final: 0.3646 (ttm170) REVERT: a 265 GLU cc_start: 0.7773 (tt0) cc_final: 0.7493 (tt0) REVERT: a 350 TYR cc_start: 0.9521 (m-80) cc_final: 0.8986 (m-80) REVERT: a 361 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7305 (p90) REVERT: a 403 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8411 (pp20) REVERT: b 149 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.6805 (p90) REVERT: b 157 TYR cc_start: 0.7680 (m-80) cc_final: 0.7454 (m-80) REVERT: b 195 MET cc_start: 0.9081 (tpt) cc_final: 0.8760 (tpt) REVERT: b 249 ARG cc_start: 0.5810 (tpt170) cc_final: 0.3543 (ttm170) REVERT: b 403 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8507 (pp20) REVERT: c 37 LYS cc_start: 0.8624 (ptmt) cc_final: 0.8374 (pttt) REVERT: c 74 ASP cc_start: 0.7093 (p0) cc_final: 0.6803 (p0) REVERT: c 99 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8497 (mp10) REVERT: c 149 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.7974 (p90) REVERT: c 153 LYS cc_start: 0.8791 (ttmt) cc_final: 0.8380 (ttmt) REVERT: c 205 MET cc_start: 0.8448 (mmp) cc_final: 0.8230 (mmp) REVERT: c 249 ARG cc_start: 0.5770 (tpt170) cc_final: 0.3694 (ttm170) REVERT: c 290 LYS cc_start: 0.8684 (mmmt) cc_final: 0.8431 (tptp) REVERT: c 361 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7739 (p90) REVERT: c 391 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8531 (t70) REVERT: c 403 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8526 (pp20) REVERT: d 99 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8494 (mp10) REVERT: d 108 MET cc_start: 0.8513 (ttp) cc_final: 0.8296 (mtp) REVERT: d 149 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.6930 (p90) REVERT: d 205 MET cc_start: 0.7494 (mtm) cc_final: 0.7197 (mtt) REVERT: d 249 ARG cc_start: 0.5914 (tpt170) cc_final: 0.3637 (ttm170) REVERT: d 265 GLU cc_start: 0.7775 (tt0) cc_final: 0.7494 (tt0) REVERT: d 350 TYR cc_start: 0.9524 (m-80) cc_final: 0.8990 (m-80) REVERT: d 361 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7306 (p90) REVERT: d 403 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8414 (pp20) REVERT: e 149 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.6803 (p90) REVERT: e 157 TYR cc_start: 0.7684 (m-80) cc_final: 0.7457 (m-80) REVERT: e 195 MET cc_start: 0.9084 (tpt) cc_final: 0.8767 (tpt) REVERT: e 249 ARG cc_start: 0.5802 (tpt170) cc_final: 0.3530 (ttm170) REVERT: e 403 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8510 (pp20) REVERT: f 37 LYS cc_start: 0.8620 (ptmt) cc_final: 0.8372 (pttt) REVERT: f 99 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8497 (mp10) REVERT: f 149 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.7975 (p90) REVERT: f 153 LYS cc_start: 0.8793 (ttmt) cc_final: 0.8379 (ttmt) REVERT: f 249 ARG cc_start: 0.5768 (tpt170) cc_final: 0.3688 (ttm170) REVERT: f 265 GLU cc_start: 0.7779 (tt0) cc_final: 0.7394 (tt0) REVERT: f 290 LYS cc_start: 0.8685 (mmmt) cc_final: 0.8428 (tptp) REVERT: f 361 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7745 (p90) REVERT: f 391 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8528 (t70) REVERT: f 403 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8526 (pp20) outliers start: 160 outliers final: 109 residues processed: 784 average time/residue: 0.4567 time to fit residues: 582.2463 Evaluate side-chains 793 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 648 time to evaluate : 3.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 149 PHE Chi-restraints excluded: chain U residue 208 ASP Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 245 VAL Chi-restraints excluded: chain U residue 246 THR Chi-restraints excluded: chain U residue 345 THR Chi-restraints excluded: chain U residue 361 PHE Chi-restraints excluded: chain U residue 371 PHE Chi-restraints excluded: chain U residue 372 ASP Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 403 GLU Chi-restraints excluded: chain V residue 149 PHE Chi-restraints excluded: chain V residue 241 SER Chi-restraints excluded: chain V residue 245 VAL Chi-restraints excluded: chain V residue 246 THR Chi-restraints excluded: chain V residue 397 THR Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 38 ASN Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 149 PHE Chi-restraints excluded: chain W residue 201 ILE Chi-restraints excluded: chain W residue 209 VAL Chi-restraints excluded: chain W residue 236 ASP Chi-restraints excluded: chain W residue 246 THR Chi-restraints excluded: chain W residue 258 GLU Chi-restraints excluded: chain W residue 267 LYS Chi-restraints excluded: chain W residue 272 ASN Chi-restraints excluded: chain W residue 345 THR Chi-restraints excluded: chain W residue 361 PHE Chi-restraints excluded: chain W residue 371 PHE Chi-restraints excluded: chain W residue 391 ASP Chi-restraints excluded: chain W residue 397 THR Chi-restraints excluded: chain W residue 403 GLU Chi-restraints excluded: chain X residue 38 ASN Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain X residue 149 PHE Chi-restraints excluded: chain X residue 208 ASP Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 245 VAL Chi-restraints excluded: chain X residue 246 THR Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 361 PHE Chi-restraints excluded: chain X residue 371 PHE Chi-restraints excluded: chain X residue 372 ASP Chi-restraints excluded: chain X residue 397 THR Chi-restraints excluded: chain X residue 403 GLU Chi-restraints excluded: chain Y residue 149 PHE Chi-restraints excluded: chain Y residue 241 SER Chi-restraints excluded: chain Y residue 245 VAL Chi-restraints excluded: chain Y residue 246 THR Chi-restraints excluded: chain Y residue 397 THR Chi-restraints excluded: chain Y residue 403 GLU Chi-restraints excluded: chain Z residue 38 ASN Chi-restraints excluded: chain Z residue 102 GLN Chi-restraints excluded: chain Z residue 131 VAL Chi-restraints excluded: chain Z residue 149 PHE Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 209 VAL Chi-restraints excluded: chain Z residue 236 ASP Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 267 LYS Chi-restraints excluded: chain Z residue 272 ASN Chi-restraints excluded: chain Z residue 345 THR Chi-restraints excluded: chain Z residue 361 PHE Chi-restraints excluded: chain Z residue 371 PHE Chi-restraints excluded: chain Z residue 391 ASP Chi-restraints excluded: chain Z residue 397 THR Chi-restraints excluded: chain Z residue 403 GLU Chi-restraints excluded: chain a residue 38 ASN Chi-restraints excluded: chain a residue 131 VAL Chi-restraints excluded: chain a residue 149 PHE Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 245 VAL Chi-restraints excluded: chain a residue 246 THR Chi-restraints excluded: chain a residue 345 THR Chi-restraints excluded: chain a residue 361 PHE Chi-restraints excluded: chain a residue 371 PHE Chi-restraints excluded: chain a residue 372 ASP Chi-restraints excluded: chain a residue 397 THR Chi-restraints excluded: chain a residue 403 GLU Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 241 SER Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 246 THR Chi-restraints excluded: chain b residue 258 GLU Chi-restraints excluded: chain b residue 397 THR Chi-restraints excluded: chain b residue 403 GLU Chi-restraints excluded: chain c residue 38 ASN Chi-restraints excluded: chain c residue 102 GLN Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 149 PHE Chi-restraints excluded: chain c residue 201 ILE Chi-restraints excluded: chain c residue 209 VAL Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 246 THR Chi-restraints excluded: chain c residue 258 GLU Chi-restraints excluded: chain c residue 267 LYS Chi-restraints excluded: chain c residue 272 ASN Chi-restraints excluded: chain c residue 345 THR Chi-restraints excluded: chain c residue 361 PHE Chi-restraints excluded: chain c residue 371 PHE Chi-restraints excluded: chain c residue 391 ASP Chi-restraints excluded: chain c residue 397 THR Chi-restraints excluded: chain c residue 403 GLU Chi-restraints excluded: chain d residue 38 ASN Chi-restraints excluded: chain d residue 131 VAL Chi-restraints excluded: chain d residue 149 PHE Chi-restraints excluded: chain d residue 208 ASP Chi-restraints excluded: chain d residue 209 VAL Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 246 THR Chi-restraints excluded: chain d residue 345 THR Chi-restraints excluded: chain d residue 361 PHE Chi-restraints excluded: chain d residue 371 PHE Chi-restraints excluded: chain d residue 372 ASP Chi-restraints excluded: chain d residue 397 THR Chi-restraints excluded: chain d residue 403 GLU Chi-restraints excluded: chain e residue 149 PHE Chi-restraints excluded: chain e residue 241 SER Chi-restraints excluded: chain e residue 245 VAL Chi-restraints excluded: chain e residue 246 THR Chi-restraints excluded: chain e residue 258 GLU Chi-restraints excluded: chain e residue 397 THR Chi-restraints excluded: chain e residue 403 GLU Chi-restraints excluded: chain f residue 38 ASN Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 149 PHE Chi-restraints excluded: chain f residue 201 ILE Chi-restraints excluded: chain f residue 209 VAL Chi-restraints excluded: chain f residue 236 ASP Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 258 GLU Chi-restraints excluded: chain f residue 267 LYS Chi-restraints excluded: chain f residue 345 THR Chi-restraints excluded: chain f residue 361 PHE Chi-restraints excluded: chain f residue 371 PHE Chi-restraints excluded: chain f residue 391 ASP Chi-restraints excluded: chain f residue 397 THR Chi-restraints excluded: chain f residue 403 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 221 optimal weight: 4.9990 chunk 287 optimal weight: 1.9990 chunk 385 optimal weight: 0.4980 chunk 110 optimal weight: 6.9990 chunk 333 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 362 optimal weight: 0.0970 chunk 151 optimal weight: 0.1980 chunk 372 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.141656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102639 restraints weight = 54248.795| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.94 r_work: 0.3086 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36000 Z= 0.165 Angle : 0.602 7.660 48672 Z= 0.302 Chirality : 0.042 0.175 5268 Planarity : 0.004 0.049 6420 Dihedral : 4.786 28.328 4904 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 3.78 % Allowed : 25.62 % Favored : 70.61 % 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: -1.10 (0.13), residues: 4524 helix: 1.14 (0.13), residues: 1968 sheet: -0.82 (0.26), residues: 504 loop : -2.71 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 143 HIS 0.001 0.000 HIS e 297 PHE 0.016 0.001 PHE W 361 TYR 0.015 0.001 TYR Y 350 ARG 0.010 0.000 ARG X 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10488.88 seconds wall clock time: 189 minutes 34.94 seconds (11374.94 seconds total)