Starting phenix.real_space_refine on Sat Mar 16 00:44:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl0_24512/03_2024/7rl0_24512_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl0_24512/03_2024/7rl0_24512.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl0_24512/03_2024/7rl0_24512_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl0_24512/03_2024/7rl0_24512_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl0_24512/03_2024/7rl0_24512_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl0_24512/03_2024/7rl0_24512.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl0_24512/03_2024/7rl0_24512.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl0_24512/03_2024/7rl0_24512_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl0_24512/03_2024/7rl0_24512_trim_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.343 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 23156 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 72 5.49 5 Mg 24 5.21 5 S 240 5.16 5 C 33528 2.51 5 N 9168 2.21 5 O 10332 1.98 5 H 52716 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 66": "OE1" <-> "OE2" Residue "A ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A ARG 334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 394": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A GLU 494": "OE1" <-> "OE2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 219": "OE1" <-> "OE2" Residue "B ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B GLU 327": "OE1" <-> "OE2" Residue "B ARG 334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 394": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 432": "OE1" <-> "OE2" Residue "B GLU 438": "OE1" <-> "OE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B GLU 494": "OE1" <-> "OE2" Residue "B GLU 504": "OE1" <-> "OE2" Residue "B GLU 515": "OE1" <-> "OE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B GLU 539": "OE1" <-> "OE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 219": "OE1" <-> "OE2" Residue "C ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C GLU 327": "OE1" <-> "OE2" Residue "C ARG 334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 348": "OE1" <-> "OE2" Residue "C ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 394": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 432": "OE1" <-> "OE2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C GLU 494": "OE1" <-> "OE2" Residue "C GLU 504": "OE1" <-> "OE2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "C GLU 524": "OE1" <-> "OE2" Residue "C GLU 539": "OE1" <-> "OE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 66": "OE1" <-> "OE2" Residue "D ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 219": "OE1" <-> "OE2" Residue "D ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 272": "OE1" <-> "OE2" Residue "D GLU 327": "OE1" <-> "OE2" Residue "D ARG 334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 348": "OE1" <-> "OE2" Residue "D ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 394": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 432": "OE1" <-> "OE2" Residue "D GLU 438": "OE1" <-> "OE2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "D GLU 484": "OE1" <-> "OE2" Residue "D GLU 494": "OE1" <-> "OE2" Residue "D GLU 504": "OE1" <-> "OE2" Residue "D GLU 515": "OE1" <-> "OE2" Residue "D GLU 524": "OE1" <-> "OE2" Residue "D GLU 539": "OE1" <-> "OE2" Residue "D GLU 546": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E GLU 66": "OE1" <-> "OE2" Residue "E ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 219": "OE1" <-> "OE2" Residue "E ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 272": "OE1" <-> "OE2" Residue "E GLU 327": "OE1" <-> "OE2" Residue "E ARG 334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 348": "OE1" <-> "OE2" Residue "E ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 394": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 432": "OE1" <-> "OE2" Residue "E GLU 438": "OE1" <-> "OE2" Residue "E GLU 471": "OE1" <-> "OE2" Residue "E GLU 484": "OE1" <-> "OE2" Residue "E GLU 494": "OE1" <-> "OE2" Residue "E GLU 504": "OE1" <-> "OE2" Residue "E GLU 515": "OE1" <-> "OE2" Residue "E GLU 524": "OE1" <-> "OE2" Residue "E GLU 539": "OE1" <-> "OE2" Residue "E GLU 546": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F GLU 66": "OE1" <-> "OE2" Residue "F ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 219": "OE1" <-> "OE2" Residue "F ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 272": "OE1" <-> "OE2" Residue "F GLU 327": "OE1" <-> "OE2" Residue "F ARG 334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 348": "OE1" <-> "OE2" Residue "F ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 394": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 432": "OE1" <-> "OE2" Residue "F GLU 438": "OE1" <-> "OE2" Residue "F GLU 471": "OE1" <-> "OE2" Residue "F GLU 484": "OE1" <-> "OE2" Residue "F GLU 494": "OE1" <-> "OE2" Residue "F GLU 504": "OE1" <-> "OE2" Residue "F GLU 515": "OE1" <-> "OE2" Residue "F GLU 524": "OE1" <-> "OE2" Residue "F GLU 539": "OE1" <-> "OE2" Residue "F GLU 546": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G GLU 66": "OE1" <-> "OE2" Residue "G ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 219": "OE1" <-> "OE2" Residue "G ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 272": "OE1" <-> "OE2" Residue "G GLU 327": "OE1" <-> "OE2" Residue "G ARG 334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 348": "OE1" <-> "OE2" Residue "G ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 394": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 432": "OE1" <-> "OE2" Residue "G GLU 438": "OE1" <-> "OE2" Residue "G GLU 471": "OE1" <-> "OE2" Residue "G GLU 484": "OE1" <-> "OE2" Residue "G GLU 494": "OE1" <-> "OE2" Residue "G GLU 504": "OE1" <-> "OE2" Residue "G GLU 515": "OE1" <-> "OE2" Residue "G GLU 524": "OE1" <-> "OE2" Residue "G GLU 539": "OE1" <-> "OE2" Residue "G GLU 546": "OE1" <-> "OE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H GLU 66": "OE1" <-> "OE2" Residue "H ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 219": "OE1" <-> "OE2" Residue "H ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 272": "OE1" <-> "OE2" Residue "H GLU 327": "OE1" <-> "OE2" Residue "H ARG 334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 348": "OE1" <-> "OE2" Residue "H ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 394": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 432": "OE1" <-> "OE2" Residue "H GLU 438": "OE1" <-> "OE2" Residue "H GLU 471": "OE1" <-> "OE2" Residue "H GLU 484": "OE1" <-> "OE2" Residue "H GLU 494": "OE1" <-> "OE2" Residue "H GLU 504": "OE1" <-> "OE2" Residue "H GLU 515": "OE1" <-> "OE2" Residue "H GLU 524": "OE1" <-> "OE2" Residue "H GLU 539": "OE1" <-> "OE2" Residue "H GLU 546": "OE1" <-> "OE2" Residue "W GLU 57": "OE1" <-> "OE2" Residue "W GLU 66": "OE1" <-> "OE2" Residue "W ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W GLU 219": "OE1" <-> "OE2" Residue "W ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W GLU 272": "OE1" <-> "OE2" Residue "W GLU 327": "OE1" <-> "OE2" Residue "W ARG 334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W GLU 348": "OE1" <-> "OE2" Residue "W ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 394": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 432": "OE1" <-> "OE2" Residue "W GLU 438": "OE1" <-> "OE2" Residue "W GLU 471": "OE1" <-> "OE2" Residue "W GLU 484": "OE1" <-> "OE2" Residue "W GLU 494": "OE1" <-> "OE2" Residue "W GLU 504": "OE1" <-> "OE2" Residue "W GLU 515": "OE1" <-> "OE2" Residue "W GLU 524": "OE1" <-> "OE2" Residue "W GLU 539": "OE1" <-> "OE2" Residue "W GLU 546": "OE1" <-> "OE2" Residue "X GLU 57": "OE1" <-> "OE2" Residue "X GLU 66": "OE1" <-> "OE2" Residue "X ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X GLU 219": "OE1" <-> "OE2" Residue "X ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X GLU 272": "OE1" <-> "OE2" Residue "X GLU 327": "OE1" <-> "OE2" Residue "X ARG 334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X GLU 348": "OE1" <-> "OE2" Residue "X ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 394": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X GLU 432": "OE1" <-> "OE2" Residue "X GLU 438": "OE1" <-> "OE2" Residue "X GLU 471": "OE1" <-> "OE2" Residue "X GLU 484": "OE1" <-> "OE2" Residue "X GLU 494": "OE1" <-> "OE2" Residue "X GLU 504": "OE1" <-> "OE2" Residue "X GLU 515": "OE1" <-> "OE2" Residue "X GLU 524": "OE1" <-> "OE2" Residue "X GLU 539": "OE1" <-> "OE2" Residue "X GLU 546": "OE1" <-> "OE2" Residue "Y GLU 57": "OE1" <-> "OE2" Residue "Y GLU 66": "OE1" <-> "OE2" Residue "Y ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y GLU 219": "OE1" <-> "OE2" Residue "Y ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y GLU 272": "OE1" <-> "OE2" Residue "Y GLU 327": "OE1" <-> "OE2" Residue "Y ARG 334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y GLU 348": "OE1" <-> "OE2" Residue "Y ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 394": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y GLU 432": "OE1" <-> "OE2" Residue "Y GLU 438": "OE1" <-> "OE2" Residue "Y GLU 471": "OE1" <-> "OE2" Residue "Y GLU 484": "OE1" <-> "OE2" Residue "Y GLU 494": "OE1" <-> "OE2" Residue "Y GLU 504": "OE1" <-> "OE2" Residue "Y GLU 515": "OE1" <-> "OE2" Residue "Y GLU 524": "OE1" <-> "OE2" Residue "Y GLU 539": "OE1" <-> "OE2" Residue "Y GLU 546": "OE1" <-> "OE2" Residue "Z GLU 57": "OE1" <-> "OE2" Residue "Z GLU 66": "OE1" <-> "OE2" Residue "Z ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z GLU 219": "OE1" <-> "OE2" Residue "Z ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z GLU 272": "OE1" <-> "OE2" Residue "Z GLU 327": "OE1" <-> "OE2" Residue "Z ARG 334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z GLU 348": "OE1" <-> "OE2" Residue "Z ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 394": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z GLU 432": "OE1" <-> "OE2" Residue "Z GLU 438": "OE1" <-> "OE2" Residue "Z GLU 471": "OE1" <-> "OE2" Residue "Z GLU 484": "OE1" <-> "OE2" Residue "Z GLU 494": "OE1" <-> "OE2" Residue "Z GLU 504": "OE1" <-> "OE2" Residue "Z GLU 515": "OE1" <-> "OE2" Residue "Z GLU 524": "OE1" <-> "OE2" Residue "Z GLU 539": "OE1" <-> "OE2" Residue "Z GLU 546": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 106080 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 8778 Classifications: {'peptide': 559} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534} Chain breaks: 1 Chain: "B" Number of atoms: 8778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 8778 Classifications: {'peptide': 559} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534} Chain breaks: 1 Chain: "C" Number of atoms: 8778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 8778 Classifications: {'peptide': 559} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534} Chain breaks: 1 Chain: "D" Number of atoms: 8778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 8778 Classifications: {'peptide': 559} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534} Chain breaks: 1 Chain: "E" Number of atoms: 8778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 8778 Classifications: {'peptide': 559} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534} Chain breaks: 1 Chain: "F" Number of atoms: 8778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 8778 Classifications: {'peptide': 559} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534} Chain breaks: 1 Chain: "G" Number of atoms: 8778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 8778 Classifications: {'peptide': 559} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534} Chain breaks: 1 Chain: "H" Number of atoms: 8778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 8778 Classifications: {'peptide': 559} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534} Chain breaks: 1 Chain: "W" Number of atoms: 8778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 8778 Classifications: {'peptide': 559} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534} Chain breaks: 1 Chain: "X" Number of atoms: 8778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 8778 Classifications: {'peptide': 559} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534} Chain breaks: 1 Chain: "Y" Number of atoms: 8778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 8778 Classifications: {'peptide': 559} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534} Chain breaks: 1 Chain: "Z" Number of atoms: 8778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 8778 Classifications: {'peptide': 559} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534} Chain breaks: 1 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "W" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "X" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "Y" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "Z" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 32.74, per 1000 atoms: 0.31 Number of scatterers: 106080 At special positions: 0 Unit cell: (134.4, 110.25, 337.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 240 16.00 P 72 15.00 Mg 24 11.99 O 10332 8.00 N 9168 7.00 C 33528 6.00 H 52716 1.00 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: 61.06 Conformation dependent library (CDL) restraints added in 7.5 seconds 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12288 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 312 helices and 36 sheets defined 55.1% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 21.02 Creating SS restraints... Processing helix chain 'A' and resid 15 through 31 removed outlier: 3.959A pdb=" N LEU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 78 removed outlier: 4.030A pdb=" N GLY A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 88 removed outlier: 4.380A pdb=" N ASN A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 88' Processing helix chain 'A' and resid 89 through 104 removed outlier: 3.537A pdb=" N ARG A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 131 removed outlier: 3.603A pdb=" N LYS A 130 " --> pdb=" O GLN A 126 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 170 Proline residue: A 158 - end of helix removed outlier: 4.186A pdb=" N PHE A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.855A pdb=" N PHE A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ALA A 176 " --> pdb=" O ARG A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 171 through 176' Processing helix chain 'A' and resid 192 through 206 Processing helix chain 'A' and resid 221 through 233 removed outlier: 5.101A pdb=" N HIS A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.999A pdb=" N VAL A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL A 240 " --> pdb=" O PRO A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 235 through 240' Processing helix chain 'A' and resid 247 through 259 removed outlier: 4.298A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 260 through 269 removed outlier: 3.610A pdb=" N SER A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 300 removed outlier: 3.878A pdb=" N SER A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.497A pdb=" N TYR A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 320' Processing helix chain 'A' and resid 321 through 334 Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.626A pdb=" N LEU A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 343 through 348' Processing helix chain 'A' and resid 349 through 355 removed outlier: 3.937A pdb=" N GLU A 353 " --> pdb=" O PRO A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 382 through 397 removed outlier: 3.675A pdb=" N LEU A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 418 removed outlier: 4.479A pdb=" N LEU A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 408 " --> pdb=" O CYS A 404 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.590A pdb=" N LEU A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 480 removed outlier: 3.807A pdb=" N GLY A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 507 removed outlier: 3.524A pdb=" N VAL A 500 " --> pdb=" O ASN A 496 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN A 501 " --> pdb=" O PRO A 497 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP A 502 " --> pdb=" O LYS A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 removed outlier: 4.851A pdb=" N THR A 541 " --> pdb=" O HIS A 537 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A 542 " --> pdb=" O PRO A 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 537 through 542' Processing helix chain 'A' and resid 548 through 560 Processing helix chain 'A' and resid 561 through 571 removed outlier: 3.560A pdb=" N LEU A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 31 removed outlier: 3.961A pdb=" N LEU B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 78 removed outlier: 4.031A pdb=" N GLY B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 88 removed outlier: 4.379A pdb=" N ASN B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE B 88 " --> pdb=" O ARG B 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 83 through 88' Processing helix chain 'B' and resid 89 through 104 removed outlier: 3.537A pdb=" N ARG B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 131 removed outlier: 3.602A pdb=" N LYS B 130 " --> pdb=" O GLN B 126 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 170 Proline residue: B 158 - end of helix removed outlier: 4.187A pdb=" N PHE B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.855A pdb=" N PHE B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ALA B 176 " --> pdb=" O ARG B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 171 through 176' Processing helix chain 'B' and resid 192 through 206 Processing helix chain 'B' and resid 221 through 233 removed outlier: 5.100A pdb=" N HIS B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.999A pdb=" N VAL B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL B 240 " --> pdb=" O PRO B 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 235 through 240' Processing helix chain 'B' and resid 247 through 259 removed outlier: 4.297A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Proline residue: B 252 - end of helix Processing helix chain 'B' and resid 260 through 269 removed outlier: 3.611A pdb=" N SER B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 300 removed outlier: 3.878A pdb=" N SER B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 300 " --> pdb=" O ASN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 320 removed outlier: 4.498A pdb=" N TYR B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 315 through 320' Processing helix chain 'B' and resid 321 through 334 Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.627A pdb=" N LEU B 347 " --> pdb=" O GLU B 343 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU B 348 " --> pdb=" O ALA B 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 343 through 348' Processing helix chain 'B' and resid 349 through 355 removed outlier: 3.937A pdb=" N GLU B 353 " --> pdb=" O PRO B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 369 Processing helix chain 'B' and resid 382 through 397 removed outlier: 3.675A pdb=" N LEU B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 418 removed outlier: 4.479A pdb=" N LEU B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 408 " --> pdb=" O CYS B 404 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 431 removed outlier: 3.590A pdb=" N LEU B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 480 removed outlier: 3.808A pdb=" N GLY B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 507 removed outlier: 3.525A pdb=" N VAL B 500 " --> pdb=" O ASN B 496 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN B 501 " --> pdb=" O PRO B 497 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP B 502 " --> pdb=" O LYS B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 removed outlier: 4.851A pdb=" N THR B 541 " --> pdb=" O HIS B 537 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER B 542 " --> pdb=" O PRO B 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 537 through 542' Processing helix chain 'B' and resid 548 through 560 Processing helix chain 'B' and resid 561 through 571 removed outlier: 3.559A pdb=" N LEU B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 31 removed outlier: 3.959A pdb=" N LEU C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY C 31 " --> pdb=" O LEU C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 78 removed outlier: 4.030A pdb=" N GLY C 72 " --> pdb=" O ASP C 68 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 88 removed outlier: 4.380A pdb=" N ASN C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE C 88 " --> pdb=" O ARG C 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 83 through 88' Processing helix chain 'C' and resid 89 through 104 removed outlier: 3.537A pdb=" N ARG C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 131 removed outlier: 3.602A pdb=" N LYS C 130 " --> pdb=" O GLN C 126 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 170 Proline residue: C 158 - end of helix removed outlier: 4.186A pdb=" N PHE C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 176 removed outlier: 3.855A pdb=" N PHE C 175 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ALA C 176 " --> pdb=" O ARG C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 171 through 176' Processing helix chain 'C' and resid 192 through 206 Processing helix chain 'C' and resid 221 through 233 removed outlier: 5.100A pdb=" N HIS C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 240 removed outlier: 4.000A pdb=" N VAL C 239 " --> pdb=" O GLY C 235 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL C 240 " --> pdb=" O PRO C 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 235 through 240' Processing helix chain 'C' and resid 247 through 259 removed outlier: 4.298A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Proline residue: C 252 - end of helix Processing helix chain 'C' and resid 260 through 269 removed outlier: 3.611A pdb=" N SER C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 300 removed outlier: 3.878A pdb=" N SER C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER C 300 " --> pdb=" O ASN C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 320 removed outlier: 4.497A pdb=" N TYR C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 315 through 320' Processing helix chain 'C' and resid 321 through 334 Processing helix chain 'C' and resid 343 through 348 removed outlier: 3.628A pdb=" N LEU C 347 " --> pdb=" O GLU C 343 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 343 through 348' Processing helix chain 'C' and resid 349 through 355 removed outlier: 3.937A pdb=" N GLU C 353 " --> pdb=" O PRO C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 369 Processing helix chain 'C' and resid 382 through 397 removed outlier: 3.674A pdb=" N LEU C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 418 removed outlier: 4.479A pdb=" N LEU C 407 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 408 " --> pdb=" O CYS C 404 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 410 " --> pdb=" O GLY C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.591A pdb=" N LEU C 430 " --> pdb=" O SER C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 480 removed outlier: 3.808A pdb=" N GLY C 480 " --> pdb=" O ARG C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 507 removed outlier: 3.523A pdb=" N VAL C 500 " --> pdb=" O ASN C 496 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN C 501 " --> pdb=" O PRO C 497 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASP C 502 " --> pdb=" O LYS C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 542 removed outlier: 4.851A pdb=" N THR C 541 " --> pdb=" O HIS C 537 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER C 542 " --> pdb=" O PRO C 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 537 through 542' Processing helix chain 'C' and resid 548 through 560 Processing helix chain 'C' and resid 561 through 571 removed outlier: 3.559A pdb=" N LEU C 571 " --> pdb=" O LYS C 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 31 removed outlier: 3.959A pdb=" N LEU D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY D 31 " --> pdb=" O LEU D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 removed outlier: 4.029A pdb=" N GLY D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 88 removed outlier: 4.378A pdb=" N ASN D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE D 88 " --> pdb=" O ARG D 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 83 through 88' Processing helix chain 'D' and resid 89 through 104 removed outlier: 3.537A pdb=" N ARG D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 131 removed outlier: 3.602A pdb=" N LYS D 130 " --> pdb=" O GLN D 126 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 170 Proline residue: D 158 - end of helix removed outlier: 4.186A pdb=" N PHE D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 176 removed outlier: 3.855A pdb=" N PHE D 175 " --> pdb=" O GLY D 171 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ALA D 176 " --> pdb=" O ARG D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 171 through 176' Processing helix chain 'D' and resid 192 through 206 Processing helix chain 'D' and resid 221 through 233 removed outlier: 5.100A pdb=" N HIS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 240 removed outlier: 3.999A pdb=" N VAL D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL D 240 " --> pdb=" O PRO D 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 235 through 240' Processing helix chain 'D' and resid 247 through 259 removed outlier: 4.298A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Proline residue: D 252 - end of helix Processing helix chain 'D' and resid 260 through 269 removed outlier: 3.610A pdb=" N SER D 266 " --> pdb=" O ASP D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 300 removed outlier: 3.878A pdb=" N SER D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER D 300 " --> pdb=" O ASN D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 320 removed outlier: 4.498A pdb=" N TYR D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU D 320 " --> pdb=" O LYS D 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 315 through 320' Processing helix chain 'D' and resid 321 through 334 Processing helix chain 'D' and resid 343 through 348 removed outlier: 3.626A pdb=" N LEU D 347 " --> pdb=" O GLU D 343 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU D 348 " --> pdb=" O ALA D 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 343 through 348' Processing helix chain 'D' and resid 349 through 355 removed outlier: 3.937A pdb=" N GLU D 353 " --> pdb=" O PRO D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 369 Processing helix chain 'D' and resid 382 through 397 removed outlier: 3.675A pdb=" N LEU D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 418 removed outlier: 4.478A pdb=" N LEU D 407 " --> pdb=" O VAL D 403 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN D 408 " --> pdb=" O CYS D 404 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA D 410 " --> pdb=" O GLY D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 431 removed outlier: 3.591A pdb=" N LEU D 430 " --> pdb=" O SER D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 480 removed outlier: 3.809A pdb=" N GLY D 480 " --> pdb=" O ARG D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 507 removed outlier: 3.523A pdb=" N VAL D 500 " --> pdb=" O ASN D 496 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN D 501 " --> pdb=" O PRO D 497 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP D 502 " --> pdb=" O LYS D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 542 removed outlier: 4.850A pdb=" N THR D 541 " --> pdb=" O HIS D 537 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER D 542 " --> pdb=" O PRO D 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 537 through 542' Processing helix chain 'D' and resid 548 through 560 Processing helix chain 'D' and resid 561 through 571 removed outlier: 3.560A pdb=" N LEU D 571 " --> pdb=" O LYS D 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 31 removed outlier: 3.959A pdb=" N LEU E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY E 31 " --> pdb=" O LEU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 78 removed outlier: 4.030A pdb=" N GLY E 72 " --> pdb=" O ASP E 68 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN E 73 " --> pdb=" O LEU E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 88 removed outlier: 4.380A pdb=" N ASN E 87 " --> pdb=" O SER E 83 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE E 88 " --> pdb=" O ARG E 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 83 through 88' Processing helix chain 'E' and resid 89 through 104 removed outlier: 3.538A pdb=" N ARG E 103 " --> pdb=" O SER E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 131 removed outlier: 3.603A pdb=" N LYS E 130 " --> pdb=" O GLN E 126 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE E 131 " --> pdb=" O ARG E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 170 Proline residue: E 158 - end of helix removed outlier: 4.187A pdb=" N PHE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 176 removed outlier: 3.854A pdb=" N PHE E 175 " --> pdb=" O GLY E 171 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ALA E 176 " --> pdb=" O ARG E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 171 through 176' Processing helix chain 'E' and resid 192 through 206 Processing helix chain 'E' and resid 221 through 233 removed outlier: 5.100A pdb=" N HIS E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 240 removed outlier: 3.999A pdb=" N VAL E 239 " --> pdb=" O GLY E 235 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL E 240 " --> pdb=" O PRO E 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 235 through 240' Processing helix chain 'E' and resid 247 through 259 removed outlier: 4.298A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) Proline residue: E 252 - end of helix Processing helix chain 'E' and resid 260 through 269 removed outlier: 3.611A pdb=" N SER E 266 " --> pdb=" O ASP E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 300 removed outlier: 3.878A pdb=" N SER E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER E 300 " --> pdb=" O ASN E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 320 removed outlier: 4.496A pdb=" N TYR E 319 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU E 320 " --> pdb=" O LYS E 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 315 through 320' Processing helix chain 'E' and resid 321 through 334 Processing helix chain 'E' and resid 343 through 348 removed outlier: 3.627A pdb=" N LEU E 347 " --> pdb=" O GLU E 343 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU E 348 " --> pdb=" O ALA E 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 343 through 348' Processing helix chain 'E' and resid 349 through 355 removed outlier: 3.938A pdb=" N GLU E 353 " --> pdb=" O PRO E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 369 Processing helix chain 'E' and resid 382 through 397 removed outlier: 3.675A pdb=" N LEU E 388 " --> pdb=" O GLU E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 418 removed outlier: 4.479A pdb=" N LEU E 407 " --> pdb=" O VAL E 403 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN E 408 " --> pdb=" O CYS E 404 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA E 410 " --> pdb=" O GLY E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 431 removed outlier: 3.591A pdb=" N LEU E 430 " --> pdb=" O SER E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 480 removed outlier: 3.807A pdb=" N GLY E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 507 removed outlier: 3.524A pdb=" N VAL E 500 " --> pdb=" O ASN E 496 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN E 501 " --> pdb=" O PRO E 497 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP E 502 " --> pdb=" O LYS E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 542 removed outlier: 4.851A pdb=" N THR E 541 " --> pdb=" O HIS E 537 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER E 542 " --> pdb=" O PRO E 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 537 through 542' Processing helix chain 'E' and resid 548 through 560 Processing helix chain 'E' and resid 561 through 571 removed outlier: 3.560A pdb=" N LEU E 571 " --> pdb=" O LYS E 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 31 removed outlier: 3.960A pdb=" N LEU F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY F 31 " --> pdb=" O LEU F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 78 removed outlier: 4.031A pdb=" N GLY F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN F 73 " --> pdb=" O LEU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 88 removed outlier: 4.378A pdb=" N ASN F 87 " --> pdb=" O SER F 83 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE F 88 " --> pdb=" O ARG F 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 83 through 88' Processing helix chain 'F' and resid 89 through 104 removed outlier: 3.538A pdb=" N ARG F 103 " --> pdb=" O SER F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 131 removed outlier: 3.602A pdb=" N LYS F 130 " --> pdb=" O GLN F 126 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE F 131 " --> pdb=" O ARG F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 170 Proline residue: F 158 - end of helix removed outlier: 4.186A pdb=" N PHE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 176 removed outlier: 3.854A pdb=" N PHE F 175 " --> pdb=" O GLY F 171 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ALA F 176 " --> pdb=" O ARG F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 171 through 176' Processing helix chain 'F' and resid 192 through 206 Processing helix chain 'F' and resid 221 through 233 removed outlier: 5.101A pdb=" N HIS F 233 " --> pdb=" O ALA F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 240 removed outlier: 3.998A pdb=" N VAL F 239 " --> pdb=" O GLY F 235 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL F 240 " --> pdb=" O PRO F 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 235 through 240' Processing helix chain 'F' and resid 247 through 259 removed outlier: 4.297A pdb=" N VAL F 251 " --> pdb=" O SER F 247 " (cutoff:3.500A) Proline residue: F 252 - end of helix Processing helix chain 'F' and resid 260 through 269 removed outlier: 3.611A pdb=" N SER F 266 " --> pdb=" O ASP F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 300 removed outlier: 3.878A pdb=" N SER F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER F 300 " --> pdb=" O ASN F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 320 removed outlier: 4.499A pdb=" N TYR F 319 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU F 320 " --> pdb=" O LYS F 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 315 through 320' Processing helix chain 'F' and resid 321 through 334 Processing helix chain 'F' and resid 343 through 348 removed outlier: 3.627A pdb=" N LEU F 347 " --> pdb=" O GLU F 343 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU F 348 " --> pdb=" O ALA F 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 343 through 348' Processing helix chain 'F' and resid 349 through 355 removed outlier: 3.937A pdb=" N GLU F 353 " --> pdb=" O PRO F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 369 Processing helix chain 'F' and resid 382 through 397 removed outlier: 3.675A pdb=" N LEU F 388 " --> pdb=" O GLU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 418 removed outlier: 4.480A pdb=" N LEU F 407 " --> pdb=" O VAL F 403 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN F 408 " --> pdb=" O CYS F 404 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA F 410 " --> pdb=" O GLY F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 431 removed outlier: 3.590A pdb=" N LEU F 430 " --> pdb=" O SER F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 480 removed outlier: 3.808A pdb=" N GLY F 480 " --> pdb=" O ARG F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 507 removed outlier: 3.525A pdb=" N VAL F 500 " --> pdb=" O ASN F 496 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN F 501 " --> pdb=" O PRO F 497 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP F 502 " --> pdb=" O LYS F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 542 removed outlier: 4.851A pdb=" N THR F 541 " --> pdb=" O HIS F 537 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER F 542 " --> pdb=" O PRO F 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 537 through 542' Processing helix chain 'F' and resid 548 through 560 Processing helix chain 'F' and resid 561 through 571 removed outlier: 3.560A pdb=" N LEU F 571 " --> pdb=" O LYS F 567 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 31 removed outlier: 3.959A pdb=" N LEU G 30 " --> pdb=" O LEU G 26 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY G 31 " --> pdb=" O LEU G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 78 removed outlier: 4.029A pdb=" N GLY G 72 " --> pdb=" O ASP G 68 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN G 73 " --> pdb=" O LEU G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 88 removed outlier: 4.380A pdb=" N ASN G 87 " --> pdb=" O SER G 83 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE G 88 " --> pdb=" O ARG G 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 83 through 88' Processing helix chain 'G' and resid 89 through 104 removed outlier: 3.538A pdb=" N ARG G 103 " --> pdb=" O SER G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 131 removed outlier: 3.602A pdb=" N LYS G 130 " --> pdb=" O GLN G 126 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE G 131 " --> pdb=" O ARG G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 170 Proline residue: G 158 - end of helix removed outlier: 4.186A pdb=" N PHE G 168 " --> pdb=" O ARG G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 176 removed outlier: 3.854A pdb=" N PHE G 175 " --> pdb=" O GLY G 171 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ALA G 176 " --> pdb=" O ARG G 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 171 through 176' Processing helix chain 'G' and resid 192 through 206 Processing helix chain 'G' and resid 221 through 233 removed outlier: 5.101A pdb=" N HIS G 233 " --> pdb=" O ALA G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 240 removed outlier: 3.999A pdb=" N VAL G 239 " --> pdb=" O GLY G 235 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL G 240 " --> pdb=" O PRO G 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 235 through 240' Processing helix chain 'G' and resid 247 through 259 removed outlier: 4.299A pdb=" N VAL G 251 " --> pdb=" O SER G 247 " (cutoff:3.500A) Proline residue: G 252 - end of helix Processing helix chain 'G' and resid 260 through 269 removed outlier: 3.610A pdb=" N SER G 266 " --> pdb=" O ASP G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 300 removed outlier: 3.878A pdb=" N SER G 284 " --> pdb=" O LYS G 280 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER G 300 " --> pdb=" O ASN G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 315 through 320 removed outlier: 4.498A pdb=" N TYR G 319 " --> pdb=" O LEU G 315 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU G 320 " --> pdb=" O LYS G 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 315 through 320' Processing helix chain 'G' and resid 321 through 334 Processing helix chain 'G' and resid 343 through 348 removed outlier: 3.628A pdb=" N LEU G 347 " --> pdb=" O GLU G 343 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU G 348 " --> pdb=" O ALA G 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 343 through 348' Processing helix chain 'G' and resid 349 through 355 removed outlier: 3.937A pdb=" N GLU G 353 " --> pdb=" O PRO G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 369 Processing helix chain 'G' and resid 382 through 397 removed outlier: 3.675A pdb=" N LEU G 388 " --> pdb=" O GLU G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 403 through 418 removed outlier: 4.478A pdb=" N LEU G 407 " --> pdb=" O VAL G 403 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN G 408 " --> pdb=" O CYS G 404 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA G 410 " --> pdb=" O GLY G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 431 removed outlier: 3.591A pdb=" N LEU G 430 " --> pdb=" O SER G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 473 through 480 removed outlier: 3.807A pdb=" N GLY G 480 " --> pdb=" O ARG G 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 507 removed outlier: 3.523A pdb=" N VAL G 500 " --> pdb=" O ASN G 496 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN G 501 " --> pdb=" O PRO G 497 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASP G 502 " --> pdb=" O LYS G 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 542 removed outlier: 4.851A pdb=" N THR G 541 " --> pdb=" O HIS G 537 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER G 542 " --> pdb=" O PRO G 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 537 through 542' Processing helix chain 'G' and resid 548 through 560 Processing helix chain 'G' and resid 561 through 571 removed outlier: 3.560A pdb=" N LEU G 571 " --> pdb=" O LYS G 567 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 31 removed outlier: 3.959A pdb=" N LEU H 30 " --> pdb=" O LEU H 26 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY H 31 " --> pdb=" O LEU H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 78 removed outlier: 4.030A pdb=" N GLY H 72 " --> pdb=" O ASP H 68 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN H 73 " --> pdb=" O LEU H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 removed outlier: 4.379A pdb=" N ASN H 87 " --> pdb=" O SER H 83 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE H 88 " --> pdb=" O ARG H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 88' Processing helix chain 'H' and resid 89 through 104 removed outlier: 3.538A pdb=" N ARG H 103 " --> pdb=" O SER H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 131 removed outlier: 3.602A pdb=" N LYS H 130 " --> pdb=" O GLN H 126 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE H 131 " --> pdb=" O ARG H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 170 Proline residue: H 158 - end of helix removed outlier: 4.186A pdb=" N PHE H 168 " --> pdb=" O ARG H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 3.855A pdb=" N PHE H 175 " --> pdb=" O GLY H 171 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ALA H 176 " --> pdb=" O ARG H 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 171 through 176' Processing helix chain 'H' and resid 192 through 206 Processing helix chain 'H' and resid 221 through 233 removed outlier: 5.101A pdb=" N HIS H 233 " --> pdb=" O ALA H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 240 removed outlier: 3.999A pdb=" N VAL H 239 " --> pdb=" O GLY H 235 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL H 240 " --> pdb=" O PRO H 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 235 through 240' Processing helix chain 'H' and resid 247 through 259 removed outlier: 4.298A pdb=" N VAL H 251 " --> pdb=" O SER H 247 " (cutoff:3.500A) Proline residue: H 252 - end of helix Processing helix chain 'H' and resid 260 through 269 removed outlier: 3.611A pdb=" N SER H 266 " --> pdb=" O ASP H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 300 removed outlier: 3.878A pdb=" N SER H 284 " --> pdb=" O LYS H 280 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER H 300 " --> pdb=" O ASN H 296 " (cutoff:3.500A) Processing helix chain 'H' and resid 315 through 320 removed outlier: 4.497A pdb=" N TYR H 319 " --> pdb=" O LEU H 315 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU H 320 " --> pdb=" O LYS H 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 315 through 320' Processing helix chain 'H' and resid 321 through 334 Processing helix chain 'H' and resid 343 through 348 removed outlier: 3.627A pdb=" N LEU H 347 " --> pdb=" O GLU H 343 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU H 348 " --> pdb=" O ALA H 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 343 through 348' Processing helix chain 'H' and resid 349 through 355 removed outlier: 3.937A pdb=" N GLU H 353 " --> pdb=" O PRO H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 369 Processing helix chain 'H' and resid 382 through 397 removed outlier: 3.675A pdb=" N LEU H 388 " --> pdb=" O GLU H 384 " (cutoff:3.500A) Processing helix chain 'H' and resid 403 through 418 removed outlier: 4.479A pdb=" N LEU H 407 " --> pdb=" O VAL H 403 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN H 408 " --> pdb=" O CYS H 404 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA H 410 " --> pdb=" O GLY H 406 " (cutoff:3.500A) Processing helix chain 'H' and resid 426 through 431 removed outlier: 3.590A pdb=" N LEU H 430 " --> pdb=" O SER H 426 " (cutoff:3.500A) Processing helix chain 'H' and resid 473 through 480 removed outlier: 3.808A pdb=" N GLY H 480 " --> pdb=" O ARG H 476 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 507 removed outlier: 3.524A pdb=" N VAL H 500 " --> pdb=" O ASN H 496 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN H 501 " --> pdb=" O PRO H 497 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP H 502 " --> pdb=" O LYS H 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 537 through 542 removed outlier: 4.851A pdb=" N THR H 541 " --> pdb=" O HIS H 537 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER H 542 " --> pdb=" O PRO H 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 537 through 542' Processing helix chain 'H' and resid 548 through 560 Processing helix chain 'H' and resid 561 through 571 removed outlier: 3.560A pdb=" N LEU H 571 " --> pdb=" O LYS H 567 " (cutoff:3.500A) Processing helix chain 'W' and resid 15 through 31 removed outlier: 3.960A pdb=" N LEU W 30 " --> pdb=" O LEU W 26 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY W 31 " --> pdb=" O LEU W 27 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 78 removed outlier: 4.031A pdb=" N GLY W 72 " --> pdb=" O ASP W 68 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN W 73 " --> pdb=" O LEU W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 88 removed outlier: 4.380A pdb=" N ASN W 87 " --> pdb=" O SER W 83 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE W 88 " --> pdb=" O ARG W 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 83 through 88' Processing helix chain 'W' and resid 89 through 104 removed outlier: 3.538A pdb=" N ARG W 103 " --> pdb=" O SER W 99 " (cutoff:3.500A) Processing helix chain 'W' and resid 115 through 131 removed outlier: 3.602A pdb=" N LYS W 130 " --> pdb=" O GLN W 126 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE W 131 " --> pdb=" O ARG W 127 " (cutoff:3.500A) Processing helix chain 'W' and resid 153 through 170 Proline residue: W 158 - end of helix removed outlier: 4.186A pdb=" N PHE W 168 " --> pdb=" O ARG W 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 171 through 176 removed outlier: 3.855A pdb=" N PHE W 175 " --> pdb=" O GLY W 171 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ALA W 176 " --> pdb=" O ARG W 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 171 through 176' Processing helix chain 'W' and resid 192 through 206 Processing helix chain 'W' and resid 221 through 233 removed outlier: 5.101A pdb=" N HIS W 233 " --> pdb=" O ALA W 229 " (cutoff:3.500A) Processing helix chain 'W' and resid 235 through 240 removed outlier: 3.998A pdb=" N VAL W 239 " --> pdb=" O GLY W 235 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL W 240 " --> pdb=" O PRO W 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 235 through 240' Processing helix chain 'W' and resid 247 through 259 removed outlier: 4.297A pdb=" N VAL W 251 " --> pdb=" O SER W 247 " (cutoff:3.500A) Proline residue: W 252 - end of helix Processing helix chain 'W' and resid 260 through 269 removed outlier: 3.611A pdb=" N SER W 266 " --> pdb=" O ASP W 262 " (cutoff:3.500A) Processing helix chain 'W' and resid 276 through 300 removed outlier: 3.877A pdb=" N SER W 284 " --> pdb=" O LYS W 280 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER W 300 " --> pdb=" O ASN W 296 " (cutoff:3.500A) Processing helix chain 'W' and resid 315 through 320 removed outlier: 4.497A pdb=" N TYR W 319 " --> pdb=" O LEU W 315 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU W 320 " --> pdb=" O LYS W 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 315 through 320' Processing helix chain 'W' and resid 321 through 334 Processing helix chain 'W' and resid 343 through 348 removed outlier: 3.627A pdb=" N LEU W 347 " --> pdb=" O GLU W 343 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU W 348 " --> pdb=" O ALA W 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 343 through 348' Processing helix chain 'W' and resid 349 through 355 removed outlier: 3.937A pdb=" N GLU W 353 " --> pdb=" O PRO W 349 " (cutoff:3.500A) Processing helix chain 'W' and resid 356 through 369 Processing helix chain 'W' and resid 382 through 397 removed outlier: 3.675A pdb=" N LEU W 388 " --> pdb=" O GLU W 384 " (cutoff:3.500A) Processing helix chain 'W' and resid 403 through 418 removed outlier: 4.478A pdb=" N LEU W 407 " --> pdb=" O VAL W 403 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN W 408 " --> pdb=" O CYS W 404 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA W 410 " --> pdb=" O GLY W 406 " (cutoff:3.500A) Processing helix chain 'W' and resid 426 through 431 removed outlier: 3.590A pdb=" N LEU W 430 " --> pdb=" O SER W 426 " (cutoff:3.500A) Processing helix chain 'W' and resid 473 through 480 removed outlier: 3.808A pdb=" N GLY W 480 " --> pdb=" O ARG W 476 " (cutoff:3.500A) Processing helix chain 'W' and resid 496 through 507 removed outlier: 3.524A pdb=" N VAL W 500 " --> pdb=" O ASN W 496 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN W 501 " --> pdb=" O PRO W 497 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP W 502 " --> pdb=" O LYS W 498 " (cutoff:3.500A) Processing helix chain 'W' and resid 537 through 542 removed outlier: 4.851A pdb=" N THR W 541 " --> pdb=" O HIS W 537 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER W 542 " --> pdb=" O PRO W 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 537 through 542' Processing helix chain 'W' and resid 548 through 560 Processing helix chain 'W' and resid 561 through 571 removed outlier: 3.559A pdb=" N LEU W 571 " --> pdb=" O LYS W 567 " (cutoff:3.500A) Processing helix chain 'X' and resid 15 through 31 removed outlier: 3.960A pdb=" N LEU X 30 " --> pdb=" O LEU X 26 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY X 31 " --> pdb=" O LEU X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 68 through 78 removed outlier: 4.031A pdb=" N GLY X 72 " --> pdb=" O ASP X 68 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN X 73 " --> pdb=" O LEU X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 88 removed outlier: 4.379A pdb=" N ASN X 87 " --> pdb=" O SER X 83 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE X 88 " --> pdb=" O ARG X 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 83 through 88' Processing helix chain 'X' and resid 89 through 104 removed outlier: 3.538A pdb=" N ARG X 103 " --> pdb=" O SER X 99 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 131 removed outlier: 3.602A pdb=" N LYS X 130 " --> pdb=" O GLN X 126 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE X 131 " --> pdb=" O ARG X 127 " (cutoff:3.500A) Processing helix chain 'X' and resid 153 through 170 Proline residue: X 158 - end of helix removed outlier: 4.186A pdb=" N PHE X 168 " --> pdb=" O ARG X 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 171 through 176 removed outlier: 3.855A pdb=" N PHE X 175 " --> pdb=" O GLY X 171 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ALA X 176 " --> pdb=" O ARG X 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 171 through 176' Processing helix chain 'X' and resid 192 through 206 Processing helix chain 'X' and resid 221 through 233 removed outlier: 5.100A pdb=" N HIS X 233 " --> pdb=" O ALA X 229 " (cutoff:3.500A) Processing helix chain 'X' and resid 235 through 240 removed outlier: 3.999A pdb=" N VAL X 239 " --> pdb=" O GLY X 235 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL X 240 " --> pdb=" O PRO X 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 235 through 240' Processing helix chain 'X' and resid 247 through 259 removed outlier: 4.298A pdb=" N VAL X 251 " --> pdb=" O SER X 247 " (cutoff:3.500A) Proline residue: X 252 - end of helix Processing helix chain 'X' and resid 260 through 269 removed outlier: 3.612A pdb=" N SER X 266 " --> pdb=" O ASP X 262 " (cutoff:3.500A) Processing helix chain 'X' and resid 276 through 300 removed outlier: 3.878A pdb=" N SER X 284 " --> pdb=" O LYS X 280 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER X 300 " --> pdb=" O ASN X 296 " (cutoff:3.500A) Processing helix chain 'X' and resid 315 through 320 removed outlier: 4.498A pdb=" N TYR X 319 " --> pdb=" O LEU X 315 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU X 320 " --> pdb=" O LYS X 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 315 through 320' Processing helix chain 'X' and resid 321 through 334 Processing helix chain 'X' and resid 343 through 348 removed outlier: 3.627A pdb=" N LEU X 347 " --> pdb=" O GLU X 343 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU X 348 " --> pdb=" O ALA X 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 343 through 348' Processing helix chain 'X' and resid 349 through 355 removed outlier: 3.937A pdb=" N GLU X 353 " --> pdb=" O PRO X 349 " (cutoff:3.500A) Processing helix chain 'X' and resid 356 through 369 Processing helix chain 'X' and resid 382 through 397 removed outlier: 3.675A pdb=" N LEU X 388 " --> pdb=" O GLU X 384 " (cutoff:3.500A) Processing helix chain 'X' and resid 403 through 418 removed outlier: 4.480A pdb=" N LEU X 407 " --> pdb=" O VAL X 403 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN X 408 " --> pdb=" O CYS X 404 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA X 410 " --> pdb=" O GLY X 406 " (cutoff:3.500A) Processing helix chain 'X' and resid 426 through 431 removed outlier: 3.590A pdb=" N LEU X 430 " --> pdb=" O SER X 426 " (cutoff:3.500A) Processing helix chain 'X' and resid 473 through 480 removed outlier: 3.808A pdb=" N GLY X 480 " --> pdb=" O ARG X 476 " (cutoff:3.500A) Processing helix chain 'X' and resid 496 through 507 removed outlier: 3.524A pdb=" N VAL X 500 " --> pdb=" O ASN X 496 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN X 501 " --> pdb=" O PRO X 497 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP X 502 " --> pdb=" O LYS X 498 " (cutoff:3.500A) Processing helix chain 'X' and resid 537 through 542 removed outlier: 4.851A pdb=" N THR X 541 " --> pdb=" O HIS X 537 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER X 542 " --> pdb=" O PRO X 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 537 through 542' Processing helix chain 'X' and resid 548 through 560 Processing helix chain 'X' and resid 561 through 571 removed outlier: 3.560A pdb=" N LEU X 571 " --> pdb=" O LYS X 567 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 31 removed outlier: 3.959A pdb=" N LEU Y 30 " --> pdb=" O LEU Y 26 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY Y 31 " --> pdb=" O LEU Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 68 through 78 removed outlier: 4.029A pdb=" N GLY Y 72 " --> pdb=" O ASP Y 68 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN Y 73 " --> pdb=" O LEU Y 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 83 through 88 removed outlier: 4.380A pdb=" N ASN Y 87 " --> pdb=" O SER Y 83 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE Y 88 " --> pdb=" O ARG Y 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 83 through 88' Processing helix chain 'Y' and resid 89 through 104 removed outlier: 3.537A pdb=" N ARG Y 103 " --> pdb=" O SER Y 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 115 through 131 removed outlier: 3.603A pdb=" N LYS Y 130 " --> pdb=" O GLN Y 126 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE Y 131 " --> pdb=" O ARG Y 127 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 170 Proline residue: Y 158 - end of helix removed outlier: 4.186A pdb=" N PHE Y 168 " --> pdb=" O ARG Y 164 " (cutoff:3.500A) Processing helix chain 'Y' and resid 171 through 176 removed outlier: 3.855A pdb=" N PHE Y 175 " --> pdb=" O GLY Y 171 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ALA Y 176 " --> pdb=" O ARG Y 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 171 through 176' Processing helix chain 'Y' and resid 192 through 206 Processing helix chain 'Y' and resid 221 through 233 removed outlier: 5.101A pdb=" N HIS Y 233 " --> pdb=" O ALA Y 229 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 240 removed outlier: 3.999A pdb=" N VAL Y 239 " --> pdb=" O GLY Y 235 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL Y 240 " --> pdb=" O PRO Y 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 235 through 240' Processing helix chain 'Y' and resid 247 through 259 removed outlier: 4.298A pdb=" N VAL Y 251 " --> pdb=" O SER Y 247 " (cutoff:3.500A) Proline residue: Y 252 - end of helix Processing helix chain 'Y' and resid 260 through 269 removed outlier: 3.611A pdb=" N SER Y 266 " --> pdb=" O ASP Y 262 " (cutoff:3.500A) Processing helix chain 'Y' and resid 276 through 300 removed outlier: 3.877A pdb=" N SER Y 284 " --> pdb=" O LYS Y 280 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER Y 300 " --> pdb=" O ASN Y 296 " (cutoff:3.500A) Processing helix chain 'Y' and resid 315 through 320 removed outlier: 4.497A pdb=" N TYR Y 319 " --> pdb=" O LEU Y 315 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU Y 320 " --> pdb=" O LYS Y 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 315 through 320' Processing helix chain 'Y' and resid 321 through 334 Processing helix chain 'Y' and resid 343 through 348 removed outlier: 3.628A pdb=" N LEU Y 347 " --> pdb=" O GLU Y 343 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU Y 348 " --> pdb=" O ALA Y 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 343 through 348' Processing helix chain 'Y' and resid 349 through 355 removed outlier: 3.938A pdb=" N GLU Y 353 " --> pdb=" O PRO Y 349 " (cutoff:3.500A) Processing helix chain 'Y' and resid 356 through 369 Processing helix chain 'Y' and resid 382 through 397 removed outlier: 3.676A pdb=" N LEU Y 388 " --> pdb=" O GLU Y 384 " (cutoff:3.500A) Processing helix chain 'Y' and resid 403 through 418 removed outlier: 4.479A pdb=" N LEU Y 407 " --> pdb=" O VAL Y 403 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN Y 408 " --> pdb=" O CYS Y 404 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA Y 410 " --> pdb=" O GLY Y 406 " (cutoff:3.500A) Processing helix chain 'Y' and resid 426 through 431 removed outlier: 3.591A pdb=" N LEU Y 430 " --> pdb=" O SER Y 426 " (cutoff:3.500A) Processing helix chain 'Y' and resid 473 through 480 removed outlier: 3.807A pdb=" N GLY Y 480 " --> pdb=" O ARG Y 476 " (cutoff:3.500A) Processing helix chain 'Y' and resid 496 through 507 removed outlier: 3.523A pdb=" N VAL Y 500 " --> pdb=" O ASN Y 496 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN Y 501 " --> pdb=" O PRO Y 497 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP Y 502 " --> pdb=" O LYS Y 498 " (cutoff:3.500A) Processing helix chain 'Y' and resid 537 through 542 removed outlier: 4.851A pdb=" N THR Y 541 " --> pdb=" O HIS Y 537 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER Y 542 " --> pdb=" O PRO Y 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 537 through 542' Processing helix chain 'Y' and resid 548 through 560 Processing helix chain 'Y' and resid 561 through 571 removed outlier: 3.560A pdb=" N LEU Y 571 " --> pdb=" O LYS Y 567 " (cutoff:3.500A) Processing helix chain 'Z' and resid 15 through 31 removed outlier: 3.959A pdb=" N LEU Z 30 " --> pdb=" O LEU Z 26 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY Z 31 " --> pdb=" O LEU Z 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 78 removed outlier: 4.030A pdb=" N GLY Z 72 " --> pdb=" O ASP Z 68 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN Z 73 " --> pdb=" O LEU Z 69 " (cutoff:3.500A) Processing helix chain 'Z' and resid 83 through 88 removed outlier: 4.379A pdb=" N ASN Z 87 " --> pdb=" O SER Z 83 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE Z 88 " --> pdb=" O ARG Z 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 83 through 88' Processing helix chain 'Z' and resid 89 through 104 removed outlier: 3.537A pdb=" N ARG Z 103 " --> pdb=" O SER Z 99 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 131 removed outlier: 3.603A pdb=" N LYS Z 130 " --> pdb=" O GLN Z 126 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE Z 131 " --> pdb=" O ARG Z 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 153 through 170 Proline residue: Z 158 - end of helix removed outlier: 4.185A pdb=" N PHE Z 168 " --> pdb=" O ARG Z 164 " (cutoff:3.500A) Processing helix chain 'Z' and resid 171 through 176 removed outlier: 3.855A pdb=" N PHE Z 175 " --> pdb=" O GLY Z 171 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ALA Z 176 " --> pdb=" O ARG Z 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 171 through 176' Processing helix chain 'Z' and resid 192 through 206 Processing helix chain 'Z' and resid 221 through 233 removed outlier: 5.101A pdb=" N HIS Z 233 " --> pdb=" O ALA Z 229 " (cutoff:3.500A) Processing helix chain 'Z' and resid 235 through 240 removed outlier: 3.999A pdb=" N VAL Z 239 " --> pdb=" O GLY Z 235 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL Z 240 " --> pdb=" O PRO Z 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 235 through 240' Processing helix chain 'Z' and resid 247 through 259 removed outlier: 4.297A pdb=" N VAL Z 251 " --> pdb=" O SER Z 247 " (cutoff:3.500A) Proline residue: Z 252 - end of helix Processing helix chain 'Z' and resid 260 through 269 removed outlier: 3.611A pdb=" N SER Z 266 " --> pdb=" O ASP Z 262 " (cutoff:3.500A) Processing helix chain 'Z' and resid 276 through 300 removed outlier: 3.877A pdb=" N SER Z 284 " --> pdb=" O LYS Z 280 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER Z 300 " --> pdb=" O ASN Z 296 " (cutoff:3.500A) Processing helix chain 'Z' and resid 315 through 320 removed outlier: 4.497A pdb=" N TYR Z 319 " --> pdb=" O LEU Z 315 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU Z 320 " --> pdb=" O LYS Z 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 315 through 320' Processing helix chain 'Z' and resid 321 through 334 Processing helix chain 'Z' and resid 343 through 348 removed outlier: 3.627A pdb=" N LEU Z 347 " --> pdb=" O GLU Z 343 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU Z 348 " --> pdb=" O ALA Z 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 343 through 348' Processing helix chain 'Z' and resid 349 through 355 removed outlier: 3.937A pdb=" N GLU Z 353 " --> pdb=" O PRO Z 349 " (cutoff:3.500A) Processing helix chain 'Z' and resid 356 through 369 Processing helix chain 'Z' and resid 382 through 397 removed outlier: 3.675A pdb=" N LEU Z 388 " --> pdb=" O GLU Z 384 " (cutoff:3.500A) Processing helix chain 'Z' and resid 403 through 418 removed outlier: 4.479A pdb=" N LEU Z 407 " --> pdb=" O VAL Z 403 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN Z 408 " --> pdb=" O CYS Z 404 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA Z 410 " --> pdb=" O GLY Z 406 " (cutoff:3.500A) Processing helix chain 'Z' and resid 426 through 431 removed outlier: 3.591A pdb=" N LEU Z 430 " --> pdb=" O SER Z 426 " (cutoff:3.500A) Processing helix chain 'Z' and resid 473 through 480 removed outlier: 3.808A pdb=" N GLY Z 480 " --> pdb=" O ARG Z 476 " (cutoff:3.500A) Processing helix chain 'Z' and resid 496 through 507 removed outlier: 3.523A pdb=" N VAL Z 500 " --> pdb=" O ASN Z 496 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN Z 501 " --> pdb=" O PRO Z 497 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP Z 502 " --> pdb=" O LYS Z 498 " (cutoff:3.500A) Processing helix chain 'Z' and resid 537 through 542 removed outlier: 4.849A pdb=" N THR Z 541 " --> pdb=" O HIS Z 537 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER Z 542 " --> pdb=" O PRO Z 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 537 through 542' Processing helix chain 'Z' and resid 548 through 560 Processing helix chain 'Z' and resid 561 through 571 removed outlier: 3.560A pdb=" N LEU Z 571 " --> pdb=" O LYS Z 567 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 33 through 40 removed outlier: 4.049A pdb=" N GLY A 8 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 9 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU A 182 " --> pdb=" O GLY A 9 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 335 through 342 removed outlier: 5.388A pdb=" N TYR A 531 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 484 through 489 removed outlier: 6.579A pdb=" N VAL A 511 " --> pdb=" O GLN A 467 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 33 through 40 removed outlier: 4.048A pdb=" N GLY B 8 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY B 9 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU B 182 " --> pdb=" O GLY B 9 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 335 through 342 removed outlier: 5.388A pdb=" N TYR B 531 " --> pdb=" O LEU B 525 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 484 through 489 removed outlier: 6.578A pdb=" N VAL B 511 " --> pdb=" O GLN B 467 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 33 through 40 removed outlier: 4.049A pdb=" N GLY C 8 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY C 9 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU C 182 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 335 through 342 removed outlier: 5.389A pdb=" N TYR C 531 " --> pdb=" O LEU C 525 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 484 through 489 removed outlier: 6.577A pdb=" N VAL C 511 " --> pdb=" O GLN C 467 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 33 through 40 removed outlier: 4.049A pdb=" N GLY D 8 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY D 9 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU D 182 " --> pdb=" O GLY D 9 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 335 through 342 removed outlier: 5.389A pdb=" N TYR D 531 " --> pdb=" O LEU D 525 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 484 through 489 removed outlier: 6.580A pdb=" N VAL D 511 " --> pdb=" O GLN D 467 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 33 through 40 removed outlier: 4.048A pdb=" N GLY E 8 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY E 9 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU E 182 " --> pdb=" O GLY E 9 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 335 through 342 removed outlier: 5.388A pdb=" N TYR E 531 " --> pdb=" O LEU E 525 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 484 through 489 removed outlier: 6.578A pdb=" N VAL E 511 " --> pdb=" O GLN E 467 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 33 through 40 removed outlier: 4.049A pdb=" N GLY F 8 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY F 9 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU F 182 " --> pdb=" O GLY F 9 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 335 through 342 removed outlier: 5.388A pdb=" N TYR F 531 " --> pdb=" O LEU F 525 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'F' and resid 484 through 489 removed outlier: 6.578A pdb=" N VAL F 511 " --> pdb=" O GLN F 467 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 33 through 40 removed outlier: 4.049A pdb=" N GLY G 8 " --> pdb=" O LEU G 147 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY G 9 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU G 182 " --> pdb=" O GLY G 9 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 335 through 342 removed outlier: 5.389A pdb=" N TYR G 531 " --> pdb=" O LEU G 525 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'G' and resid 484 through 489 removed outlier: 6.578A pdb=" N VAL G 511 " --> pdb=" O GLN G 467 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 33 through 40 removed outlier: 4.049A pdb=" N GLY H 8 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY H 9 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU H 182 " --> pdb=" O GLY H 9 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 335 through 342 removed outlier: 5.388A pdb=" N TYR H 531 " --> pdb=" O LEU H 525 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'H' and resid 484 through 489 removed outlier: 6.579A pdb=" N VAL H 511 " --> pdb=" O GLN H 467 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'W' and resid 33 through 40 removed outlier: 4.048A pdb=" N GLY W 8 " --> pdb=" O LEU W 147 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY W 9 " --> pdb=" O VAL W 180 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU W 182 " --> pdb=" O GLY W 9 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'W' and resid 335 through 342 removed outlier: 5.388A pdb=" N TYR W 531 " --> pdb=" O LEU W 525 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'W' and resid 484 through 489 removed outlier: 6.579A pdb=" N VAL W 511 " --> pdb=" O GLN W 467 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'X' and resid 33 through 40 removed outlier: 4.048A pdb=" N GLY X 8 " --> pdb=" O LEU X 147 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY X 9 " --> pdb=" O VAL X 180 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU X 182 " --> pdb=" O GLY X 9 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'X' and resid 335 through 342 removed outlier: 5.388A pdb=" N TYR X 531 " --> pdb=" O LEU X 525 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'X' and resid 484 through 489 removed outlier: 6.578A pdb=" N VAL X 511 " --> pdb=" O GLN X 467 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Y' and resid 33 through 40 removed outlier: 4.049A pdb=" N GLY Y 8 " --> pdb=" O LEU Y 147 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY Y 9 " --> pdb=" O VAL Y 180 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU Y 182 " --> pdb=" O GLY Y 9 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Y' and resid 335 through 342 removed outlier: 5.388A pdb=" N TYR Y 531 " --> pdb=" O LEU Y 525 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Y' and resid 484 through 489 removed outlier: 6.578A pdb=" N VAL Y 511 " --> pdb=" O GLN Y 467 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Z' and resid 33 through 40 removed outlier: 4.049A pdb=" N GLY Z 8 " --> pdb=" O LEU Z 147 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY Z 9 " --> pdb=" O VAL Z 180 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU Z 182 " --> pdb=" O GLY Z 9 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Z' and resid 335 through 342 removed outlier: 5.389A pdb=" N TYR Z 531 " --> pdb=" O LEU Z 525 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Z' and resid 484 through 489 removed outlier: 6.579A pdb=" N VAL Z 511 " --> pdb=" O GLN Z 467 " (cutoff:3.500A) 2484 hydrogen bonds defined for protein. 7380 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: 40.26 Time building geometry restraints manager: 64.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 52620 1.09 - 1.28: 9024 1.28 - 1.46: 14882 1.46 - 1.64: 30214 1.64 - 1.82: 384 Bond restraints: 107124 Sorted by residual: bond pdb=" C2' UTP B 604 " pdb=" C3' UTP B 604 " ideal model delta sigma weight residual 1.301 1.538 -0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C2' UTP G 602 " pdb=" C3' UTP G 602 " ideal model delta sigma weight residual 1.301 1.537 -0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C2' UTP Y 602 " pdb=" C3' UTP Y 602 " ideal model delta sigma weight residual 1.301 1.537 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C2' UTP C 603 " pdb=" C3' UTP C 603 " ideal model delta sigma weight residual 1.301 1.537 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C2' UTP H 602 " pdb=" C3' UTP H 602 " ideal model delta sigma weight residual 1.301 1.537 -0.236 2.00e-02 2.50e+03 1.39e+02 ... (remaining 107119 not shown) Histogram of bond angle deviations from ideal: 76.67 - 89.19: 36 89.19 - 101.71: 300 101.71 - 114.23: 128859 114.23 - 126.75: 63445 126.75 - 139.27: 1352 Bond angle restraints: 193992 Sorted by residual: angle pdb=" N SER E 217 " pdb=" CA SER E 217 " pdb=" HA SER E 217 " ideal model delta sigma weight residual 110.00 76.94 33.06 3.00e+00 1.11e-01 1.21e+02 angle pdb=" N SER G 217 " pdb=" CA SER G 217 " pdb=" HA SER G 217 " ideal model delta sigma weight residual 110.00 76.95 33.05 3.00e+00 1.11e-01 1.21e+02 angle pdb=" N SER F 217 " pdb=" CA SER F 217 " pdb=" HA SER F 217 " ideal model delta sigma weight residual 110.00 76.95 33.05 3.00e+00 1.11e-01 1.21e+02 angle pdb=" N SER Y 217 " pdb=" CA SER Y 217 " pdb=" HA SER Y 217 " ideal model delta sigma weight residual 110.00 76.96 33.04 3.00e+00 1.11e-01 1.21e+02 angle pdb=" N SER C 217 " pdb=" CA SER C 217 " pdb=" HA SER C 217 " ideal model delta sigma weight residual 110.00 76.96 33.04 3.00e+00 1.11e-01 1.21e+02 ... (remaining 193987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 44448 18.00 - 35.99: 3572 35.99 - 53.99: 1120 53.99 - 71.98: 900 71.98 - 89.98: 84 Dihedral angle restraints: 50124 sinusoidal: 28080 harmonic: 22044 Sorted by residual: dihedral pdb=" C SER W 217 " pdb=" N SER W 217 " pdb=" CA SER W 217 " pdb=" CB SER W 217 " ideal model delta harmonic sigma weight residual -122.60 -138.16 15.56 0 2.50e+00 1.60e-01 3.87e+01 dihedral pdb=" C SER Z 217 " pdb=" N SER Z 217 " pdb=" CA SER Z 217 " pdb=" CB SER Z 217 " ideal model delta harmonic sigma weight residual -122.60 -138.15 15.55 0 2.50e+00 1.60e-01 3.87e+01 dihedral pdb=" C SER F 217 " pdb=" N SER F 217 " pdb=" CA SER F 217 " pdb=" CB SER F 217 " ideal model delta harmonic sigma weight residual -122.60 -138.14 15.54 0 2.50e+00 1.60e-01 3.87e+01 ... (remaining 50121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 6717 0.134 - 0.268: 1458 0.268 - 0.402: 141 0.402 - 0.536: 24 0.536 - 0.670: 12 Chirality restraints: 8352 Sorted by residual: chirality pdb=" CA SER F 217 " pdb=" N SER F 217 " pdb=" C SER F 217 " pdb=" CB SER F 217 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" CA SER W 217 " pdb=" N SER W 217 " pdb=" C SER W 217 " pdb=" CB SER W 217 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" CA SER B 217 " pdb=" N SER B 217 " pdb=" C SER B 217 " pdb=" CB SER B 217 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.12e+01 ... (remaining 8349 not shown) Planarity restraints: 15792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN Z 241 " 0.121 2.00e-02 2.50e+03 1.19e-01 2.13e+02 pdb=" CG ASN Z 241 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN Z 241 " -0.077 2.00e-02 2.50e+03 pdb=" ND2 ASN Z 241 " -0.125 2.00e-02 2.50e+03 pdb="HD21 ASN Z 241 " -0.089 2.00e-02 2.50e+03 pdb="HD22 ASN Z 241 " 0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 241 " -0.121 2.00e-02 2.50e+03 1.19e-01 2.13e+02 pdb=" CG ASN F 241 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN F 241 " 0.077 2.00e-02 2.50e+03 pdb=" ND2 ASN F 241 " 0.126 2.00e-02 2.50e+03 pdb="HD21 ASN F 241 " 0.089 2.00e-02 2.50e+03 pdb="HD22 ASN F 241 " -0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 241 " 0.121 2.00e-02 2.50e+03 1.19e-01 2.13e+02 pdb=" CG ASN B 241 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B 241 " -0.078 2.00e-02 2.50e+03 pdb=" ND2 ASN B 241 " -0.125 2.00e-02 2.50e+03 pdb="HD21 ASN B 241 " -0.090 2.00e-02 2.50e+03 pdb="HD22 ASN B 241 " 0.200 2.00e-02 2.50e+03 ... (remaining 15789 not shown) Histogram of nonbonded interaction distances: 1.11 - 1.81: 650 1.81 - 2.50: 66528 2.50 - 3.20: 336513 3.20 - 3.90: 443427 3.90 - 4.60: 683216 Nonbonded interactions: 1530334 Sorted by model distance: nonbonded pdb=" H THR A 192 " pdb=" O1G UTP A 604 " model vdw 1.108 1.850 nonbonded pdb=" H THR W 192 " pdb=" O1G UTP W 604 " model vdw 1.108 1.850 nonbonded pdb=" H THR E 192 " pdb=" O1G UTP E 604 " model vdw 1.109 1.850 nonbonded pdb=" H THR H 192 " pdb=" O1G UTP H 602 " model vdw 1.123 1.850 nonbonded pdb=" H THR Z 192 " pdb=" O1G UTP Z 602 " model vdw 1.124 1.850 ... (remaining 1530329 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 571) selection = (chain 'B' and resid 1 through 571) selection = (chain 'C' and resid 1 through 571) selection = (chain 'D' and resid 1 through 571) selection = (chain 'E' and resid 1 through 571) selection = (chain 'F' and resid 1 through 571) selection = (chain 'G' and resid 1 through 571) selection = (chain 'H' and resid 1 through 571) selection = (chain 'W' and resid 1 through 571) selection = (chain 'X' and resid 1 through 571) selection = (chain 'Y' and resid 1 through 571) selection = (chain 'Z' and resid 1 through 571) } 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.550 Construct map_model_manager: 1.150 Extract box with map and model: 10.230 Check model and map are aligned: 1.140 Set scattering table: 0.690 Process input model: 258.560 Find NCS groups from input model: 5.540 Set up NCS constraints: 0.480 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:9.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 289.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4773 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 : 0.014 0.237 54408 Z= 0.923 Angle : 2.041 20.342 73860 Z= 1.343 Chirality : 0.111 0.670 8352 Planarity : 0.017 0.153 9396 Dihedral : 15.071 89.976 20544 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.52 % Favored : 97.30 % Rotamer: Outliers : 1.08 % Allowed : 3.43 % Favored : 95.49 % Cbeta Deviations : 0.78 % Peptide Plane: Cis-proline : 4.17 % 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: -1.35 (0.09), residues: 6660 helix: -1.73 (0.07), residues: 2904 sheet: 0.78 (0.16), residues: 984 loop : -0.34 (0.12), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.019 TRP B 392 HIS 0.020 0.005 HIS E 179 PHE 0.081 0.018 PHE F 508 TYR 0.107 0.024 TYR B 42 ARG 0.024 0.002 ARG Y 267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2112 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 2049 time to evaluate : 5.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 339 ILE cc_start: 0.7690 (mt) cc_final: 0.7294 (tt) REVERT: B 340 LEU cc_start: 0.7329 (mt) cc_final: 0.6839 (mt) REVERT: B 394 ARG cc_start: 0.6606 (ttp80) cc_final: 0.5579 (ttp-110) REVERT: C 366 LEU cc_start: 0.7940 (tp) cc_final: 0.7714 (tp) REVERT: C 388 LEU cc_start: 0.7721 (mt) cc_final: 0.6927 (mt) REVERT: E 28 LYS cc_start: 0.7989 (tttm) cc_final: 0.7785 (mtmt) REVERT: E 257 LYS cc_start: 0.7020 (mttp) cc_final: 0.6653 (mptt) REVERT: E 305 LYS cc_start: 0.7675 (mttm) cc_final: 0.7397 (mtpp) REVERT: E 499 ILE cc_start: 0.7562 (mt) cc_final: 0.7321 (mm) REVERT: F 75 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7321 (mm-30) REVERT: F 189 GLU cc_start: 0.7726 (tt0) cc_final: 0.7353 (tt0) REVERT: F 282 ARG cc_start: 0.7005 (mtp-110) cc_final: 0.5903 (mpt-90) REVERT: F 320 LEU cc_start: 0.8655 (tp) cc_final: 0.8450 (tp) REVERT: F 384 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6818 (mm-30) REVERT: G 257 LYS cc_start: 0.6899 (mttp) cc_final: 0.6601 (mptt) REVERT: G 305 LYS cc_start: 0.7918 (mttm) cc_final: 0.7542 (mtpt) REVERT: H 189 GLU cc_start: 0.7704 (tt0) cc_final: 0.7269 (tt0) REVERT: H 195 THR cc_start: 0.9005 (t) cc_final: 0.8703 (m) REVERT: H 305 LYS cc_start: 0.7816 (mttm) cc_final: 0.7493 (mtpp) REVERT: W 134 ASP cc_start: 0.6680 (m-30) cc_final: 0.6246 (t70) REVERT: W 365 LYS cc_start: 0.7206 (mtmt) cc_final: 0.6529 (mptt) REVERT: W 373 LEU cc_start: 0.6894 (tp) cc_final: 0.6061 (mt) REVERT: X 303 VAL cc_start: 0.6073 (t) cc_final: 0.5658 (p) REVERT: Y 226 ASP cc_start: 0.4534 (m-30) cc_final: 0.3572 (m-30) REVERT: Y 279 ASP cc_start: 0.3754 (m-30) cc_final: 0.2844 (m-30) REVERT: Y 350 GLU cc_start: 0.5373 (tt0) cc_final: 0.4985 (tp30) REVERT: Y 353 GLU cc_start: 0.4142 (mt-10) cc_final: 0.3686 (mt-10) REVERT: Z 294 THR cc_start: 0.5655 (p) cc_final: 0.5420 (p) REVERT: Z 304 VAL cc_start: 0.7855 (p) cc_final: 0.7603 (t) REVERT: Z 391 LYS cc_start: 0.6797 (ttpt) cc_final: 0.5907 (tmtp) outliers start: 63 outliers final: 14 residues processed: 2087 average time/residue: 2.4012 time to fit residues: 6596.6124 Evaluate side-chains 1491 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1477 time to evaluate : 5.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 93 ILE Chi-restraints excluded: chain Z residue 262 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 557 optimal weight: 10.0000 chunk 500 optimal weight: 10.0000 chunk 277 optimal weight: 0.7980 chunk 170 optimal weight: 9.9990 chunk 337 optimal weight: 0.7980 chunk 267 optimal weight: 0.8980 chunk 517 optimal weight: 8.9990 chunk 200 optimal weight: 9.9990 chunk 314 optimal weight: 0.9990 chunk 385 optimal weight: 0.6980 chunk 599 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 167 GLN ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 ASN A 265 HIS A 289 ASN B 73 ASN B 165 GLN B 537 HIS C 86 HIS C 87 ASN C 165 GLN C 238 GLN C 259 HIS C 483 ASN D 165 GLN D 221 ASN E 165 GLN E 167 GLN E 221 ASN E 296 ASN F 165 GLN F 221 ASN F 241 ASN F 467 GLN G 165 GLN G 221 ASN H 165 GLN H 167 GLN H 221 ASN H 296 ASN W 87 ASN W 165 GLN W 221 ASN W 238 GLN W 259 HIS W 336 GLN W 467 GLN W 483 ASN X 165 GLN X 167 GLN ** X 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN X 233 HIS X 265 HIS Y 165 GLN Y 221 ASN ** Y 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 73 ASN Z 364 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4875 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 54408 Z= 0.218 Angle : 0.700 8.724 73860 Z= 0.366 Chirality : 0.049 0.383 8352 Planarity : 0.005 0.065 9396 Dihedral : 9.579 117.502 7769 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.41 % Favored : 98.41 % Rotamer: Outliers : 2.85 % Allowed : 16.65 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.28 (0.10), residues: 6660 helix: 0.32 (0.09), residues: 2904 sheet: 0.37 (0.15), residues: 1044 loop : 0.18 (0.13), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 363 HIS 0.009 0.002 HIS W 259 PHE 0.023 0.003 PHE F 508 TYR 0.019 0.002 TYR A 42 ARG 0.011 0.001 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1755 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1588 time to evaluate : 5.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 GLU cc_start: 0.5724 (OUTLIER) cc_final: 0.3910 (tm-30) REVERT: B 339 ILE cc_start: 0.7837 (mt) cc_final: 0.7448 (tt) REVERT: B 373 LEU cc_start: 0.6902 (tp) cc_final: 0.5382 (mt) REVERT: C 101 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.5139 (tp30) REVERT: C 353 GLU cc_start: 0.4788 (mp0) cc_final: 0.4116 (mp0) REVERT: C 366 LEU cc_start: 0.8209 (tp) cc_final: 0.7958 (tp) REVERT: C 386 MET cc_start: 0.7002 (mpt) cc_final: 0.6364 (mpt) REVERT: C 388 LEU cc_start: 0.7599 (mt) cc_final: 0.7060 (mt) REVERT: D 61 LEU cc_start: 0.4009 (OUTLIER) cc_final: 0.3791 (tp) REVERT: D 571 LEU cc_start: 0.3345 (OUTLIER) cc_final: 0.0443 (mt) REVERT: E 105 ASP cc_start: 0.7149 (m-30) cc_final: 0.6780 (m-30) REVERT: E 130 LYS cc_start: 0.7904 (mtmm) cc_final: 0.7347 (mttm) REVERT: E 139 GLU cc_start: 0.6889 (pt0) cc_final: 0.6607 (tt0) REVERT: E 226 ASP cc_start: 0.7584 (m-30) cc_final: 0.7319 (t70) REVERT: E 249 TYR cc_start: 0.8003 (m-80) cc_final: 0.6991 (m-80) REVERT: E 257 LYS cc_start: 0.6856 (mttp) cc_final: 0.6388 (mptt) REVERT: E 305 LYS cc_start: 0.7356 (mttm) cc_final: 0.7099 (mtpp) REVERT: E 481 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6729 (mm-30) REVERT: F 82 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8362 (mp) REVERT: F 110 THR cc_start: 0.8320 (t) cc_final: 0.8118 (m) REVERT: F 130 LYS cc_start: 0.7861 (mtmm) cc_final: 0.7096 (mptt) REVERT: F 138 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7671 (mt) REVERT: F 568 ASP cc_start: 0.5231 (OUTLIER) cc_final: 0.4363 (t0) REVERT: G 110 THR cc_start: 0.8410 (t) cc_final: 0.8156 (m) REVERT: G 123 ASP cc_start: 0.6978 (m-30) cc_final: 0.6723 (m-30) REVERT: G 257 LYS cc_start: 0.6864 (mttp) cc_final: 0.6488 (mptt) REVERT: G 305 LYS cc_start: 0.7543 (mttm) cc_final: 0.6832 (mttm) REVERT: H 164 ARG cc_start: 0.7785 (ttt90) cc_final: 0.7440 (ttp-110) REVERT: H 185 VAL cc_start: 0.8913 (p) cc_final: 0.8681 (t) REVERT: H 200 LYS cc_start: 0.7664 (mtpt) cc_final: 0.7359 (mttp) REVERT: H 282 ARG cc_start: 0.6724 (mtp-110) cc_final: 0.5793 (mpt-90) REVERT: H 305 LYS cc_start: 0.7514 (mttm) cc_final: 0.7054 (mtpp) REVERT: W 101 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.3552 (tp30) REVERT: W 291 GLU cc_start: 0.6665 (tm-30) cc_final: 0.6434 (tm-30) REVERT: W 388 LEU cc_start: 0.7840 (mt) cc_final: 0.7237 (mt) REVERT: X 331 MET cc_start: 0.3475 (mmm) cc_final: 0.2994 (mmp) REVERT: Z 53 LEU cc_start: 0.7945 (pp) cc_final: 0.7603 (pp) REVERT: Z 101 GLU cc_start: 0.5886 (OUTLIER) cc_final: 0.4705 (tp30) outliers start: 167 outliers final: 61 residues processed: 1663 average time/residue: 2.1623 time to fit residues: 4923.3440 Evaluate side-chains 1358 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1288 time to evaluate : 5.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 92 LYS Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain F residue 542 SER Chi-restraints excluded: chain F residue 568 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 542 SER Chi-restraints excluded: chain H residue 542 SER Chi-restraints excluded: chain W residue 19 LEU Chi-restraints excluded: chain W residue 101 GLU Chi-restraints excluded: chain W residue 141 ASP Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 183 VAL Chi-restraints excluded: chain W residue 251 VAL Chi-restraints excluded: chain W residue 314 ASN Chi-restraints excluded: chain W residue 427 THR Chi-restraints excluded: chain W residue 542 SER Chi-restraints excluded: chain X residue 297 LEU Chi-restraints excluded: chain X residue 562 LEU Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 87 ASN Chi-restraints excluded: chain Y residue 193 LYS Chi-restraints excluded: chain Y residue 355 ASP Chi-restraints excluded: chain Y residue 566 ILE Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 28 LYS Chi-restraints excluded: chain Z residue 42 TYR Chi-restraints excluded: chain Z residue 101 GLU Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 275 LEU Chi-restraints excluded: chain Z residue 337 LEU Chi-restraints excluded: chain Z residue 339 ILE Chi-restraints excluded: chain Z residue 356 LYS Chi-restraints excluded: chain Z residue 403 VAL Chi-restraints excluded: chain Z residue 430 LEU Chi-restraints excluded: chain Z residue 459 LEU Chi-restraints excluded: chain Z residue 542 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 333 optimal weight: 1.9990 chunk 186 optimal weight: 40.0000 chunk 498 optimal weight: 20.0000 chunk 408 optimal weight: 1.9990 chunk 165 optimal weight: 50.0000 chunk 600 optimal weight: 50.0000 chunk 648 optimal weight: 7.9990 chunk 534 optimal weight: 9.9990 chunk 595 optimal weight: 9.9990 chunk 204 optimal weight: 50.0000 chunk 481 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 167 GLN ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 HIS ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 165 GLN C 467 GLN ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 HIS E 174 ASN E 296 ASN ** E 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 GLN F 174 ASN F 285 GLN F 292 ASN F 486 HIS ** F 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 HIS G 174 ASN G 196 GLN G 486 HIS ** G 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 ASN H 196 GLN H 296 ASN W 87 ASN W 265 HIS ** W 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 265 HIS Z 417 ASN Z 537 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5075 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.115 54408 Z= 0.640 Angle : 0.829 9.774 73860 Z= 0.442 Chirality : 0.056 0.404 8352 Planarity : 0.007 0.086 9396 Dihedral : 9.431 88.764 7745 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.52 % Favored : 97.22 % Rotamer: Outliers : 4.73 % Allowed : 19.35 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.06 % 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: -0.26 (0.10), residues: 6660 helix: -0.04 (0.09), residues: 3000 sheet: 0.20 (0.15), residues: 972 loop : -0.26 (0.13), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 124 HIS 0.014 0.002 HIS E 528 PHE 0.028 0.003 PHE F 508 TYR 0.039 0.003 TYR A 263 ARG 0.010 0.001 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1568 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 1291 time to evaluate : 5.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 141 ASP cc_start: 0.3900 (m-30) cc_final: 0.3695 (m-30) REVERT: A 212 ILE cc_start: 0.3827 (OUTLIER) cc_final: 0.3409 (tp) REVERT: A 339 ILE cc_start: 0.5767 (tp) cc_final: 0.5533 (tp) REVERT: B 101 GLU cc_start: 0.5819 (OUTLIER) cc_final: 0.5153 (mm-30) REVERT: B 348 GLU cc_start: 0.6395 (mt-10) cc_final: 0.6145 (mt-10) REVERT: B 395 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.6184 (tp30) REVERT: B 484 GLU cc_start: 0.6114 (OUTLIER) cc_final: 0.5689 (mm-30) REVERT: C 101 GLU cc_start: 0.5909 (OUTLIER) cc_final: 0.5479 (tp30) REVERT: C 353 GLU cc_start: 0.5179 (mp0) cc_final: 0.4382 (mp0) REVERT: C 357 ASN cc_start: 0.6764 (OUTLIER) cc_final: 0.6385 (t0) REVERT: C 366 LEU cc_start: 0.8001 (tp) cc_final: 0.7788 (tp) REVERT: C 391 LYS cc_start: 0.7207 (ttpt) cc_final: 0.6984 (ttpp) REVERT: E 130 LYS cc_start: 0.7968 (mtmm) cc_final: 0.7435 (mttm) REVERT: E 226 ASP cc_start: 0.7557 (m-30) cc_final: 0.7326 (t70) REVERT: E 257 LYS cc_start: 0.6871 (mttp) cc_final: 0.6361 (mptt) REVERT: E 272 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6074 (mp0) REVERT: E 281 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6842 (tm-30) REVERT: E 305 LYS cc_start: 0.7449 (mttm) cc_final: 0.6883 (mtpp) REVERT: E 499 ILE cc_start: 0.7474 (mt) cc_final: 0.7176 (mm) REVERT: F 130 LYS cc_start: 0.7855 (mtmm) cc_final: 0.7019 (mmtm) REVERT: F 146 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7635 (tt0) REVERT: F 282 ARG cc_start: 0.7155 (mtp-110) cc_final: 0.5916 (mpt-90) REVERT: F 317 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6974 (t0) REVERT: G 257 LYS cc_start: 0.6951 (mttp) cc_final: 0.6568 (mptt) REVERT: G 262 ASP cc_start: 0.6422 (OUTLIER) cc_final: 0.6112 (t0) REVERT: G 305 LYS cc_start: 0.7726 (mttm) cc_final: 0.7135 (mttt) REVERT: G 481 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: G 487 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7142 (mm-30) REVERT: G 492 ARG cc_start: 0.7989 (ttm-80) cc_final: 0.7699 (ttm110) REVERT: H 200 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7561 (mttp) REVERT: H 272 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.5867 (mp0) REVERT: H 281 GLU cc_start: 0.7279 (tp30) cc_final: 0.7003 (tm-30) REVERT: H 282 ARG cc_start: 0.7333 (mtp-110) cc_final: 0.5819 (mpt90) REVERT: H 305 LYS cc_start: 0.7493 (mttm) cc_final: 0.7088 (mtpp) REVERT: H 336 GLN cc_start: 0.7848 (tt0) cc_final: 0.7591 (tt0) REVERT: W 101 GLU cc_start: 0.5573 (OUTLIER) cc_final: 0.4425 (tp30) REVERT: W 187 HIS cc_start: 0.6233 (OUTLIER) cc_final: 0.5979 (t70) REVERT: X 331 MET cc_start: 0.3303 (mmm) cc_final: 0.3048 (mmp) REVERT: X 337 LEU cc_start: 0.6324 (tm) cc_final: 0.6094 (tp) REVERT: X 495 ILE cc_start: 0.5537 (mm) cc_final: 0.5321 (mm) REVERT: Y 55 HIS cc_start: 0.5911 (OUTLIER) cc_final: 0.5080 (p-80) REVERT: Z 101 GLU cc_start: 0.5641 (OUTLIER) cc_final: 0.5261 (tp30) REVERT: Z 324 LYS cc_start: 0.6070 (mmtp) cc_final: 0.5779 (mmmt) outliers start: 277 outliers final: 141 residues processed: 1471 average time/residue: 2.0594 time to fit residues: 4202.4417 Evaluate side-chains 1350 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1192 time to evaluate : 5.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 489 HIS Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 319 TYR Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 262 ASP Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 542 SER Chi-restraints excluded: chain F residue 565 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 481 GLU Chi-restraints excluded: chain G residue 485 VAL Chi-restraints excluded: chain G residue 542 SER Chi-restraints excluded: chain G residue 565 VAL Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 542 SER Chi-restraints excluded: chain W residue 19 LEU Chi-restraints excluded: chain W residue 101 GLU Chi-restraints excluded: chain W residue 141 ASP Chi-restraints excluded: chain W residue 183 VAL Chi-restraints excluded: chain W residue 187 HIS Chi-restraints excluded: chain W residue 202 LEU Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain W residue 251 VAL Chi-restraints excluded: chain W residue 313 THR Chi-restraints excluded: chain W residue 314 ASN Chi-restraints excluded: chain W residue 333 CYS Chi-restraints excluded: chain W residue 357 ASN Chi-restraints excluded: chain W residue 373 LEU Chi-restraints excluded: chain W residue 384 GLU Chi-restraints excluded: chain W residue 403 VAL Chi-restraints excluded: chain W residue 427 THR Chi-restraints excluded: chain W residue 542 SER Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 264 LEU Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 297 LEU Chi-restraints excluded: chain X residue 355 ASP Chi-restraints excluded: chain X residue 366 LEU Chi-restraints excluded: chain X residue 562 LEU Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 55 HIS Chi-restraints excluded: chain Y residue 95 SER Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Y residue 122 GLN Chi-restraints excluded: chain Y residue 147 LEU Chi-restraints excluded: chain Y residue 150 THR Chi-restraints excluded: chain Y residue 192 THR Chi-restraints excluded: chain Y residue 193 LYS Chi-restraints excluded: chain Y residue 264 LEU Chi-restraints excluded: chain Y residue 289 ASN Chi-restraints excluded: chain Y residue 297 LEU Chi-restraints excluded: chain Y residue 486 HIS Chi-restraints excluded: chain Y residue 511 VAL Chi-restraints excluded: chain Z residue 28 LYS Chi-restraints excluded: chain Z residue 101 GLU Chi-restraints excluded: chain Z residue 141 ASP Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 251 VAL Chi-restraints excluded: chain Z residue 293 MET Chi-restraints excluded: chain Z residue 313 THR Chi-restraints excluded: chain Z residue 337 LEU Chi-restraints excluded: chain Z residue 347 LEU Chi-restraints excluded: chain Z residue 356 LYS Chi-restraints excluded: chain Z residue 395 GLU Chi-restraints excluded: chain Z residue 403 VAL Chi-restraints excluded: chain Z residue 407 LEU Chi-restraints excluded: chain Z residue 430 LEU Chi-restraints excluded: chain Z residue 542 SER Chi-restraints excluded: chain Z residue 559 SER Chi-restraints excluded: chain Z residue 567 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 593 optimal weight: 50.0000 chunk 451 optimal weight: 9.9990 chunk 311 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 286 optimal weight: 0.4980 chunk 403 optimal weight: 0.6980 chunk 602 optimal weight: 50.0000 chunk 637 optimal weight: 0.8980 chunk 314 optimal weight: 0.9980 chunk 571 optimal weight: 40.0000 chunk 171 optimal weight: 40.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 HIS ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 ASN E 296 ASN ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 ASN ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 486 HIS G 238 GLN ** G 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 HIS H 165 GLN H 238 GLN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 ASN ** H 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 196 GLN Y 87 ASN ** Y 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 174 ASN ** Z 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 233 HIS ** Z 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 537 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4975 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 54408 Z= 0.185 Angle : 0.599 8.805 73860 Z= 0.309 Chirality : 0.047 0.385 8352 Planarity : 0.004 0.070 9396 Dihedral : 8.843 89.303 7745 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.12 % Favored : 97.70 % Rotamer: Outliers : 2.87 % Allowed : 22.08 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.10), residues: 6660 helix: 0.64 (0.09), residues: 3036 sheet: 0.16 (0.15), residues: 960 loop : -0.02 (0.13), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 363 HIS 0.008 0.001 HIS X 233 PHE 0.026 0.002 PHE A 168 TYR 0.019 0.001 TYR A 263 ARG 0.006 0.000 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1487 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1319 time to evaluate : 5.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 212 ILE cc_start: 0.3943 (OUTLIER) cc_final: 0.3664 (tp) REVERT: A 286 LEU cc_start: 0.6361 (mm) cc_final: 0.5807 (mp) REVERT: B 348 GLU cc_start: 0.6313 (mt-10) cc_final: 0.6082 (mt-10) REVERT: C 101 GLU cc_start: 0.6009 (OUTLIER) cc_final: 0.5623 (tp30) REVERT: C 352 GLN cc_start: 0.5955 (tt0) cc_final: 0.5719 (tt0) REVERT: C 366 LEU cc_start: 0.8081 (tp) cc_final: 0.7775 (tp) REVERT: D 186 ILE cc_start: 0.7190 (tp) cc_final: 0.6786 (mm) REVERT: E 130 LYS cc_start: 0.8048 (mtmm) cc_final: 0.7484 (mttm) REVERT: E 257 LYS cc_start: 0.6844 (mttp) cc_final: 0.6427 (mptt) REVERT: E 272 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.5800 (mp0) REVERT: E 281 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6925 (tm-30) REVERT: E 305 LYS cc_start: 0.7270 (mttm) cc_final: 0.6861 (mtpt) REVERT: E 361 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7101 (m-30) REVERT: E 499 ILE cc_start: 0.7307 (mt) cc_final: 0.7044 (mm) REVERT: F 130 LYS cc_start: 0.7778 (mtmm) cc_final: 0.6875 (mmtm) REVERT: F 282 ARG cc_start: 0.7045 (mtp-110) cc_final: 0.5716 (mpt-90) REVERT: F 317 ASP cc_start: 0.7152 (OUTLIER) cc_final: 0.6944 (t0) REVERT: F 348 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6550 (tm-30) REVERT: G 123 ASP cc_start: 0.7091 (m-30) cc_final: 0.6809 (m-30) REVERT: G 211 MET cc_start: 0.7225 (mmm) cc_final: 0.6906 (mmt) REVERT: G 249 TYR cc_start: 0.7990 (m-80) cc_final: 0.7316 (m-80) REVERT: G 257 LYS cc_start: 0.6871 (mttp) cc_final: 0.6506 (mptt) REVERT: G 282 ARG cc_start: 0.7557 (mtp-110) cc_final: 0.7331 (mtp-110) REVERT: G 487 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7046 (mm-30) REVERT: G 492 ARG cc_start: 0.7859 (ttm-80) cc_final: 0.7629 (ttm110) REVERT: H 200 LYS cc_start: 0.8015 (mtpt) cc_final: 0.7389 (mttt) REVERT: H 272 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.5537 (mp0) REVERT: H 282 ARG cc_start: 0.7261 (mtp-110) cc_final: 0.5972 (mpt-90) REVERT: H 305 LYS cc_start: 0.7419 (mttm) cc_final: 0.6976 (mtpp) REVERT: H 336 GLN cc_start: 0.7748 (tt0) cc_final: 0.7519 (tt0) REVERT: W 101 GLU cc_start: 0.5575 (OUTLIER) cc_final: 0.4843 (tp30) REVERT: W 187 HIS cc_start: 0.6238 (OUTLIER) cc_final: 0.5969 (t70) REVERT: X 37 ILE cc_start: 0.4152 (mm) cc_final: 0.3596 (mm) REVERT: X 61 LEU cc_start: 0.4413 (OUTLIER) cc_final: 0.4148 (mt) REVERT: X 77 TYR cc_start: 0.4492 (m-80) cc_final: 0.4174 (m-80) REVERT: X 212 ILE cc_start: 0.4160 (OUTLIER) cc_final: 0.3902 (tp) REVERT: X 339 ILE cc_start: 0.4202 (tp) cc_final: 0.3726 (tp) REVERT: X 419 ILE cc_start: -0.0804 (OUTLIER) cc_final: -0.1599 (mt) REVERT: Y 55 HIS cc_start: 0.6096 (OUTLIER) cc_final: 0.5196 (p-80) REVERT: Y 286 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5393 (mp) outliers start: 168 outliers final: 97 residues processed: 1420 average time/residue: 2.0464 time to fit residues: 4043.5501 Evaluate side-chains 1344 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1232 time to evaluate : 5.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 361 ASP Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 542 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 542 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 345 SER Chi-restraints excluded: chain H residue 542 SER Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain W residue 19 LEU Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain W residue 101 GLU Chi-restraints excluded: chain W residue 141 ASP Chi-restraints excluded: chain W residue 165 GLN Chi-restraints excluded: chain W residue 183 VAL Chi-restraints excluded: chain W residue 187 HIS Chi-restraints excluded: chain W residue 251 VAL Chi-restraints excluded: chain W residue 313 THR Chi-restraints excluded: chain W residue 314 ASN Chi-restraints excluded: chain W residue 357 ASN Chi-restraints excluded: chain W residue 373 LEU Chi-restraints excluded: chain W residue 384 GLU Chi-restraints excluded: chain W residue 428 GLU Chi-restraints excluded: chain W residue 542 SER Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 95 SER Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 212 ILE Chi-restraints excluded: chain X residue 264 LEU Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 337 LEU Chi-restraints excluded: chain X residue 419 ILE Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 55 HIS Chi-restraints excluded: chain Y residue 73 ASN Chi-restraints excluded: chain Y residue 95 SER Chi-restraints excluded: chain Y residue 110 THR Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Y residue 122 GLN Chi-restraints excluded: chain Y residue 147 LEU Chi-restraints excluded: chain Y residue 193 LYS Chi-restraints excluded: chain Y residue 286 LEU Chi-restraints excluded: chain Y residue 289 ASN Chi-restraints excluded: chain Y residue 298 ASP Chi-restraints excluded: chain Y residue 355 ASP Chi-restraints excluded: chain Y residue 486 HIS Chi-restraints excluded: chain Y residue 499 ILE Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 93 ILE Chi-restraints excluded: chain Z residue 141 ASP Chi-restraints excluded: chain Z residue 239 VAL Chi-restraints excluded: chain Z residue 313 THR Chi-restraints excluded: chain Z residue 347 LEU Chi-restraints excluded: chain Z residue 356 LYS Chi-restraints excluded: chain Z residue 430 LEU Chi-restraints excluded: chain Z residue 542 SER Chi-restraints excluded: chain Z residue 567 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 531 optimal weight: 30.0000 chunk 362 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 475 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 544 optimal weight: 50.0000 chunk 440 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 325 optimal weight: 1.9990 chunk 572 optimal weight: 20.0000 chunk 160 optimal weight: 40.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN C 165 GLN C 238 GLN E 167 GLN E 196 GLN E 296 ASN ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 ASN ** F 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 HIS ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 486 HIS H 167 GLN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 ASN ** H 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 238 GLN Y 87 ASN ** Y 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 96 HIS ** Z 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 537 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5055 moved from start: 0.5929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 54408 Z= 0.403 Angle : 0.673 8.888 73860 Z= 0.351 Chirality : 0.051 0.806 8352 Planarity : 0.005 0.069 9396 Dihedral : 8.796 88.970 7744 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.58 % Favored : 97.21 % Rotamer: Outliers : 4.01 % Allowed : 22.06 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.21 (0.10), residues: 6660 helix: 0.58 (0.09), residues: 3036 sheet: 0.04 (0.15), residues: 960 loop : -0.17 (0.13), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 472 HIS 0.011 0.002 HIS B 486 PHE 0.023 0.002 PHE F 508 TYR 0.020 0.002 TYR X 42 ARG 0.011 0.001 ARG Z 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1459 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1224 time to evaluate : 5.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 212 ILE cc_start: 0.4384 (OUTLIER) cc_final: 0.4092 (tp) REVERT: A 457 MET cc_start: 0.4885 (mmm) cc_final: 0.3927 (mmm) REVERT: B 101 GLU cc_start: 0.5667 (OUTLIER) cc_final: 0.5402 (mm-30) REVERT: B 348 GLU cc_start: 0.6494 (mt-10) cc_final: 0.6284 (mt-10) REVERT: C 101 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5498 (tp30) REVERT: C 366 LEU cc_start: 0.8049 (tp) cc_final: 0.7797 (tp) REVERT: D 186 ILE cc_start: 0.7342 (tp) cc_final: 0.6550 (pp) REVERT: D 304 VAL cc_start: 0.6196 (p) cc_final: 0.5362 (t) REVERT: D 374 VAL cc_start: 0.1747 (t) cc_final: 0.1429 (t) REVERT: E 130 LYS cc_start: 0.7948 (mtmm) cc_final: 0.7435 (mttm) REVERT: E 257 LYS cc_start: 0.6823 (mttp) cc_final: 0.6332 (mptt) REVERT: E 272 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.5980 (mp0) REVERT: E 281 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6916 (tm-30) REVERT: E 301 ASP cc_start: 0.6342 (t0) cc_final: 0.6098 (t70) REVERT: E 305 LYS cc_start: 0.7252 (mttm) cc_final: 0.6932 (mtpp) REVERT: E 331 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7329 (mtt) REVERT: E 343 GLU cc_start: 0.7389 (tp30) cc_final: 0.7121 (tm-30) REVERT: E 467 GLN cc_start: 0.6378 (OUTLIER) cc_final: 0.6114 (mm110) REVERT: E 499 ILE cc_start: 0.7363 (mt) cc_final: 0.7096 (mm) REVERT: F 130 LYS cc_start: 0.7831 (mtmm) cc_final: 0.6992 (mmtm) REVERT: F 282 ARG cc_start: 0.7211 (mtp-110) cc_final: 0.6872 (ttm-80) REVERT: F 317 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6940 (t0) REVERT: F 331 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.7159 (mtt) REVERT: F 335 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6272 (mtm180) REVERT: G 82 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8432 (mp) REVERT: G 211 MET cc_start: 0.7536 (mmm) cc_final: 0.7177 (mmt) REVERT: G 257 LYS cc_start: 0.6826 (mttp) cc_final: 0.6448 (mptt) REVERT: G 335 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6459 (mtm180) REVERT: G 361 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7397 (m-30) REVERT: G 487 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7088 (mm-30) REVERT: G 492 ARG cc_start: 0.7891 (ttm-80) cc_final: 0.7640 (ttm110) REVERT: H 130 LYS cc_start: 0.7945 (mtmt) cc_final: 0.7502 (mttp) REVERT: H 200 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7431 (mttp) REVERT: H 272 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.5823 (mp0) REVERT: H 282 ARG cc_start: 0.7375 (mtp-110) cc_final: 0.5783 (mpt90) REVERT: H 305 LYS cc_start: 0.7439 (mttm) cc_final: 0.6976 (mttt) REVERT: W 101 GLU cc_start: 0.5584 (OUTLIER) cc_final: 0.5109 (tp30) REVERT: W 187 HIS cc_start: 0.6172 (OUTLIER) cc_final: 0.5906 (t70) REVERT: X 37 ILE cc_start: 0.4020 (mm) cc_final: 0.3545 (mp) REVERT: X 61 LEU cc_start: 0.4426 (OUTLIER) cc_final: 0.4205 (mt) REVERT: X 77 TYR cc_start: 0.4563 (m-80) cc_final: 0.4197 (m-80) REVERT: X 339 ILE cc_start: 0.4722 (tp) cc_final: 0.4437 (tp) REVERT: Y 55 HIS cc_start: 0.6017 (OUTLIER) cc_final: 0.5112 (p-80) REVERT: Y 286 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5579 (mp) REVERT: Z 350 GLU cc_start: 0.6605 (mp0) cc_final: 0.5267 (mp0) REVERT: Z 352 GLN cc_start: 0.5488 (tt0) cc_final: 0.5269 (tt0) outliers start: 235 outliers final: 137 residues processed: 1365 average time/residue: 2.0699 time to fit residues: 3926.0826 Evaluate side-chains 1328 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1172 time to evaluate : 5.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 535 GLN Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 92 LYS Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 319 TYR Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 467 GLN Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain E residue 568 ASP Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 331 MET Chi-restraints excluded: chain F residue 335 ARG Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 542 SER Chi-restraints excluded: chain F residue 568 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 332 LYS Chi-restraints excluded: chain G residue 335 ARG Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 361 ASP Chi-restraints excluded: chain G residue 485 VAL Chi-restraints excluded: chain G residue 542 SER Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 345 SER Chi-restraints excluded: chain H residue 542 SER Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain W residue 19 LEU Chi-restraints excluded: chain W residue 101 GLU Chi-restraints excluded: chain W residue 141 ASP Chi-restraints excluded: chain W residue 165 GLN Chi-restraints excluded: chain W residue 183 VAL Chi-restraints excluded: chain W residue 187 HIS Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 241 ASN Chi-restraints excluded: chain W residue 251 VAL Chi-restraints excluded: chain W residue 298 ASP Chi-restraints excluded: chain W residue 313 THR Chi-restraints excluded: chain W residue 314 ASN Chi-restraints excluded: chain W residue 357 ASN Chi-restraints excluded: chain W residue 373 LEU Chi-restraints excluded: chain W residue 428 GLU Chi-restraints excluded: chain W residue 443 ILE Chi-restraints excluded: chain W residue 503 MET Chi-restraints excluded: chain W residue 542 SER Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 123 ASP Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 264 LEU Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 366 LEU Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 55 HIS Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Y residue 73 ASN Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 93 ILE Chi-restraints excluded: chain Y residue 95 SER Chi-restraints excluded: chain Y residue 110 THR Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Y residue 122 GLN Chi-restraints excluded: chain Y residue 147 LEU Chi-restraints excluded: chain Y residue 193 LYS Chi-restraints excluded: chain Y residue 286 LEU Chi-restraints excluded: chain Y residue 289 ASN Chi-restraints excluded: chain Y residue 298 ASP Chi-restraints excluded: chain Y residue 486 HIS Chi-restraints excluded: chain Y residue 499 ILE Chi-restraints excluded: chain Y residue 511 VAL Chi-restraints excluded: chain Z residue 134 ASP Chi-restraints excluded: chain Z residue 141 ASP Chi-restraints excluded: chain Z residue 239 VAL Chi-restraints excluded: chain Z residue 251 VAL Chi-restraints excluded: chain Z residue 313 THR Chi-restraints excluded: chain Z residue 347 LEU Chi-restraints excluded: chain Z residue 356 LYS Chi-restraints excluded: chain Z residue 430 LEU Chi-restraints excluded: chain Z residue 542 SER Chi-restraints excluded: chain Z residue 559 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 214 optimal weight: 50.0000 chunk 574 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 chunk 374 optimal weight: 2.9990 chunk 157 optimal weight: 20.0000 chunk 638 optimal weight: 6.9990 chunk 530 optimal weight: 7.9990 chunk 295 optimal weight: 0.8980 chunk 53 optimal weight: 50.0000 chunk 211 optimal weight: 30.0000 chunk 335 optimal weight: 1.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN C 165 GLN C 352 GLN D 243 HIS E 167 GLN E 296 ASN ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 196 GLN ** F 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 486 HIS ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 486 HIS H 165 GLN H 167 GLN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 ASN ** H 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 55 HIS ** X 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 112 GLN ** Y 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 96 HIS ** Z 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 537 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5088 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 54408 Z= 0.493 Angle : 0.705 8.614 73860 Z= 0.371 Chirality : 0.052 0.411 8352 Planarity : 0.006 0.073 9396 Dihedral : 8.816 89.497 7744 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.23 % Favored : 96.56 % Rotamer: Outliers : 4.41 % Allowed : 22.83 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.02 (0.10), residues: 6660 helix: 0.45 (0.09), residues: 3036 sheet: -0.07 (0.15), residues: 984 loop : -0.30 (0.13), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP Z 124 HIS 0.011 0.002 HIS X 233 PHE 0.027 0.002 PHE F 508 TYR 0.021 0.002 TYR A 3 ARG 0.011 0.001 ARG G 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1435 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1177 time to evaluate : 5.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 212 ILE cc_start: 0.4501 (OUTLIER) cc_final: 0.4137 (tp) REVERT: B 101 GLU cc_start: 0.5746 (OUTLIER) cc_final: 0.5234 (tm-30) REVERT: B 141 ASP cc_start: 0.4586 (OUTLIER) cc_final: 0.4028 (m-30) REVERT: B 350 GLU cc_start: 0.6196 (mp0) cc_final: 0.5072 (mp0) REVERT: B 361 ASP cc_start: 0.6611 (m-30) cc_final: 0.6393 (t0) REVERT: C 101 GLU cc_start: 0.6057 (OUTLIER) cc_final: 0.5828 (tp30) REVERT: C 350 GLU cc_start: 0.6536 (mp0) cc_final: 0.5318 (mp0) REVERT: C 356 LYS cc_start: 0.7400 (mttt) cc_final: 0.7144 (mttm) REVERT: D 186 ILE cc_start: 0.7195 (tp) cc_final: 0.6464 (pp) REVERT: E 43 MET cc_start: 0.7711 (mtp) cc_final: 0.7469 (mtp) REVERT: E 130 LYS cc_start: 0.8133 (mtmm) cc_final: 0.7546 (mttm) REVERT: E 257 LYS cc_start: 0.6886 (mttp) cc_final: 0.6350 (mptt) REVERT: E 272 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.5902 (mp0) REVERT: E 281 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6929 (tm-30) REVERT: E 305 LYS cc_start: 0.7198 (mttm) cc_final: 0.6896 (mtpp) REVERT: E 331 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7286 (mtt) REVERT: E 343 GLU cc_start: 0.7455 (tp30) cc_final: 0.7215 (tm-30) REVERT: E 361 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7175 (m-30) REVERT: E 487 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7589 (mm-30) REVERT: E 499 ILE cc_start: 0.7408 (mt) cc_final: 0.7169 (mm) REVERT: F 130 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7023 (mmtm) REVERT: F 282 ARG cc_start: 0.7211 (mtp-110) cc_final: 0.6870 (ttm-80) REVERT: F 317 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6958 (t0) REVERT: F 331 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7197 (mtt) REVERT: F 335 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6286 (mtm180) REVERT: G 28 LYS cc_start: 0.8631 (mtpm) cc_final: 0.8262 (mttm) REVERT: G 211 MET cc_start: 0.7513 (mmm) cc_final: 0.7175 (mmt) REVERT: G 257 LYS cc_start: 0.6871 (mttp) cc_final: 0.6537 (mptt) REVERT: G 331 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.7061 (mtt) REVERT: G 335 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6443 (mtm180) REVERT: G 361 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7355 (m-30) REVERT: G 487 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7122 (mm-30) REVERT: G 492 ARG cc_start: 0.7919 (ttm-80) cc_final: 0.7656 (ttm110) REVERT: H 130 LYS cc_start: 0.8012 (mtmt) cc_final: 0.7573 (mttm) REVERT: H 272 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.5854 (mp0) REVERT: H 282 ARG cc_start: 0.7491 (mtp-110) cc_final: 0.7163 (mtp-110) REVERT: H 305 LYS cc_start: 0.7458 (mttm) cc_final: 0.6999 (mttt) REVERT: H 467 GLN cc_start: 0.6331 (OUTLIER) cc_final: 0.5564 (mm110) REVERT: W 101 GLU cc_start: 0.5547 (OUTLIER) cc_final: 0.5125 (tp30) REVERT: W 187 HIS cc_start: 0.6151 (OUTLIER) cc_final: 0.5883 (t70) REVERT: X 37 ILE cc_start: 0.4036 (mm) cc_final: 0.3650 (mm) REVERT: X 77 TYR cc_start: 0.4510 (m-80) cc_final: 0.4134 (m-80) REVERT: X 339 ILE cc_start: 0.4178 (tp) cc_final: 0.3978 (tp) REVERT: Y 55 HIS cc_start: 0.5955 (OUTLIER) cc_final: 0.4999 (p-80) REVERT: Y 286 LEU cc_start: 0.5996 (OUTLIER) cc_final: 0.5555 (mp) REVERT: Z 45 ILE cc_start: 0.6423 (OUTLIER) cc_final: 0.6164 (pt) REVERT: Z 260 MET cc_start: 0.5357 (OUTLIER) cc_final: 0.5033 (tpp) REVERT: Z 350 GLU cc_start: 0.6921 (mp0) cc_final: 0.5336 (mp0) REVERT: Z 352 GLN cc_start: 0.5893 (tt0) cc_final: 0.5501 (tt0) REVERT: Z 356 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7308 (mttp) outliers start: 258 outliers final: 158 residues processed: 1344 average time/residue: 1.9572 time to fit residues: 3652.7438 Evaluate side-chains 1315 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1134 time to evaluate : 5.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 92 LYS Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 319 TYR Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 361 ASP Chi-restraints excluded: chain E residue 541 THR Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain E residue 568 ASP Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 331 MET Chi-restraints excluded: chain F residue 335 ARG Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 542 SER Chi-restraints excluded: chain F residue 565 VAL Chi-restraints excluded: chain F residue 568 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 331 MET Chi-restraints excluded: chain G residue 335 ARG Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 361 ASP Chi-restraints excluded: chain G residue 485 VAL Chi-restraints excluded: chain G residue 565 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 345 SER Chi-restraints excluded: chain H residue 467 GLN Chi-restraints excluded: chain H residue 485 VAL Chi-restraints excluded: chain H residue 539 GLU Chi-restraints excluded: chain H residue 542 SER Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain W residue 19 LEU Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain W residue 101 GLU Chi-restraints excluded: chain W residue 141 ASP Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 165 GLN Chi-restraints excluded: chain W residue 172 ARG Chi-restraints excluded: chain W residue 183 VAL Chi-restraints excluded: chain W residue 187 HIS Chi-restraints excluded: chain W residue 202 LEU Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 241 ASN Chi-restraints excluded: chain W residue 251 VAL Chi-restraints excluded: chain W residue 298 ASP Chi-restraints excluded: chain W residue 313 THR Chi-restraints excluded: chain W residue 314 ASN Chi-restraints excluded: chain W residue 330 SER Chi-restraints excluded: chain W residue 357 ASN Chi-restraints excluded: chain W residue 373 LEU Chi-restraints excluded: chain W residue 384 GLU Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 428 GLU Chi-restraints excluded: chain W residue 542 SER Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 95 SER Chi-restraints excluded: chain X residue 123 ASP Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 264 LEU Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 495 ILE Chi-restraints excluded: chain X residue 566 ILE Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 55 HIS Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Y residue 73 ASN Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 95 SER Chi-restraints excluded: chain Y residue 110 THR Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Y residue 122 GLN Chi-restraints excluded: chain Y residue 147 LEU Chi-restraints excluded: chain Y residue 193 LYS Chi-restraints excluded: chain Y residue 286 LEU Chi-restraints excluded: chain Y residue 289 ASN Chi-restraints excluded: chain Y residue 298 ASP Chi-restraints excluded: chain Y residue 355 ASP Chi-restraints excluded: chain Y residue 486 HIS Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 45 ILE Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 141 ASP Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 251 VAL Chi-restraints excluded: chain Z residue 260 MET Chi-restraints excluded: chain Z residue 313 THR Chi-restraints excluded: chain Z residue 347 LEU Chi-restraints excluded: chain Z residue 351 THR Chi-restraints excluded: chain Z residue 356 LYS Chi-restraints excluded: chain Z residue 395 GLU Chi-restraints excluded: chain Z residue 542 SER Chi-restraints excluded: chain Z residue 559 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 615 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 363 optimal weight: 0.9990 chunk 466 optimal weight: 30.0000 chunk 361 optimal weight: 0.8980 chunk 537 optimal weight: 50.0000 chunk 356 optimal weight: 0.5980 chunk 636 optimal weight: 0.0170 chunk 398 optimal weight: 0.7980 chunk 387 optimal weight: 0.5980 chunk 293 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN E 296 ASN ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS F 292 ASN ** F 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 486 HIS G 196 GLN ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 GLN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 ASN ** H 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 423 ASN ** Y 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 96 HIS ** Z 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 537 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4995 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 54408 Z= 0.167 Angle : 0.574 8.646 73860 Z= 0.293 Chirality : 0.046 0.382 8352 Planarity : 0.004 0.072 9396 Dihedral : 8.307 89.942 7744 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.22 % Favored : 97.58 % Rotamer: Outliers : 2.63 % Allowed : 24.64 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.56 (0.11), residues: 6660 helix: 1.03 (0.10), residues: 3048 sheet: -0.04 (0.15), residues: 984 loop : -0.10 (0.13), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 472 HIS 0.009 0.001 HIS Z 96 PHE 0.021 0.001 PHE D 359 TYR 0.033 0.001 TYR Y 263 ARG 0.008 0.000 ARG Y 164 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1377 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1223 time to evaluate : 5.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 128 VAL cc_start: 0.3202 (t) cc_final: 0.2759 (p) REVERT: A 212 ILE cc_start: 0.4531 (OUTLIER) cc_final: 0.4072 (tp) REVERT: A 339 ILE cc_start: 0.5581 (tp) cc_final: 0.5367 (tp) REVERT: A 418 VAL cc_start: 0.3938 (t) cc_final: 0.3549 (t) REVERT: B 101 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.4975 (mm-30) REVERT: B 260 MET cc_start: 0.5375 (OUTLIER) cc_final: 0.5032 (tpp) REVERT: C 101 GLU cc_start: 0.5971 (OUTLIER) cc_final: 0.5581 (tp30) REVERT: D 63 ASP cc_start: 0.4288 (p0) cc_final: 0.4085 (p0) REVERT: D 186 ILE cc_start: 0.7148 (tp) cc_final: 0.6462 (pp) REVERT: D 457 MET cc_start: 0.4437 (mmm) cc_final: 0.4209 (mmm) REVERT: E 130 LYS cc_start: 0.8036 (mtmm) cc_final: 0.7487 (mttm) REVERT: E 146 GLU cc_start: 0.7576 (tt0) cc_final: 0.6972 (tt0) REVERT: E 257 LYS cc_start: 0.6910 (mttp) cc_final: 0.6412 (mptt) REVERT: E 281 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: E 305 LYS cc_start: 0.7272 (mttm) cc_final: 0.6923 (mtpt) REVERT: E 331 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7359 (mtt) REVERT: E 343 GLU cc_start: 0.7312 (tp30) cc_final: 0.6961 (tm-30) REVERT: E 345 SER cc_start: 0.7527 (p) cc_final: 0.6911 (p) REVERT: E 361 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7078 (m-30) REVERT: E 499 ILE cc_start: 0.7318 (mt) cc_final: 0.7068 (mm) REVERT: F 82 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8558 (mt) REVERT: F 130 LYS cc_start: 0.7765 (mtmm) cc_final: 0.6926 (mmtm) REVERT: F 281 GLU cc_start: 0.7425 (tp30) cc_final: 0.7223 (tm-30) REVERT: F 317 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6943 (t0) REVERT: F 568 ASP cc_start: 0.5216 (OUTLIER) cc_final: 0.4963 (t70) REVERT: G 123 ASP cc_start: 0.7073 (m-30) cc_final: 0.6804 (m-30) REVERT: G 257 LYS cc_start: 0.6821 (mttp) cc_final: 0.6479 (mptt) REVERT: G 335 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6248 (mtm180) REVERT: G 361 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7339 (m-30) REVERT: G 487 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6971 (mm-30) REVERT: G 492 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7657 (ttm110) REVERT: H 130 LYS cc_start: 0.7877 (mtmt) cc_final: 0.7455 (mttp) REVERT: H 200 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7331 (mttp) REVERT: H 272 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.5469 (mp0) REVERT: H 282 ARG cc_start: 0.7279 (mtp-110) cc_final: 0.6980 (mtp-110) REVERT: H 305 LYS cc_start: 0.7391 (mttm) cc_final: 0.6967 (mttt) REVERT: W 25 MET cc_start: 0.4299 (ttp) cc_final: 0.4047 (ttm) REVERT: W 187 HIS cc_start: 0.6107 (OUTLIER) cc_final: 0.5852 (t70) REVERT: W 230 MET cc_start: 0.6888 (tmm) cc_final: 0.6330 (ttp) REVERT: X 37 ILE cc_start: 0.3814 (mm) cc_final: 0.3471 (mp) REVERT: X 77 TYR cc_start: 0.4207 (m-80) cc_final: 0.3816 (m-80) REVERT: Y 286 LEU cc_start: 0.5888 (OUTLIER) cc_final: 0.5582 (mp) REVERT: Z 45 ILE cc_start: 0.6344 (OUTLIER) cc_final: 0.6069 (pt) REVERT: Z 350 GLU cc_start: 0.6382 (mp0) cc_final: 0.4975 (mp0) REVERT: Z 352 GLN cc_start: 0.5658 (tt0) cc_final: 0.5339 (tt0) REVERT: Z 356 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.7122 (mttp) outliers start: 154 outliers final: 101 residues processed: 1313 average time/residue: 2.0379 time to fit residues: 3737.6666 Evaluate side-chains 1273 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1155 time to evaluate : 5.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 421 ARG Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 535 GLN Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 92 LYS Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 265 HIS Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 361 ASP Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 542 SER Chi-restraints excluded: chain F residue 568 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 335 ARG Chi-restraints excluded: chain G residue 361 ASP Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 345 SER Chi-restraints excluded: chain H residue 542 SER Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain W residue 19 LEU Chi-restraints excluded: chain W residue 165 GLN Chi-restraints excluded: chain W residue 183 VAL Chi-restraints excluded: chain W residue 187 HIS Chi-restraints excluded: chain W residue 202 LEU Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 313 THR Chi-restraints excluded: chain W residue 357 ASN Chi-restraints excluded: chain W residue 373 LEU Chi-restraints excluded: chain W residue 427 THR Chi-restraints excluded: chain W residue 503 MET Chi-restraints excluded: chain W residue 542 SER Chi-restraints excluded: chain X residue 95 SER Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 264 LEU Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 440 GLN Chi-restraints excluded: chain X residue 495 ILE Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 55 HIS Chi-restraints excluded: chain Y residue 73 ASN Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 122 GLN Chi-restraints excluded: chain Y residue 147 LEU Chi-restraints excluded: chain Y residue 193 LYS Chi-restraints excluded: chain Y residue 286 LEU Chi-restraints excluded: chain Y residue 289 ASN Chi-restraints excluded: chain Y residue 298 ASP Chi-restraints excluded: chain Y residue 355 ASP Chi-restraints excluded: chain Y residue 511 VAL Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 45 ILE Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 141 ASP Chi-restraints excluded: chain Z residue 239 VAL Chi-restraints excluded: chain Z residue 313 THR Chi-restraints excluded: chain Z residue 347 LEU Chi-restraints excluded: chain Z residue 356 LYS Chi-restraints excluded: chain Z residue 542 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 393 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 379 optimal weight: 1.9990 chunk 191 optimal weight: 50.0000 chunk 124 optimal weight: 20.0000 chunk 123 optimal weight: 8.9990 chunk 404 optimal weight: 1.9990 chunk 433 optimal weight: 3.9990 chunk 314 optimal weight: 0.4980 chunk 59 optimal weight: 6.9990 chunk 500 optimal weight: 20.0000 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN E 296 ASN ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** F 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 486 HIS G 174 ASN ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 GLN H 167 GLN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 ASN ** H 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 112 GLN ** Y 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 259 HIS Z 96 HIS ** Z 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 467 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5035 moved from start: 0.6519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 54408 Z= 0.270 Angle : 0.609 9.098 73860 Z= 0.314 Chirality : 0.048 0.395 8352 Planarity : 0.005 0.102 9396 Dihedral : 8.270 83.171 7744 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.82 % Favored : 96.98 % Rotamer: Outliers : 2.77 % Allowed : 25.15 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.54 (0.11), residues: 6660 helix: 1.06 (0.10), residues: 3036 sheet: -0.05 (0.15), residues: 984 loop : -0.17 (0.13), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 472 HIS 0.010 0.001 HIS Z 96 PHE 0.023 0.002 PHE D 359 TYR 0.023 0.002 TYR Y 263 ARG 0.026 0.000 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1165 time to evaluate : 5.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 212 ILE cc_start: 0.4594 (OUTLIER) cc_final: 0.4083 (tp) REVERT: A 339 ILE cc_start: 0.5735 (tp) cc_final: 0.5485 (tp) REVERT: A 457 MET cc_start: 0.4650 (tpt) cc_final: 0.4012 (mmm) REVERT: B 101 GLU cc_start: 0.5820 (OUTLIER) cc_final: 0.5191 (mm-30) REVERT: B 350 GLU cc_start: 0.6072 (mp0) cc_final: 0.5341 (tp30) REVERT: C 101 GLU cc_start: 0.5983 (OUTLIER) cc_final: 0.5527 (tp30) REVERT: C 350 GLU cc_start: 0.6107 (mp0) cc_final: 0.5169 (mp0) REVERT: D 63 ASP cc_start: 0.4295 (p0) cc_final: 0.4082 (p0) REVERT: D 186 ILE cc_start: 0.7121 (tp) cc_final: 0.6472 (pp) REVERT: E 130 LYS cc_start: 0.8076 (mtmm) cc_final: 0.7528 (mttm) REVERT: E 257 LYS cc_start: 0.6860 (mttp) cc_final: 0.6327 (mptt) REVERT: E 272 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.5796 (mp0) REVERT: E 281 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.7006 (tm-30) REVERT: E 305 LYS cc_start: 0.7240 (mttm) cc_final: 0.6876 (mtpt) REVERT: E 331 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7297 (mtt) REVERT: E 343 GLU cc_start: 0.7391 (tp30) cc_final: 0.7065 (tm-30) REVERT: E 345 SER cc_start: 0.7592 (p) cc_final: 0.7087 (p) REVERT: E 499 ILE cc_start: 0.7344 (mt) cc_final: 0.7077 (mm) REVERT: F 130 LYS cc_start: 0.7823 (mtmm) cc_final: 0.6996 (mmtm) REVERT: F 282 ARG cc_start: 0.7236 (mtp-110) cc_final: 0.6717 (ttm-80) REVERT: F 317 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6954 (t0) REVERT: F 331 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7212 (mtt) REVERT: F 335 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6312 (mtm180) REVERT: F 568 ASP cc_start: 0.5293 (OUTLIER) cc_final: 0.4807 (t70) REVERT: G 257 LYS cc_start: 0.6801 (mttp) cc_final: 0.6478 (mptt) REVERT: G 335 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6340 (mtm180) REVERT: G 487 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6982 (mm-30) REVERT: G 492 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7694 (ttm110) REVERT: H 130 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7495 (mttm) REVERT: H 272 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.5841 (mp0) REVERT: H 282 ARG cc_start: 0.7381 (mtp-110) cc_final: 0.5801 (mpt90) REVERT: H 305 LYS cc_start: 0.7389 (mttm) cc_final: 0.6974 (mttt) REVERT: H 331 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7640 (mtt) REVERT: W 25 MET cc_start: 0.4492 (ttp) cc_final: 0.4266 (ttm) REVERT: W 187 HIS cc_start: 0.6072 (OUTLIER) cc_final: 0.5817 (t70) REVERT: W 230 MET cc_start: 0.6844 (tmm) cc_final: 0.6373 (ttp) REVERT: X 37 ILE cc_start: 0.3835 (mm) cc_final: 0.3419 (mm) REVERT: X 43 MET cc_start: 0.2682 (mmm) cc_final: 0.2237 (mmm) REVERT: X 77 TYR cc_start: 0.4390 (m-80) cc_final: 0.3984 (m-80) REVERT: Y 286 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5681 (mp) REVERT: Y 331 MET cc_start: 0.1866 (mmm) cc_final: 0.1239 (mmm) REVERT: Z 45 ILE cc_start: 0.6330 (OUTLIER) cc_final: 0.6052 (pt) REVERT: Z 350 GLU cc_start: 0.6570 (mp0) cc_final: 0.5137 (mp0) REVERT: Z 352 GLN cc_start: 0.5760 (tt0) cc_final: 0.5442 (tt0) REVERT: Z 356 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6458 (mtmp) outliers start: 162 outliers final: 116 residues processed: 1266 average time/residue: 2.0429 time to fit residues: 3655.9260 Evaluate side-chains 1258 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1125 time to evaluate : 5.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 535 GLN Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 92 LYS Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 265 HIS Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain E residue 568 ASP Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 50 MET Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 331 MET Chi-restraints excluded: chain F residue 335 ARG Chi-restraints excluded: chain F residue 542 SER Chi-restraints excluded: chain F residue 568 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 335 ARG Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 331 MET Chi-restraints excluded: chain H residue 345 SER Chi-restraints excluded: chain H residue 541 THR Chi-restraints excluded: chain H residue 542 SER Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain W residue 141 ASP Chi-restraints excluded: chain W residue 183 VAL Chi-restraints excluded: chain W residue 187 HIS Chi-restraints excluded: chain W residue 202 LEU Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 313 THR Chi-restraints excluded: chain W residue 314 ASN Chi-restraints excluded: chain W residue 357 ASN Chi-restraints excluded: chain W residue 373 LEU Chi-restraints excluded: chain W residue 427 THR Chi-restraints excluded: chain W residue 503 MET Chi-restraints excluded: chain W residue 542 SER Chi-restraints excluded: chain X residue 95 SER Chi-restraints excluded: chain X residue 123 ASP Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 202 LEU Chi-restraints excluded: chain X residue 256 LEU Chi-restraints excluded: chain X residue 264 LEU Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 297 LEU Chi-restraints excluded: chain X residue 304 VAL Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 55 HIS Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Y residue 73 ASN Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 95 SER Chi-restraints excluded: chain Y residue 122 GLN Chi-restraints excluded: chain Y residue 147 LEU Chi-restraints excluded: chain Y residue 193 LYS Chi-restraints excluded: chain Y residue 286 LEU Chi-restraints excluded: chain Y residue 289 ASN Chi-restraints excluded: chain Y residue 298 ASP Chi-restraints excluded: chain Y residue 511 VAL Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 45 ILE Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 141 ASP Chi-restraints excluded: chain Z residue 165 GLN Chi-restraints excluded: chain Z residue 313 THR Chi-restraints excluded: chain Z residue 347 LEU Chi-restraints excluded: chain Z residue 356 LYS Chi-restraints excluded: chain Z residue 542 SER Chi-restraints excluded: chain Z residue 559 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 578 optimal weight: 30.0000 chunk 609 optimal weight: 30.0000 chunk 556 optimal weight: 50.0000 chunk 592 optimal weight: 50.0000 chunk 356 optimal weight: 0.9980 chunk 258 optimal weight: 3.9990 chunk 465 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 chunk 535 optimal weight: 50.0000 chunk 560 optimal weight: 20.0000 chunk 590 optimal weight: 50.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** C 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN D 179 HIS ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 HIS E 73 ASN E 167 GLN E 296 ASN ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 HIS F 238 GLN ** F 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 174 ASN G 196 GLN ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 486 HIS H 73 ASN H 296 ASN ** H 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 474 ASN ** W 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 112 GLN ** Y 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 96 HIS ** Z 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5178 moved from start: 0.6891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.162 54408 Z= 0.927 Angle : 0.924 12.311 73860 Z= 0.495 Chirality : 0.066 0.449 8352 Planarity : 0.008 0.108 9396 Dihedral : 8.971 83.617 7744 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.41 % Favored : 95.29 % Rotamer: Outliers : 3.91 % Allowed : 24.62 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.53 (0.10), residues: 6660 helix: 0.07 (0.09), residues: 3060 sheet: -0.20 (0.15), residues: 984 loop : -0.75 (0.13), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP C 472 HIS 0.018 0.002 HIS E 528 PHE 0.036 0.004 PHE F 508 TYR 0.026 0.003 TYR E 249 ARG 0.013 0.001 ARG F 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1344 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1115 time to evaluate : 5.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 457 MET cc_start: 0.4625 (tpt) cc_final: 0.4064 (mmm) REVERT: B 89 THR cc_start: 0.5749 (OUTLIER) cc_final: 0.5380 (p) REVERT: B 341 TRP cc_start: 0.6900 (m100) cc_final: 0.6427 (m-90) REVERT: B 350 GLU cc_start: 0.6654 (mp0) cc_final: 0.5335 (mp0) REVERT: B 438 GLU cc_start: 0.6158 (OUTLIER) cc_final: 0.5889 (mm-30) REVERT: C 101 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.5552 (tp30) REVERT: C 350 GLU cc_start: 0.6861 (mp0) cc_final: 0.5165 (mp0) REVERT: D 45 ILE cc_start: 0.3043 (mp) cc_final: 0.2455 (mt) REVERT: E 43 MET cc_start: 0.7916 (mtp) cc_final: 0.7619 (mtp) REVERT: E 130 LYS cc_start: 0.8184 (mtmm) cc_final: 0.7569 (mttp) REVERT: E 257 LYS cc_start: 0.6951 (mttp) cc_final: 0.6426 (mptt) REVERT: E 272 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.5815 (mp0) REVERT: E 305 LYS cc_start: 0.7283 (mttm) cc_final: 0.6958 (mtpp) REVERT: E 331 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7187 (mtt) REVERT: E 499 ILE cc_start: 0.7422 (mt) cc_final: 0.7216 (mm) REVERT: F 130 LYS cc_start: 0.7947 (mtmm) cc_final: 0.7077 (mmtm) REVERT: F 282 ARG cc_start: 0.7296 (mtp-110) cc_final: 0.6851 (mtp-110) REVERT: F 331 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.7114 (mtt) REVERT: F 335 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6393 (mtm180) REVERT: G 161 GLU cc_start: 0.7647 (tp30) cc_final: 0.7305 (tp30) REVERT: G 169 GLU cc_start: 0.6294 (mt-10) cc_final: 0.6064 (mt-10) REVERT: G 257 LYS cc_start: 0.7013 (mttp) cc_final: 0.6620 (mptt) REVERT: G 295 LYS cc_start: 0.6933 (tptp) cc_final: 0.6690 (tppt) REVERT: G 335 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6513 (mtm180) REVERT: G 487 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7293 (mm-30) REVERT: H 130 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7667 (mttp) REVERT: H 272 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.5676 (mp0) REVERT: H 282 ARG cc_start: 0.7570 (mtp-110) cc_final: 0.7223 (mtp-110) REVERT: H 305 LYS cc_start: 0.7472 (mttm) cc_final: 0.7090 (mtpp) REVERT: H 331 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7776 (mtt) REVERT: W 187 HIS cc_start: 0.6127 (OUTLIER) cc_final: 0.5881 (t70) REVERT: W 230 MET cc_start: 0.6755 (tmm) cc_final: 0.6304 (ttp) REVERT: X 366 LEU cc_start: 0.4793 (OUTLIER) cc_final: 0.4469 (tm) REVERT: Y 55 HIS cc_start: 0.5867 (OUTLIER) cc_final: 0.4955 (p-80) REVERT: Y 186 ILE cc_start: 0.6517 (tp) cc_final: 0.5881 (pp) REVERT: Y 286 LEU cc_start: 0.6030 (OUTLIER) cc_final: 0.5710 (mp) REVERT: Y 331 MET cc_start: 0.1693 (mmm) cc_final: 0.1333 (mmm) REVERT: Z 45 ILE cc_start: 0.6375 (OUTLIER) cc_final: 0.6118 (pt) REVERT: Z 352 GLN cc_start: 0.6083 (tt0) cc_final: 0.5572 (tt0) REVERT: Z 356 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.7179 (mttp) outliers start: 229 outliers final: 143 residues processed: 1248 average time/residue: 2.0614 time to fit residues: 3584.2507 Evaluate side-chains 1231 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1072 time to evaluate : 5.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 92 LYS Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain D residue 491 HIS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 265 HIS Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 541 THR Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 50 MET Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 331 MET Chi-restraints excluded: chain F residue 335 ARG Chi-restraints excluded: chain F residue 464 THR Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 542 SER Chi-restraints excluded: chain F residue 565 VAL Chi-restraints excluded: chain F residue 568 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 335 ARG Chi-restraints excluded: chain G residue 485 VAL Chi-restraints excluded: chain G residue 565 VAL Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 331 MET Chi-restraints excluded: chain H residue 345 SER Chi-restraints excluded: chain H residue 541 THR Chi-restraints excluded: chain H residue 542 SER Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain W residue 55 HIS Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain W residue 69 LEU Chi-restraints excluded: chain W residue 141 ASP Chi-restraints excluded: chain W residue 163 LEU Chi-restraints excluded: chain W residue 183 VAL Chi-restraints excluded: chain W residue 187 HIS Chi-restraints excluded: chain W residue 202 LEU Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 241 ASN Chi-restraints excluded: chain W residue 251 VAL Chi-restraints excluded: chain W residue 313 THR Chi-restraints excluded: chain W residue 357 ASN Chi-restraints excluded: chain W residue 373 LEU Chi-restraints excluded: chain W residue 384 GLU Chi-restraints excluded: chain W residue 398 VAL Chi-restraints excluded: chain W residue 427 THR Chi-restraints excluded: chain W residue 495 ILE Chi-restraints excluded: chain W residue 503 MET Chi-restraints excluded: chain W residue 542 SER Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 95 SER Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 202 LEU Chi-restraints excluded: chain X residue 264 LEU Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 297 LEU Chi-restraints excluded: chain X residue 304 VAL Chi-restraints excluded: chain X residue 366 LEU Chi-restraints excluded: chain Y residue 55 HIS Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Y residue 73 ASN Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 122 GLN Chi-restraints excluded: chain Y residue 147 LEU Chi-restraints excluded: chain Y residue 193 LYS Chi-restraints excluded: chain Y residue 286 LEU Chi-restraints excluded: chain Y residue 289 ASN Chi-restraints excluded: chain Y residue 298 ASP Chi-restraints excluded: chain Y residue 511 VAL Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 45 ILE Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 141 ASP Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 163 LEU Chi-restraints excluded: chain Z residue 165 GLN Chi-restraints excluded: chain Z residue 251 VAL Chi-restraints excluded: chain Z residue 313 THR Chi-restraints excluded: chain Z residue 317 ASP Chi-restraints excluded: chain Z residue 337 LEU Chi-restraints excluded: chain Z residue 347 LEU Chi-restraints excluded: chain Z residue 356 LYS Chi-restraints excluded: chain Z residue 542 SER Chi-restraints excluded: chain Z residue 559 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 389 optimal weight: 0.6980 chunk 626 optimal weight: 0.8980 chunk 382 optimal weight: 0.8980 chunk 297 optimal weight: 0.5980 chunk 435 optimal weight: 0.5980 chunk 657 optimal weight: 3.9990 chunk 605 optimal weight: 20.0000 chunk 523 optimal weight: 30.0000 chunk 54 optimal weight: 0.0070 chunk 404 optimal weight: 0.6980 chunk 321 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 GLN E 241 ASN E 296 ASN ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 474 ASN G 296 ASN ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 535 GLN ** Y 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 196 GLN Z 96 HIS ** Z 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5016 moved from start: 0.6904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 54408 Z= 0.176 Angle : 0.610 11.622 73860 Z= 0.312 Chirality : 0.047 0.389 8352 Planarity : 0.005 0.075 9396 Dihedral : 8.323 83.960 7744 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.55 % Favored : 97.25 % Rotamer: Outliers : 1.74 % Allowed : 27.39 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.27 (0.10), residues: 6660 helix: 0.88 (0.10), residues: 3036 sheet: -0.18 (0.15), residues: 984 loop : -0.37 (0.13), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 472 HIS 0.026 0.001 HIS D 491 PHE 0.028 0.002 PHE D 59 TYR 0.022 0.002 TYR Z 263 ARG 0.010 0.001 ARG Y 164 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13320 Ramachandran restraints generated. 6660 Oldfield, 0 Emsley, 6660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1134 time to evaluate : 6.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 457 MET cc_start: 0.4544 (tpt) cc_final: 0.3998 (mmm) REVERT: B 89 THR cc_start: 0.5156 (OUTLIER) cc_final: 0.4847 (p) REVERT: B 350 GLU cc_start: 0.6164 (mp0) cc_final: 0.5316 (tp30) REVERT: B 438 GLU cc_start: 0.5879 (OUTLIER) cc_final: 0.5377 (mm-30) REVERT: C 101 GLU cc_start: 0.5916 (OUTLIER) cc_final: 0.5651 (tp30) REVERT: C 350 GLU cc_start: 0.6154 (mp0) cc_final: 0.4906 (mp0) REVERT: D 37 ILE cc_start: 0.3992 (mm) cc_final: 0.3669 (mp) REVERT: D 45 ILE cc_start: 0.3606 (mp) cc_final: 0.3048 (mt) REVERT: D 457 MET cc_start: 0.4365 (mmm) cc_final: 0.4148 (mmm) REVERT: E 130 LYS cc_start: 0.8070 (mtmm) cc_final: 0.7499 (mttp) REVERT: E 167 GLN cc_start: 0.7669 (tt0) cc_final: 0.7450 (tt0) REVERT: E 257 LYS cc_start: 0.6930 (mttp) cc_final: 0.6395 (mptt) REVERT: E 281 GLU cc_start: 0.7252 (tp30) cc_final: 0.6952 (tm-30) REVERT: E 305 LYS cc_start: 0.7167 (mttm) cc_final: 0.6839 (mtpt) REVERT: E 331 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7340 (mtt) REVERT: E 343 GLU cc_start: 0.7154 (tp30) cc_final: 0.6952 (tm-30) REVERT: E 499 ILE cc_start: 0.7342 (mt) cc_final: 0.7112 (mm) REVERT: F 130 LYS cc_start: 0.7914 (mtmm) cc_final: 0.7084 (mmtm) REVERT: F 282 ARG cc_start: 0.7184 (mtp-110) cc_final: 0.6709 (ttm-80) REVERT: F 335 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6237 (mtm180) REVERT: F 568 ASP cc_start: 0.5150 (OUTLIER) cc_final: 0.4940 (t70) REVERT: G 123 ASP cc_start: 0.7066 (m-30) cc_final: 0.6570 (m-30) REVERT: G 257 LYS cc_start: 0.6858 (mttp) cc_final: 0.6488 (mptt) REVERT: G 335 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6358 (mtm180) REVERT: G 428 GLU cc_start: 0.5824 (tp30) cc_final: 0.5612 (tp30) REVERT: G 487 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7150 (mm-30) REVERT: G 492 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7633 (ttm110) REVERT: H 130 LYS cc_start: 0.7902 (mtmt) cc_final: 0.7472 (mttp) REVERT: H 282 ARG cc_start: 0.7274 (mtp-110) cc_final: 0.6962 (mtp-110) REVERT: H 305 LYS cc_start: 0.7407 (mttm) cc_final: 0.6984 (mttt) REVERT: W 187 HIS cc_start: 0.6087 (OUTLIER) cc_final: 0.5873 (t70) REVERT: W 230 MET cc_start: 0.6664 (tmm) cc_final: 0.6304 (ttp) REVERT: Y 331 MET cc_start: 0.1563 (mmm) cc_final: 0.1258 (mmm) REVERT: Z 350 GLU cc_start: 0.6596 (mp0) cc_final: 0.5010 (mp0) REVERT: Z 356 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6866 (mttp) outliers start: 102 outliers final: 81 residues processed: 1200 average time/residue: 2.0163 time to fit residues: 3375.8963 Evaluate side-chains 1168 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1078 time to evaluate : 5.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 92 LYS Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 265 HIS Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 335 ARG Chi-restraints excluded: chain F residue 568 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 335 ARG Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 541 THR Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain W residue 53 LEU Chi-restraints excluded: chain W residue 183 VAL Chi-restraints excluded: chain W residue 187 HIS Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 241 ASN Chi-restraints excluded: chain W residue 313 THR Chi-restraints excluded: chain W residue 357 ASN Chi-restraints excluded: chain W residue 373 LEU Chi-restraints excluded: chain W residue 472 TRP Chi-restraints excluded: chain W residue 503 MET Chi-restraints excluded: chain W residue 542 SER Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 95 SER Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 202 LEU Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 297 LEU Chi-restraints excluded: chain X residue 304 VAL Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 55 HIS Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Y residue 73 ASN Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 122 GLN Chi-restraints excluded: chain Y residue 147 LEU Chi-restraints excluded: chain Y residue 289 ASN Chi-restraints excluded: chain Y residue 298 ASP Chi-restraints excluded: chain Y residue 511 VAL Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 141 ASP Chi-restraints excluded: chain Z residue 165 GLN Chi-restraints excluded: chain Z residue 313 THR Chi-restraints excluded: chain Z residue 337 LEU Chi-restraints excluded: chain Z residue 347 LEU Chi-restraints excluded: chain Z residue 356 LYS Chi-restraints excluded: chain Z residue 441 VAL Chi-restraints excluded: chain Z residue 542 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 415 optimal weight: 0.9980 chunk 557 optimal weight: 30.0000 chunk 160 optimal weight: 20.0000 chunk 482 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 145 optimal weight: 0.7980 chunk 524 optimal weight: 1.9990 chunk 219 optimal weight: 20.0000 chunk 538 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 HIS E 241 ASN E 296 ASN ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 ASN ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 GLN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 ASN ** H 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 483 ASN ** W 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 489 HIS ** Z 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.291488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.224018 restraints weight = 171033.894| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 2.22 r_work: 0.3898 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.7025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 54408 Z= 0.475 Angle : 0.704 10.925 73860 Z= 0.369 Chirality : 0.052 0.414 8352 Planarity : 0.006 0.076 9396 Dihedral : 8.523 86.404 7744 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.80 % Favored : 96.01 % Rotamer: Outliers : 2.13 % Allowed : 27.27 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.03 (0.10), residues: 6660 helix: 0.66 (0.10), residues: 3036 sheet: -0.24 (0.15), residues: 996 loop : -0.49 (0.13), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 472 HIS 0.011 0.001 HIS E 243 PHE 0.027 0.003 PHE D 59 TYR 0.021 0.002 TYR E 74 ARG 0.011 0.001 ARG D 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51837.25 seconds wall clock time: 882 minutes 58.91 seconds (52978.91 seconds total)