Starting phenix.real_space_refine on Tue Feb 13 16:04:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knq_22954/02_2024/7knq_22954.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knq_22954/02_2024/7knq_22954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knq_22954/02_2024/7knq_22954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knq_22954/02_2024/7knq_22954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knq_22954/02_2024/7knq_22954.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knq_22954/02_2024/7knq_22954.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 18170 atoms to isotropic. 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 176 5.16 5 C 23450 2.51 5 N 6615 2.21 5 O 6825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A ARG 162": "NH1" <-> "NH2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 224": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A ARG 267": "NH1" <-> "NH2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ASP 304": "OD1" <-> "OD2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 367": "OD1" <-> "OD2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A ARG 434": "NH1" <-> "NH2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 468": "NH1" <-> "NH2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "A ASP 489": "OD1" <-> "OD2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 637": "OD1" <-> "OD2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 664": "OE1" <-> "OE2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B ARG 159": "NH1" <-> "NH2" Residue "B ARG 162": "NH1" <-> "NH2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B ARG 217": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B ARG 267": "NH1" <-> "NH2" Residue "B ARG 285": "NH1" <-> "NH2" Residue "B GLU 286": "OE1" <-> "OE2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 395": "NH1" <-> "NH2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B GLU 448": "OE1" <-> "OE2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 468": "NH1" <-> "NH2" Residue "B GLU 469": "OE1" <-> "OE2" Residue "B ASP 489": "OD1" <-> "OD2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "B GLU 520": "OE1" <-> "OE2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "B PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 604": "OE1" <-> "OE2" Residue "B PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 637": "OD1" <-> "OD2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 664": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C ARG 157": "NH1" <-> "NH2" Residue "C ARG 159": "NH1" <-> "NH2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C ARG 224": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C GLU 247": "OE1" <-> "OE2" Residue "C ARG 249": "NH1" <-> "NH2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C ARG 267": "NH1" <-> "NH2" Residue "C ARG 285": "NH1" <-> "NH2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C ASP 304": "OD1" <-> "OD2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 329": "NH1" <-> "NH2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 367": "OD1" <-> "OD2" Residue "C ARG 376": "NH1" <-> "NH2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C ARG 395": "NH1" <-> "NH2" Residue "C ARG 434": "NH1" <-> "NH2" Residue "C ASP 439": "OD1" <-> "OD2" Residue "C GLU 448": "OE1" <-> "OE2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 468": "NH1" <-> "NH2" Residue "C GLU 469": "OE1" <-> "OE2" Residue "C ASP 489": "OD1" <-> "OD2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "C ARG 543": "NH1" <-> "NH2" Residue "C PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 604": "OE1" <-> "OE2" Residue "C PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 637": "OD1" <-> "OD2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 664": "OE1" <-> "OE2" Residue "C GLU 686": "OE1" <-> "OE2" Residue "C GLU 689": "OE1" <-> "OE2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D GLU 137": "OE1" <-> "OE2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D ARG 201": "NH1" <-> "NH2" Residue "D TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D ARG 217": "NH1" <-> "NH2" Residue "D ARG 224": "NH1" <-> "NH2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D GLU 247": "OE1" <-> "OE2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "D ARG 267": "NH1" <-> "NH2" Residue "D ARG 285": "NH1" <-> "NH2" Residue "D GLU 286": "OE1" <-> "OE2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D ARG 307": "NH1" <-> "NH2" Residue "D ARG 329": "NH1" <-> "NH2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D GLU 340": "OE1" <-> "OE2" Residue "D PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 367": "OD1" <-> "OD2" Residue "D ARG 376": "NH1" <-> "NH2" Residue "D ARG 392": "NH1" <-> "NH2" Residue "D ARG 395": "NH1" <-> "NH2" Residue "D ARG 434": "NH1" <-> "NH2" Residue "D ASP 441": "OD1" <-> "OD2" Residue "D GLU 448": "OE1" <-> "OE2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 468": "NH1" <-> "NH2" Residue "D GLU 469": "OE1" <-> "OE2" Residue "D GLU 472": "OE1" <-> "OE2" Residue "D ASP 489": "OD1" <-> "OD2" Residue "D ARG 517": "NH1" <-> "NH2" Residue "D GLU 520": "OE1" <-> "OE2" Residue "D ARG 543": "NH1" <-> "NH2" Residue "D PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 604": "OE1" <-> "OE2" Residue "D PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 637": "OD1" <-> "OD2" Residue "D GLU 661": "OE1" <-> "OE2" Residue "D GLU 664": "OE1" <-> "OE2" Residue "D GLU 686": "OE1" <-> "OE2" Residue "D GLU 689": "OE1" <-> "OE2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "E ARG 141": "NH1" <-> "NH2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E ARG 159": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E GLU 174": "OE1" <-> "OE2" Residue "E ARG 182": "NH1" <-> "NH2" Residue "E ARG 201": "NH1" <-> "NH2" Residue "E ARG 216": "NH1" <-> "NH2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E ARG 224": "NH1" <-> "NH2" Residue "E ARG 243": "NH1" <-> "NH2" Residue "E ARG 244": "NH1" <-> "NH2" Residue "E GLU 247": "OE1" <-> "OE2" Residue "E ARG 249": "NH1" <-> "NH2" Residue "E PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 262": "OE1" <-> "OE2" Residue "E ARG 267": "NH1" <-> "NH2" Residue "E ARG 285": "NH1" <-> "NH2" Residue "E GLU 286": "OE1" <-> "OE2" Residue "E ARG 289": "NH1" <-> "NH2" Residue "E GLU 297": "OE1" <-> "OE2" Residue "E ASP 304": "OD1" <-> "OD2" Residue "E ARG 307": "NH1" <-> "NH2" Residue "E ARG 329": "NH1" <-> "NH2" Residue "E ARG 338": "NH1" <-> "NH2" Residue "E GLU 340": "OE1" <-> "OE2" Residue "E PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 376": "NH1" <-> "NH2" Residue "E ARG 392": "NH1" <-> "NH2" Residue "E ARG 395": "NH1" <-> "NH2" Residue "E ARG 434": "NH1" <-> "NH2" Residue "E GLU 448": "OE1" <-> "OE2" Residue "E ARG 465": "NH1" <-> "NH2" Residue "E PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 468": "NH1" <-> "NH2" Residue "E GLU 469": "OE1" <-> "OE2" Residue "E ASP 489": "OD1" <-> "OD2" Residue "E ARG 517": "NH1" <-> "NH2" Residue "E GLU 520": "OE1" <-> "OE2" Residue "E ARG 543": "NH1" <-> "NH2" Residue "E PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 604": "OE1" <-> "OE2" Residue "E PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 637": "OD1" <-> "OD2" Residue "E GLU 661": "OE1" <-> "OE2" Residue "E GLU 664": "OE1" <-> "OE2" Residue "E GLU 686": "OE1" <-> "OE2" Residue "E GLU 689": "OE1" <-> "OE2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F GLU 137": "OE1" <-> "OE2" Residue "F ARG 141": "NH1" <-> "NH2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F ARG 162": "NH1" <-> "NH2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F ARG 201": "NH1" <-> "NH2" Residue "F TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 216": "NH1" <-> "NH2" Residue "F ARG 217": "NH1" <-> "NH2" Residue "F ARG 224": "NH1" <-> "NH2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "F GLU 247": "OE1" <-> "OE2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "F PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 262": "OE1" <-> "OE2" Residue "F ARG 267": "NH1" <-> "NH2" Residue "F ARG 285": "NH1" <-> "NH2" Residue "F GLU 286": "OE1" <-> "OE2" Residue "F ARG 289": "NH1" <-> "NH2" Residue "F ASP 304": "OD1" <-> "OD2" Residue "F ARG 307": "NH1" <-> "NH2" Residue "F ARG 329": "NH1" <-> "NH2" Residue "F ARG 338": "NH1" <-> "NH2" Residue "F GLU 340": "OE1" <-> "OE2" Residue "F PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 376": "NH1" <-> "NH2" Residue "F ARG 392": "NH1" <-> "NH2" Residue "F ARG 395": "NH1" <-> "NH2" Residue "F ARG 434": "NH1" <-> "NH2" Residue "F ASP 441": "OD1" <-> "OD2" Residue "F GLU 448": "OE1" <-> "OE2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 468": "NH1" <-> "NH2" Residue "F GLU 469": "OE1" <-> "OE2" Residue "F ASP 489": "OD1" <-> "OD2" Residue "F ARG 517": "NH1" <-> "NH2" Residue "F GLU 520": "OE1" <-> "OE2" Residue "F ARG 543": "NH1" <-> "NH2" Residue "F PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 604": "OE1" <-> "OE2" Residue "F PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 637": "OD1" <-> "OD2" Residue "F GLU 661": "OE1" <-> "OE2" Residue "F GLU 664": "OE1" <-> "OE2" Residue "F GLU 686": "OE1" <-> "OE2" Residue "F GLU 689": "OE1" <-> "OE2" Residue "G ARG 86": "NH1" <-> "NH2" Residue "G ARG 121": "NH1" <-> "NH2" Residue "G GLU 137": "OE1" <-> "OE2" Residue "G ARG 141": "NH1" <-> "NH2" Residue "G ARG 157": "NH1" <-> "NH2" Residue "G ARG 159": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "G ARG 182": "NH1" <-> "NH2" Residue "G ARG 201": "NH1" <-> "NH2" Residue "G ARG 216": "NH1" <-> "NH2" Residue "G ARG 217": "NH1" <-> "NH2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ARG 244": "NH1" <-> "NH2" Residue "G GLU 247": "OE1" <-> "OE2" Residue "G ARG 249": "NH1" <-> "NH2" Residue "G GLU 262": "OE1" <-> "OE2" Residue "G ARG 267": "NH1" <-> "NH2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G GLU 286": "OE1" <-> "OE2" Residue "G ARG 289": "NH1" <-> "NH2" Residue "G GLU 297": "OE1" <-> "OE2" Residue "G ASP 304": "OD1" <-> "OD2" Residue "G ARG 307": "NH1" <-> "NH2" Residue "G ARG 329": "NH1" <-> "NH2" Residue "G ARG 338": "NH1" <-> "NH2" Residue "G GLU 340": "OE1" <-> "OE2" Residue "G PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 367": "OD1" <-> "OD2" Residue "G ARG 376": "NH1" <-> "NH2" Residue "G ARG 392": "NH1" <-> "NH2" Residue "G ARG 395": "NH1" <-> "NH2" Residue "G ARG 434": "NH1" <-> "NH2" Residue "G GLU 448": "OE1" <-> "OE2" Residue "G ARG 465": "NH1" <-> "NH2" Residue "G PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 468": "NH1" <-> "NH2" Residue "G GLU 469": "OE1" <-> "OE2" Residue "G ASP 489": "OD1" <-> "OD2" Residue "G ARG 517": "NH1" <-> "NH2" Residue "G GLU 520": "OE1" <-> "OE2" Residue "G ARG 543": "NH1" <-> "NH2" Residue "G PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 604": "OE1" <-> "OE2" Residue "G PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 637": "OD1" <-> "OD2" Residue "G GLU 661": "OE1" <-> "OE2" Residue "G GLU 664": "OE1" <-> "OE2" Residue "G GLU 686": "OE1" <-> "OE2" Residue "G GLU 689": "OE1" <-> "OE2" Residue "H ARG 86": "NH1" <-> "NH2" Residue "H ARG 121": "NH1" <-> "NH2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "H ARG 141": "NH1" <-> "NH2" Residue "H ARG 157": "NH1" <-> "NH2" Residue "H ARG 159": "NH1" <-> "NH2" Residue "H ARG 162": "NH1" <-> "NH2" Residue "H ARG 182": "NH1" <-> "NH2" Residue "H ARG 201": "NH1" <-> "NH2" Residue "H TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 216": "NH1" <-> "NH2" Residue "H ARG 217": "NH1" <-> "NH2" Residue "H ARG 224": "NH1" <-> "NH2" Residue "H ARG 243": "NH1" <-> "NH2" Residue "H ARG 244": "NH1" <-> "NH2" Residue "H GLU 247": "OE1" <-> "OE2" Residue "H ARG 249": "NH1" <-> "NH2" Residue "H PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 262": "OE1" <-> "OE2" Residue "H ARG 267": "NH1" <-> "NH2" Residue "H ARG 285": "NH1" <-> "NH2" Residue "H GLU 286": "OE1" <-> "OE2" Residue "H ARG 289": "NH1" <-> "NH2" Residue "H ARG 307": "NH1" <-> "NH2" Residue "H ARG 329": "NH1" <-> "NH2" Residue "H ARG 338": "NH1" <-> "NH2" Residue "H GLU 340": "OE1" <-> "OE2" Residue "H PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 352": "OE1" <-> "OE2" Residue "H ASP 367": "OD1" <-> "OD2" Residue "H ARG 376": "NH1" <-> "NH2" Residue "H ARG 392": "NH1" <-> "NH2" Residue "H ARG 395": "NH1" <-> "NH2" Residue "H ARG 434": "NH1" <-> "NH2" Residue "H ASP 441": "OD1" <-> "OD2" Residue "H GLU 448": "OE1" <-> "OE2" Residue "H ARG 465": "NH1" <-> "NH2" Residue "H PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 468": "NH1" <-> "NH2" Residue "H GLU 469": "OE1" <-> "OE2" Residue "H ASP 489": "OD1" <-> "OD2" Residue "H ARG 517": "NH1" <-> "NH2" Residue "H GLU 520": "OE1" <-> "OE2" Residue "H ARG 543": "NH1" <-> "NH2" Residue "H PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 604": "OE1" <-> "OE2" Residue "H PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 637": "OD1" <-> "OD2" Residue "H GLU 661": "OE1" <-> "OE2" Residue "H GLU 664": "OE1" <-> "OE2" Residue "H GLU 686": "OE1" <-> "OE2" Residue "H GLU 689": "OE1" <-> "OE2" 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: 37066 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 588, 4611 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 588, 4611 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4665 Chain: "B" Number of atoms: 4633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 588, 4611 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 588, 4611 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4665 Chain: "C" Number of atoms: 4635 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 588, 4611 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 588, 4611 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4663 Chain: "D" Number of atoms: 4632 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 588, 4611 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 588, 4611 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4666 Chain: "E" Number of atoms: 4633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 588, 4611 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 588, 4611 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4665 Chain: "F" Number of atoms: 4633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 588, 4611 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 588, 4611 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4665 Chain: "G" Number of atoms: 4634 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 588, 4611 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 588, 4611 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4664 Chain: "H" Number of atoms: 4633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 588, 4611 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 588, 4611 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4665 Residues with excluded nonbonded symmetry interactions: 23 residue: pdb=" N ASER A 574 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 574 " occ=0.50 residue: pdb=" N AGLN A 575 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 575 " occ=0.50 residue: pdb=" N ASER A 590 " occ=0.58 ... (10 atoms not shown) pdb=" OG BSER A 590 " occ=0.42 residue: pdb=" N ASER B 574 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 574 " occ=0.50 residue: pdb=" N AGLN B 575 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 575 " occ=0.50 residue: pdb=" N ASER B 590 " occ=0.58 ... (10 atoms not shown) pdb=" OG BSER B 590 " occ=0.42 residue: pdb=" N ASER C 574 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 574 " occ=0.50 residue: pdb=" N AGLN C 575 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C 575 " occ=0.50 residue: pdb=" N ASER C 590 " occ=0.58 ... (10 atoms not shown) pdb=" OG BSER C 590 " occ=0.42 residue: pdb=" N ASER D 574 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 574 " occ=0.50 residue: pdb=" N AGLN D 575 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN D 575 " occ=0.50 residue: pdb=" N ASER E 574 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER E 574 " occ=0.50 ... (remaining 11 not shown) Time building chain proxies: 26.54, per 1000 atoms: 0.72 Number of scatterers: 37066 At special positions: 0 Unit cell: (201.3, 201.3, 78.375, 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 176 16.00 O 6825 8.00 N 6615 7.00 C 23450 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: 10.87 Conformation dependent library (CDL) restraints added in 10.0 seconds 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8820 Finding SS restraints... Secondary structure from input PDB file: 318 helices and 8 sheets defined 63.2% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.40 Creating SS restraints... Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.676A pdb=" N GLU A 100 " --> pdb=" O GLN A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 135 Processing helix chain 'A' and resid 137 through 149 removed outlier: 3.522A pdb=" N ARG A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 164 removed outlier: 3.620A pdb=" N ARG A 157 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 180 through 193 removed outlier: 3.873A pdb=" N GLY A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.704A pdb=" N CYS A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.675A pdb=" N VAL A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 236 removed outlier: 4.189A pdb=" N LEU A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 248 removed outlier: 3.858A pdb=" N ARG A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 259 Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.790A pdb=" N ALA A 273 " --> pdb=" O HIS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 291 removed outlier: 4.526A pdb=" N ARG A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 304 through 308 removed outlier: 4.066A pdb=" N PHE A 308 " --> pdb=" O PRO A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 329 Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 338 through 355 removed outlier: 4.236A pdb=" N ILE A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.781A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 398 removed outlier: 3.668A pdb=" N LYS A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 412 removed outlier: 3.694A pdb=" N SER A 411 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 461 through 475 removed outlier: 3.710A pdb=" N PHE A 467 " --> pdb=" O ARG A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 512 through 516 removed outlier: 3.914A pdb=" N LEU A 515 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS A 516 " --> pdb=" O SER A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 512 through 516' Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 531 through 545 Processing helix chain 'A' and resid 573 through 586 removed outlier: 3.519A pdb=" N LEU A 579 " --> pdb=" O AGLN A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 597 removed outlier: 3.742A pdb=" N GLU A 596 " --> pdb=" O ILE A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 removed outlier: 3.646A pdb=" N VAL A 611 " --> pdb=" O LEU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 647 removed outlier: 4.001A pdb=" N LEU A 647 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 removed outlier: 4.490A pdb=" N ALA A 674 " --> pdb=" O GLU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 697 removed outlier: 4.270A pdb=" N ARG A 697 " --> pdb=" O GLU A 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.515A pdb=" N GLU B 100 " --> pdb=" O GLN B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 137 through 149 Processing helix chain 'B' and resid 153 through 164 removed outlier: 3.596A pdb=" N ILE B 163 " --> pdb=" O ARG B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 180 through 192 removed outlier: 3.894A pdb=" N GLY B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 removed outlier: 3.732A pdb=" N CYS B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.641A pdb=" N VAL B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 236 removed outlier: 4.142A pdb=" N LEU B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 248 removed outlier: 3.916A pdb=" N ARG B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 259 Proline residue: B 256 - end of helix Processing helix chain 'B' and resid 263 through 278 removed outlier: 3.776A pdb=" N ALA B 273 " --> pdb=" O HIS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 291 removed outlier: 3.511A pdb=" N GLU B 284 " --> pdb=" O ASN B 280 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLU B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 326 through 329 Processing helix chain 'B' and resid 330 through 335 Processing helix chain 'B' and resid 338 through 355 removed outlier: 4.197A pdb=" N ILE B 344 " --> pdb=" O GLU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'B' and resid 369 through 380 removed outlier: 3.815A pdb=" N SER B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR B 380 " --> pdb=" O ARG B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 398 removed outlier: 3.673A pdb=" N LYS B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 removed outlier: 3.703A pdb=" N SER B 411 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 424 Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 431 through 436 Processing helix chain 'B' and resid 447 through 454 Processing helix chain 'B' and resid 461 through 475 removed outlier: 3.677A pdb=" N PHE B 467 " --> pdb=" O ARG B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 498 through 500 No H-bonds generated for 'chain 'B' and resid 498 through 500' Processing helix chain 'B' and resid 501 through 507 Processing helix chain 'B' and resid 512 through 516 removed outlier: 3.882A pdb=" N LEU B 515 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS B 516 " --> pdb=" O SER B 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 512 through 516' Processing helix chain 'B' and resid 519 through 526 Processing helix chain 'B' and resid 531 through 545 removed outlier: 3.641A pdb=" N MET B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 586 removed outlier: 3.596A pdb=" N LEU B 579 " --> pdb=" O AGLN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 597 No H-bonds generated for 'chain 'B' and resid 595 through 597' Processing helix chain 'B' and resid 607 through 614 Processing helix chain 'B' and resid 637 through 647 removed outlier: 4.047A pdb=" N LEU B 647 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 674 removed outlier: 4.477A pdb=" N ALA B 674 " --> pdb=" O GLU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 697 removed outlier: 4.095A pdb=" N ARG B 697 " --> pdb=" O GLU B 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.565A pdb=" N GLU C 100 " --> pdb=" O GLN C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 135 Processing helix chain 'C' and resid 137 through 149 removed outlier: 3.519A pdb=" N ARG C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 164 removed outlier: 3.587A pdb=" N ILE C 163 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 180 through 193 removed outlier: 3.889A pdb=" N GLY C 186 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.692A pdb=" N CYS C 199 " --> pdb=" O SER C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.672A pdb=" N VAL C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 236 removed outlier: 4.178A pdb=" N LEU C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 248 removed outlier: 3.849A pdb=" N ARG C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 259 Proline residue: C 256 - end of helix Processing helix chain 'C' and resid 263 through 278 removed outlier: 3.789A pdb=" N ALA C 273 " --> pdb=" O HIS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 291 removed outlier: 4.547A pdb=" N ARG C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N GLU C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY C 291 " --> pdb=" O VAL C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 296 through 301 Processing helix chain 'C' and resid 304 through 308 removed outlier: 4.048A pdb=" N PHE C 308 " --> pdb=" O PRO C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 329 Processing helix chain 'C' and resid 330 through 335 removed outlier: 3.518A pdb=" N LEU C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 355 removed outlier: 4.235A pdb=" N ILE C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 368 Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.813A pdb=" N SER C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR C 380 " --> pdb=" O ARG C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 398 removed outlier: 3.692A pdb=" N LYS C 391 " --> pdb=" O SER C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 412 removed outlier: 3.687A pdb=" N SER C 411 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 424 Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 429 through 436 Processing helix chain 'C' and resid 447 through 454 Processing helix chain 'C' and resid 461 through 475 removed outlier: 3.707A pdb=" N PHE C 467 " --> pdb=" O ARG C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 498 through 500 No H-bonds generated for 'chain 'C' and resid 498 through 500' Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 512 through 516 removed outlier: 3.928A pdb=" N LEU C 515 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS C 516 " --> pdb=" O SER C 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 512 through 516' Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 531 through 545 Processing helix chain 'C' and resid 573 through 586 removed outlier: 3.516A pdb=" N LEU C 579 " --> pdb=" O AGLN C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 597 removed outlier: 3.756A pdb=" N GLU C 596 " --> pdb=" O ILE C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.585A pdb=" N VAL C 611 " --> pdb=" O LEU C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 650 removed outlier: 3.919A pdb=" N LEU C 647 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER C 648 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N CYS C 649 " --> pdb=" O THR C 645 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY C 650 " --> pdb=" O ALA C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 removed outlier: 4.471A pdb=" N ALA C 674 " --> pdb=" O GLU C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 697 removed outlier: 4.057A pdb=" N ARG C 697 " --> pdb=" O GLU C 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.612A pdb=" N GLU D 100 " --> pdb=" O GLN D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 135 Processing helix chain 'D' and resid 137 through 149 removed outlier: 3.501A pdb=" N ARG D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 164 removed outlier: 3.609A pdb=" N ILE D 163 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.900A pdb=" N GLY D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.725A pdb=" N CYS D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 removed outlier: 3.634A pdb=" N VAL D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 236 removed outlier: 4.112A pdb=" N LEU D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 248 removed outlier: 3.905A pdb=" N ARG D 244 " --> pdb=" O ALA D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 259 Proline residue: D 256 - end of helix Processing helix chain 'D' and resid 263 through 278 removed outlier: 3.806A pdb=" N ALA D 273 " --> pdb=" O HIS D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 291 removed outlier: 3.522A pdb=" N GLU D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG D 285 " --> pdb=" O LYS D 281 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLU D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 295 No H-bonds generated for 'chain 'D' and resid 293 through 295' Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 304 through 308 removed outlier: 3.819A pdb=" N PHE D 308 " --> pdb=" O PRO D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 329 Processing helix chain 'D' and resid 330 through 335 Processing helix chain 'D' and resid 338 through 355 removed outlier: 4.213A pdb=" N ILE D 344 " --> pdb=" O GLU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 368 Processing helix chain 'D' and resid 369 through 380 removed outlier: 3.772A pdb=" N SER D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 398 removed outlier: 3.699A pdb=" N LYS D 391 " --> pdb=" O SER D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 412 removed outlier: 3.702A pdb=" N SER D 411 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 424 Processing helix chain 'D' and resid 426 through 428 No H-bonds generated for 'chain 'D' and resid 426 through 428' Processing helix chain 'D' and resid 429 through 436 Processing helix chain 'D' and resid 447 through 454 Processing helix chain 'D' and resid 461 through 475 removed outlier: 3.683A pdb=" N PHE D 467 " --> pdb=" O ARG D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 498 through 500 No H-bonds generated for 'chain 'D' and resid 498 through 500' Processing helix chain 'D' and resid 501 through 507 Processing helix chain 'D' and resid 512 through 516 removed outlier: 3.859A pdb=" N LEU D 515 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS D 516 " --> pdb=" O SER D 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 512 through 516' Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 531 through 545 removed outlier: 3.630A pdb=" N MET D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 586 removed outlier: 3.626A pdb=" N LEU D 579 " --> pdb=" O AGLN D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 597 removed outlier: 3.739A pdb=" N GLU D 596 " --> pdb=" O ILE D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 614 removed outlier: 3.569A pdb=" N VAL D 611 " --> pdb=" O LEU D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 647 removed outlier: 4.012A pdb=" N LEU D 647 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 697 removed outlier: 4.119A pdb=" N ARG D 697 " --> pdb=" O GLU D 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.564A pdb=" N GLU E 100 " --> pdb=" O GLN E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 135 Processing helix chain 'E' and resid 137 through 149 removed outlier: 3.513A pdb=" N ARG E 141 " --> pdb=" O GLU E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 removed outlier: 3.519A pdb=" N ILE E 163 " --> pdb=" O ARG E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 174 Processing helix chain 'E' and resid 180 through 193 removed outlier: 3.884A pdb=" N GLY E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 removed outlier: 3.704A pdb=" N CYS E 199 " --> pdb=" O SER E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 215 removed outlier: 3.674A pdb=" N VAL E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 236 removed outlier: 4.171A pdb=" N LEU E 228 " --> pdb=" O ARG E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 248 removed outlier: 3.873A pdb=" N ARG E 244 " --> pdb=" O ALA E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 259 Proline residue: E 256 - end of helix Processing helix chain 'E' and resid 263 through 278 removed outlier: 3.789A pdb=" N ALA E 273 " --> pdb=" O HIS E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 291 removed outlier: 4.528A pdb=" N ARG E 285 " --> pdb=" O LYS E 281 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLU E 286 " --> pdb=" O GLU E 282 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY E 291 " --> pdb=" O VAL E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 295 No H-bonds generated for 'chain 'E' and resid 293 through 295' Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 304 through 308 removed outlier: 4.103A pdb=" N PHE E 308 " --> pdb=" O PRO E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 329 Processing helix chain 'E' and resid 330 through 335 Processing helix chain 'E' and resid 338 through 355 removed outlier: 4.241A pdb=" N ILE E 344 " --> pdb=" O GLU E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 368 Processing helix chain 'E' and resid 369 through 380 removed outlier: 3.816A pdb=" N SER E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR E 380 " --> pdb=" O ARG E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 398 removed outlier: 3.669A pdb=" N LYS E 391 " --> pdb=" O SER E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 412 removed outlier: 3.678A pdb=" N SER E 411 " --> pdb=" O SER E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 424 Processing helix chain 'E' and resid 426 through 428 No H-bonds generated for 'chain 'E' and resid 426 through 428' Processing helix chain 'E' and resid 429 through 436 Processing helix chain 'E' and resid 447 through 454 Processing helix chain 'E' and resid 461 through 475 removed outlier: 3.705A pdb=" N PHE E 467 " --> pdb=" O ARG E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 492 Processing helix chain 'E' and resid 498 through 500 No H-bonds generated for 'chain 'E' and resid 498 through 500' Processing helix chain 'E' and resid 501 through 507 Processing helix chain 'E' and resid 512 through 516 removed outlier: 3.914A pdb=" N LEU E 515 " --> pdb=" O ARG E 512 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N HIS E 516 " --> pdb=" O SER E 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 512 through 516' Processing helix chain 'E' and resid 519 through 526 Processing helix chain 'E' and resid 531 through 545 Processing helix chain 'E' and resid 573 through 586 removed outlier: 3.541A pdb=" N LEU E 579 " --> pdb=" O AGLN E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 593 through 597 removed outlier: 3.720A pdb=" N GLU E 596 " --> pdb=" O ILE E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 607 through 614 removed outlier: 3.580A pdb=" N VAL E 611 " --> pdb=" O LEU E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 637 through 647 removed outlier: 3.944A pdb=" N LEU E 647 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 669 through 674 removed outlier: 4.415A pdb=" N ALA E 674 " --> pdb=" O GLU E 670 " (cutoff:3.500A) Processing helix chain 'E' and resid 687 through 697 removed outlier: 4.063A pdb=" N ARG E 697 " --> pdb=" O GLU E 693 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.535A pdb=" N GLU F 100 " --> pdb=" O GLN F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 135 Processing helix chain 'F' and resid 137 through 149 removed outlier: 3.519A pdb=" N ARG F 141 " --> pdb=" O GLU F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 164 removed outlier: 3.584A pdb=" N ILE F 163 " --> pdb=" O ARG F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 174 Processing helix chain 'F' and resid 180 through 193 removed outlier: 3.867A pdb=" N GLY F 186 " --> pdb=" O ARG F 182 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.726A pdb=" N CYS F 199 " --> pdb=" O SER F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 215 removed outlier: 3.644A pdb=" N VAL F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 236 removed outlier: 4.101A pdb=" N LEU F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 248 removed outlier: 3.908A pdb=" N ARG F 244 " --> pdb=" O ALA F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 259 Proline residue: F 256 - end of helix Processing helix chain 'F' and resid 263 through 278 removed outlier: 3.829A pdb=" N ALA F 273 " --> pdb=" O HIS F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 291 removed outlier: 3.515A pdb=" N GLU F 284 " --> pdb=" O ASN F 280 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG F 285 " --> pdb=" O LYS F 281 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLU F 286 " --> pdb=" O GLU F 282 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY F 291 " --> pdb=" O VAL F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 295 No H-bonds generated for 'chain 'F' and resid 293 through 295' Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 326 through 329 Processing helix chain 'F' and resid 330 through 335 Processing helix chain 'F' and resid 338 through 355 removed outlier: 4.223A pdb=" N ILE F 344 " --> pdb=" O GLU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 368 Processing helix chain 'F' and resid 369 through 380 removed outlier: 3.774A pdb=" N SER F 373 " --> pdb=" O GLY F 369 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR F 380 " --> pdb=" O ARG F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 398 removed outlier: 3.678A pdb=" N LYS F 391 " --> pdb=" O SER F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 412 removed outlier: 3.700A pdb=" N SER F 411 " --> pdb=" O SER F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 424 Processing helix chain 'F' and resid 426 through 430 Processing helix chain 'F' and resid 431 through 436 Processing helix chain 'F' and resid 447 through 454 Processing helix chain 'F' and resid 461 through 475 removed outlier: 3.694A pdb=" N PHE F 467 " --> pdb=" O ARG F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 487 through 492 Processing helix chain 'F' and resid 498 through 500 No H-bonds generated for 'chain 'F' and resid 498 through 500' Processing helix chain 'F' and resid 501 through 507 Processing helix chain 'F' and resid 512 through 516 removed outlier: 3.841A pdb=" N LEU F 515 " --> pdb=" O ARG F 512 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS F 516 " --> pdb=" O SER F 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 512 through 516' Processing helix chain 'F' and resid 519 through 526 Processing helix chain 'F' and resid 531 through 545 removed outlier: 3.590A pdb=" N MET F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 586 removed outlier: 3.603A pdb=" N LEU F 579 " --> pdb=" O AGLN F 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 593 through 597 removed outlier: 3.760A pdb=" N GLU F 596 " --> pdb=" O ILE F 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 614 removed outlier: 3.609A pdb=" N VAL F 611 " --> pdb=" O LEU F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 637 through 647 removed outlier: 4.047A pdb=" N LEU F 647 " --> pdb=" O ILE F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 669 through 674 removed outlier: 4.413A pdb=" N ALA F 674 " --> pdb=" O GLU F 670 " (cutoff:3.500A) Processing helix chain 'F' and resid 687 through 697 removed outlier: 4.048A pdb=" N ARG F 697 " --> pdb=" O GLU F 693 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.581A pdb=" N GLU G 100 " --> pdb=" O GLN G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 135 Processing helix chain 'G' and resid 137 through 149 Processing helix chain 'G' and resid 153 through 164 removed outlier: 3.604A pdb=" N ILE G 163 " --> pdb=" O ARG G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 180 through 193 removed outlier: 3.881A pdb=" N GLY G 186 " --> pdb=" O ARG G 182 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS G 193 " --> pdb=" O GLU G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 removed outlier: 3.711A pdb=" N CYS G 199 " --> pdb=" O SER G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 215 removed outlier: 3.667A pdb=" N VAL G 211 " --> pdb=" O GLY G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 236 removed outlier: 4.143A pdb=" N LEU G 228 " --> pdb=" O ARG G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 248 removed outlier: 3.891A pdb=" N ARG G 244 " --> pdb=" O ALA G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 259 Proline residue: G 256 - end of helix Processing helix chain 'G' and resid 263 through 278 removed outlier: 3.792A pdb=" N ALA G 273 " --> pdb=" O HIS G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 291 removed outlier: 4.527A pdb=" N ARG G 285 " --> pdb=" O LYS G 281 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLU G 286 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY G 291 " --> pdb=" O VAL G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 295 No H-bonds generated for 'chain 'G' and resid 293 through 295' Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 304 through 308 removed outlier: 4.063A pdb=" N PHE G 308 " --> pdb=" O PRO G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 329 Processing helix chain 'G' and resid 330 through 335 Processing helix chain 'G' and resid 338 through 355 removed outlier: 4.222A pdb=" N ILE G 344 " --> pdb=" O GLU G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 363 through 368 Processing helix chain 'G' and resid 369 through 380 removed outlier: 3.796A pdb=" N SER G 373 " --> pdb=" O GLY G 369 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR G 380 " --> pdb=" O ARG G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 384 through 398 removed outlier: 3.670A pdb=" N LYS G 391 " --> pdb=" O SER G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 412 removed outlier: 3.685A pdb=" N SER G 411 " --> pdb=" O SER G 408 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 424 Processing helix chain 'G' and resid 426 through 428 No H-bonds generated for 'chain 'G' and resid 426 through 428' Processing helix chain 'G' and resid 429 through 436 Processing helix chain 'G' and resid 447 through 454 Processing helix chain 'G' and resid 461 through 475 removed outlier: 3.706A pdb=" N PHE G 467 " --> pdb=" O ARG G 463 " (cutoff:3.500A) Processing helix chain 'G' and resid 487 through 492 Processing helix chain 'G' and resid 498 through 500 No H-bonds generated for 'chain 'G' and resid 498 through 500' Processing helix chain 'G' and resid 501 through 507 Processing helix chain 'G' and resid 512 through 516 removed outlier: 3.927A pdb=" N LEU G 515 " --> pdb=" O ARG G 512 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS G 516 " --> pdb=" O SER G 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 512 through 516' Processing helix chain 'G' and resid 519 through 526 Processing helix chain 'G' and resid 531 through 545 Processing helix chain 'G' and resid 573 through 586 removed outlier: 3.520A pdb=" N LEU G 579 " --> pdb=" O AGLN G 575 " (cutoff:3.500A) Processing helix chain 'G' and resid 595 through 597 No H-bonds generated for 'chain 'G' and resid 595 through 597' Processing helix chain 'G' and resid 607 through 614 removed outlier: 3.544A pdb=" N VAL G 611 " --> pdb=" O LEU G 607 " (cutoff:3.500A) Processing helix chain 'G' and resid 637 through 647 removed outlier: 3.983A pdb=" N LEU G 647 " --> pdb=" O ILE G 643 " (cutoff:3.500A) Processing helix chain 'G' and resid 669 through 674 removed outlier: 4.472A pdb=" N ALA G 674 " --> pdb=" O GLU G 670 " (cutoff:3.500A) Processing helix chain 'G' and resid 687 through 697 removed outlier: 4.070A pdb=" N ARG G 697 " --> pdb=" O GLU G 693 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 101 removed outlier: 3.542A pdb=" N GLU H 100 " --> pdb=" O GLN H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 135 Processing helix chain 'H' and resid 137 through 149 removed outlier: 3.515A pdb=" N ARG H 141 " --> pdb=" O GLU H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 164 removed outlier: 3.613A pdb=" N ILE H 163 " --> pdb=" O ARG H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 174 Processing helix chain 'H' and resid 180 through 193 removed outlier: 3.870A pdb=" N GLY H 186 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS H 193 " --> pdb=" O GLU H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 205 removed outlier: 3.736A pdb=" N CYS H 199 " --> pdb=" O SER H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 215 removed outlier: 3.657A pdb=" N VAL H 211 " --> pdb=" O GLY H 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 236 removed outlier: 4.101A pdb=" N LEU H 228 " --> pdb=" O ARG H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 248 removed outlier: 3.941A pdb=" N ARG H 244 " --> pdb=" O ALA H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 259 Proline residue: H 256 - end of helix Processing helix chain 'H' and resid 263 through 278 removed outlier: 3.826A pdb=" N ALA H 273 " --> pdb=" O HIS H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 291 removed outlier: 3.518A pdb=" N GLU H 284 " --> pdb=" O ASN H 280 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLU H 286 " --> pdb=" O GLU H 282 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY H 291 " --> pdb=" O VAL H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 295 No H-bonds generated for 'chain 'H' and resid 293 through 295' Processing helix chain 'H' and resid 296 through 301 Processing helix chain 'H' and resid 304 through 308 removed outlier: 3.801A pdb=" N PHE H 308 " --> pdb=" O PRO H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 329 Processing helix chain 'H' and resid 330 through 335 removed outlier: 3.525A pdb=" N LEU H 334 " --> pdb=" O LEU H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 355 removed outlier: 4.196A pdb=" N ILE H 344 " --> pdb=" O GLU H 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 363 through 368 Processing helix chain 'H' and resid 369 through 380 removed outlier: 3.768A pdb=" N SER H 373 " --> pdb=" O GLY H 369 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR H 380 " --> pdb=" O ARG H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 398 removed outlier: 3.681A pdb=" N LYS H 391 " --> pdb=" O SER H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 412 removed outlier: 3.681A pdb=" N SER H 411 " --> pdb=" O SER H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 413 through 424 Processing helix chain 'H' and resid 426 through 428 No H-bonds generated for 'chain 'H' and resid 426 through 428' Processing helix chain 'H' and resid 429 through 436 Processing helix chain 'H' and resid 447 through 454 Processing helix chain 'H' and resid 461 through 475 removed outlier: 3.666A pdb=" N PHE H 467 " --> pdb=" O ARG H 463 " (cutoff:3.500A) Processing helix chain 'H' and resid 487 through 492 Processing helix chain 'H' and resid 498 through 500 No H-bonds generated for 'chain 'H' and resid 498 through 500' Processing helix chain 'H' and resid 501 through 507 Processing helix chain 'H' and resid 512 through 516 removed outlier: 3.843A pdb=" N LEU H 515 " --> pdb=" O ARG H 512 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS H 516 " --> pdb=" O SER H 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 512 through 516' Processing helix chain 'H' and resid 519 through 526 Processing helix chain 'H' and resid 531 through 545 removed outlier: 3.516A pdb=" N MET H 545 " --> pdb=" O ALA H 541 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 586 removed outlier: 3.524A pdb=" N LEU H 579 " --> pdb=" O AGLN H 575 " (cutoff:3.500A) Processing helix chain 'H' and resid 593 through 597 removed outlier: 3.762A pdb=" N GLU H 596 " --> pdb=" O ILE H 593 " (cutoff:3.500A) Processing helix chain 'H' and resid 607 through 614 removed outlier: 3.583A pdb=" N VAL H 611 " --> pdb=" O LEU H 607 " (cutoff:3.500A) Processing helix chain 'H' and resid 625 through 630 removed outlier: 4.656A pdb=" N CYS H 629 " --> pdb=" O ALA H 625 " (cutoff:3.500A) Processing helix chain 'H' and resid 637 through 647 removed outlier: 4.096A pdb=" N LEU H 647 " --> pdb=" O ILE H 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 669 through 674 removed outlier: 4.473A pdb=" N ALA H 674 " --> pdb=" O GLU H 670 " (cutoff:3.500A) Processing helix chain 'H' and resid 687 through 697 removed outlier: 4.153A pdb=" N ARG H 697 " --> pdb=" O GLU H 693 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 591 through 592 removed outlier: 6.767A pdb=" N VAL A 564 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N PHE A 565 " --> pdb=" O VAL A 618 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL A 620 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N SER A 567 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE A 656 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU A 619 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 591 through 593 removed outlier: 6.732A pdb=" N VAL B 564 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHE B 565 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 620 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER B 567 " --> pdb=" O VAL B 620 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE B 656 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU B 619 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 591 through 592 removed outlier: 6.752A pdb=" N VAL C 564 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE C 565 " --> pdb=" O VAL C 618 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL C 620 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N SER C 567 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU C 619 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 591 through 592 removed outlier: 6.750A pdb=" N VAL D 564 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE D 565 " --> pdb=" O VAL D 618 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL D 620 " --> pdb=" O PHE D 565 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER D 567 " --> pdb=" O VAL D 620 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE D 656 " --> pdb=" O PHE D 617 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU D 619 " --> pdb=" O ILE D 656 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 591 through 592 removed outlier: 6.813A pdb=" N VAL E 564 " --> pdb=" O PHE E 592 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE E 565 " --> pdb=" O VAL E 618 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL E 620 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N SER E 567 " --> pdb=" O VAL E 620 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE E 656 " --> pdb=" O PHE E 617 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU E 619 " --> pdb=" O ILE E 656 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 591 through 592 removed outlier: 6.770A pdb=" N VAL F 564 " --> pdb=" O PHE F 592 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE F 565 " --> pdb=" O VAL F 618 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N VAL F 620 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER F 567 " --> pdb=" O VAL F 620 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU F 619 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 591 through 593 removed outlier: 6.747A pdb=" N VAL G 564 " --> pdb=" O PHE G 592 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE G 565 " --> pdb=" O VAL G 618 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL G 620 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N SER G 567 " --> pdb=" O VAL G 620 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU G 619 " --> pdb=" O ILE G 656 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 591 through 592 removed outlier: 6.754A pdb=" N VAL H 564 " --> pdb=" O PHE H 592 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE H 565 " --> pdb=" O VAL H 618 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL H 620 " --> pdb=" O PHE H 565 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N SER H 567 " --> pdb=" O VAL H 620 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU H 619 " --> pdb=" O ILE H 656 " (cutoff:3.500A) 1534 hydrogen bonds defined for protein. 4482 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: 10.23 Time building geometry restraints manager: 11.95 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: 12565 1.34 - 1.46: 5513 1.46 - 1.57: 19396 1.57 - 1.69: 0 1.69 - 1.81: 232 Bond restraints: 37706 Sorted by residual: bond pdb=" CG LEU D 451 " pdb=" CD2 LEU D 451 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.36e+00 bond pdb=" CB ASP G 441 " pdb=" CG ASP G 441 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.33e+00 bond pdb=" CB ASP E 441 " pdb=" CG ASP E 441 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.28e+00 bond pdb=" CB ASP C 441 " pdb=" CG ASP C 441 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.24e+00 bond pdb=" CB ASP A 441 " pdb=" CG ASP A 441 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.22e+00 ... (remaining 37701 not shown) Histogram of bond angle deviations from ideal: 95.64 - 103.35: 302 103.35 - 111.06: 14386 111.06 - 118.78: 16302 118.78 - 126.49: 19478 126.49 - 134.20: 528 Bond angle restraints: 50996 Sorted by residual: angle pdb=" N LEU E 442 " pdb=" CA LEU E 442 " pdb=" C LEU E 442 " ideal model delta sigma weight residual 112.93 106.24 6.69 1.12e+00 7.97e-01 3.56e+01 angle pdb=" N LEU C 442 " pdb=" CA LEU C 442 " pdb=" C LEU C 442 " ideal model delta sigma weight residual 112.93 106.39 6.54 1.12e+00 7.97e-01 3.41e+01 angle pdb=" N LEU A 442 " pdb=" CA LEU A 442 " pdb=" C LEU A 442 " ideal model delta sigma weight residual 112.93 106.39 6.54 1.12e+00 7.97e-01 3.41e+01 angle pdb=" N LEU G 442 " pdb=" CA LEU G 442 " pdb=" C LEU G 442 " ideal model delta sigma weight residual 112.93 106.42 6.51 1.12e+00 7.97e-01 3.38e+01 angle pdb=" N LEU B 442 " pdb=" CA LEU B 442 " pdb=" C LEU B 442 " ideal model delta sigma weight residual 113.21 106.71 6.50 1.15e+00 7.56e-01 3.19e+01 ... (remaining 50991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 20048 16.76 - 33.52: 2263 33.52 - 50.28: 533 50.28 - 67.03: 80 67.03 - 83.79: 16 Dihedral angle restraints: 22940 sinusoidal: 9328 harmonic: 13612 Sorted by residual: dihedral pdb=" CA ARG H 403 " pdb=" C ARG H 403 " pdb=" N PRO H 404 " pdb=" CA PRO H 404 " ideal model delta harmonic sigma weight residual 180.00 146.34 33.66 0 5.00e+00 4.00e-02 4.53e+01 dihedral pdb=" CA ARG F 403 " pdb=" C ARG F 403 " pdb=" N PRO F 404 " pdb=" CA PRO F 404 " ideal model delta harmonic sigma weight residual 180.00 146.48 33.52 0 5.00e+00 4.00e-02 4.49e+01 dihedral pdb=" CA ARG B 403 " pdb=" C ARG B 403 " pdb=" N PRO B 404 " pdb=" CA PRO B 404 " ideal model delta harmonic sigma weight residual 180.00 147.02 32.98 0 5.00e+00 4.00e-02 4.35e+01 ... (remaining 22937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3888 0.047 - 0.094: 1579 0.094 - 0.140: 329 0.140 - 0.187: 26 0.187 - 0.234: 4 Chirality restraints: 5826 Sorted by residual: chirality pdb=" CG LEU D 444 " pdb=" CB LEU D 444 " pdb=" CD1 LEU D 444 " pdb=" CD2 LEU D 444 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CG LEU H 444 " pdb=" CB LEU H 444 " pdb=" CD1 LEU H 444 " pdb=" CD2 LEU H 444 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CG LEU F 444 " pdb=" CB LEU F 444 " pdb=" CD1 LEU F 444 " pdb=" CD2 LEU F 444 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 5823 not shown) Planarity restraints: 6608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 561 " 0.045 5.00e-02 4.00e+02 6.78e-02 7.36e+00 pdb=" N PRO E 562 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO E 562 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 562 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 561 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.65e+00 pdb=" N PRO G 562 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO G 562 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 562 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 331 " 0.037 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO D 332 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 332 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 332 " 0.031 5.00e-02 4.00e+02 ... (remaining 6605 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 719 2.65 - 3.21: 38275 3.21 - 3.77: 55726 3.77 - 4.34: 78752 4.34 - 4.90: 127405 Nonbonded interactions: 300877 Sorted by model distance: nonbonded pdb=" O ALA A 102 " pdb=" NH2 ARG A 110 " model vdw 2.083 2.520 nonbonded pdb=" O ALA F 102 " pdb=" NH2 ARG F 110 " model vdw 2.100 2.520 nonbonded pdb=" OE1 GLU A 189 " pdb=" ND1 HIS A 225 " model vdw 2.114 2.520 nonbonded pdb=" OE1 GLU C 189 " pdb=" ND1 HIS C 225 " model vdw 2.150 2.520 nonbonded pdb=" OE1 GLU E 189 " pdb=" ND1 HIS E 225 " model vdw 2.152 2.520 ... (remaining 300872 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 'A' and (resid 84 through 573 or resid 576 through 589 or resid 591 throu \ gh 647 or resid 649 through 700)) selection = (chain 'B' and (resid 84 through 573 or resid 576 through 589 or resid 591 throu \ gh 647 or resid 649 through 700)) selection = (chain 'C' and (resid 84 through 573 or resid 576 through 589 or resid 591 throu \ gh 647 or resid 649 through 700)) selection = (chain 'D' and (resid 84 through 573 or resid 576 through 589 or resid 591 throu \ gh 647 or resid 649 through 700)) selection = (chain 'E' and (resid 84 through 573 or resid 576 through 589 or resid 591 throu \ gh 647 or resid 649 through 700)) selection = (chain 'F' and (resid 84 through 573 or resid 576 through 589 or resid 591 throu \ gh 647 or resid 649 through 700)) selection = (chain 'G' and (resid 84 through 573 or resid 576 through 589 or resid 591 throu \ gh 647 or resid 649 through 700)) selection = (chain 'H' and (resid 84 through 573 or resid 576 through 589 or resid 591 throu \ gh 647 or resid 649 through 700)) } 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=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.280 Construct map_model_manager: 0.020 Extract box with map and model: 10.600 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 92.090 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.180 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: 0.010 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 : 0.009 0.076 37706 Z= 0.574 Angle : 0.924 13.421 50996 Z= 0.501 Chirality : 0.050 0.234 5826 Planarity : 0.005 0.068 6608 Dihedral : 14.564 83.792 14120 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 0.38 % Allowed : 0.20 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -2.88 (0.12), residues: 4711 helix: -1.63 (0.09), residues: 2632 sheet: -1.73 (0.40), residues: 168 loop : -2.18 (0.15), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 662 HIS 0.007 0.001 HIS E 640 PHE 0.034 0.002 PHE E 259 TYR 0.025 0.003 TYR B 213 ARG 0.015 0.001 ARG H 543 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 421 time to evaluate : 3.213 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: B 441 ASP cc_start: 0.7759 (m-30) cc_final: 0.7491 (m-30) REVERT: D 175 ARG cc_start: 0.8743 (tpp80) cc_final: 0.7660 (tpp80) REVERT: G 259 PHE cc_start: 0.7713 (t80) cc_final: 0.7341 (t80) outliers start: 7 outliers final: 6 residues processed: 421 average time/residue: 0.4824 time to fit residues: 309.5666 Evaluate side-chains 337 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 331 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain F residue 156 ASN Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain H residue 156 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 391 optimal weight: 0.7980 chunk 351 optimal weight: 0.0270 chunk 195 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 237 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 363 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 221 optimal weight: 6.9990 chunk 270 optimal weight: 1.9990 chunk 421 optimal weight: 6.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 ASN C 232 ASN D 156 ASN F 616 ASN ** H 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37706 Z= 0.217 Angle : 0.685 8.505 50996 Z= 0.347 Chirality : 0.042 0.156 5826 Planarity : 0.006 0.084 6608 Dihedral : 5.510 32.199 5164 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.19 % Allowed : 7.42 % Favored : 91.39 % 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: -2.03 (0.12), residues: 4711 helix: -0.92 (0.10), residues: 2712 sheet: -1.38 (0.42), residues: 168 loop : -1.84 (0.16), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 638 HIS 0.003 0.001 HIS H 236 PHE 0.025 0.001 PHE B 259 TYR 0.028 0.002 TYR C 503 ARG 0.008 0.001 ARG D 543 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 384 time to evaluate : 3.089 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: A 612 MET cc_start: 0.7827 (mpp) cc_final: 0.7555 (mmm) REVERT: B 293 LEU cc_start: 0.8615 (tp) cc_final: 0.8390 (tp) REVERT: C 131 ARG cc_start: 0.7708 (mtp-110) cc_final: 0.7354 (ptm-80) REVERT: C 299 LEU cc_start: 0.8759 (tp) cc_final: 0.8524 (tp) REVERT: D 131 ARG cc_start: 0.7736 (mtp-110) cc_final: 0.7467 (ptm160) REVERT: D 293 LEU cc_start: 0.8584 (tp) cc_final: 0.8358 (tp) REVERT: D 441 ASP cc_start: 0.7498 (t0) cc_final: 0.7182 (t0) REVERT: F 293 LEU cc_start: 0.8599 (tp) cc_final: 0.8371 (tp) REVERT: F 441 ASP cc_start: 0.7514 (t0) cc_final: 0.7200 (t0) REVERT: H 131 ARG cc_start: 0.7634 (mtp-110) cc_final: 0.7324 (ptm160) REVERT: H 293 LEU cc_start: 0.8620 (tp) cc_final: 0.8401 (tp) REVERT: H 441 ASP cc_start: 0.7502 (t0) cc_final: 0.7191 (t0) REVERT: H 615 ARG cc_start: 0.7085 (mmp-170) cc_final: 0.6742 (mmp-170) outliers start: 39 outliers final: 21 residues processed: 409 average time/residue: 0.4897 time to fit residues: 300.4627 Evaluate side-chains 361 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 340 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 454 ASP Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 454 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 234 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 350 optimal weight: 2.9990 chunk 286 optimal weight: 4.9990 chunk 116 optimal weight: 20.0000 chunk 422 optimal weight: 0.8980 chunk 456 optimal weight: 5.9990 chunk 375 optimal weight: 4.9990 chunk 418 optimal weight: 0.7980 chunk 143 optimal weight: 7.9990 chunk 338 optimal weight: 8.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 ASN B 156 ASN C 232 ASN D 156 ASN F 156 ASN H 156 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 37706 Z= 0.351 Angle : 0.708 9.695 50996 Z= 0.354 Chirality : 0.044 0.234 5826 Planarity : 0.005 0.061 6608 Dihedral : 5.386 29.638 5158 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 1.99 % Allowed : 10.28 % Favored : 87.73 % 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: -2.00 (0.13), residues: 4711 helix: -0.95 (0.10), residues: 2744 sheet: -0.84 (0.45), residues: 152 loop : -1.78 (0.16), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 214 HIS 0.003 0.001 HIS H 236 PHE 0.016 0.002 PHE A 259 TYR 0.015 0.002 TYR B 503 ARG 0.005 0.000 ARG H 543 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 351 time to evaluate : 3.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 293 LEU cc_start: 0.8664 (tp) cc_final: 0.8449 (tp) REVERT: C 131 ARG cc_start: 0.7769 (mtp-110) cc_final: 0.7389 (ptm-80) REVERT: C 259 PHE cc_start: 0.7491 (t80) cc_final: 0.7111 (t80) REVERT: D 293 LEU cc_start: 0.8660 (tp) cc_final: 0.8447 (tp) REVERT: D 441 ASP cc_start: 0.7640 (t0) cc_final: 0.7379 (t0) REVERT: D 612 MET cc_start: 0.8045 (mpp) cc_final: 0.7438 (mmm) REVERT: D 615 ARG cc_start: 0.6997 (mmp-170) cc_final: 0.6663 (mmp-170) REVERT: F 293 LEU cc_start: 0.8603 (tp) cc_final: 0.8389 (tp) REVERT: F 441 ASP cc_start: 0.7683 (t0) cc_final: 0.7423 (t0) REVERT: G 259 PHE cc_start: 0.7388 (t80) cc_final: 0.7025 (t80) REVERT: H 293 LEU cc_start: 0.8620 (tp) cc_final: 0.8413 (tp) REVERT: H 441 ASP cc_start: 0.7660 (t0) cc_final: 0.7396 (t0) REVERT: H 615 ARG cc_start: 0.7114 (mmp-170) cc_final: 0.6803 (mmp-170) outliers start: 71 outliers final: 57 residues processed: 383 average time/residue: 0.5113 time to fit residues: 300.3364 Evaluate side-chains 387 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 330 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 526 ASP Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 526 ASP Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 526 ASP Chi-restraints excluded: chain E residue 571 ASN Chi-restraints excluded: chain E residue 594 ASP Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 454 ASP Chi-restraints excluded: chain F residue 526 ASP Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 526 ASP Chi-restraints excluded: chain G residue 571 ASN Chi-restraints excluded: chain G residue 594 ASP Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 344 ILE Chi-restraints excluded: chain H residue 454 ASP Chi-restraints excluded: chain H residue 526 ASP Chi-restraints excluded: chain H residue 594 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 417 optimal weight: 8.9990 chunk 317 optimal weight: 4.9990 chunk 219 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 chunk 283 optimal weight: 5.9990 chunk 423 optimal weight: 0.9990 chunk 448 optimal weight: 0.9980 chunk 221 optimal weight: 10.0000 chunk 401 optimal weight: 30.0000 chunk 120 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 37706 Z= 0.265 Angle : 0.655 8.246 50996 Z= 0.328 Chirality : 0.042 0.153 5826 Planarity : 0.005 0.061 6608 Dihedral : 5.144 28.250 5158 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.02 % Allowed : 11.06 % Favored : 86.92 % 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: -1.76 (0.13), residues: 4711 helix: -0.80 (0.10), residues: 2752 sheet: -0.59 (0.46), residues: 152 loop : -1.64 (0.17), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 214 HIS 0.003 0.001 HIS C 236 PHE 0.011 0.001 PHE B 433 TYR 0.013 0.002 TYR F 503 ARG 0.008 0.000 ARG F 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 370 time to evaluate : 3.092 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: B 293 LEU cc_start: 0.8558 (tp) cc_final: 0.8353 (tp) REVERT: C 131 ARG cc_start: 0.7761 (mtp-110) cc_final: 0.7385 (ptm-80) REVERT: C 612 MET cc_start: 0.7924 (mpp) cc_final: 0.7237 (mpp) REVERT: C 630 MET cc_start: 0.3796 (mmm) cc_final: 0.3517 (mmm) REVERT: D 612 MET cc_start: 0.8075 (mpp) cc_final: 0.7585 (mmm) REVERT: E 441 ASP cc_start: 0.7784 (m-30) cc_final: 0.7552 (t0) REVERT: E 612 MET cc_start: 0.7923 (mpp) cc_final: 0.7317 (mpp) REVERT: F 612 MET cc_start: 0.8068 (mpp) cc_final: 0.7546 (mmm) REVERT: G 612 MET cc_start: 0.7992 (mpp) cc_final: 0.7338 (mpp) REVERT: H 131 ARG cc_start: 0.7646 (mtp-110) cc_final: 0.7300 (ptm160) REVERT: H 570 ARG cc_start: 0.6907 (mtp85) cc_final: 0.6381 (ttm170) REVERT: H 615 ARG cc_start: 0.7064 (mmp-170) cc_final: 0.6857 (mmp-170) outliers start: 72 outliers final: 57 residues processed: 411 average time/residue: 0.4920 time to fit residues: 304.2944 Evaluate side-chains 396 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 339 time to evaluate : 3.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 526 ASP Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 526 ASP Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 526 ASP Chi-restraints excluded: chain E residue 571 ASN Chi-restraints excluded: chain E residue 594 ASP Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 454 ASP Chi-restraints excluded: chain F residue 526 ASP Chi-restraints excluded: chain F residue 594 ASP Chi-restraints excluded: chain G residue 110 ARG Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 472 GLU Chi-restraints excluded: chain G residue 526 ASP Chi-restraints excluded: chain G residue 571 ASN Chi-restraints excluded: chain G residue 594 ASP Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 344 ILE Chi-restraints excluded: chain H residue 454 ASP Chi-restraints excluded: chain H residue 526 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 373 optimal weight: 0.8980 chunk 254 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 333 optimal weight: 0.6980 chunk 185 optimal weight: 3.9990 chunk 382 optimal weight: 0.7980 chunk 310 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 229 optimal weight: 0.0030 chunk 402 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 575 GLN A Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 37706 Z= 0.172 Angle : 0.611 9.265 50996 Z= 0.307 Chirality : 0.040 0.209 5826 Planarity : 0.005 0.070 6608 Dihedral : 4.821 26.954 5158 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.49 % Allowed : 12.37 % Favored : 86.14 % 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: -1.45 (0.13), residues: 4711 helix: -0.57 (0.10), residues: 2752 sheet: -0.35 (0.45), residues: 152 loop : -1.47 (0.17), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 214 HIS 0.003 0.001 HIS B 534 PHE 0.009 0.001 PHE G 259 TYR 0.013 0.001 TYR D 429 ARG 0.008 0.000 ARG F 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 424 time to evaluate : 3.113 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: A 297 GLU cc_start: 0.7865 (tp30) cc_final: 0.7652 (mm-30) REVERT: A 570 ARG cc_start: 0.6968 (mtp85) cc_final: 0.6412 (ttm170) REVERT: B 200 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7761 (mp10) REVERT: C 131 ARG cc_start: 0.7741 (mtp-110) cc_final: 0.7344 (ptm-80) REVERT: C 293 LEU cc_start: 0.8479 (tp) cc_final: 0.8211 (tp) REVERT: C 297 GLU cc_start: 0.7756 (tp30) cc_final: 0.7464 (mm-30) REVERT: C 422 GLN cc_start: 0.7579 (mt0) cc_final: 0.7031 (mm-40) REVERT: C 612 MET cc_start: 0.7913 (mpp) cc_final: 0.7318 (mpp) REVERT: D 200 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7728 (mp10) REVERT: D 570 ARG cc_start: 0.6870 (mtp85) cc_final: 0.6657 (ttm170) REVERT: D 612 MET cc_start: 0.8054 (mpp) cc_final: 0.7570 (mmm) REVERT: E 200 GLN cc_start: 0.8155 (mp10) cc_final: 0.7856 (mp10) REVERT: E 422 GLN cc_start: 0.7587 (mt0) cc_final: 0.7008 (mm-40) REVERT: E 612 MET cc_start: 0.7841 (mpp) cc_final: 0.7256 (mpp) REVERT: F 200 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7704 (mp10) REVERT: F 297 GLU cc_start: 0.7679 (tp30) cc_final: 0.7443 (mm-30) REVERT: F 403 ARG cc_start: 0.5084 (mmp80) cc_final: 0.4856 (mmp80) REVERT: F 612 MET cc_start: 0.8044 (mpp) cc_final: 0.7558 (mmm) REVERT: G 422 GLN cc_start: 0.7580 (mt0) cc_final: 0.7027 (mm-40) REVERT: H 131 ARG cc_start: 0.7596 (mtp-110) cc_final: 0.7258 (ptm160) REVERT: H 200 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7700 (mp10) outliers start: 51 outliers final: 29 residues processed: 458 average time/residue: 0.4690 time to fit residues: 327.3580 Evaluate side-chains 368 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 335 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 594 ASP Chi-restraints excluded: chain F residue 200 GLN Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 454 ASP Chi-restraints excluded: chain G residue 110 ARG Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 594 ASP Chi-restraints excluded: chain H residue 200 GLN Chi-restraints excluded: chain H residue 344 ILE Chi-restraints excluded: chain H residue 454 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 150 optimal weight: 0.0980 chunk 403 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 263 optimal weight: 0.0170 chunk 110 optimal weight: 0.8980 chunk 448 optimal weight: 0.7980 chunk 372 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 235 optimal weight: 0.0670 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN C 156 ASN C 337 ASN E 156 ASN E 232 ASN E 337 ASN F 232 ASN G 337 ASN H 232 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 37706 Z= 0.158 Angle : 0.616 9.620 50996 Z= 0.304 Chirality : 0.040 0.270 5826 Planarity : 0.005 0.082 6608 Dihedral : 4.592 26.350 5154 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.49 % Allowed : 13.59 % Favored : 84.92 % 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: -1.29 (0.13), residues: 4711 helix: -0.50 (0.10), residues: 2792 sheet: -0.16 (0.44), residues: 152 loop : -1.33 (0.17), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 638 HIS 0.003 0.001 HIS C 269 PHE 0.007 0.001 PHE C 259 TYR 0.010 0.001 TYR D 429 ARG 0.009 0.000 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 396 time to evaluate : 3.109 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: A 200 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: A 422 GLN cc_start: 0.7503 (mt0) cc_final: 0.7271 (mt0) REVERT: B 200 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7750 (mp10) REVERT: C 131 ARG cc_start: 0.7737 (mtp-110) cc_final: 0.7328 (ptm-80) REVERT: C 200 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7872 (mp10) REVERT: D 200 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7719 (mp10) REVERT: D 403 ARG cc_start: 0.5193 (mmp80) cc_final: 0.4898 (mmp80) REVERT: D 422 GLN cc_start: 0.7581 (mt0) cc_final: 0.7131 (mm-40) REVERT: D 570 ARG cc_start: 0.6878 (mtp85) cc_final: 0.6426 (ttm110) REVERT: D 612 MET cc_start: 0.8000 (mpp) cc_final: 0.7498 (mmm) REVERT: E 200 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7829 (mp10) REVERT: E 232 ASN cc_start: 0.7651 (m-40) cc_final: 0.7120 (m110) REVERT: E 473 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7758 (tp) REVERT: E 612 MET cc_start: 0.7858 (mpp) cc_final: 0.7216 (mpp) REVERT: F 200 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7788 (mp10) REVERT: F 403 ARG cc_start: 0.5010 (mmp80) cc_final: 0.4712 (mmp80) REVERT: F 422 GLN cc_start: 0.7497 (mt0) cc_final: 0.7104 (mm-40) REVERT: F 612 MET cc_start: 0.8026 (mpp) cc_final: 0.7567 (mmm) REVERT: G 200 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7927 (mp10) REVERT: G 612 MET cc_start: 0.7971 (mpp) cc_final: 0.7345 (mpp) REVERT: H 131 ARG cc_start: 0.7604 (mtp-110) cc_final: 0.7286 (ptm160) REVERT: H 422 GLN cc_start: 0.7588 (mt0) cc_final: 0.7132 (mm-40) outliers start: 51 outliers final: 25 residues processed: 430 average time/residue: 0.4934 time to fit residues: 319.8937 Evaluate side-chains 374 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 341 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain E residue 200 GLN Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain F residue 200 GLN Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 439 ASP Chi-restraints excluded: chain F residue 454 ASP Chi-restraints excluded: chain G residue 110 ARG Chi-restraints excluded: chain G residue 200 GLN Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain H residue 344 ILE Chi-restraints excluded: chain H residue 454 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 255 optimal weight: 0.5980 chunk 327 optimal weight: 2.9990 chunk 254 optimal weight: 8.9990 chunk 377 optimal weight: 1.9990 chunk 250 optimal weight: 0.9980 chunk 447 optimal weight: 3.9990 chunk 279 optimal weight: 4.9990 chunk 272 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN C 575 GLN A ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 37706 Z= 0.239 Angle : 0.647 13.974 50996 Z= 0.316 Chirality : 0.042 0.255 5826 Planarity : 0.005 0.086 6608 Dihedral : 4.616 26.890 5152 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.36 % Allowed : 15.00 % Favored : 83.64 % 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: -1.29 (0.13), residues: 4711 helix: -0.54 (0.10), residues: 2792 sheet: -0.15 (0.44), residues: 152 loop : -1.24 (0.17), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 214 HIS 0.003 0.001 HIS C 236 PHE 0.010 0.001 PHE H 476 TYR 0.011 0.001 TYR A 429 ARG 0.007 0.000 ARG H 570 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 342 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7907 (mp10) REVERT: B 200 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7735 (mp10) REVERT: B 672 MET cc_start: 0.3333 (ptt) cc_final: 0.3119 (ptt) REVERT: C 131 ARG cc_start: 0.7728 (mtp-110) cc_final: 0.7318 (ptm-80) REVERT: C 200 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7922 (mp10) REVERT: D 200 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7749 (mp10) REVERT: E 200 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7882 (mp10) REVERT: E 612 MET cc_start: 0.7901 (mpp) cc_final: 0.7313 (mpp) REVERT: F 200 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7720 (mp10) REVERT: F 612 MET cc_start: 0.8035 (mpp) cc_final: 0.7530 (mmm) REVERT: G 200 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7961 (mp10) REVERT: H 131 ARG cc_start: 0.7633 (mtp-110) cc_final: 0.7297 (ptm-80) REVERT: H 200 GLN cc_start: 0.7835 (mp10) cc_final: 0.7470 (mp10) outliers start: 46 outliers final: 33 residues processed: 378 average time/residue: 0.5062 time to fit residues: 290.4501 Evaluate side-chains 364 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 324 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 526 ASP Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain E residue 200 GLN Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 526 ASP Chi-restraints excluded: chain F residue 200 GLN Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 439 ASP Chi-restraints excluded: chain F residue 454 ASP Chi-restraints excluded: chain G residue 110 ARG Chi-restraints excluded: chain G residue 200 GLN Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 526 ASP Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 344 ILE Chi-restraints excluded: chain H residue 454 ASP Chi-restraints excluded: chain H residue 594 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 276 optimal weight: 0.6980 chunk 178 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 284 optimal weight: 0.0370 chunk 304 optimal weight: 0.9980 chunk 221 optimal weight: 10.0000 chunk 41 optimal weight: 0.0030 chunk 351 optimal weight: 3.9990 overall best weight: 0.5268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37706 Z= 0.162 Angle : 0.624 13.019 50996 Z= 0.304 Chirality : 0.040 0.225 5826 Planarity : 0.005 0.077 6608 Dihedral : 4.470 25.764 5152 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.08 % Favored : 93.88 % Rotamer: Outliers : 1.29 % Allowed : 15.38 % Favored : 83.33 % 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: 4711 helix: -0.41 (0.10), residues: 2800 sheet: 0.05 (0.45), residues: 152 loop : -1.14 (0.17), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 214 HIS 0.003 0.001 HIS E 534 PHE 0.006 0.001 PHE C 467 TYR 0.012 0.001 TYR D 568 ARG 0.014 0.000 ARG D 570 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 347 time to evaluate : 3.219 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: A 200 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7903 (mp10) REVERT: A 570 ARG cc_start: 0.6507 (mtp85) cc_final: 0.6103 (ttm-80) REVERT: B 200 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7749 (mp10) REVERT: C 131 ARG cc_start: 0.7730 (mtp-110) cc_final: 0.7324 (ptm-80) REVERT: C 200 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7886 (mp10) REVERT: D 403 ARG cc_start: 0.4952 (mmp80) cc_final: 0.4709 (mmp80) REVERT: D 422 GLN cc_start: 0.7560 (mt0) cc_final: 0.7094 (mm-40) REVERT: D 612 MET cc_start: 0.6894 (mmm) cc_final: 0.6646 (mmm) REVERT: E 200 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7867 (mp10) REVERT: E 473 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7696 (tp) REVERT: F 200 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7765 (mp10) REVERT: F 612 MET cc_start: 0.7986 (mpp) cc_final: 0.7534 (mmm) REVERT: G 200 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7938 (mp10) REVERT: H 131 ARG cc_start: 0.7598 (mtp-110) cc_final: 0.7267 (ptm160) REVERT: H 200 GLN cc_start: 0.7798 (mp10) cc_final: 0.7419 (mp10) REVERT: H 422 GLN cc_start: 0.7588 (mt0) cc_final: 0.7132 (mm-40) REVERT: H 568 TYR cc_start: 0.7220 (p90) cc_final: 0.6980 (p90) outliers start: 43 outliers final: 32 residues processed: 381 average time/residue: 0.4790 time to fit residues: 278.3891 Evaluate side-chains 377 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 338 time to evaluate : 3.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain E residue 200 GLN Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain F residue 200 GLN Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 439 ASP Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 454 ASP Chi-restraints excluded: chain G residue 110 ARG Chi-restraints excluded: chain G residue 200 GLN Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 344 ILE Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 454 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 406 optimal weight: 20.0000 chunk 428 optimal weight: 8.9990 chunk 390 optimal weight: 0.5980 chunk 416 optimal weight: 4.9990 chunk 250 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 327 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 376 optimal weight: 5.9990 chunk 394 optimal weight: 8.9990 chunk 415 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 37706 Z= 0.203 Angle : 0.634 12.773 50996 Z= 0.308 Chirality : 0.041 0.190 5826 Planarity : 0.005 0.079 6608 Dihedral : 4.473 27.388 5152 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.24 % Allowed : 15.76 % Favored : 83.01 % 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: -1.07 (0.13), residues: 4711 helix: -0.38 (0.10), residues: 2800 sheet: 0.06 (0.45), residues: 152 loop : -1.14 (0.17), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 214 HIS 0.003 0.001 HIS G 534 PHE 0.008 0.001 PHE F 433 TYR 0.011 0.001 TYR A 503 ARG 0.012 0.000 ARG D 570 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 345 time to evaluate : 3.090 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: A 200 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7927 (mp10) REVERT: A 403 ARG cc_start: 0.5252 (mmp80) cc_final: 0.4782 (mmp80) REVERT: A 570 ARG cc_start: 0.6514 (mtp85) cc_final: 0.6089 (ttm-80) REVERT: B 200 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7762 (mp10) REVERT: C 131 ARG cc_start: 0.7773 (mtp-110) cc_final: 0.7347 (ptm-80) REVERT: C 200 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7922 (mp10) REVERT: D 200 GLN cc_start: 0.7874 (mp10) cc_final: 0.7505 (mp10) REVERT: D 403 ARG cc_start: 0.4907 (mmp80) cc_final: 0.4622 (mmp80) REVERT: D 612 MET cc_start: 0.6857 (mmm) cc_final: 0.6571 (mmm) REVERT: E 200 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7879 (mp10) REVERT: E 473 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7713 (tp) REVERT: F 200 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7763 (mp10) REVERT: F 612 MET cc_start: 0.8000 (mpp) cc_final: 0.7495 (mmm) REVERT: G 200 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: H 200 GLN cc_start: 0.7815 (mp10) cc_final: 0.7435 (mp10) REVERT: H 403 ARG cc_start: 0.5317 (mmp80) cc_final: 0.4886 (mmp80) REVERT: H 568 TYR cc_start: 0.7272 (p90) cc_final: 0.7044 (p90) outliers start: 41 outliers final: 34 residues processed: 378 average time/residue: 0.5052 time to fit residues: 291.1355 Evaluate side-chains 375 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 334 time to evaluate : 3.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain E residue 200 GLN Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain F residue 200 GLN Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 439 ASP Chi-restraints excluded: chain F residue 454 ASP Chi-restraints excluded: chain G residue 110 ARG Chi-restraints excluded: chain G residue 200 GLN Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 526 ASP Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 344 ILE Chi-restraints excluded: chain H residue 454 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 273 optimal weight: 1.9990 chunk 440 optimal weight: 0.9990 chunk 268 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 306 optimal weight: 0.9990 chunk 462 optimal weight: 20.0000 chunk 425 optimal weight: 4.9990 chunk 368 optimal weight: 7.9990 chunk 38 optimal weight: 0.0770 chunk 284 optimal weight: 9.9990 chunk 225 optimal weight: 0.7980 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 37706 Z= 0.168 Angle : 0.621 12.546 50996 Z= 0.301 Chirality : 0.040 0.166 5826 Planarity : 0.005 0.075 6608 Dihedral : 4.378 26.958 5152 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.31 % Allowed : 15.81 % Favored : 82.88 % 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: -0.92 (0.13), residues: 4711 helix: -0.30 (0.10), residues: 2808 sheet: 0.07 (0.46), residues: 152 loop : -1.00 (0.17), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 214 HIS 0.003 0.001 HIS B 534 PHE 0.006 0.001 PHE H 476 TYR 0.023 0.001 TYR B 213 ARG 0.013 0.000 ARG D 570 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 365 time to evaluate : 3.622 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: A 200 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7927 (mp10) REVERT: A 403 ARG cc_start: 0.5050 (mmp80) cc_final: 0.4627 (mmp80) REVERT: B 200 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7787 (mp10) REVERT: B 569 ARG cc_start: 0.6539 (tpm170) cc_final: 0.6323 (tpp-160) REVERT: C 131 ARG cc_start: 0.7773 (mtp-110) cc_final: 0.7330 (ptm-80) REVERT: C 200 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7930 (mp10) REVERT: C 569 ARG cc_start: 0.6844 (tpm170) cc_final: 0.6610 (tpp-160) REVERT: D 200 GLN cc_start: 0.7882 (mp10) cc_final: 0.7518 (mp10) REVERT: E 200 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7885 (mp10) REVERT: E 403 ARG cc_start: 0.5167 (mmp80) cc_final: 0.4807 (mmp80) REVERT: E 473 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7774 (tp) REVERT: F 200 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7766 (mp10) REVERT: F 403 ARG cc_start: 0.4784 (mmp80) cc_final: 0.4527 (mmp80) REVERT: F 612 MET cc_start: 0.7961 (mpp) cc_final: 0.7505 (mmm) REVERT: G 200 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: H 200 GLN cc_start: 0.7793 (mp10) cc_final: 0.7408 (mp10) REVERT: H 403 ARG cc_start: 0.5156 (mmp80) cc_final: 0.4808 (mmp80) REVERT: H 568 TYR cc_start: 0.7251 (p90) cc_final: 0.7046 (p90) outliers start: 44 outliers final: 36 residues processed: 395 average time/residue: 0.4941 time to fit residues: 297.1840 Evaluate side-chains 387 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 344 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain E residue 200 GLN Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain F residue 200 GLN Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 439 ASP Chi-restraints excluded: chain F residue 454 ASP Chi-restraints excluded: chain G residue 110 ARG Chi-restraints excluded: chain G residue 200 GLN Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 344 ILE Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 454 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 292 optimal weight: 8.9990 chunk 392 optimal weight: 0.8980 chunk 112 optimal weight: 20.0000 chunk 339 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 368 optimal weight: 5.9990 chunk 154 optimal weight: 0.0970 chunk 378 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 67 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.197168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.142647 restraints weight = 206718.880| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 6.55 r_work: 0.3308 rms_B_bonded: 6.30 restraints_weight: 2.0000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37706 Z= 0.163 Angle : 0.620 12.666 50996 Z= 0.300 Chirality : 0.040 0.173 5826 Planarity : 0.005 0.077 6608 Dihedral : 4.313 24.600 5152 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.86 % Favored : 94.12 % Rotamer: Outliers : 1.31 % Allowed : 15.83 % Favored : 82.85 % 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: -0.80 (0.13), residues: 4711 helix: -0.20 (0.10), residues: 2808 sheet: 0.13 (0.46), residues: 152 loop : -0.94 (0.17), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 214 HIS 0.003 0.001 HIS B 534 PHE 0.006 0.001 PHE H 467 TYR 0.021 0.001 TYR F 213 ARG 0.013 0.000 ARG D 570 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6933.30 seconds wall clock time: 123 minutes 14.25 seconds (7394.25 seconds total)