Starting phenix.real_space_refine on Tue Apr 16 23:18:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2l_17369/04_2024/8p2l_17369_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2l_17369/04_2024/8p2l_17369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2l_17369/04_2024/8p2l_17369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2l_17369/04_2024/8p2l_17369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2l_17369/04_2024/8p2l_17369_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2l_17369/04_2024/8p2l_17369_updated.pdb" } resolution = 2.68 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= 0.004 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 176 5.16 5 C 25672 2.51 5 N 7328 2.21 5 O 7584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 110": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A ARG 162": "NH1" <-> "NH2" Residue "A ARG 175": "NH1" <-> "NH2" 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 ARG 249": "NH1" <-> "NH2" Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 267": "NH1" <-> "NH2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 434": "NH1" <-> "NH2" Residue "A ARG 445": "NH1" <-> "NH2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A ARG 468": "NH1" <-> "NH2" Residue "A ARG 484": "NH1" <-> "NH2" Residue "A ARG 497": "NH1" <-> "NH2" Residue "A ARG 499": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B ARG 131": "NH1" <-> "NH2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B ARG 159": "NH1" <-> "NH2" Residue "B ARG 162": "NH1" <-> "NH2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 201": "NH1" <-> "NH2" 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 PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 267": "NH1" <-> "NH2" Residue "B ARG 285": "NH1" <-> "NH2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 395": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ARG 445": "NH1" <-> "NH2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B ARG 468": "NH1" <-> "NH2" Residue "B ARG 484": "NH1" <-> "NH2" Residue "B ARG 497": "NH1" <-> "NH2" Residue "B ARG 499": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "B ARG 535": "NH1" <-> "NH2" Residue "B ARG 537": "NH1" <-> "NH2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 157": "NH1" <-> "NH2" Residue "C ARG 159": "NH1" <-> "NH2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C ARG 175": "NH1" <-> "NH2" 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 ARG 249": "NH1" <-> "NH2" Residue "C PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 267": "NH1" <-> "NH2" Residue "C ARG 285": "NH1" <-> "NH2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C ARG 322": "NH1" <-> "NH2" Residue "C ARG 329": "NH1" <-> "NH2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C ARG 376": "NH1" <-> "NH2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C ARG 395": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C ARG 434": "NH1" <-> "NH2" Residue "C ARG 445": "NH1" <-> "NH2" Residue "C ARG 463": "NH1" <-> "NH2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C ARG 468": "NH1" <-> "NH2" Residue "C ARG 484": "NH1" <-> "NH2" Residue "C ARG 497": "NH1" <-> "NH2" Residue "C ARG 499": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "C ARG 535": "NH1" <-> "NH2" Residue "C ARG 537": "NH1" <-> "NH2" Residue "C ARG 543": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 175": "NH1" <-> "NH2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D ARG 201": "NH1" <-> "NH2" 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 ARG 249": "NH1" <-> "NH2" Residue "D PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 267": "NH1" <-> "NH2" Residue "D ARG 285": "NH1" <-> "NH2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D ARG 307": "NH1" <-> "NH2" Residue "D ARG 310": "NH1" <-> "NH2" Residue "D ARG 322": "NH1" <-> "NH2" Residue "D ARG 329": "NH1" <-> "NH2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D ARG 376": "NH1" <-> "NH2" Residue "D ARG 392": "NH1" <-> "NH2" Residue "D ARG 395": "NH1" <-> "NH2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D ARG 434": "NH1" <-> "NH2" Residue "D ARG 445": "NH1" <-> "NH2" Residue "D ARG 463": "NH1" <-> "NH2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D ARG 468": "NH1" <-> "NH2" Residue "D ARG 484": "NH1" <-> "NH2" Residue "D ARG 497": "NH1" <-> "NH2" Residue "D ARG 499": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "D ARG 517": "NH1" <-> "NH2" Residue "D ARG 535": "NH1" <-> "NH2" Residue "D ARG 537": "NH1" <-> "NH2" Residue "D ARG 543": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 141": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E ARG 159": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 175": "NH1" <-> "NH2" 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 ARG 249": "NH1" <-> "NH2" Residue "E PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 267": "NH1" <-> "NH2" Residue "E ARG 285": "NH1" <-> "NH2" Residue "E ARG 289": "NH1" <-> "NH2" Residue "E ARG 307": "NH1" <-> "NH2" Residue "E ARG 310": "NH1" <-> "NH2" Residue "E ARG 322": "NH1" <-> "NH2" Residue "E ARG 329": "NH1" <-> "NH2" Residue "E ARG 338": "NH1" <-> "NH2" Residue "E ARG 376": "NH1" <-> "NH2" Residue "E ARG 392": "NH1" <-> "NH2" Residue "E ARG 395": "NH1" <-> "NH2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E ARG 434": "NH1" <-> "NH2" Residue "E ARG 445": "NH1" <-> "NH2" Residue "E ARG 463": "NH1" <-> "NH2" Residue "E ARG 465": "NH1" <-> "NH2" Residue "E ARG 468": "NH1" <-> "NH2" Residue "E ARG 484": "NH1" <-> "NH2" Residue "E ARG 497": "NH1" <-> "NH2" Residue "E ARG 499": "NH1" <-> "NH2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "E ARG 517": "NH1" <-> "NH2" Residue "E ARG 535": "NH1" <-> "NH2" Residue "E ARG 537": "NH1" <-> "NH2" Residue "E ARG 543": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F ARG 131": "NH1" <-> "NH2" Residue "F ARG 141": "NH1" <-> "NH2" Residue "F ARG 146": "NH1" <-> "NH2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F ARG 162": "NH1" <-> "NH2" Residue "F ARG 175": "NH1" <-> "NH2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F ARG 201": "NH1" <-> "NH2" 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 ARG 249": "NH1" <-> "NH2" Residue "F PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 267": "NH1" <-> "NH2" Residue "F ARG 285": "NH1" <-> "NH2" Residue "F ARG 289": "NH1" <-> "NH2" Residue "F ARG 307": "NH1" <-> "NH2" Residue "F ARG 310": "NH1" <-> "NH2" Residue "F ARG 322": "NH1" <-> "NH2" Residue "F ARG 329": "NH1" <-> "NH2" Residue "F ARG 338": "NH1" <-> "NH2" Residue "F ARG 376": "NH1" <-> "NH2" Residue "F ARG 392": "NH1" <-> "NH2" Residue "F ARG 395": "NH1" <-> "NH2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F ARG 434": "NH1" <-> "NH2" Residue "F ARG 445": "NH1" <-> "NH2" Residue "F ARG 463": "NH1" <-> "NH2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F ARG 468": "NH1" <-> "NH2" Residue "F ARG 484": "NH1" <-> "NH2" Residue "F ARG 497": "NH1" <-> "NH2" Residue "F ARG 499": "NH1" <-> "NH2" Residue "F ARG 512": "NH1" <-> "NH2" Residue "F ARG 517": "NH1" <-> "NH2" Residue "F ARG 535": "NH1" <-> "NH2" Residue "F ARG 537": "NH1" <-> "NH2" Residue "F ARG 543": "NH1" <-> "NH2" Residue "G ARG 67": "NH1" <-> "NH2" Residue "G ARG 86": "NH1" <-> "NH2" Residue "G ARG 110": "NH1" <-> "NH2" Residue "G ARG 121": "NH1" <-> "NH2" Residue "G ARG 131": "NH1" <-> "NH2" Residue "G ARG 141": "NH1" <-> "NH2" Residue "G ARG 146": "NH1" <-> "NH2" Residue "G ARG 157": "NH1" <-> "NH2" Residue "G ARG 159": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 175": "NH1" <-> "NH2" 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 ARG 249": "NH1" <-> "NH2" Residue "G PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 267": "NH1" <-> "NH2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G ARG 289": "NH1" <-> "NH2" Residue "G ARG 307": "NH1" <-> "NH2" Residue "G ARG 310": "NH1" <-> "NH2" Residue "G ARG 322": "NH1" <-> "NH2" Residue "G ARG 329": "NH1" <-> "NH2" Residue "G ARG 338": "NH1" <-> "NH2" Residue "G ARG 376": "NH1" <-> "NH2" Residue "G ARG 392": "NH1" <-> "NH2" Residue "G ARG 395": "NH1" <-> "NH2" Residue "G ARG 403": "NH1" <-> "NH2" Residue "G ARG 434": "NH1" <-> "NH2" Residue "G ARG 445": "NH1" <-> "NH2" Residue "G ARG 463": "NH1" <-> "NH2" Residue "G ARG 465": "NH1" <-> "NH2" Residue "G ARG 468": "NH1" <-> "NH2" Residue "G ARG 484": "NH1" <-> "NH2" Residue "G ARG 497": "NH1" <-> "NH2" Residue "G ARG 499": "NH1" <-> "NH2" Residue "G ARG 512": "NH1" <-> "NH2" Residue "G ARG 517": "NH1" <-> "NH2" Residue "G ARG 535": "NH1" <-> "NH2" Residue "G ARG 537": "NH1" <-> "NH2" Residue "G ARG 543": "NH1" <-> "NH2" Residue "H ARG 67": "NH1" <-> "NH2" Residue "H ARG 86": "NH1" <-> "NH2" Residue "H ARG 110": "NH1" <-> "NH2" Residue "H ARG 121": "NH1" <-> "NH2" Residue "H ARG 131": "NH1" <-> "NH2" Residue "H ARG 141": "NH1" <-> "NH2" Residue "H ARG 146": "NH1" <-> "NH2" Residue "H ARG 157": "NH1" <-> "NH2" Residue "H ARG 159": "NH1" <-> "NH2" Residue "H ARG 162": "NH1" <-> "NH2" Residue "H ARG 175": "NH1" <-> "NH2" Residue "H ARG 182": "NH1" <-> "NH2" Residue "H ARG 201": "NH1" <-> "NH2" 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 ARG 249": "NH1" <-> "NH2" Residue "H PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 267": "NH1" <-> "NH2" Residue "H ARG 285": "NH1" <-> "NH2" Residue "H ARG 289": "NH1" <-> "NH2" Residue "H ARG 307": "NH1" <-> "NH2" Residue "H ARG 310": "NH1" <-> "NH2" Residue "H ARG 322": "NH1" <-> "NH2" Residue "H ARG 329": "NH1" <-> "NH2" Residue "H ARG 338": "NH1" <-> "NH2" Residue "H ARG 376": "NH1" <-> "NH2" Residue "H ARG 392": "NH1" <-> "NH2" Residue "H ARG 395": "NH1" <-> "NH2" Residue "H ARG 403": "NH1" <-> "NH2" Residue "H ARG 434": "NH1" <-> "NH2" Residue "H ARG 445": "NH1" <-> "NH2" Residue "H ARG 463": "NH1" <-> "NH2" Residue "H ARG 465": "NH1" <-> "NH2" Residue "H ARG 468": "NH1" <-> "NH2" Residue "H ARG 484": "NH1" <-> "NH2" Residue "H ARG 497": "NH1" <-> "NH2" Residue "H ARG 499": "NH1" <-> "NH2" Residue "H ARG 512": "NH1" <-> "NH2" Residue "H ARG 517": "NH1" <-> "NH2" Residue "H ARG 535": "NH1" <-> "NH2" Residue "H ARG 537": "NH1" <-> "NH2" Residue "H ARG 543": "NH1" <-> "NH2" Residue "J ARG 715": "NH1" <-> "NH2" Residue "J ARG 716": "NH1" <-> "NH2" Residue "J ARG 733": "NH1" <-> "NH2" Residue "J ARG 736": "NH1" <-> "NH2" Residue "J ARG 774": "NH1" <-> "NH2" Residue "J ARG 821": "NH1" <-> "NH2" Residue "J ARG 845": "NH1" <-> "NH2" Residue "I ARG 715": "NH1" <-> "NH2" Residue "I ARG 716": "NH1" <-> "NH2" Residue "I ARG 733": "NH1" <-> "NH2" Residue "I ARG 736": "NH1" <-> "NH2" Residue "I PHE 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 774": "NH1" <-> "NH2" Residue "I ARG 821": "NH1" <-> "NH2" Residue "I ARG 845": "NH1" <-> "NH2" Residue "K ARG 715": "NH1" <-> "NH2" Residue "K ARG 716": "NH1" <-> "NH2" Residue "K ARG 733": "NH1" <-> "NH2" Residue "K ARG 736": "NH1" <-> "NH2" Residue "K PHE 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 774": "NH1" <-> "NH2" Residue "K ARG 821": "NH1" <-> "NH2" Residue "K ARG 845": "NH1" <-> "NH2" Residue "L ARG 715": "NH1" <-> "NH2" Residue "L ARG 716": "NH1" <-> "NH2" Residue "L ARG 733": "NH1" <-> "NH2" Residue "L ARG 736": "NH1" <-> "NH2" Residue "L ARG 774": "NH1" <-> "NH2" Residue "L ARG 821": "NH1" <-> "NH2" Residue "L ARG 845": "NH1" <-> "NH2" Residue "M ARG 715": "NH1" <-> "NH2" Residue "M ARG 716": "NH1" <-> "NH2" Residue "M ARG 733": "NH1" <-> "NH2" Residue "M ARG 736": "NH1" <-> "NH2" Residue "M ARG 774": "NH1" <-> "NH2" Residue "M ARG 821": "NH1" <-> "NH2" Residue "M ARG 845": "NH1" <-> "NH2" Residue "N ARG 715": "NH1" <-> "NH2" Residue "N ARG 716": "NH1" <-> "NH2" Residue "N ARG 733": "NH1" <-> "NH2" Residue "N ARG 736": "NH1" <-> "NH2" Residue "N ARG 774": "NH1" <-> "NH2" Residue "N ARG 821": "NH1" <-> "NH2" Residue "N ARG 845": "NH1" <-> "NH2" Residue "O ARG 715": "NH1" <-> "NH2" Residue "O ARG 716": "NH1" <-> "NH2" Residue "O ARG 733": "NH1" <-> "NH2" Residue "O ARG 736": "NH1" <-> "NH2" Residue "O PHE 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 774": "NH1" <-> "NH2" Residue "O ARG 821": "NH1" <-> "NH2" Residue "O ARG 845": "NH1" <-> "NH2" Residue "P ARG 715": "NH1" <-> "NH2" Residue "P ARG 716": "NH1" <-> "NH2" Residue "P ARG 733": "NH1" <-> "NH2" Residue "P ARG 736": "NH1" <-> "NH2" Residue "P ARG 774": "NH1" <-> "NH2" Residue "P ARG 821": "NH1" <-> "NH2" Residue "P ARG 845": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 40776 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3845 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 17, 'TRANS': 478} Chain: "B" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3845 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 17, 'TRANS': 478} Chain: "C" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3845 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 17, 'TRANS': 478} Chain: "D" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3845 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 17, 'TRANS': 478} Chain: "E" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3845 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 17, 'TRANS': 478} Chain: "F" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3845 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 17, 'TRANS': 478} Chain: "G" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3845 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 17, 'TRANS': 478} Chain: "H" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3845 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 17, 'TRANS': 478} Chain: "J" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1208 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "I" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1208 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "K" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1208 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "L" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1208 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "M" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1208 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "N" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1208 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "O" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1208 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "P" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1208 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.22, per 1000 atoms: 0.47 Number of scatterers: 40776 At special positions: 0 Unit cell: (210.84, 210.84, 87.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 176 16.00 P 16 15.00 O 7584 8.00 N 7328 7.00 C 25672 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: 16.33 Conformation dependent library (CDL) restraints added in 7.5 seconds 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9632 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 320 helices and 8 sheets defined 65.7% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.32 Creating SS restraints... Processing helix chain 'A' and resid 57 through 80 removed outlier: 4.741A pdb=" N LEU A 69 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Proline residue: A 70 - end of helix removed outlier: 3.545A pdb=" N LEU A 76 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 104 Processing helix chain 'A' and resid 109 through 122 Processing helix chain 'A' and resid 125 through 134 removed outlier: 4.533A pdb=" N LEU A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 154 through 160 Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.968A pdb=" N LYS A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.505A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.690A pdb=" N VAL A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 236 Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 250 through 253 No H-bonds generated for 'chain 'A' and resid 250 through 253' Processing helix chain 'A' and resid 255 through 258 No H-bonds generated for 'chain 'A' and resid 255 through 258' Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 292 through 302 removed outlier: 4.705A pdb=" N GLU A 297 " --> pdb=" O ALA A 294 " (cutoff:3.500A) Proline residue: A 298 - end of helix removed outlier: 3.678A pdb=" N ALA A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 311 removed outlier: 3.840A pdb=" N PHE A 308 " --> pdb=" O PRO A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 removed outlier: 4.144A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Proline residue: A 332 - end of helix Processing helix chain 'A' and resid 339 through 359 Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 384 through 396 Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 427 through 435 removed outlier: 4.743A pdb=" N GLU A 431 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 460 through 476 Processing helix chain 'A' and resid 487 through 494 Processing helix chain 'A' and resid 496 through 507 removed outlier: 4.089A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR A 503 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 506 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A 507 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 532 through 549 removed outlier: 3.906A pdb=" N LEU A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N HIS A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N SER A 548 " --> pdb=" O GLU A 544 " (cutoff:3.500A) Proline residue: A 549 - end of helix Processing helix chain 'B' and resid 57 through 80 removed outlier: 4.742A pdb=" N LEU B 69 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Proline residue: B 70 - end of helix removed outlier: 3.544A pdb=" N LEU B 76 " --> pdb=" O GLN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 104 Processing helix chain 'B' and resid 109 through 122 Processing helix chain 'B' and resid 125 through 134 removed outlier: 4.533A pdb=" N LEU B 129 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.968A pdb=" N LYS B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 removed outlier: 3.506A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.691A pdb=" N VAL B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 236 Processing helix chain 'B' and resid 238 through 247 Processing helix chain 'B' and resid 250 through 253 No H-bonds generated for 'chain 'B' and resid 250 through 253' Processing helix chain 'B' and resid 255 through 258 No H-bonds generated for 'chain 'B' and resid 255 through 258' Processing helix chain 'B' and resid 264 through 279 Processing helix chain 'B' and resid 284 through 289 Processing helix chain 'B' and resid 292 through 302 removed outlier: 4.706A pdb=" N GLU B 297 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Proline residue: B 298 - end of helix removed outlier: 3.680A pdb=" N ALA B 301 " --> pdb=" O PRO B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 311 removed outlier: 3.841A pdb=" N PHE B 308 " --> pdb=" O PRO B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 removed outlier: 4.142A pdb=" N LEU B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Proline residue: B 332 - end of helix Processing helix chain 'B' and resid 339 through 359 Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 370 through 379 Processing helix chain 'B' and resid 384 through 396 Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 414 through 423 Processing helix chain 'B' and resid 427 through 435 removed outlier: 4.744A pdb=" N GLU B 431 " --> pdb=" O LYS B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 445 Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 460 through 476 Processing helix chain 'B' and resid 487 through 494 Processing helix chain 'B' and resid 496 through 507 removed outlier: 4.088A pdb=" N GLN B 500 " --> pdb=" O ARG B 497 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR B 503 " --> pdb=" O GLN B 500 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 506 " --> pdb=" O TYR B 503 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B 507 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 517 No H-bonds generated for 'chain 'B' and resid 515 through 517' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 532 through 549 removed outlier: 3.905A pdb=" N LEU B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N HIS B 547 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N SER B 548 " --> pdb=" O GLU B 544 " (cutoff:3.500A) Proline residue: B 549 - end of helix Processing helix chain 'C' and resid 57 through 80 removed outlier: 4.745A pdb=" N LEU C 69 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Proline residue: C 70 - end of helix removed outlier: 3.545A pdb=" N LEU C 76 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 104 Processing helix chain 'C' and resid 109 through 122 Processing helix chain 'C' and resid 125 through 134 removed outlier: 4.531A pdb=" N LEU C 129 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.966A pdb=" N LYS C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 removed outlier: 3.505A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 204 Processing helix chain 'C' and resid 207 through 216 removed outlier: 3.691A pdb=" N VAL C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 236 Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'C' and resid 250 through 253 No H-bonds generated for 'chain 'C' and resid 250 through 253' Processing helix chain 'C' and resid 255 through 258 No H-bonds generated for 'chain 'C' and resid 255 through 258' Processing helix chain 'C' and resid 264 through 279 Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 292 through 302 removed outlier: 4.706A pdb=" N GLU C 297 " --> pdb=" O ALA C 294 " (cutoff:3.500A) Proline residue: C 298 - end of helix removed outlier: 3.681A pdb=" N ALA C 301 " --> pdb=" O PRO C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 311 removed outlier: 3.841A pdb=" N PHE C 308 " --> pdb=" O PRO C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 4.142A pdb=" N LEU C 330 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL C 331 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Proline residue: C 332 - end of helix Processing helix chain 'C' and resid 339 through 359 Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 370 through 379 Processing helix chain 'C' and resid 384 through 396 Processing helix chain 'C' and resid 409 through 411 No H-bonds generated for 'chain 'C' and resid 409 through 411' Processing helix chain 'C' and resid 414 through 423 Processing helix chain 'C' and resid 427 through 435 removed outlier: 4.744A pdb=" N GLU C 431 " --> pdb=" O LYS C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 448 through 453 Processing helix chain 'C' and resid 460 through 476 Processing helix chain 'C' and resid 487 through 494 Processing helix chain 'C' and resid 496 through 507 removed outlier: 4.090A pdb=" N GLN C 500 " --> pdb=" O ARG C 497 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR C 503 " --> pdb=" O GLN C 500 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL C 506 " --> pdb=" O TYR C 503 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C 507 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 517 No H-bonds generated for 'chain 'C' and resid 515 through 517' Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 532 through 549 removed outlier: 3.906A pdb=" N LEU C 546 " --> pdb=" O ALA C 542 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N HIS C 547 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N SER C 548 " --> pdb=" O GLU C 544 " (cutoff:3.500A) Proline residue: C 549 - end of helix Processing helix chain 'D' and resid 57 through 80 removed outlier: 4.743A pdb=" N LEU D 69 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Proline residue: D 70 - end of helix removed outlier: 3.545A pdb=" N LEU D 76 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 104 Processing helix chain 'D' and resid 109 through 122 Processing helix chain 'D' and resid 125 through 134 removed outlier: 4.532A pdb=" N LEU D 129 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 150 Processing helix chain 'D' and resid 154 through 160 Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.969A pdb=" N LYS D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 193 removed outlier: 3.505A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 204 Processing helix chain 'D' and resid 207 through 216 removed outlier: 3.693A pdb=" N VAL D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 236 Processing helix chain 'D' and resid 238 through 247 Processing helix chain 'D' and resid 250 through 253 No H-bonds generated for 'chain 'D' and resid 250 through 253' Processing helix chain 'D' and resid 255 through 258 No H-bonds generated for 'chain 'D' and resid 255 through 258' Processing helix chain 'D' and resid 264 through 279 Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'D' and resid 292 through 302 removed outlier: 4.706A pdb=" N GLU D 297 " --> pdb=" O ALA D 294 " (cutoff:3.500A) Proline residue: D 298 - end of helix removed outlier: 3.681A pdb=" N ALA D 301 " --> pdb=" O PRO D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 311 removed outlier: 3.842A pdb=" N PHE D 308 " --> pdb=" O PRO D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 removed outlier: 4.144A pdb=" N LEU D 330 " --> pdb=" O ASP D 326 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Proline residue: D 332 - end of helix Processing helix chain 'D' and resid 339 through 359 Processing helix chain 'D' and resid 362 through 367 Processing helix chain 'D' and resid 370 through 379 Processing helix chain 'D' and resid 384 through 396 Processing helix chain 'D' and resid 409 through 411 No H-bonds generated for 'chain 'D' and resid 409 through 411' Processing helix chain 'D' and resid 414 through 423 Processing helix chain 'D' and resid 427 through 435 removed outlier: 4.743A pdb=" N GLU D 431 " --> pdb=" O LYS D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 445 Processing helix chain 'D' and resid 448 through 453 Processing helix chain 'D' and resid 460 through 476 Processing helix chain 'D' and resid 487 through 494 Processing helix chain 'D' and resid 496 through 507 removed outlier: 4.087A pdb=" N GLN D 500 " --> pdb=" O ARG D 497 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR D 503 " --> pdb=" O GLN D 500 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL D 506 " --> pdb=" O TYR D 503 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER D 507 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 517 No H-bonds generated for 'chain 'D' and resid 515 through 517' Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 532 through 549 removed outlier: 3.905A pdb=" N LEU D 546 " --> pdb=" O ALA D 542 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N HIS D 547 " --> pdb=" O ARG D 543 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N SER D 548 " --> pdb=" O GLU D 544 " (cutoff:3.500A) Proline residue: D 549 - end of helix Processing helix chain 'E' and resid 57 through 80 removed outlier: 4.741A pdb=" N LEU E 69 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Proline residue: E 70 - end of helix removed outlier: 3.545A pdb=" N LEU E 76 " --> pdb=" O GLN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 104 Processing helix chain 'E' and resid 109 through 122 Processing helix chain 'E' and resid 125 through 134 removed outlier: 4.531A pdb=" N LEU E 129 " --> pdb=" O GLY E 125 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 150 Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 165 through 173 removed outlier: 3.969A pdb=" N LYS E 173 " --> pdb=" O LEU E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 193 removed outlier: 3.506A pdb=" N SER E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 204 Processing helix chain 'E' and resid 207 through 216 removed outlier: 3.690A pdb=" N VAL E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 236 Processing helix chain 'E' and resid 238 through 247 Processing helix chain 'E' and resid 250 through 253 No H-bonds generated for 'chain 'E' and resid 250 through 253' Processing helix chain 'E' and resid 255 through 258 No H-bonds generated for 'chain 'E' and resid 255 through 258' Processing helix chain 'E' and resid 264 through 279 Processing helix chain 'E' and resid 284 through 289 Processing helix chain 'E' and resid 292 through 302 removed outlier: 4.706A pdb=" N GLU E 297 " --> pdb=" O ALA E 294 " (cutoff:3.500A) Proline residue: E 298 - end of helix removed outlier: 3.681A pdb=" N ALA E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 311 removed outlier: 3.840A pdb=" N PHE E 308 " --> pdb=" O PRO E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 335 removed outlier: 4.144A pdb=" N LEU E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL E 331 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Proline residue: E 332 - end of helix Processing helix chain 'E' and resid 339 through 359 Processing helix chain 'E' and resid 362 through 367 Processing helix chain 'E' and resid 370 through 379 Processing helix chain 'E' and resid 384 through 396 Processing helix chain 'E' and resid 409 through 411 No H-bonds generated for 'chain 'E' and resid 409 through 411' Processing helix chain 'E' and resid 414 through 423 Processing helix chain 'E' and resid 427 through 435 removed outlier: 4.743A pdb=" N GLU E 431 " --> pdb=" O LYS E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 445 Processing helix chain 'E' and resid 448 through 453 Processing helix chain 'E' and resid 460 through 476 Processing helix chain 'E' and resid 487 through 494 Processing helix chain 'E' and resid 496 through 507 removed outlier: 4.089A pdb=" N GLN E 500 " --> pdb=" O ARG E 497 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR E 503 " --> pdb=" O GLN E 500 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL E 506 " --> pdb=" O TYR E 503 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER E 507 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 517 No H-bonds generated for 'chain 'E' and resid 515 through 517' Processing helix chain 'E' and resid 520 through 525 Processing helix chain 'E' and resid 532 through 549 removed outlier: 3.904A pdb=" N LEU E 546 " --> pdb=" O ALA E 542 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N HIS E 547 " --> pdb=" O ARG E 543 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N SER E 548 " --> pdb=" O GLU E 544 " (cutoff:3.500A) Proline residue: E 549 - end of helix Processing helix chain 'F' and resid 57 through 80 removed outlier: 4.743A pdb=" N LEU F 69 " --> pdb=" O GLU F 66 " (cutoff:3.500A) Proline residue: F 70 - end of helix removed outlier: 3.545A pdb=" N LEU F 76 " --> pdb=" O GLN F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 104 Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 125 through 134 removed outlier: 4.532A pdb=" N LEU F 129 " --> pdb=" O GLY F 125 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 150 Processing helix chain 'F' and resid 154 through 160 Processing helix chain 'F' and resid 165 through 173 removed outlier: 3.967A pdb=" N LYS F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 193 removed outlier: 3.506A pdb=" N SER F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 204 Processing helix chain 'F' and resid 207 through 216 removed outlier: 3.690A pdb=" N VAL F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 236 Processing helix chain 'F' and resid 238 through 247 Processing helix chain 'F' and resid 250 through 253 No H-bonds generated for 'chain 'F' and resid 250 through 253' Processing helix chain 'F' and resid 255 through 258 No H-bonds generated for 'chain 'F' and resid 255 through 258' Processing helix chain 'F' and resid 264 through 279 Processing helix chain 'F' and resid 284 through 289 Processing helix chain 'F' and resid 292 through 302 removed outlier: 4.706A pdb=" N GLU F 297 " --> pdb=" O ALA F 294 " (cutoff:3.500A) Proline residue: F 298 - end of helix removed outlier: 3.680A pdb=" N ALA F 301 " --> pdb=" O PRO F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 311 removed outlier: 3.841A pdb=" N PHE F 308 " --> pdb=" O PRO F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 335 removed outlier: 4.143A pdb=" N LEU F 330 " --> pdb=" O ASP F 326 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL F 331 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Proline residue: F 332 - end of helix Processing helix chain 'F' and resid 339 through 359 Processing helix chain 'F' and resid 362 through 367 Processing helix chain 'F' and resid 370 through 379 Processing helix chain 'F' and resid 384 through 396 Processing helix chain 'F' and resid 409 through 411 No H-bonds generated for 'chain 'F' and resid 409 through 411' Processing helix chain 'F' and resid 414 through 423 Processing helix chain 'F' and resid 427 through 435 removed outlier: 4.743A pdb=" N GLU F 431 " --> pdb=" O LYS F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 445 Processing helix chain 'F' and resid 448 through 453 Processing helix chain 'F' and resid 460 through 476 Processing helix chain 'F' and resid 487 through 494 Processing helix chain 'F' and resid 496 through 507 removed outlier: 4.087A pdb=" N GLN F 500 " --> pdb=" O ARG F 497 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR F 503 " --> pdb=" O GLN F 500 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL F 506 " --> pdb=" O TYR F 503 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER F 507 " --> pdb=" O GLY F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 517 No H-bonds generated for 'chain 'F' and resid 515 through 517' Processing helix chain 'F' and resid 520 through 525 Processing helix chain 'F' and resid 532 through 549 removed outlier: 3.905A pdb=" N LEU F 546 " --> pdb=" O ALA F 542 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N HIS F 547 " --> pdb=" O ARG F 543 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N SER F 548 " --> pdb=" O GLU F 544 " (cutoff:3.500A) Proline residue: F 549 - end of helix Processing helix chain 'G' and resid 57 through 80 removed outlier: 4.742A pdb=" N LEU G 69 " --> pdb=" O GLU G 66 " (cutoff:3.500A) Proline residue: G 70 - end of helix removed outlier: 3.545A pdb=" N LEU G 76 " --> pdb=" O GLN G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 104 Processing helix chain 'G' and resid 109 through 122 Processing helix chain 'G' and resid 125 through 134 removed outlier: 4.533A pdb=" N LEU G 129 " --> pdb=" O GLY G 125 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 154 through 160 Processing helix chain 'G' and resid 165 through 173 removed outlier: 3.967A pdb=" N LYS G 173 " --> pdb=" O LEU G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 193 removed outlier: 3.506A pdb=" N SER G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 204 Processing helix chain 'G' and resid 207 through 216 removed outlier: 3.689A pdb=" N VAL G 211 " --> pdb=" O GLY G 207 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG G 216 " --> pdb=" O LEU G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 236 Processing helix chain 'G' and resid 238 through 247 Processing helix chain 'G' and resid 250 through 253 No H-bonds generated for 'chain 'G' and resid 250 through 253' Processing helix chain 'G' and resid 255 through 258 No H-bonds generated for 'chain 'G' and resid 255 through 258' Processing helix chain 'G' and resid 264 through 279 Processing helix chain 'G' and resid 284 through 289 Processing helix chain 'G' and resid 292 through 302 removed outlier: 4.706A pdb=" N GLU G 297 " --> pdb=" O ALA G 294 " (cutoff:3.500A) Proline residue: G 298 - end of helix removed outlier: 3.679A pdb=" N ALA G 301 " --> pdb=" O PRO G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 311 removed outlier: 3.841A pdb=" N PHE G 308 " --> pdb=" O PRO G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 335 removed outlier: 4.142A pdb=" N LEU G 330 " --> pdb=" O ASP G 326 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL G 331 " --> pdb=" O LEU G 327 " (cutoff:3.500A) Proline residue: G 332 - end of helix Processing helix chain 'G' and resid 339 through 359 Processing helix chain 'G' and resid 362 through 367 Processing helix chain 'G' and resid 370 through 379 Processing helix chain 'G' and resid 384 through 396 Processing helix chain 'G' and resid 409 through 411 No H-bonds generated for 'chain 'G' and resid 409 through 411' Processing helix chain 'G' and resid 414 through 423 Processing helix chain 'G' and resid 427 through 435 removed outlier: 4.743A pdb=" N GLU G 431 " --> pdb=" O LYS G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 445 Processing helix chain 'G' and resid 448 through 453 Processing helix chain 'G' and resid 460 through 476 Processing helix chain 'G' and resid 487 through 494 Processing helix chain 'G' and resid 496 through 507 removed outlier: 4.087A pdb=" N GLN G 500 " --> pdb=" O ARG G 497 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR G 503 " --> pdb=" O GLN G 500 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL G 506 " --> pdb=" O TYR G 503 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER G 507 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 515 through 517 No H-bonds generated for 'chain 'G' and resid 515 through 517' Processing helix chain 'G' and resid 520 through 525 Processing helix chain 'G' and resid 532 through 549 removed outlier: 3.905A pdb=" N LEU G 546 " --> pdb=" O ALA G 542 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N HIS G 547 " --> pdb=" O ARG G 543 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N SER G 548 " --> pdb=" O GLU G 544 " (cutoff:3.500A) Proline residue: G 549 - end of helix Processing helix chain 'H' and resid 57 through 80 removed outlier: 4.740A pdb=" N LEU H 69 " --> pdb=" O GLU H 66 " (cutoff:3.500A) Proline residue: H 70 - end of helix removed outlier: 3.545A pdb=" N LEU H 76 " --> pdb=" O GLN H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 104 Processing helix chain 'H' and resid 109 through 122 Processing helix chain 'H' and resid 125 through 134 removed outlier: 4.531A pdb=" N LEU H 129 " --> pdb=" O GLY H 125 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 150 Processing helix chain 'H' and resid 154 through 160 Processing helix chain 'H' and resid 165 through 173 removed outlier: 3.969A pdb=" N LYS H 173 " --> pdb=" O LEU H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.506A pdb=" N SER H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 204 Processing helix chain 'H' and resid 207 through 216 removed outlier: 3.688A pdb=" N VAL H 211 " --> pdb=" O GLY H 207 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG H 216 " --> pdb=" O LEU H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 236 Processing helix chain 'H' and resid 238 through 247 Processing helix chain 'H' and resid 250 through 253 No H-bonds generated for 'chain 'H' and resid 250 through 253' Processing helix chain 'H' and resid 255 through 258 No H-bonds generated for 'chain 'H' and resid 255 through 258' Processing helix chain 'H' and resid 264 through 279 Processing helix chain 'H' and resid 284 through 289 Processing helix chain 'H' and resid 292 through 302 removed outlier: 4.706A pdb=" N GLU H 297 " --> pdb=" O ALA H 294 " (cutoff:3.500A) Proline residue: H 298 - end of helix removed outlier: 3.680A pdb=" N ALA H 301 " --> pdb=" O PRO H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 305 through 311 removed outlier: 3.840A pdb=" N PHE H 308 " --> pdb=" O PRO H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 335 removed outlier: 4.142A pdb=" N LEU H 330 " --> pdb=" O ASP H 326 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL H 331 " --> pdb=" O LEU H 327 " (cutoff:3.500A) Proline residue: H 332 - end of helix Processing helix chain 'H' and resid 339 through 359 Processing helix chain 'H' and resid 362 through 367 Processing helix chain 'H' and resid 370 through 379 Processing helix chain 'H' and resid 384 through 396 Processing helix chain 'H' and resid 409 through 411 No H-bonds generated for 'chain 'H' and resid 409 through 411' Processing helix chain 'H' and resid 414 through 423 Processing helix chain 'H' and resid 427 through 435 removed outlier: 4.744A pdb=" N GLU H 431 " --> pdb=" O LYS H 428 " (cutoff:3.500A) Processing helix chain 'H' and resid 440 through 445 Processing helix chain 'H' and resid 448 through 453 Processing helix chain 'H' and resid 460 through 476 Processing helix chain 'H' and resid 487 through 494 Processing helix chain 'H' and resid 496 through 507 removed outlier: 4.089A pdb=" N GLN H 500 " --> pdb=" O ARG H 497 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR H 503 " --> pdb=" O GLN H 500 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL H 506 " --> pdb=" O TYR H 503 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER H 507 " --> pdb=" O GLY H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 515 through 517 No H-bonds generated for 'chain 'H' and resid 515 through 517' Processing helix chain 'H' and resid 520 through 525 Processing helix chain 'H' and resid 532 through 549 removed outlier: 3.905A pdb=" N LEU H 546 " --> pdb=" O ALA H 542 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N HIS H 547 " --> pdb=" O ARG H 543 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N SER H 548 " --> pdb=" O GLU H 544 " (cutoff:3.500A) Proline residue: H 549 - end of helix Processing helix chain 'J' and resid 720 through 732 Processing helix chain 'J' and resid 751 through 759 Processing helix chain 'J' and resid 771 through 775 removed outlier: 4.259A pdb=" N ARG J 774 " --> pdb=" O SER J 771 " (cutoff:3.500A) Processing helix chain 'J' and resid 784 through 794 Processing helix chain 'J' and resid 821 through 825 Processing helix chain 'J' and resid 836 through 848 Processing helix chain 'I' and resid 720 through 732 Processing helix chain 'I' and resid 751 through 759 Processing helix chain 'I' and resid 771 through 775 removed outlier: 4.257A pdb=" N ARG I 774 " --> pdb=" O SER I 771 " (cutoff:3.500A) Processing helix chain 'I' and resid 784 through 794 Processing helix chain 'I' and resid 821 through 825 Processing helix chain 'I' and resid 836 through 848 Processing helix chain 'K' and resid 720 through 732 Processing helix chain 'K' and resid 751 through 759 Processing helix chain 'K' and resid 771 through 775 removed outlier: 4.259A pdb=" N ARG K 774 " --> pdb=" O SER K 771 " (cutoff:3.500A) Processing helix chain 'K' and resid 784 through 794 Processing helix chain 'K' and resid 821 through 825 Processing helix chain 'K' and resid 836 through 848 Processing helix chain 'L' and resid 720 through 732 Processing helix chain 'L' and resid 751 through 759 Processing helix chain 'L' and resid 771 through 775 removed outlier: 4.257A pdb=" N ARG L 774 " --> pdb=" O SER L 771 " (cutoff:3.500A) Processing helix chain 'L' and resid 784 through 794 Processing helix chain 'L' and resid 821 through 825 Processing helix chain 'L' and resid 836 through 848 Processing helix chain 'M' and resid 720 through 732 Processing helix chain 'M' and resid 751 through 759 Processing helix chain 'M' and resid 771 through 775 removed outlier: 4.257A pdb=" N ARG M 774 " --> pdb=" O SER M 771 " (cutoff:3.500A) Processing helix chain 'M' and resid 784 through 794 Processing helix chain 'M' and resid 821 through 825 Processing helix chain 'M' and resid 836 through 848 Processing helix chain 'N' and resid 720 through 732 Processing helix chain 'N' and resid 751 through 759 Processing helix chain 'N' and resid 771 through 775 removed outlier: 4.257A pdb=" N ARG N 774 " --> pdb=" O SER N 771 " (cutoff:3.500A) Processing helix chain 'N' and resid 784 through 794 Processing helix chain 'N' and resid 821 through 825 Processing helix chain 'N' and resid 836 through 848 Processing helix chain 'O' and resid 720 through 732 Processing helix chain 'O' and resid 751 through 759 Processing helix chain 'O' and resid 771 through 775 removed outlier: 4.257A pdb=" N ARG O 774 " --> pdb=" O SER O 771 " (cutoff:3.500A) Processing helix chain 'O' and resid 784 through 794 Processing helix chain 'O' and resid 821 through 825 Processing helix chain 'O' and resid 836 through 848 Processing helix chain 'P' and resid 720 through 732 Processing helix chain 'P' and resid 751 through 759 Processing helix chain 'P' and resid 771 through 775 removed outlier: 4.261A pdb=" N ARG P 774 " --> pdb=" O SER P 771 " (cutoff:3.500A) Processing helix chain 'P' and resid 784 through 794 Processing helix chain 'P' and resid 821 through 825 Processing helix chain 'P' and resid 836 through 848 Processing sheet with id= A, first strand: chain 'J' and resid 710 through 714 removed outlier: 6.575A pdb=" N HIS J 762 " --> pdb=" O PHE J 711 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N SER J 713 " --> pdb=" O HIS J 762 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE J 764 " --> pdb=" O SER J 713 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASN J 798 " --> pdb=" O PHE J 763 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU J 765 " --> pdb=" O ASN J 798 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE J 800 " --> pdb=" O LEU J 765 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU J 767 " --> pdb=" O ILE J 800 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE J 802 " --> pdb=" O LEU J 767 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'I' and resid 710 through 714 removed outlier: 6.574A pdb=" N HIS I 762 " --> pdb=" O PHE I 711 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N SER I 713 " --> pdb=" O HIS I 762 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE I 764 " --> pdb=" O SER I 713 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ASN I 798 " --> pdb=" O PHE I 763 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU I 765 " --> pdb=" O ASN I 798 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE I 800 " --> pdb=" O LEU I 765 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU I 767 " --> pdb=" O ILE I 800 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE I 802 " --> pdb=" O LEU I 767 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 710 through 714 removed outlier: 6.575A pdb=" N HIS K 762 " --> pdb=" O PHE K 711 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N SER K 713 " --> pdb=" O HIS K 762 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE K 764 " --> pdb=" O SER K 713 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASN K 798 " --> pdb=" O PHE K 763 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU K 765 " --> pdb=" O ASN K 798 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE K 800 " --> pdb=" O LEU K 765 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU K 767 " --> pdb=" O ILE K 800 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE K 802 " --> pdb=" O LEU K 767 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 710 through 714 removed outlier: 6.574A pdb=" N HIS L 762 " --> pdb=" O PHE L 711 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N SER L 713 " --> pdb=" O HIS L 762 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE L 764 " --> pdb=" O SER L 713 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASN L 798 " --> pdb=" O PHE L 763 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU L 765 " --> pdb=" O ASN L 798 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE L 800 " --> pdb=" O LEU L 765 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU L 767 " --> pdb=" O ILE L 800 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE L 802 " --> pdb=" O LEU L 767 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'M' and resid 710 through 714 removed outlier: 6.574A pdb=" N HIS M 762 " --> pdb=" O PHE M 711 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N SER M 713 " --> pdb=" O HIS M 762 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE M 764 " --> pdb=" O SER M 713 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASN M 798 " --> pdb=" O PHE M 763 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU M 765 " --> pdb=" O ASN M 798 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE M 800 " --> pdb=" O LEU M 765 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU M 767 " --> pdb=" O ILE M 800 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE M 802 " --> pdb=" O LEU M 767 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'N' and resid 710 through 714 removed outlier: 6.573A pdb=" N HIS N 762 " --> pdb=" O PHE N 711 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N SER N 713 " --> pdb=" O HIS N 762 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE N 764 " --> pdb=" O SER N 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASN N 798 " --> pdb=" O PHE N 763 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU N 765 " --> pdb=" O ASN N 798 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE N 800 " --> pdb=" O LEU N 765 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU N 767 " --> pdb=" O ILE N 800 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE N 802 " --> pdb=" O LEU N 767 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'O' and resid 710 through 714 removed outlier: 6.573A pdb=" N HIS O 762 " --> pdb=" O PHE O 711 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N SER O 713 " --> pdb=" O HIS O 762 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE O 764 " --> pdb=" O SER O 713 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ASN O 798 " --> pdb=" O PHE O 763 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU O 765 " --> pdb=" O ASN O 798 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE O 800 " --> pdb=" O LEU O 765 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU O 767 " --> pdb=" O ILE O 800 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE O 802 " --> pdb=" O LEU O 767 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'P' and resid 710 through 714 removed outlier: 6.573A pdb=" N HIS P 762 " --> pdb=" O PHE P 711 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N SER P 713 " --> pdb=" O HIS P 762 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE P 764 " --> pdb=" O SER P 713 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASN P 798 " --> pdb=" O PHE P 763 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU P 765 " --> pdb=" O ASN P 798 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE P 800 " --> pdb=" O LEU P 765 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU P 767 " --> pdb=" O ILE P 800 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE P 802 " --> pdb=" O LEU P 767 " (cutoff:3.500A) 1952 hydrogen bonds defined for protein. 4800 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: 14.63 Time building geometry restraints manager: 17.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9819 1.34 - 1.47: 12820 1.47 - 1.60: 18577 1.60 - 1.72: 32 1.72 - 1.85: 224 Bond restraints: 41472 Sorted by residual: bond pdb=" CA ALA A 536 " pdb=" CB ALA A 536 " ideal model delta sigma weight residual 1.528 1.466 0.062 1.56e-02 4.11e+03 1.60e+01 bond pdb=" CA ALA H 536 " pdb=" CB ALA H 536 " ideal model delta sigma weight residual 1.528 1.466 0.062 1.56e-02 4.11e+03 1.59e+01 bond pdb=" CA ALA G 536 " pdb=" CB ALA G 536 " ideal model delta sigma weight residual 1.528 1.467 0.061 1.56e-02 4.11e+03 1.55e+01 bond pdb=" CA ALA C 536 " pdb=" CB ALA C 536 " ideal model delta sigma weight residual 1.528 1.467 0.061 1.56e-02 4.11e+03 1.55e+01 bond pdb=" CA ALA E 536 " pdb=" CB ALA E 536 " ideal model delta sigma weight residual 1.528 1.467 0.061 1.56e-02 4.11e+03 1.55e+01 ... (remaining 41467 not shown) Histogram of bond angle deviations from ideal: 98.48 - 105.82: 934 105.82 - 113.15: 19858 113.15 - 120.49: 20297 120.49 - 127.82: 14766 127.82 - 135.16: 289 Bond angle restraints: 56144 Sorted by residual: angle pdb=" C ARG F 465 " pdb=" CA ARG F 465 " pdb=" CB ARG F 465 " ideal model delta sigma weight residual 110.85 100.65 10.20 1.70e+00 3.46e-01 3.60e+01 angle pdb=" C ARG D 465 " pdb=" CA ARG D 465 " pdb=" CB ARG D 465 " ideal model delta sigma weight residual 110.85 100.70 10.15 1.70e+00 3.46e-01 3.57e+01 angle pdb=" C ARG H 465 " pdb=" CA ARG H 465 " pdb=" CB ARG H 465 " ideal model delta sigma weight residual 110.85 100.70 10.15 1.70e+00 3.46e-01 3.56e+01 angle pdb=" C ARG A 465 " pdb=" CA ARG A 465 " pdb=" CB ARG A 465 " ideal model delta sigma weight residual 110.85 100.71 10.14 1.70e+00 3.46e-01 3.56e+01 angle pdb=" C ARG E 465 " pdb=" CA ARG E 465 " pdb=" CB ARG E 465 " ideal model delta sigma weight residual 110.85 100.71 10.14 1.70e+00 3.46e-01 3.56e+01 ... (remaining 56139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 22856 16.14 - 32.28: 2082 32.28 - 48.42: 423 48.42 - 64.56: 119 64.56 - 80.71: 40 Dihedral angle restraints: 25520 sinusoidal: 10656 harmonic: 14864 Sorted by residual: dihedral pdb=" CA ASP D 367 " pdb=" C ASP D 367 " pdb=" N ILE D 368 " pdb=" CA ILE D 368 " ideal model delta harmonic sigma weight residual 180.00 155.40 24.60 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA ASP F 367 " pdb=" C ASP F 367 " pdb=" N ILE F 368 " pdb=" CA ILE F 368 " ideal model delta harmonic sigma weight residual 180.00 155.42 24.58 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA ASP B 367 " pdb=" C ASP B 367 " pdb=" N ILE B 368 " pdb=" CA ILE B 368 " ideal model delta harmonic sigma weight residual 180.00 155.42 24.58 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 25517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3784 0.089 - 0.179: 1895 0.179 - 0.268: 602 0.268 - 0.357: 118 0.357 - 0.447: 17 Chirality restraints: 6416 Sorted by residual: chirality pdb=" CA ARG H 497 " pdb=" N ARG H 497 " pdb=" C ARG H 497 " pdb=" CB ARG H 497 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" CA ARG D 497 " pdb=" N ARG D 497 " pdb=" C ARG D 497 " pdb=" CB ARG D 497 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CA ARG G 497 " pdb=" N ARG G 497 " pdb=" C ARG G 497 " pdb=" CB ARG G 497 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.86e+00 ... (remaining 6413 not shown) Planarity restraints: 7256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD F 901 " -0.058 2.00e-02 2.50e+03 4.90e-02 4.80e+01 pdb=" C2N NAD F 901 " 0.093 2.00e-02 2.50e+03 pdb=" C3N NAD F 901 " -0.003 2.00e-02 2.50e+03 pdb=" C4N NAD F 901 " -0.065 2.00e-02 2.50e+03 pdb=" C5N NAD F 901 " 0.048 2.00e-02 2.50e+03 pdb=" C6N NAD F 901 " -0.006 2.00e-02 2.50e+03 pdb=" C7N NAD F 901 " -0.022 2.00e-02 2.50e+03 pdb=" N1N NAD F 901 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 901 " -0.060 2.00e-02 2.50e+03 4.77e-02 4.55e+01 pdb=" C2N NAD B 901 " 0.089 2.00e-02 2.50e+03 pdb=" C3N NAD B 901 " -0.003 2.00e-02 2.50e+03 pdb=" C4N NAD B 901 " -0.065 2.00e-02 2.50e+03 pdb=" C5N NAD B 901 " 0.043 2.00e-02 2.50e+03 pdb=" C6N NAD B 901 " 0.002 2.00e-02 2.50e+03 pdb=" C7N NAD B 901 " -0.019 2.00e-02 2.50e+03 pdb=" N1N NAD B 901 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 901 " -0.057 2.00e-02 2.50e+03 4.71e-02 4.44e+01 pdb=" C2N NAD D 901 " 0.086 2.00e-02 2.50e+03 pdb=" C3N NAD D 901 " -0.003 2.00e-02 2.50e+03 pdb=" C4N NAD D 901 " -0.066 2.00e-02 2.50e+03 pdb=" C5N NAD D 901 " 0.047 2.00e-02 2.50e+03 pdb=" C6N NAD D 901 " -0.002 2.00e-02 2.50e+03 pdb=" C7N NAD D 901 " -0.018 2.00e-02 2.50e+03 pdb=" N1N NAD D 901 " 0.013 2.00e-02 2.50e+03 ... (remaining 7253 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 18910 2.97 - 3.45: 44434 3.45 - 3.93: 69700 3.93 - 4.42: 82405 4.42 - 4.90: 127423 Nonbonded interactions: 342872 Sorted by model distance: nonbonded pdb=" O GLU E 149 " pdb=" O3D NAD E 901 " model vdw 2.486 2.440 nonbonded pdb=" O GLU C 149 " pdb=" O3D NAD C 901 " model vdw 2.488 2.440 nonbonded pdb=" O GLU G 149 " pdb=" O3D NAD G 901 " model vdw 2.491 2.440 nonbonded pdb=" O GLU D 149 " pdb=" O3D NAD D 901 " model vdw 2.494 2.440 nonbonded pdb=" O GLU H 149 " pdb=" O3D NAD H 901 " model vdw 2.498 2.440 ... (remaining 342867 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.040 Check model and map are aligned: 0.610 Set scattering table: 0.390 Process input model: 104.730 Find NCS groups from input model: 2.900 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 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 : 0.010 0.071 41472 Z= 0.625 Angle : 1.603 10.339 56144 Z= 1.055 Chirality : 0.114 0.447 6416 Planarity : 0.009 0.050 7256 Dihedral : 13.677 80.706 15888 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.56 % Allowed : 3.95 % Favored : 95.49 % Cbeta Deviations : 0.98 % 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: -1.64 (0.11), residues: 5120 helix: -1.40 (0.07), residues: 3544 sheet: 0.28 (0.41), residues: 120 loop : 0.26 (0.18), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.010 TRP D 103 HIS 0.015 0.004 HIS G 534 PHE 0.039 0.009 PHE H 467 TYR 0.055 0.012 TYR C 429 ARG 0.023 0.003 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 4304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1028 time to evaluate : 5.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 0 residues processed: 1036 average time/residue: 1.8107 time to fit residues: 2221.3285 Evaluate side-chains 590 residues out of total 4304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 590 time to evaluate : 4.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 425 optimal weight: 9.9990 chunk 382 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 395 optimal weight: 5.9990 chunk 152 optimal weight: 50.0000 chunk 240 optimal weight: 0.9980 chunk 294 optimal weight: 40.0000 chunk 457 optimal weight: 40.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 232 ASN J 852 ASN I 731 GLN ** I 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 852 ASN K 731 GLN ** K 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 852 ASN M 731 GLN ** M 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 852 ASN N 852 ASN O 731 GLN ** O 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 852 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 41472 Z= 0.327 Angle : 0.762 10.551 56144 Z= 0.375 Chirality : 0.043 0.258 6416 Planarity : 0.005 0.034 7256 Dihedral : 6.635 69.627 6080 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.67 % Allowed : 12.55 % Favored : 85.78 % 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: 0.36 (0.12), residues: 5120 helix: 0.18 (0.09), residues: 3512 sheet: 1.09 (0.43), residues: 136 loop : 0.75 (0.18), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 214 HIS 0.006 0.001 HIS O 795 PHE 0.015 0.002 PHE N 763 TYR 0.009 0.001 TYR B 429 ARG 0.009 0.001 ARG G 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 4304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 639 time to evaluate : 3.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 20 residues processed: 690 average time/residue: 1.6635 time to fit residues: 1382.0040 Evaluate side-chains 507 residues out of total 4304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 487 time to evaluate : 4.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain H residue 260 SER Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain I residue 768 THR Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain K residue 845 ARG Chi-restraints excluded: chain L residue 768 THR Chi-restraints excluded: chain M residue 768 THR Chi-restraints excluded: chain M residue 845 ARG Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain O residue 768 THR Chi-restraints excluded: chain O residue 845 ARG Chi-restraints excluded: chain P residue 768 THR Chi-restraints excluded: chain P residue 827 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 254 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 380 optimal weight: 0.9980 chunk 311 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 458 optimal weight: 50.0000 chunk 495 optimal weight: 7.9990 chunk 408 optimal weight: 9.9990 chunk 454 optimal weight: 0.6980 chunk 156 optimal weight: 7.9990 chunk 367 optimal weight: 0.0020 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 758 GLN ** P 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 798 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 41472 Z= 0.210 Angle : 0.674 13.340 56144 Z= 0.323 Chirality : 0.040 0.236 6416 Planarity : 0.004 0.056 7256 Dihedral : 6.128 67.995 6080 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.86 % Allowed : 13.82 % Favored : 84.32 % 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: 0.77 (0.12), residues: 5120 helix: 0.57 (0.09), residues: 3568 sheet: 1.68 (0.45), residues: 136 loop : 0.64 (0.18), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 831 HIS 0.007 0.001 HIS I 786 PHE 0.023 0.001 PHE M 738 TYR 0.007 0.001 TYR P 735 ARG 0.008 0.001 ARG P 845 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 4304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 588 time to evaluate : 4.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 ARG cc_start: 0.7429 (mmm-85) cc_final: 0.7136 (mmm-85) REVERT: C 249 ARG cc_start: 0.7435 (mmm-85) cc_final: 0.7141 (mmm-85) REVERT: E 249 ARG cc_start: 0.7436 (mmm-85) cc_final: 0.7135 (mmm-85) REVERT: G 249 ARG cc_start: 0.7431 (mmm-85) cc_final: 0.7125 (mmm-85) outliers start: 80 outliers final: 29 residues processed: 629 average time/residue: 1.6614 time to fit residues: 1257.6525 Evaluate side-chains 530 residues out of total 4304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 501 time to evaluate : 5.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 260 SER Chi-restraints excluded: chain H residue 366 SER Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain I residue 768 THR Chi-restraints excluded: chain I residue 827 ASN Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain K residue 824 THR Chi-restraints excluded: chain L residue 768 THR Chi-restraints excluded: chain M residue 768 THR Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain O residue 768 THR Chi-restraints excluded: chain P residue 768 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 453 optimal weight: 40.0000 chunk 344 optimal weight: 5.9990 chunk 237 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 218 optimal weight: 9.9990 chunk 307 optimal weight: 6.9990 chunk 460 optimal weight: 20.0000 chunk 487 optimal weight: 6.9990 chunk 240 optimal weight: 0.7980 chunk 436 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 798 ASN ** M 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 798 ASN ** O 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 41472 Z= 0.421 Angle : 0.707 11.712 56144 Z= 0.337 Chirality : 0.043 0.234 6416 Planarity : 0.005 0.040 7256 Dihedral : 6.002 68.194 6080 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.07 % Allowed : 15.36 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.12), residues: 5120 helix: 0.55 (0.09), residues: 3536 sheet: 1.98 (0.44), residues: 136 loop : 0.49 (0.18), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 831 HIS 0.005 0.001 HIS D 190 PHE 0.024 0.002 PHE J 738 TYR 0.020 0.001 TYR D 213 ARG 0.011 0.001 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 4304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 559 time to evaluate : 5.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 ASP cc_start: 0.4895 (OUTLIER) cc_final: 0.4564 (p0) outliers start: 89 outliers final: 38 residues processed: 605 average time/residue: 1.6407 time to fit residues: 1201.4568 Evaluate side-chains 515 residues out of total 4304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 476 time to evaluate : 5.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain H residue 260 SER Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain I residue 768 THR Chi-restraints excluded: chain I residue 795 HIS Chi-restraints excluded: chain I residue 827 ASN Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain K residue 795 HIS Chi-restraints excluded: chain K residue 824 THR Chi-restraints excluded: chain K residue 845 ARG Chi-restraints excluded: chain L residue 768 THR Chi-restraints excluded: chain M residue 768 THR Chi-restraints excluded: chain M residue 795 HIS Chi-restraints excluded: chain M residue 845 ARG Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain N residue 827 ASN Chi-restraints excluded: chain O residue 768 THR Chi-restraints excluded: chain O residue 824 THR Chi-restraints excluded: chain O residue 845 ARG Chi-restraints excluded: chain P residue 768 THR Chi-restraints excluded: chain P residue 827 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 405 optimal weight: 20.0000 chunk 276 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 362 optimal weight: 3.9990 chunk 201 optimal weight: 6.9990 chunk 415 optimal weight: 50.0000 chunk 336 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 248 optimal weight: 5.9990 chunk 437 optimal weight: 6.9990 chunk 122 optimal weight: 0.0770 overall best weight: 3.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 798 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 41472 Z= 0.303 Angle : 0.674 14.562 56144 Z= 0.321 Chirality : 0.041 0.243 6416 Planarity : 0.004 0.042 7256 Dihedral : 5.872 67.868 6080 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.44 % Allowed : 16.43 % Favored : 81.13 % 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: 0.81 (0.12), residues: 5120 helix: 0.63 (0.09), residues: 3544 sheet: 1.83 (0.43), residues: 136 loop : 0.54 (0.18), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 831 HIS 0.004 0.001 HIS M 786 PHE 0.025 0.001 PHE L 738 TYR 0.007 0.001 TYR B 429 ARG 0.009 0.001 ARG F 249 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 4304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 536 time to evaluate : 4.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 51 residues processed: 604 average time/residue: 1.5774 time to fit residues: 1157.5583 Evaluate side-chains 545 residues out of total 4304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 494 time to evaluate : 5.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 260 SER Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain I residue 768 THR Chi-restraints excluded: chain I residue 795 HIS Chi-restraints excluded: chain I residue 846 PHE Chi-restraints excluded: chain K residue 752 SER Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain K residue 795 HIS Chi-restraints excluded: chain K residue 845 ARG Chi-restraints excluded: chain L residue 768 THR Chi-restraints excluded: chain L residue 846 PHE Chi-restraints excluded: chain M residue 768 THR Chi-restraints excluded: chain M residue 795 HIS Chi-restraints excluded: chain M residue 845 ARG Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain N residue 846 PHE Chi-restraints excluded: chain O residue 768 THR Chi-restraints excluded: chain O residue 795 HIS Chi-restraints excluded: chain O residue 845 ARG Chi-restraints excluded: chain P residue 768 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 163 optimal weight: 9.9990 chunk 438 optimal weight: 40.0000 chunk 96 optimal weight: 0.2980 chunk 286 optimal weight: 0.6980 chunk 120 optimal weight: 8.9990 chunk 487 optimal weight: 8.9990 chunk 404 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 798 ASN ** I 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 798 ASN ** M 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 798 ASN O 758 GLN ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41472 Z= 0.214 Angle : 0.654 14.395 56144 Z= 0.310 Chirality : 0.040 0.260 6416 Planarity : 0.004 0.041 7256 Dihedral : 5.745 67.827 6080 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.11 % Allowed : 17.03 % Favored : 80.86 % 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: 0.87 (0.12), residues: 5120 helix: 0.71 (0.09), residues: 3536 sheet: 1.67 (0.42), residues: 136 loop : 0.47 (0.18), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 490 HIS 0.004 0.001 HIS I 795 PHE 0.029 0.002 PHE K 738 TYR 0.011 0.001 TYR O 826 ARG 0.010 0.000 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 4304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 544 time to evaluate : 4.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 45 residues processed: 601 average time/residue: 1.5626 time to fit residues: 1143.8940 Evaluate side-chains 528 residues out of total 4304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 483 time to evaluate : 5.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 260 SER Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain I residue 768 THR Chi-restraints excluded: chain I residue 795 HIS Chi-restraints excluded: chain I residue 827 ASN Chi-restraints excluded: chain I residue 846 PHE Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain K residue 795 HIS Chi-restraints excluded: chain L residue 768 THR Chi-restraints excluded: chain L residue 846 PHE Chi-restraints excluded: chain M residue 768 THR Chi-restraints excluded: chain M residue 795 HIS Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain N residue 846 PHE Chi-restraints excluded: chain O residue 768 THR Chi-restraints excluded: chain P residue 768 THR Chi-restraints excluded: chain P residue 827 ASN Chi-restraints excluded: chain P residue 846 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 470 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 277 optimal weight: 4.9990 chunk 356 optimal weight: 10.0000 chunk 275 optimal weight: 7.9990 chunk 410 optimal weight: 9.9990 chunk 272 optimal weight: 0.0670 chunk 485 optimal weight: 50.0000 chunk 304 optimal weight: 0.8980 chunk 296 optimal weight: 7.9990 chunk 224 optimal weight: 5.9990 overall best weight: 3.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 798 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 41472 Z= 0.335 Angle : 0.687 14.766 56144 Z= 0.329 Chirality : 0.042 0.264 6416 Planarity : 0.004 0.038 7256 Dihedral : 5.712 68.018 6080 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.11 % Allowed : 18.10 % Favored : 79.79 % 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: 0.78 (0.12), residues: 5120 helix: 0.66 (0.09), residues: 3544 sheet: 1.53 (0.40), residues: 136 loop : 0.40 (0.18), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 214 HIS 0.003 0.001 HIS I 795 PHE 0.028 0.001 PHE L 738 TYR 0.022 0.001 TYR D 213 ARG 0.011 0.001 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 4304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 526 time to evaluate : 4.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 45 residues processed: 589 average time/residue: 1.5739 time to fit residues: 1129.1829 Evaluate side-chains 530 residues out of total 4304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 485 time to evaluate : 4.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 260 SER Chi-restraints excluded: chain H residue 366 SER Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain J residue 827 ASN Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain I residue 768 THR Chi-restraints excluded: chain I residue 795 HIS Chi-restraints excluded: chain I residue 846 PHE Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain L residue 768 THR Chi-restraints excluded: chain M residue 768 THR Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain N residue 795 HIS Chi-restraints excluded: chain O residue 768 THR Chi-restraints excluded: chain P residue 768 THR Chi-restraints excluded: chain P residue 795 HIS Chi-restraints excluded: chain P residue 827 ASN Chi-restraints excluded: chain P residue 846 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 300 optimal weight: 6.9990 chunk 193 optimal weight: 0.6980 chunk 290 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 330 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 381 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN D 328 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 731 GLN ** I 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 41472 Z= 0.212 Angle : 0.671 15.645 56144 Z= 0.318 Chirality : 0.041 0.274 6416 Planarity : 0.004 0.042 7256 Dihedral : 5.648 68.145 6080 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.72 % Allowed : 18.80 % Favored : 79.48 % 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: 0.85 (0.12), residues: 5120 helix: 0.72 (0.09), residues: 3544 sheet: 1.44 (0.39), residues: 136 loop : 0.42 (0.18), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 214 HIS 0.003 0.001 HIS I 795 PHE 0.031 0.002 PHE J 738 TYR 0.013 0.001 TYR A 213 ARG 0.010 0.001 ARG J 845 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 4304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 513 time to evaluate : 5.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 840 MET cc_start: 0.6059 (tpp) cc_final: 0.5827 (tpt) outliers start: 74 outliers final: 44 residues processed: 570 average time/residue: 1.5763 time to fit residues: 1093.7011 Evaluate side-chains 529 residues out of total 4304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 485 time to evaluate : 4.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 260 SER Chi-restraints excluded: chain H residue 366 SER Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain J residue 795 HIS Chi-restraints excluded: chain J residue 827 ASN Chi-restraints excluded: chain I residue 768 THR Chi-restraints excluded: chain I residue 846 PHE Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain K residue 846 PHE Chi-restraints excluded: chain L residue 768 THR Chi-restraints excluded: chain L residue 795 HIS Chi-restraints excluded: chain L residue 846 PHE Chi-restraints excluded: chain M residue 768 THR Chi-restraints excluded: chain M residue 846 PHE Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain N residue 795 HIS Chi-restraints excluded: chain N residue 846 PHE Chi-restraints excluded: chain O residue 768 THR Chi-restraints excluded: chain O residue 846 PHE Chi-restraints excluded: chain P residue 768 THR Chi-restraints excluded: chain P residue 795 HIS Chi-restraints excluded: chain P residue 827 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 441 optimal weight: 40.0000 chunk 465 optimal weight: 8.9990 chunk 424 optimal weight: 0.9980 chunk 452 optimal weight: 20.0000 chunk 272 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 355 optimal weight: 0.4980 chunk 138 optimal weight: 0.9990 chunk 409 optimal weight: 20.0000 chunk 428 optimal weight: 8.9990 chunk 451 optimal weight: 30.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 41472 Z= 0.235 Angle : 0.700 16.907 56144 Z= 0.333 Chirality : 0.041 0.279 6416 Planarity : 0.004 0.051 7256 Dihedral : 5.598 68.254 6080 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.32 % Allowed : 19.45 % Favored : 79.23 % 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: 0.87 (0.12), residues: 5120 helix: 0.74 (0.09), residues: 3528 sheet: 1.42 (0.39), residues: 136 loop : 0.43 (0.18), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 214 HIS 0.003 0.001 HIS I 795 PHE 0.030 0.001 PHE M 738 TYR 0.024 0.001 TYR H 213 ARG 0.023 0.001 ARG B 131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 4304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 503 time to evaluate : 4.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 40 residues processed: 549 average time/residue: 1.6342 time to fit residues: 1114.9923 Evaluate side-chains 524 residues out of total 4304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 484 time to evaluate : 5.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 260 SER Chi-restraints excluded: chain H residue 366 SER Chi-restraints excluded: chain H residue 368 ILE Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain J residue 795 HIS Chi-restraints excluded: chain J residue 827 ASN Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain I residue 768 THR Chi-restraints excluded: chain I residue 846 PHE Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain L residue 768 THR Chi-restraints excluded: chain L residue 846 PHE Chi-restraints excluded: chain M residue 768 THR Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain N residue 795 HIS Chi-restraints excluded: chain N residue 846 PHE Chi-restraints excluded: chain O residue 768 THR Chi-restraints excluded: chain P residue 768 THR Chi-restraints excluded: chain P residue 827 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 297 optimal weight: 5.9990 chunk 478 optimal weight: 10.0000 chunk 292 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 332 optimal weight: 3.9990 chunk 502 optimal weight: 50.0000 chunk 462 optimal weight: 20.0000 chunk 399 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 245 optimal weight: 40.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 41472 Z= 0.324 Angle : 0.723 17.370 56144 Z= 0.341 Chirality : 0.043 0.278 6416 Planarity : 0.004 0.042 7256 Dihedral : 5.600 68.279 6080 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.21 % Allowed : 19.61 % Favored : 79.18 % 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: 0.81 (0.12), residues: 5120 helix: 0.70 (0.09), residues: 3520 sheet: 1.40 (0.38), residues: 136 loop : 0.39 (0.18), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 214 HIS 0.003 0.001 HIS I 795 PHE 0.029 0.002 PHE I 738 TYR 0.017 0.001 TYR A 213 ARG 0.019 0.001 ARG B 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 4304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 516 time to evaluate : 5.089 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 outliers start: 52 outliers final: 45 residues processed: 557 average time/residue: 1.5353 time to fit residues: 1049.6624 Evaluate side-chains 544 residues out of total 4304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 499 time to evaluate : 4.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 368 ILE Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 260 SER Chi-restraints excluded: chain H residue 368 ILE Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain J residue 795 HIS Chi-restraints excluded: chain J residue 827 ASN Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain I residue 768 THR Chi-restraints excluded: chain I residue 846 PHE Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain L residue 768 THR Chi-restraints excluded: chain L residue 795 HIS Chi-restraints excluded: chain L residue 846 PHE Chi-restraints excluded: chain M residue 768 THR Chi-restraints excluded: chain M residue 846 PHE Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain N residue 795 HIS Chi-restraints excluded: chain N residue 846 PHE Chi-restraints excluded: chain O residue 768 THR Chi-restraints excluded: chain O residue 846 PHE Chi-restraints excluded: chain P residue 768 THR Chi-restraints excluded: chain P residue 795 HIS Chi-restraints excluded: chain P residue 827 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 317 optimal weight: 1.9990 chunk 425 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 368 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 400 optimal weight: 50.0000 chunk 167 optimal weight: 0.3980 chunk 411 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.138915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.076382 restraints weight = 80159.383| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.08 r_work: 0.2808 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 41472 Z= 0.243 Angle : 0.731 18.800 56144 Z= 0.344 Chirality : 0.041 0.260 6416 Planarity : 0.004 0.041 7256 Dihedral : 5.576 68.398 6080 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.02 % Allowed : 20.17 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.12), residues: 5120 helix: 0.70 (0.09), residues: 3520 sheet: 1.37 (0.38), residues: 136 loop : 0.41 (0.18), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 214 HIS 0.003 0.001 HIS O 786 PHE 0.031 0.001 PHE M 738 TYR 0.005 0.001 TYR B 429 ARG 0.021 0.001 ARG F 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18925.38 seconds wall clock time: 337 minutes 39.93 seconds (20259.93 seconds total)