Starting phenix.real_space_refine on Sat Feb 24 07:20:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5q_13844/02_2024/7q5q_13844.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5q_13844/02_2024/7q5q_13844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5q_13844/02_2024/7q5q_13844.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5q_13844/02_2024/7q5q_13844.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5q_13844/02_2024/7q5q_13844.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5q_13844/02_2024/7q5q_13844.pdb" } resolution = 4.38 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= 0.001 sd= 0.147 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 240 5.16 5 C 26856 2.51 5 N 7392 2.21 5 O 7848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 11": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B ASP 69": "OD1" <-> "OD2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "A GLU 11": "OE1" <-> "OE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 36": "OE1" <-> "OE2" Residue "A PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "C GLU 11": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C ASP 69": "OD1" <-> "OD2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C ASP 116": "OD1" <-> "OD2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C GLU 221": "OE1" <-> "OE2" Residue "D GLU 11": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 44": "OE1" <-> "OE2" Residue "D ASP 69": "OD1" <-> "OD2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D ASP 116": "OD1" <-> "OD2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D GLU 221": "OE1" <-> "OE2" Residue "E GLU 11": "OE1" <-> "OE2" Residue "E GLU 28": "OE1" <-> "OE2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E ASP 69": "OD1" <-> "OD2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E GLU 113": "OE1" <-> "OE2" Residue "E ASP 116": "OD1" <-> "OD2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "E PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E GLU 188": "OE1" <-> "OE2" Residue "E TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 208": "OE1" <-> "OE2" Residue "E PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E GLU 221": "OE1" <-> "OE2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F GLU 28": "OE1" <-> "OE2" Residue "F GLU 36": "OE1" <-> "OE2" Residue "F PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 44": "OE1" <-> "OE2" Residue "F ASP 69": "OD1" <-> "OD2" Residue "F GLU 78": "OE1" <-> "OE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "F GLU 113": "OE1" <-> "OE2" Residue "F ASP 116": "OD1" <-> "OD2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 178": "OE1" <-> "OE2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "F TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 208": "OE1" <-> "OE2" Residue "F PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 218": "OE1" <-> "OE2" Residue "F GLU 221": "OE1" <-> "OE2" Residue "G GLU 11": "OE1" <-> "OE2" Residue "G GLU 28": "OE1" <-> "OE2" Residue "G GLU 36": "OE1" <-> "OE2" Residue "G PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G ASP 69": "OD1" <-> "OD2" Residue "G GLU 78": "OE1" <-> "OE2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 101": "OE1" <-> "OE2" Residue "G GLU 113": "OE1" <-> "OE2" Residue "G ASP 116": "OD1" <-> "OD2" Residue "G GLU 121": "OE1" <-> "OE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 178": "OE1" <-> "OE2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 208": "OE1" <-> "OE2" Residue "G PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G GLU 221": "OE1" <-> "OE2" Residue "H GLU 11": "OE1" <-> "OE2" Residue "H GLU 28": "OE1" <-> "OE2" Residue "H GLU 36": "OE1" <-> "OE2" Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 44": "OE1" <-> "OE2" Residue "H ASP 69": "OD1" <-> "OD2" Residue "H GLU 78": "OE1" <-> "OE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 101": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H ASP 116": "OD1" <-> "OD2" Residue "H GLU 121": "OE1" <-> "OE2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 178": "OE1" <-> "OE2" Residue "H GLU 188": "OE1" <-> "OE2" Residue "H TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 208": "OE1" <-> "OE2" Residue "H PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 218": "OE1" <-> "OE2" Residue "H GLU 221": "OE1" <-> "OE2" Residue "I GLU 11": "OE1" <-> "OE2" Residue "I GLU 28": "OE1" <-> "OE2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "I PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I ASP 69": "OD1" <-> "OD2" Residue "I GLU 78": "OE1" <-> "OE2" Residue "I TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 101": "OE1" <-> "OE2" Residue "I GLU 113": "OE1" <-> "OE2" Residue "I ASP 116": "OD1" <-> "OD2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "I GLU 126": "OE1" <-> "OE2" Residue "I GLU 139": "OE1" <-> "OE2" Residue "I PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 178": "OE1" <-> "OE2" Residue "I GLU 188": "OE1" <-> "OE2" Residue "I TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 208": "OE1" <-> "OE2" Residue "I PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 218": "OE1" <-> "OE2" Residue "I GLU 221": "OE1" <-> "OE2" Residue "J GLU 11": "OE1" <-> "OE2" Residue "J GLU 28": "OE1" <-> "OE2" Residue "J GLU 36": "OE1" <-> "OE2" Residue "J PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 44": "OE1" <-> "OE2" Residue "J ASP 69": "OD1" <-> "OD2" Residue "J GLU 78": "OE1" <-> "OE2" Residue "J TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 101": "OE1" <-> "OE2" Residue "J GLU 113": "OE1" <-> "OE2" Residue "J ASP 116": "OD1" <-> "OD2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J GLU 126": "OE1" <-> "OE2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 178": "OE1" <-> "OE2" Residue "J GLU 188": "OE1" <-> "OE2" Residue "J TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 208": "OE1" <-> "OE2" Residue "J PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 218": "OE1" <-> "OE2" Residue "J GLU 221": "OE1" <-> "OE2" Residue "K GLU 11": "OE1" <-> "OE2" Residue "K GLU 28": "OE1" <-> "OE2" Residue "K GLU 36": "OE1" <-> "OE2" Residue "K PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 44": "OE1" <-> "OE2" Residue "K ASP 69": "OD1" <-> "OD2" Residue "K GLU 78": "OE1" <-> "OE2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 101": "OE1" <-> "OE2" Residue "K GLU 113": "OE1" <-> "OE2" Residue "K ASP 116": "OD1" <-> "OD2" Residue "K GLU 121": "OE1" <-> "OE2" Residue "K GLU 126": "OE1" <-> "OE2" Residue "K GLU 139": "OE1" <-> "OE2" Residue "K PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 178": "OE1" <-> "OE2" Residue "K GLU 188": "OE1" <-> "OE2" Residue "K TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 208": "OE1" <-> "OE2" Residue "K PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 218": "OE1" <-> "OE2" Residue "K GLU 221": "OE1" <-> "OE2" Residue "L GLU 11": "OE1" <-> "OE2" Residue "L GLU 28": "OE1" <-> "OE2" Residue "L GLU 36": "OE1" <-> "OE2" Residue "L PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 44": "OE1" <-> "OE2" Residue "L ASP 69": "OD1" <-> "OD2" Residue "L GLU 78": "OE1" <-> "OE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 101": "OE1" <-> "OE2" Residue "L GLU 113": "OE1" <-> "OE2" Residue "L ASP 116": "OD1" <-> "OD2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "L GLU 126": "OE1" <-> "OE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "L PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 178": "OE1" <-> "OE2" Residue "L GLU 188": "OE1" <-> "OE2" Residue "L TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 208": "OE1" <-> "OE2" Residue "L PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 218": "OE1" <-> "OE2" Residue "L GLU 221": "OE1" <-> "OE2" Residue "M GLU 11": "OE1" <-> "OE2" Residue "M GLU 28": "OE1" <-> "OE2" Residue "M GLU 36": "OE1" <-> "OE2" Residue "M PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M ASP 69": "OD1" <-> "OD2" Residue "M GLU 78": "OE1" <-> "OE2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 101": "OE1" <-> "OE2" Residue "M GLU 113": "OE1" <-> "OE2" Residue "M ASP 116": "OD1" <-> "OD2" Residue "M GLU 121": "OE1" <-> "OE2" Residue "M GLU 126": "OE1" <-> "OE2" Residue "M GLU 139": "OE1" <-> "OE2" Residue "M PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 178": "OE1" <-> "OE2" Residue "M GLU 188": "OE1" <-> "OE2" Residue "M TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 208": "OE1" <-> "OE2" Residue "M PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 218": "OE1" <-> "OE2" Residue "M GLU 221": "OE1" <-> "OE2" Residue "N GLU 11": "OE1" <-> "OE2" Residue "N GLU 28": "OE1" <-> "OE2" Residue "N GLU 36": "OE1" <-> "OE2" Residue "N PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 44": "OE1" <-> "OE2" Residue "N ASP 69": "OD1" <-> "OD2" Residue "N GLU 78": "OE1" <-> "OE2" Residue "N TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 101": "OE1" <-> "OE2" Residue "N GLU 113": "OE1" <-> "OE2" Residue "N ASP 116": "OD1" <-> "OD2" Residue "N GLU 121": "OE1" <-> "OE2" Residue "N GLU 126": "OE1" <-> "OE2" Residue "N GLU 139": "OE1" <-> "OE2" Residue "N PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 178": "OE1" <-> "OE2" Residue "N GLU 188": "OE1" <-> "OE2" Residue "N TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 208": "OE1" <-> "OE2" Residue "N PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 218": "OE1" <-> "OE2" Residue "N GLU 221": "OE1" <-> "OE2" Residue "O GLU 11": "OE1" <-> "OE2" Residue "O GLU 28": "OE1" <-> "OE2" Residue "O GLU 36": "OE1" <-> "OE2" Residue "O PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 44": "OE1" <-> "OE2" Residue "O ASP 69": "OD1" <-> "OD2" Residue "O GLU 78": "OE1" <-> "OE2" Residue "O TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 101": "OE1" <-> "OE2" Residue "O GLU 113": "OE1" <-> "OE2" Residue "O ASP 116": "OD1" <-> "OD2" Residue "O GLU 121": "OE1" <-> "OE2" Residue "O GLU 126": "OE1" <-> "OE2" Residue "O GLU 139": "OE1" <-> "OE2" Residue "O PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 178": "OE1" <-> "OE2" Residue "O GLU 188": "OE1" <-> "OE2" Residue "O TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 208": "OE1" <-> "OE2" Residue "O PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 218": "OE1" <-> "OE2" Residue "O GLU 221": "OE1" <-> "OE2" Residue "P GLU 11": "OE1" <-> "OE2" Residue "P GLU 28": "OE1" <-> "OE2" Residue "P GLU 36": "OE1" <-> "OE2" Residue "P PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 44": "OE1" <-> "OE2" Residue "P ASP 69": "OD1" <-> "OD2" Residue "P GLU 78": "OE1" <-> "OE2" Residue "P TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 101": "OE1" <-> "OE2" Residue "P GLU 113": "OE1" <-> "OE2" Residue "P ASP 116": "OD1" <-> "OD2" Residue "P GLU 121": "OE1" <-> "OE2" Residue "P GLU 126": "OE1" <-> "OE2" Residue "P GLU 139": "OE1" <-> "OE2" Residue "P PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 178": "OE1" <-> "OE2" Residue "P GLU 188": "OE1" <-> "OE2" Residue "P TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 208": "OE1" <-> "OE2" Residue "P PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 218": "OE1" <-> "OE2" Residue "P GLU 221": "OE1" <-> "OE2" Residue "Q GLU 11": "OE1" <-> "OE2" Residue "Q GLU 28": "OE1" <-> "OE2" Residue "Q GLU 36": "OE1" <-> "OE2" Residue "Q PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 44": "OE1" <-> "OE2" Residue "Q ASP 69": "OD1" <-> "OD2" Residue "Q GLU 78": "OE1" <-> "OE2" Residue "Q TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 101": "OE1" <-> "OE2" Residue "Q GLU 113": "OE1" <-> "OE2" Residue "Q ASP 116": "OD1" <-> "OD2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q GLU 126": "OE1" <-> "OE2" Residue "Q GLU 139": "OE1" <-> "OE2" Residue "Q PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 178": "OE1" <-> "OE2" Residue "Q GLU 188": "OE1" <-> "OE2" Residue "Q TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 208": "OE1" <-> "OE2" Residue "Q PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 218": "OE1" <-> "OE2" Residue "Q GLU 221": "OE1" <-> "OE2" Residue "R GLU 11": "OE1" <-> "OE2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "R GLU 36": "OE1" <-> "OE2" Residue "R PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 44": "OE1" <-> "OE2" Residue "R ASP 69": "OD1" <-> "OD2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "R TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 101": "OE1" <-> "OE2" Residue "R GLU 113": "OE1" <-> "OE2" Residue "R ASP 116": "OD1" <-> "OD2" Residue "R GLU 121": "OE1" <-> "OE2" Residue "R GLU 126": "OE1" <-> "OE2" Residue "R GLU 139": "OE1" <-> "OE2" Residue "R PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 178": "OE1" <-> "OE2" Residue "R GLU 188": "OE1" <-> "OE2" Residue "R TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 208": "OE1" <-> "OE2" Residue "R PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 218": "OE1" <-> "OE2" Residue "R GLU 221": "OE1" <-> "OE2" Residue "S GLU 11": "OE1" <-> "OE2" Residue "S GLU 28": "OE1" <-> "OE2" Residue "S GLU 36": "OE1" <-> "OE2" Residue "S PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 44": "OE1" <-> "OE2" Residue "S ASP 69": "OD1" <-> "OD2" Residue "S GLU 78": "OE1" <-> "OE2" Residue "S TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 101": "OE1" <-> "OE2" Residue "S GLU 113": "OE1" <-> "OE2" Residue "S ASP 116": "OD1" <-> "OD2" Residue "S GLU 121": "OE1" <-> "OE2" Residue "S GLU 126": "OE1" <-> "OE2" Residue "S GLU 139": "OE1" <-> "OE2" Residue "S PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 178": "OE1" <-> "OE2" Residue "S GLU 188": "OE1" <-> "OE2" Residue "S TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 208": "OE1" <-> "OE2" Residue "S PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 218": "OE1" <-> "OE2" Residue "S GLU 221": "OE1" <-> "OE2" Residue "T GLU 11": "OE1" <-> "OE2" Residue "T GLU 28": "OE1" <-> "OE2" Residue "T GLU 36": "OE1" <-> "OE2" Residue "T PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 44": "OE1" <-> "OE2" Residue "T ASP 69": "OD1" <-> "OD2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "T TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 101": "OE1" <-> "OE2" Residue "T GLU 113": "OE1" <-> "OE2" Residue "T ASP 116": "OD1" <-> "OD2" Residue "T GLU 121": "OE1" <-> "OE2" Residue "T GLU 126": "OE1" <-> "OE2" Residue "T GLU 139": "OE1" <-> "OE2" Residue "T PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 178": "OE1" <-> "OE2" Residue "T GLU 188": "OE1" <-> "OE2" Residue "T TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 208": "OE1" <-> "OE2" Residue "T PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 218": "OE1" <-> "OE2" Residue "T GLU 221": "OE1" <-> "OE2" Residue "V GLU 11": "OE1" <-> "OE2" Residue "V GLU 28": "OE1" <-> "OE2" Residue "V GLU 36": "OE1" <-> "OE2" Residue "V PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "V ASP 69": "OD1" <-> "OD2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "V TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 101": "OE1" <-> "OE2" Residue "V GLU 113": "OE1" <-> "OE2" Residue "V ASP 116": "OD1" <-> "OD2" Residue "V GLU 121": "OE1" <-> "OE2" Residue "V GLU 126": "OE1" <-> "OE2" Residue "V GLU 139": "OE1" <-> "OE2" Residue "V PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 178": "OE1" <-> "OE2" Residue "V GLU 188": "OE1" <-> "OE2" Residue "V TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 208": "OE1" <-> "OE2" Residue "V PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 218": "OE1" <-> "OE2" Residue "V GLU 221": "OE1" <-> "OE2" Residue "W GLU 11": "OE1" <-> "OE2" Residue "W GLU 28": "OE1" <-> "OE2" Residue "W GLU 36": "OE1" <-> "OE2" Residue "W PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 44": "OE1" <-> "OE2" Residue "W ASP 69": "OD1" <-> "OD2" Residue "W GLU 78": "OE1" <-> "OE2" Residue "W TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 101": "OE1" <-> "OE2" Residue "W GLU 113": "OE1" <-> "OE2" Residue "W ASP 116": "OD1" <-> "OD2" Residue "W GLU 121": "OE1" <-> "OE2" Residue "W GLU 126": "OE1" <-> "OE2" Residue "W GLU 139": "OE1" <-> "OE2" Residue "W PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 178": "OE1" <-> "OE2" Residue "W GLU 188": "OE1" <-> "OE2" Residue "W TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 208": "OE1" <-> "OE2" Residue "W PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 218": "OE1" <-> "OE2" Residue "W GLU 221": "OE1" <-> "OE2" Residue "X GLU 11": "OE1" <-> "OE2" Residue "X GLU 28": "OE1" <-> "OE2" Residue "X GLU 36": "OE1" <-> "OE2" Residue "X PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 44": "OE1" <-> "OE2" Residue "X ASP 69": "OD1" <-> "OD2" Residue "X GLU 78": "OE1" <-> "OE2" Residue "X TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 101": "OE1" <-> "OE2" Residue "X GLU 113": "OE1" <-> "OE2" Residue "X ASP 116": "OD1" <-> "OD2" Residue "X GLU 121": "OE1" <-> "OE2" Residue "X GLU 126": "OE1" <-> "OE2" Residue "X GLU 139": "OE1" <-> "OE2" Residue "X PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 178": "OE1" <-> "OE2" Residue "X GLU 188": "OE1" <-> "OE2" Residue "X TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 208": "OE1" <-> "OE2" Residue "X PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 218": "OE1" <-> "OE2" Residue "X GLU 221": "OE1" <-> "OE2" Residue "Y GLU 11": "OE1" <-> "OE2" Residue "Y GLU 28": "OE1" <-> "OE2" Residue "Y GLU 36": "OE1" <-> "OE2" Residue "Y PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 44": "OE1" <-> "OE2" Residue "Y ASP 69": "OD1" <-> "OD2" Residue "Y GLU 78": "OE1" <-> "OE2" Residue "Y TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 101": "OE1" <-> "OE2" Residue "Y GLU 113": "OE1" <-> "OE2" Residue "Y ASP 116": "OD1" <-> "OD2" Residue "Y GLU 121": "OE1" <-> "OE2" Residue "Y GLU 126": "OE1" <-> "OE2" Residue "Y GLU 139": "OE1" <-> "OE2" Residue "Y PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 178": "OE1" <-> "OE2" Residue "Y GLU 188": "OE1" <-> "OE2" Residue "Y TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 208": "OE1" <-> "OE2" Residue "Y PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 218": "OE1" <-> "OE2" Residue "Y GLU 221": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 42336 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "A" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "C" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "D" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "E" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "F" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "G" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "H" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "I" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "J" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "K" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "L" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "M" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "N" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "O" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "P" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "Q" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "R" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "S" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "T" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "V" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "W" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "X" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "Y" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Time building chain proxies: 21.86, per 1000 atoms: 0.52 Number of scatterers: 42336 At special positions: 0 Unit cell: (155.212, 155.212, 155.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 240 16.00 O 7848 8.00 N 7392 7.00 C 26856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.05 Conformation dependent library (CDL) restraints added in 8.1 seconds 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10128 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 96 sheets defined 50.4% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.71 Creating SS restraints... Processing helix chain 'B' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP B 43 " --> pdb=" O ASN B 39 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 70 Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 116 through 133 Processing helix chain 'B' and resid 137 through 141 Processing helix chain 'B' and resid 205 through 222 Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'A' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP A 43 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 116 through 133 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 205 through 222 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'C' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP C 43 " --> pdb=" O ASN C 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 70 Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 116 through 133 Processing helix chain 'C' and resid 137 through 141 Processing helix chain 'C' and resid 205 through 222 Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'D' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP D 43 " --> pdb=" O ASN D 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 70 Processing helix chain 'D' and resid 71 through 74 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 111 through 115 Processing helix chain 'D' and resid 116 through 133 Processing helix chain 'D' and resid 137 through 141 Processing helix chain 'D' and resid 205 through 222 Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'E' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP E 43 " --> pdb=" O ASN E 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU E 44 " --> pdb=" O LYS E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 70 Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 111 through 115 Processing helix chain 'E' and resid 116 through 133 Processing helix chain 'E' and resid 137 through 141 Processing helix chain 'E' and resid 205 through 222 Processing helix chain 'E' and resid 223 through 228 Processing helix chain 'F' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS F 14 " --> pdb=" O ALA F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP F 43 " --> pdb=" O ASN F 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU F 44 " --> pdb=" O LYS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 70 Processing helix chain 'F' and resid 71 through 74 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 111 through 115 Processing helix chain 'F' and resid 116 through 133 Processing helix chain 'F' and resid 137 through 141 Processing helix chain 'F' and resid 205 through 222 Processing helix chain 'F' and resid 223 through 228 Processing helix chain 'G' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP G 43 " --> pdb=" O ASN G 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU G 44 " --> pdb=" O LYS G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 70 Processing helix chain 'G' and resid 71 through 74 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'G' and resid 116 through 133 Processing helix chain 'G' and resid 137 through 141 Processing helix chain 'G' and resid 205 through 222 Processing helix chain 'G' and resid 223 through 228 Processing helix chain 'H' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP H 43 " --> pdb=" O ASN H 39 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLU H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 70 Processing helix chain 'H' and resid 71 through 74 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'H' and resid 111 through 115 Processing helix chain 'H' and resid 116 through 133 Processing helix chain 'H' and resid 137 through 141 Processing helix chain 'H' and resid 205 through 222 Processing helix chain 'H' and resid 223 through 228 Processing helix chain 'I' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS I 14 " --> pdb=" O ALA I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP I 43 " --> pdb=" O ASN I 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU I 44 " --> pdb=" O LYS I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 70 Processing helix chain 'I' and resid 71 through 74 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'I' and resid 111 through 115 Processing helix chain 'I' and resid 116 through 133 Processing helix chain 'I' and resid 137 through 141 Processing helix chain 'I' and resid 205 through 222 Processing helix chain 'I' and resid 223 through 228 Processing helix chain 'J' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS J 14 " --> pdb=" O ALA J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLU J 44 " --> pdb=" O LYS J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 70 Processing helix chain 'J' and resid 71 through 74 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'J' and resid 111 through 115 Processing helix chain 'J' and resid 116 through 133 Processing helix chain 'J' and resid 137 through 141 Processing helix chain 'J' and resid 205 through 222 Processing helix chain 'J' and resid 223 through 228 Processing helix chain 'K' and resid 3 through 20 removed outlier: 3.748A pdb=" N LYS K 14 " --> pdb=" O ALA K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU K 44 " --> pdb=" O LYS K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 70 Processing helix chain 'K' and resid 71 through 74 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'K' and resid 111 through 115 Processing helix chain 'K' and resid 116 through 133 Processing helix chain 'K' and resid 137 through 141 Processing helix chain 'K' and resid 205 through 222 Processing helix chain 'K' and resid 223 through 228 Processing helix chain 'L' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS L 14 " --> pdb=" O ALA L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 50 removed outlier: 5.543A pdb=" N ASP L 43 " --> pdb=" O ASN L 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU L 44 " --> pdb=" O LYS L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 70 Processing helix chain 'L' and resid 71 through 74 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 111 through 115 Processing helix chain 'L' and resid 116 through 133 Processing helix chain 'L' and resid 137 through 141 Processing helix chain 'L' and resid 205 through 222 Processing helix chain 'L' and resid 223 through 228 Processing helix chain 'M' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS M 14 " --> pdb=" O ALA M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP M 43 " --> pdb=" O ASN M 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU M 44 " --> pdb=" O LYS M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 70 Processing helix chain 'M' and resid 71 through 74 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'M' and resid 111 through 115 Processing helix chain 'M' and resid 116 through 133 Processing helix chain 'M' and resid 137 through 141 Processing helix chain 'M' and resid 205 through 222 Processing helix chain 'M' and resid 223 through 228 Processing helix chain 'N' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS N 14 " --> pdb=" O ALA N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP N 43 " --> pdb=" O ASN N 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 70 Processing helix chain 'N' and resid 71 through 74 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'N' and resid 111 through 115 Processing helix chain 'N' and resid 116 through 133 Processing helix chain 'N' and resid 137 through 141 Processing helix chain 'N' and resid 205 through 222 Processing helix chain 'N' and resid 223 through 228 Processing helix chain 'O' and resid 3 through 20 removed outlier: 3.746A pdb=" N LYS O 14 " --> pdb=" O ALA O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP O 43 " --> pdb=" O ASN O 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU O 44 " --> pdb=" O LYS O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 70 Processing helix chain 'O' and resid 71 through 74 Processing helix chain 'O' and resid 79 through 83 Processing helix chain 'O' and resid 111 through 115 Processing helix chain 'O' and resid 116 through 133 Processing helix chain 'O' and resid 137 through 141 Processing helix chain 'O' and resid 205 through 222 Processing helix chain 'O' and resid 223 through 228 Processing helix chain 'P' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS P 14 " --> pdb=" O ALA P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 50 removed outlier: 5.545A pdb=" N ASP P 43 " --> pdb=" O ASN P 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU P 44 " --> pdb=" O LYS P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 70 Processing helix chain 'P' and resid 71 through 74 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'P' and resid 111 through 115 Processing helix chain 'P' and resid 116 through 133 Processing helix chain 'P' and resid 137 through 141 Processing helix chain 'P' and resid 205 through 222 Processing helix chain 'P' and resid 223 through 228 Processing helix chain 'Q' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS Q 14 " --> pdb=" O ALA Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP Q 43 " --> pdb=" O ASN Q 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU Q 44 " --> pdb=" O LYS Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 70 Processing helix chain 'Q' and resid 71 through 74 Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'Q' and resid 111 through 115 Processing helix chain 'Q' and resid 116 through 133 Processing helix chain 'Q' and resid 137 through 141 Processing helix chain 'Q' and resid 205 through 222 Processing helix chain 'Q' and resid 223 through 228 Processing helix chain 'R' and resid 3 through 20 removed outlier: 3.748A pdb=" N LYS R 14 " --> pdb=" O ALA R 10 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP R 43 " --> pdb=" O ASN R 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU R 44 " --> pdb=" O LYS R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 70 Processing helix chain 'R' and resid 71 through 74 Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'R' and resid 111 through 115 Processing helix chain 'R' and resid 116 through 133 Processing helix chain 'R' and resid 137 through 141 Processing helix chain 'R' and resid 205 through 222 Processing helix chain 'R' and resid 223 through 228 Processing helix chain 'S' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS S 14 " --> pdb=" O ALA S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP S 43 " --> pdb=" O ASN S 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU S 44 " --> pdb=" O LYS S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 70 Processing helix chain 'S' and resid 71 through 74 Processing helix chain 'S' and resid 79 through 83 Processing helix chain 'S' and resid 111 through 115 Processing helix chain 'S' and resid 116 through 133 Processing helix chain 'S' and resid 137 through 141 Processing helix chain 'S' and resid 205 through 222 Processing helix chain 'S' and resid 223 through 228 Processing helix chain 'T' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS T 14 " --> pdb=" O ALA T 10 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP T 43 " --> pdb=" O ASN T 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU T 44 " --> pdb=" O LYS T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 70 Processing helix chain 'T' and resid 71 through 74 Processing helix chain 'T' and resid 79 through 83 Processing helix chain 'T' and resid 111 through 115 Processing helix chain 'T' and resid 116 through 133 Processing helix chain 'T' and resid 137 through 141 Processing helix chain 'T' and resid 205 through 222 Processing helix chain 'T' and resid 223 through 228 Processing helix chain 'V' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS V 14 " --> pdb=" O ALA V 10 " (cutoff:3.500A) Processing helix chain 'V' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP V 43 " --> pdb=" O ASN V 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU V 44 " --> pdb=" O LYS V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 70 Processing helix chain 'V' and resid 71 through 74 Processing helix chain 'V' and resid 79 through 83 Processing helix chain 'V' and resid 111 through 115 Processing helix chain 'V' and resid 116 through 133 Processing helix chain 'V' and resid 137 through 141 Processing helix chain 'V' and resid 205 through 222 Processing helix chain 'V' and resid 223 through 228 Processing helix chain 'W' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS W 14 " --> pdb=" O ALA W 10 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP W 43 " --> pdb=" O ASN W 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU W 44 " --> pdb=" O LYS W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 70 Processing helix chain 'W' and resid 71 through 74 Processing helix chain 'W' and resid 79 through 83 Processing helix chain 'W' and resid 111 through 115 Processing helix chain 'W' and resid 116 through 133 Processing helix chain 'W' and resid 137 through 141 Processing helix chain 'W' and resid 205 through 222 Processing helix chain 'W' and resid 223 through 228 Processing helix chain 'X' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS X 14 " --> pdb=" O ALA X 10 " (cutoff:3.500A) Processing helix chain 'X' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP X 43 " --> pdb=" O ASN X 39 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLU X 44 " --> pdb=" O LYS X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 55 through 70 Processing helix chain 'X' and resid 71 through 74 Processing helix chain 'X' and resid 79 through 83 Processing helix chain 'X' and resid 111 through 115 Processing helix chain 'X' and resid 116 through 133 Processing helix chain 'X' and resid 137 through 141 Processing helix chain 'X' and resid 205 through 222 Processing helix chain 'X' and resid 223 through 228 Processing helix chain 'Y' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS Y 14 " --> pdb=" O ALA Y 10 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP Y 43 " --> pdb=" O ASN Y 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU Y 44 " --> pdb=" O LYS Y 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 55 through 70 Processing helix chain 'Y' and resid 71 through 74 Processing helix chain 'Y' and resid 79 through 83 Processing helix chain 'Y' and resid 111 through 115 Processing helix chain 'Y' and resid 116 through 133 Processing helix chain 'Y' and resid 137 through 141 Processing helix chain 'Y' and resid 205 through 222 Processing helix chain 'Y' and resid 223 through 228 Processing sheet with id=AA1, first strand: chain 'B' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA B 196 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR B 147 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 30 Processing sheet with id=AA3, first strand: chain 'B' and resid 76 through 78 Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 100 Processing sheet with id=AA5, first strand: chain 'A' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA A 196 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR A 147 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 23 through 30 Processing sheet with id=AA7, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA8, first strand: chain 'A' and resid 98 through 100 Processing sheet with id=AA9, first strand: chain 'C' and resid 23 through 30 removed outlier: 3.520A pdb=" N ALA C 196 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR C 147 " --> pdb=" O ALA C 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 23 through 30 Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78 Processing sheet with id=AB3, first strand: chain 'C' and resid 98 through 100 Processing sheet with id=AB4, first strand: chain 'D' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA D 196 " --> pdb=" O GLY D 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR D 147 " --> pdb=" O ALA D 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 23 through 30 Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78 Processing sheet with id=AB7, first strand: chain 'D' and resid 98 through 100 Processing sheet with id=AB8, first strand: chain 'E' and resid 23 through 30 removed outlier: 3.520A pdb=" N ALA E 196 " --> pdb=" O GLY E 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR E 147 " --> pdb=" O ALA E 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 23 through 30 Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78 Processing sheet with id=AC2, first strand: chain 'E' and resid 98 through 100 Processing sheet with id=AC3, first strand: chain 'F' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA F 196 " --> pdb=" O GLY F 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR F 147 " --> pdb=" O ALA F 169 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 23 through 30 Processing sheet with id=AC5, first strand: chain 'F' and resid 76 through 78 Processing sheet with id=AC6, first strand: chain 'F' and resid 98 through 100 Processing sheet with id=AC7, first strand: chain 'G' and resid 23 through 30 removed outlier: 3.520A pdb=" N ALA G 196 " --> pdb=" O GLY G 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR G 147 " --> pdb=" O ALA G 169 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 23 through 30 Processing sheet with id=AC9, first strand: chain 'G' and resid 76 through 78 Processing sheet with id=AD1, first strand: chain 'G' and resid 98 through 100 Processing sheet with id=AD2, first strand: chain 'H' and resid 23 through 30 removed outlier: 3.520A pdb=" N ALA H 196 " --> pdb=" O GLY H 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR H 147 " --> pdb=" O ALA H 169 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 23 through 30 Processing sheet with id=AD4, first strand: chain 'H' and resid 76 through 78 Processing sheet with id=AD5, first strand: chain 'H' and resid 98 through 100 Processing sheet with id=AD6, first strand: chain 'I' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA I 196 " --> pdb=" O GLY I 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR I 147 " --> pdb=" O ALA I 169 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 23 through 30 Processing sheet with id=AD8, first strand: chain 'I' and resid 76 through 78 Processing sheet with id=AD9, first strand: chain 'I' and resid 98 through 100 Processing sheet with id=AE1, first strand: chain 'J' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA J 196 " --> pdb=" O GLY J 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR J 147 " --> pdb=" O ALA J 169 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 23 through 30 Processing sheet with id=AE3, first strand: chain 'J' and resid 76 through 78 Processing sheet with id=AE4, first strand: chain 'J' and resid 98 through 100 Processing sheet with id=AE5, first strand: chain 'K' and resid 23 through 30 removed outlier: 3.520A pdb=" N ALA K 196 " --> pdb=" O GLY K 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR K 147 " --> pdb=" O ALA K 169 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 23 through 30 Processing sheet with id=AE7, first strand: chain 'K' and resid 76 through 78 Processing sheet with id=AE8, first strand: chain 'K' and resid 98 through 100 Processing sheet with id=AE9, first strand: chain 'L' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA L 196 " --> pdb=" O GLY L 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR L 147 " --> pdb=" O ALA L 169 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 23 through 30 Processing sheet with id=AF2, first strand: chain 'L' and resid 76 through 78 Processing sheet with id=AF3, first strand: chain 'L' and resid 98 through 100 Processing sheet with id=AF4, first strand: chain 'M' and resid 23 through 30 removed outlier: 3.520A pdb=" N ALA M 196 " --> pdb=" O GLY M 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR M 147 " --> pdb=" O ALA M 169 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 23 through 30 Processing sheet with id=AF6, first strand: chain 'M' and resid 76 through 78 Processing sheet with id=AF7, first strand: chain 'M' and resid 98 through 100 Processing sheet with id=AF8, first strand: chain 'N' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA N 196 " --> pdb=" O GLY N 172 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR N 147 " --> pdb=" O ALA N 169 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 23 through 30 Processing sheet with id=AG1, first strand: chain 'N' and resid 76 through 78 Processing sheet with id=AG2, first strand: chain 'N' and resid 98 through 100 Processing sheet with id=AG3, first strand: chain 'O' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA O 196 " --> pdb=" O GLY O 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR O 147 " --> pdb=" O ALA O 169 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 23 through 30 Processing sheet with id=AG5, first strand: chain 'O' and resid 76 through 78 Processing sheet with id=AG6, first strand: chain 'O' and resid 98 through 100 Processing sheet with id=AG7, first strand: chain 'P' and resid 23 through 30 removed outlier: 3.520A pdb=" N ALA P 196 " --> pdb=" O GLY P 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR P 147 " --> pdb=" O ALA P 169 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 23 through 30 Processing sheet with id=AG9, first strand: chain 'P' and resid 76 through 78 Processing sheet with id=AH1, first strand: chain 'P' and resid 98 through 100 Processing sheet with id=AH2, first strand: chain 'Q' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA Q 196 " --> pdb=" O GLY Q 172 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR Q 147 " --> pdb=" O ALA Q 169 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 23 through 30 Processing sheet with id=AH4, first strand: chain 'Q' and resid 76 through 78 Processing sheet with id=AH5, first strand: chain 'Q' and resid 98 through 100 Processing sheet with id=AH6, first strand: chain 'R' and resid 23 through 30 removed outlier: 3.520A pdb=" N ALA R 196 " --> pdb=" O GLY R 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR R 147 " --> pdb=" O ALA R 169 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'R' and resid 23 through 30 Processing sheet with id=AH8, first strand: chain 'R' and resid 76 through 78 Processing sheet with id=AH9, first strand: chain 'R' and resid 98 through 100 Processing sheet with id=AI1, first strand: chain 'S' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA S 196 " --> pdb=" O GLY S 172 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR S 147 " --> pdb=" O ALA S 169 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'S' and resid 23 through 30 Processing sheet with id=AI3, first strand: chain 'S' and resid 76 through 78 Processing sheet with id=AI4, first strand: chain 'S' and resid 98 through 100 Processing sheet with id=AI5, first strand: chain 'T' and resid 23 through 30 removed outlier: 3.520A pdb=" N ALA T 196 " --> pdb=" O GLY T 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR T 147 " --> pdb=" O ALA T 169 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'T' and resid 23 through 30 Processing sheet with id=AI7, first strand: chain 'T' and resid 76 through 78 Processing sheet with id=AI8, first strand: chain 'T' and resid 98 through 100 Processing sheet with id=AI9, first strand: chain 'V' and resid 23 through 30 removed outlier: 3.520A pdb=" N ALA V 196 " --> pdb=" O GLY V 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR V 147 " --> pdb=" O ALA V 169 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'V' and resid 23 through 30 Processing sheet with id=AJ2, first strand: chain 'V' and resid 76 through 78 Processing sheet with id=AJ3, first strand: chain 'V' and resid 98 through 100 Processing sheet with id=AJ4, first strand: chain 'W' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA W 196 " --> pdb=" O GLY W 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR W 147 " --> pdb=" O ALA W 169 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'W' and resid 23 through 30 Processing sheet with id=AJ6, first strand: chain 'W' and resid 76 through 78 Processing sheet with id=AJ7, first strand: chain 'W' and resid 98 through 100 Processing sheet with id=AJ8, first strand: chain 'X' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA X 196 " --> pdb=" O GLY X 172 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR X 147 " --> pdb=" O ALA X 169 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'X' and resid 23 through 30 Processing sheet with id=AK1, first strand: chain 'X' and resid 76 through 78 Processing sheet with id=AK2, first strand: chain 'X' and resid 98 through 100 Processing sheet with id=AK3, first strand: chain 'Y' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA Y 196 " --> pdb=" O GLY Y 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR Y 147 " --> pdb=" O ALA Y 169 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'Y' and resid 23 through 30 Processing sheet with id=AK5, first strand: chain 'Y' and resid 76 through 78 Processing sheet with id=AK6, first strand: chain 'Y' and resid 98 through 100 2856 hydrogen bonds defined for protein. 7200 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: 18.31 Time building geometry restraints manager: 18.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10436 1.33 - 1.45: 6700 1.45 - 1.57: 25248 1.57 - 1.69: 0 1.69 - 1.81: 480 Bond restraints: 42864 Sorted by residual: bond pdb=" CZ ARG V 6 " pdb=" NH2 ARG V 6 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.86e+00 bond pdb=" CZ ARG T 6 " pdb=" NH2 ARG T 6 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.84e+00 bond pdb=" CZ ARG Y 6 " pdb=" NH2 ARG Y 6 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.82e+00 bond pdb=" CZ ARG G 6 " pdb=" NH2 ARG G 6 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.75e+00 bond pdb=" CZ ARG O 6 " pdb=" NH2 ARG O 6 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.70e+00 ... (remaining 42859 not shown) Histogram of bond angle deviations from ideal: 98.78 - 104.78: 960 104.78 - 110.78: 12289 110.78 - 116.78: 17347 116.78 - 122.78: 23064 122.78 - 128.79: 4108 Bond angle restraints: 57768 Sorted by residual: angle pdb=" C GLY M 206 " pdb=" N ARG M 207 " pdb=" CA ARG M 207 " ideal model delta sigma weight residual 120.79 125.79 -5.00 1.39e+00 5.18e-01 1.29e+01 angle pdb=" C GLY E 206 " pdb=" N ARG E 207 " pdb=" CA ARG E 207 " ideal model delta sigma weight residual 120.79 125.78 -4.99 1.39e+00 5.18e-01 1.29e+01 angle pdb=" C GLY Y 206 " pdb=" N ARG Y 207 " pdb=" CA ARG Y 207 " ideal model delta sigma weight residual 120.79 125.78 -4.99 1.39e+00 5.18e-01 1.29e+01 angle pdb=" C GLY J 206 " pdb=" N ARG J 207 " pdb=" CA ARG J 207 " ideal model delta sigma weight residual 120.79 125.78 -4.99 1.39e+00 5.18e-01 1.29e+01 angle pdb=" C GLY Q 206 " pdb=" N ARG Q 207 " pdb=" CA ARG Q 207 " ideal model delta sigma weight residual 120.79 125.77 -4.98 1.39e+00 5.18e-01 1.28e+01 ... (remaining 57763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.76: 23257 14.76 - 29.52: 2735 29.52 - 44.29: 441 44.29 - 59.05: 87 59.05 - 73.81: 72 Dihedral angle restraints: 26592 sinusoidal: 10872 harmonic: 15720 Sorted by residual: dihedral pdb=" CA ALA N 20 " pdb=" C ALA N 20 " pdb=" N ALA N 21 " pdb=" CA ALA N 21 " ideal model delta harmonic sigma weight residual 180.00 151.73 28.27 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA ALA O 20 " pdb=" C ALA O 20 " pdb=" N ALA O 21 " pdb=" CA ALA O 21 " ideal model delta harmonic sigma weight residual 180.00 151.75 28.25 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA ALA D 20 " pdb=" C ALA D 20 " pdb=" N ALA D 21 " pdb=" CA ALA D 21 " ideal model delta harmonic sigma weight residual 180.00 151.75 28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 26589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4103 0.054 - 0.108: 2117 0.108 - 0.162: 620 0.162 - 0.216: 24 0.216 - 0.271: 24 Chirality restraints: 6888 Sorted by residual: chirality pdb=" CA LEU L 203 " pdb=" N LEU L 203 " pdb=" C LEU L 203 " pdb=" CB LEU L 203 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA LEU K 203 " pdb=" N LEU K 203 " pdb=" C LEU K 203 " pdb=" CB LEU K 203 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA LEU B 203 " pdb=" N LEU B 203 " pdb=" C LEU B 203 " pdb=" CB LEU B 203 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 6885 not shown) Planarity restraints: 7344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR V 41 " 0.071 2.00e-02 2.50e+03 3.77e-02 2.84e+01 pdb=" CG TYR V 41 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR V 41 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR V 41 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR V 41 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR V 41 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR V 41 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR V 41 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 41 " -0.071 2.00e-02 2.50e+03 3.77e-02 2.84e+01 pdb=" CG TYR Q 41 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 41 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 41 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 41 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 41 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR Q 41 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR Q 41 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 41 " -0.071 2.00e-02 2.50e+03 3.76e-02 2.83e+01 pdb=" CG TYR F 41 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR F 41 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR F 41 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR F 41 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR F 41 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR F 41 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR F 41 " -0.049 2.00e-02 2.50e+03 ... (remaining 7341 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 922 2.70 - 3.25: 45478 3.25 - 3.80: 70093 3.80 - 4.35: 88227 4.35 - 4.90: 140927 Nonbonded interactions: 345647 Sorted by model distance: nonbonded pdb=" O ASP C 84 " pdb=" N MET N 2 " model vdw 2.152 2.520 nonbonded pdb=" N MET L 2 " pdb=" O ASP O 84 " model vdw 2.255 2.520 nonbonded pdb=" O ASP F 84 " pdb=" N MET M 2 " model vdw 2.260 2.520 nonbonded pdb=" O ASP M 84 " pdb=" N MET V 2 " model vdw 2.344 2.520 nonbonded pdb=" NH2 ARG I 6 " pdb=" OD2 ASP R 205 " model vdw 2.360 2.520 ... (remaining 345642 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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 group one per residue 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.760 Check model and map are aligned: 0.680 Set scattering table: 0.410 Process input model: 111.660 Find NCS groups from input model: 2.990 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 42864 Z= 0.597 Angle : 1.410 7.217 57768 Z= 0.870 Chirality : 0.067 0.271 6888 Planarity : 0.013 0.105 7344 Dihedral : 13.563 73.810 16464 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.08 % Allowed : 6.25 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.58 (0.11), residues: 5424 helix: -1.83 (0.08), residues: 2160 sheet: -1.01 (0.13), residues: 1296 loop : 0.32 (0.16), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.005 HIS I 174 PHE 0.040 0.011 PHE P 146 TYR 0.071 0.014 TYR Q 41 ARG 0.008 0.001 ARG P 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 4608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 545 time to evaluate : 5.024 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: B 193 MET cc_start: 0.8926 (ttm) cc_final: 0.8453 (ttp) REVERT: B 204 LEU cc_start: 0.9197 (mt) cc_final: 0.8810 (mt) REVERT: B 226 MET cc_start: 0.9209 (mmt) cc_final: 0.8894 (mmm) REVERT: A 193 MET cc_start: 0.8864 (ttm) cc_final: 0.8265 (ttp) REVERT: A 204 LEU cc_start: 0.9263 (mt) cc_final: 0.8957 (mt) REVERT: A 226 MET cc_start: 0.9256 (mmt) cc_final: 0.8921 (mmm) REVERT: C 56 MET cc_start: 0.9410 (mmm) cc_final: 0.8952 (mpp) REVERT: C 115 MET cc_start: 0.7687 (mtt) cc_final: 0.7087 (mtt) REVERT: C 193 MET cc_start: 0.9091 (ttm) cc_final: 0.8739 (ttp) REVERT: D 192 MET cc_start: 0.9025 (mmm) cc_final: 0.8711 (mmm) REVERT: D 193 MET cc_start: 0.8945 (ttm) cc_final: 0.8622 (ttp) REVERT: D 226 MET cc_start: 0.9337 (mmt) cc_final: 0.8907 (mmm) REVERT: E 5 MET cc_start: 0.9058 (tmt) cc_final: 0.8830 (tmm) REVERT: E 31 MET cc_start: 0.9118 (mmm) cc_final: 0.8848 (mmm) REVERT: E 193 MET cc_start: 0.8755 (ttm) cc_final: 0.8195 (ttp) REVERT: E 204 LEU cc_start: 0.9225 (mt) cc_final: 0.8917 (mt) REVERT: E 226 MET cc_start: 0.9108 (mmt) cc_final: 0.8896 (mmm) REVERT: F 192 MET cc_start: 0.9076 (mmm) cc_final: 0.8796 (mmm) REVERT: F 193 MET cc_start: 0.8954 (ttm) cc_final: 0.8576 (ttp) REVERT: F 226 MET cc_start: 0.9252 (mmt) cc_final: 0.9038 (mmt) REVERT: G 5 MET cc_start: 0.9079 (tmt) cc_final: 0.8839 (tmm) REVERT: G 31 MET cc_start: 0.9084 (mmm) cc_final: 0.8821 (mmm) REVERT: G 193 MET cc_start: 0.8766 (ttm) cc_final: 0.8194 (ttp) REVERT: G 204 LEU cc_start: 0.9142 (mt) cc_final: 0.8827 (mt) REVERT: G 226 MET cc_start: 0.9110 (mmt) cc_final: 0.8880 (mmm) REVERT: H 192 MET cc_start: 0.9014 (mmm) cc_final: 0.8792 (mmm) REVERT: H 193 MET cc_start: 0.8861 (ttm) cc_final: 0.8431 (ttp) REVERT: H 226 MET cc_start: 0.9249 (mmt) cc_final: 0.8930 (mmt) REVERT: I 192 MET cc_start: 0.8987 (mmm) cc_final: 0.8712 (mmm) REVERT: I 193 MET cc_start: 0.8857 (ttm) cc_final: 0.8537 (ttp) REVERT: I 226 MET cc_start: 0.9239 (mmt) cc_final: 0.8919 (mmt) REVERT: J 192 MET cc_start: 0.9030 (mmm) cc_final: 0.8687 (mmm) REVERT: J 193 MET cc_start: 0.8784 (ttm) cc_final: 0.8455 (ttp) REVERT: J 226 MET cc_start: 0.9117 (mmt) cc_final: 0.8889 (mmm) REVERT: K 56 MET cc_start: 0.9340 (mmm) cc_final: 0.8554 (mpp) REVERT: K 158 MET cc_start: 0.8988 (ttp) cc_final: 0.8723 (ptm) REVERT: K 192 MET cc_start: 0.9003 (mmm) cc_final: 0.8798 (mmm) REVERT: K 193 MET cc_start: 0.8766 (ttm) cc_final: 0.8380 (ttp) REVERT: K 226 MET cc_start: 0.9232 (mmt) cc_final: 0.8902 (mmt) REVERT: L 31 MET cc_start: 0.9146 (mmm) cc_final: 0.8850 (mmm) REVERT: L 52 LYS cc_start: 0.9427 (ptpp) cc_final: 0.9176 (tppt) REVERT: L 56 MET cc_start: 0.9444 (mmm) cc_final: 0.9048 (mpp) REVERT: L 193 MET cc_start: 0.9112 (ttm) cc_final: 0.8792 (ttp) REVERT: M 56 MET cc_start: 0.9386 (mmm) cc_final: 0.8939 (mpp) REVERT: M 115 MET cc_start: 0.7777 (mtt) cc_final: 0.7364 (mtt) REVERT: M 192 MET cc_start: 0.9123 (mmm) cc_final: 0.8880 (mmm) REVERT: M 193 MET cc_start: 0.9073 (ttm) cc_final: 0.8773 (ttp) REVERT: M 226 MET cc_start: 0.9059 (mmt) cc_final: 0.8850 (mmt) REVERT: N 193 MET cc_start: 0.8923 (ttm) cc_final: 0.8431 (ttp) REVERT: N 226 MET cc_start: 0.9325 (mmt) cc_final: 0.8918 (mmm) REVERT: O 31 MET cc_start: 0.9160 (mmm) cc_final: 0.8925 (mmm) REVERT: O 193 MET cc_start: 0.8785 (ttm) cc_final: 0.8395 (ttp) REVERT: P 158 MET cc_start: 0.9181 (ttp) cc_final: 0.8818 (ptm) REVERT: P 192 MET cc_start: 0.8954 (mmm) cc_final: 0.8710 (mmm) REVERT: P 193 MET cc_start: 0.8911 (ttm) cc_final: 0.8575 (ttp) REVERT: P 226 MET cc_start: 0.9277 (mmt) cc_final: 0.9039 (mmt) REVERT: Q 184 ASN cc_start: 0.9156 (m-40) cc_final: 0.8935 (m-40) REVERT: Q 193 MET cc_start: 0.8627 (ttm) cc_final: 0.8024 (ttp) REVERT: Q 204 LEU cc_start: 0.9261 (mt) cc_final: 0.8880 (mt) REVERT: R 5 MET cc_start: 0.9059 (tmt) cc_final: 0.8817 (tmm) REVERT: R 31 MET cc_start: 0.9137 (mmm) cc_final: 0.8909 (mmm) REVERT: R 193 MET cc_start: 0.8727 (ttm) cc_final: 0.8243 (ttp) REVERT: R 204 LEU cc_start: 0.9235 (mt) cc_final: 0.8856 (mt) REVERT: R 226 MET cc_start: 0.9110 (mmt) cc_final: 0.8814 (mmm) REVERT: S 31 MET cc_start: 0.9196 (mmm) cc_final: 0.8875 (mmm) REVERT: S 193 MET cc_start: 0.8795 (ttm) cc_final: 0.8351 (ttp) REVERT: S 204 LEU cc_start: 0.9254 (mt) cc_final: 0.8948 (mt) REVERT: T 31 MET cc_start: 0.9097 (mmm) cc_final: 0.8690 (mmm) REVERT: T 193 MET cc_start: 0.8555 (ttm) cc_final: 0.7907 (ttt) REVERT: T 204 LEU cc_start: 0.9206 (mt) cc_final: 0.8833 (mt) REVERT: V 192 MET cc_start: 0.9077 (mmm) cc_final: 0.8821 (mmm) REVERT: V 193 MET cc_start: 0.8913 (ttm) cc_final: 0.8502 (ttp) REVERT: V 226 MET cc_start: 0.9248 (mmt) cc_final: 0.9011 (mmt) REVERT: W 5 MET cc_start: 0.9068 (tmt) cc_final: 0.8839 (tmm) REVERT: W 31 MET cc_start: 0.9208 (mmm) cc_final: 0.8929 (mmm) REVERT: W 192 MET cc_start: 0.9033 (mmm) cc_final: 0.8832 (mmm) REVERT: W 193 MET cc_start: 0.8832 (ttm) cc_final: 0.8326 (ttp) REVERT: W 204 LEU cc_start: 0.9239 (mt) cc_final: 0.8893 (mt) REVERT: W 226 MET cc_start: 0.9127 (mmt) cc_final: 0.8878 (mmm) REVERT: X 193 MET cc_start: 0.8765 (ttm) cc_final: 0.8392 (ttp) REVERT: Y 192 MET cc_start: 0.9028 (mmm) cc_final: 0.8820 (mmm) REVERT: Y 193 MET cc_start: 0.8961 (ttm) cc_final: 0.8515 (ttp) REVERT: Y 226 MET cc_start: 0.9245 (mmt) cc_final: 0.8880 (mmt) outliers start: 96 outliers final: 36 residues processed: 641 average time/residue: 0.6097 time to fit residues: 616.1208 Evaluate side-chains 365 residues out of total 4608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 329 time to evaluate : 5.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 5.9990 chunk 400 optimal weight: 0.8980 chunk 222 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 269 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 chunk 413 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 chunk 308 optimal weight: 5.9990 chunk 479 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 184 ASN A 18 ASN A 27 ASN A 184 ASN C 27 ASN C 184 ASN D 27 ASN E 27 ASN F 27 ASN G 27 ASN G 184 ASN H 27 ASN H 184 ASN I 27 ASN J 27 ASN J 184 ASN K 27 ASN K 184 ASN ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN M 27 ASN M 184 ASN N 27 ASN ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 18 ASN P 27 ASN Q 27 ASN Q 184 ASN R 27 ASN R 184 ASN S 18 ASN S 27 ASN T 18 ASN T 27 ASN V 27 ASN V 184 ASN W 18 ASN ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 184 ASN ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 ASN Y 184 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 42864 Z= 0.215 Angle : 0.647 5.762 57768 Z= 0.355 Chirality : 0.042 0.147 6888 Planarity : 0.003 0.025 7344 Dihedral : 6.478 21.507 5952 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.83 (0.12), residues: 5424 helix: 0.85 (0.10), residues: 2136 sheet: -0.57 (0.14), residues: 1152 loop : 1.23 (0.16), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS S 174 PHE 0.031 0.002 PHE T 154 TYR 0.015 0.002 TYR X 219 ARG 0.005 0.000 ARG F 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 4608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 4.991 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: B 192 MET cc_start: 0.8895 (mmm) cc_final: 0.8667 (mmm) REVERT: B 193 MET cc_start: 0.8971 (ttp) cc_final: 0.8282 (ttt) REVERT: B 204 LEU cc_start: 0.9268 (mt) cc_final: 0.8967 (mt) REVERT: B 226 MET cc_start: 0.9148 (mmt) cc_final: 0.8939 (mmt) REVERT: A 193 MET cc_start: 0.8761 (ttp) cc_final: 0.8007 (ttt) REVERT: A 204 LEU cc_start: 0.9277 (mt) cc_final: 0.8976 (mt) REVERT: A 226 MET cc_start: 0.9180 (mmt) cc_final: 0.8905 (mmt) REVERT: C 31 MET cc_start: 0.9226 (mmp) cc_final: 0.8978 (mmm) REVERT: C 56 MET cc_start: 0.9441 (mmm) cc_final: 0.9083 (mpp) REVERT: D 192 MET cc_start: 0.8964 (mmm) cc_final: 0.8747 (mmm) REVERT: D 193 MET cc_start: 0.8788 (ttp) cc_final: 0.8157 (ttt) REVERT: D 226 MET cc_start: 0.9140 (mmt) cc_final: 0.8752 (mmt) REVERT: E 31 MET cc_start: 0.8933 (mmm) cc_final: 0.8689 (mmm) REVERT: E 184 ASN cc_start: 0.9399 (m-40) cc_final: 0.9121 (m110) REVERT: E 193 MET cc_start: 0.8528 (ttp) cc_final: 0.8164 (ttt) REVERT: E 204 LEU cc_start: 0.9283 (mt) cc_final: 0.9044 (mt) REVERT: E 226 MET cc_start: 0.9195 (mmt) cc_final: 0.8878 (mmt) REVERT: F 68 ARG cc_start: 0.9341 (ttm110) cc_final: 0.9126 (mtm110) REVERT: F 184 ASN cc_start: 0.9645 (m-40) cc_final: 0.9437 (m110) REVERT: F 192 MET cc_start: 0.9023 (mmm) cc_final: 0.8785 (mmm) REVERT: F 193 MET cc_start: 0.8890 (ttp) cc_final: 0.8262 (ttt) REVERT: G 31 MET cc_start: 0.8871 (mmm) cc_final: 0.8663 (mmm) REVERT: G 193 MET cc_start: 0.8470 (ttp) cc_final: 0.8081 (ttt) REVERT: G 204 LEU cc_start: 0.9205 (mt) cc_final: 0.8969 (mt) REVERT: G 226 MET cc_start: 0.9244 (mmt) cc_final: 0.8848 (mmt) REVERT: H 193 MET cc_start: 0.8904 (ttp) cc_final: 0.8445 (ttt) REVERT: H 226 MET cc_start: 0.9068 (mmt) cc_final: 0.8820 (mmt) REVERT: I 5 MET cc_start: 0.9009 (ptm) cc_final: 0.8702 (ppp) REVERT: I 184 ASN cc_start: 0.9616 (m-40) cc_final: 0.9394 (m110) REVERT: I 193 MET cc_start: 0.8974 (ttp) cc_final: 0.8230 (ttt) REVERT: J 192 MET cc_start: 0.8881 (mmm) cc_final: 0.8606 (mmm) REVERT: J 193 MET cc_start: 0.8928 (ttp) cc_final: 0.8296 (ttt) REVERT: J 226 MET cc_start: 0.9133 (mmt) cc_final: 0.8919 (mmt) REVERT: K 158 MET cc_start: 0.9059 (ttp) cc_final: 0.8744 (ttm) REVERT: K 193 MET cc_start: 0.9019 (ttp) cc_final: 0.8528 (ttt) REVERT: L 5 MET cc_start: 0.9051 (ptm) cc_final: 0.8704 (ppp) REVERT: L 46 LEU cc_start: 0.9869 (tp) cc_final: 0.9663 (mt) REVERT: L 56 MET cc_start: 0.9438 (mmm) cc_final: 0.9077 (mpp) REVERT: M 56 MET cc_start: 0.9419 (mmm) cc_final: 0.9072 (mpp) REVERT: M 193 MET cc_start: 0.9137 (ttp) cc_final: 0.8861 (ttt) REVERT: N 184 ASN cc_start: 0.9582 (m-40) cc_final: 0.9351 (m110) REVERT: N 193 MET cc_start: 0.8722 (ttp) cc_final: 0.8436 (ttt) REVERT: N 226 MET cc_start: 0.9203 (mmt) cc_final: 0.8992 (mmt) REVERT: O 184 ASN cc_start: 0.9542 (m-40) cc_final: 0.9297 (m110) REVERT: O 193 MET cc_start: 0.8754 (ttp) cc_final: 0.8317 (ttt) REVERT: P 158 MET cc_start: 0.9057 (ttp) cc_final: 0.8634 (ttm) REVERT: P 193 MET cc_start: 0.8861 (ttp) cc_final: 0.8356 (ttt) REVERT: Q 193 MET cc_start: 0.9121 (ttp) cc_final: 0.8122 (ttt) REVERT: Q 204 LEU cc_start: 0.9334 (mt) cc_final: 0.9068 (mt) REVERT: R 31 MET cc_start: 0.8974 (mmm) cc_final: 0.8745 (mmm) REVERT: R 193 MET cc_start: 0.8417 (ttp) cc_final: 0.8095 (ttt) REVERT: R 204 LEU cc_start: 0.9286 (mt) cc_final: 0.9043 (mt) REVERT: R 226 MET cc_start: 0.9228 (mmt) cc_final: 0.8791 (mmt) REVERT: S 184 ASN cc_start: 0.9440 (m-40) cc_final: 0.9141 (m110) REVERT: S 193 MET cc_start: 0.8710 (ttp) cc_final: 0.8332 (ttt) REVERT: S 204 LEU cc_start: 0.9299 (mt) cc_final: 0.8985 (mt) REVERT: T 31 MET cc_start: 0.8960 (mmm) cc_final: 0.8744 (mmm) REVERT: T 154 PHE cc_start: 0.8960 (m-10) cc_final: 0.8634 (m-10) REVERT: T 184 ASN cc_start: 0.9336 (m-40) cc_final: 0.9073 (m110) REVERT: T 193 MET cc_start: 0.8650 (ttp) cc_final: 0.8073 (ttt) REVERT: T 204 LEU cc_start: 0.9265 (mt) cc_final: 0.9029 (mt) REVERT: V 192 MET cc_start: 0.9026 (mmm) cc_final: 0.8743 (mmm) REVERT: V 193 MET cc_start: 0.8753 (ttp) cc_final: 0.8063 (ttt) REVERT: W 31 MET cc_start: 0.8946 (mmm) cc_final: 0.8702 (mmm) REVERT: W 193 MET cc_start: 0.8670 (ttp) cc_final: 0.8293 (ttt) REVERT: W 204 LEU cc_start: 0.9280 (mt) cc_final: 0.9043 (mt) REVERT: W 226 MET cc_start: 0.9262 (mmt) cc_final: 0.8854 (mmt) REVERT: X 31 MET cc_start: 0.9178 (mmp) cc_final: 0.8975 (mmm) REVERT: X 184 ASN cc_start: 0.9547 (m-40) cc_final: 0.9292 (m110) REVERT: X 192 MET cc_start: 0.8788 (mmm) cc_final: 0.8564 (mmm) REVERT: X 193 MET cc_start: 0.8937 (ttp) cc_final: 0.8205 (ttt) REVERT: Y 192 MET cc_start: 0.8968 (mmm) cc_final: 0.8763 (mmm) REVERT: Y 193 MET cc_start: 0.8805 (ttp) cc_final: 0.8198 (ttt) REVERT: Y 226 MET cc_start: 0.9062 (mmt) cc_final: 0.8757 (mmt) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.4787 time to fit residues: 332.3838 Evaluate side-chains 322 residues out of total 4608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 4.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 399 optimal weight: 4.9990 chunk 326 optimal weight: 0.1980 chunk 132 optimal weight: 20.0000 chunk 480 optimal weight: 6.9990 chunk 518 optimal weight: 9.9990 chunk 427 optimal weight: 2.9990 chunk 476 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 chunk 385 optimal weight: 10.0000 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 18 ASN L 27 ASN O 27 ASN S 18 ASN ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 42864 Z= 0.219 Angle : 0.603 6.485 57768 Z= 0.321 Chirality : 0.041 0.137 6888 Planarity : 0.003 0.019 7344 Dihedral : 5.756 21.501 5952 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.55 (0.12), residues: 5424 helix: 1.64 (0.11), residues: 2136 sheet: -0.22 (0.14), residues: 1104 loop : 1.37 (0.16), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS L 174 PHE 0.016 0.002 PHE Q 154 TYR 0.011 0.001 TYR M 41 ARG 0.003 0.000 ARG F 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 4608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 5.031 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: B 5 MET cc_start: 0.8561 (ppp) cc_final: 0.8343 (ppp) REVERT: B 31 MET cc_start: 0.9273 (mmp) cc_final: 0.9053 (mmm) REVERT: B 193 MET cc_start: 0.8975 (ttp) cc_final: 0.8359 (ttt) REVERT: B 226 MET cc_start: 0.9150 (mmt) cc_final: 0.8930 (mmt) REVERT: A 193 MET cc_start: 0.8891 (ttp) cc_final: 0.8050 (ttt) REVERT: A 204 LEU cc_start: 0.9239 (mt) cc_final: 0.9036 (mt) REVERT: C 31 MET cc_start: 0.9115 (mmp) cc_final: 0.8894 (mmm) REVERT: D 56 MET cc_start: 0.9210 (mpp) cc_final: 0.8956 (mpp) REVERT: D 226 MET cc_start: 0.9107 (mmt) cc_final: 0.8817 (mmt) REVERT: E 184 ASN cc_start: 0.9466 (m-40) cc_final: 0.9220 (m110) REVERT: E 193 MET cc_start: 0.8688 (ttp) cc_final: 0.8241 (ttt) REVERT: E 226 MET cc_start: 0.9233 (mmt) cc_final: 0.8924 (mmt) REVERT: F 31 MET cc_start: 0.9287 (mmp) cc_final: 0.9086 (mmm) REVERT: F 56 MET cc_start: 0.9209 (mpp) cc_final: 0.8975 (mpp) REVERT: F 193 MET cc_start: 0.9047 (ttp) cc_final: 0.8525 (ttt) REVERT: G 193 MET cc_start: 0.8590 (ttp) cc_final: 0.8145 (ttt) REVERT: G 226 MET cc_start: 0.9220 (mmt) cc_final: 0.8872 (mmt) REVERT: H 56 MET cc_start: 0.9249 (mpp) cc_final: 0.9011 (mpp) REVERT: H 193 MET cc_start: 0.9030 (ttp) cc_final: 0.8382 (ttt) REVERT: H 226 MET cc_start: 0.9063 (mmt) cc_final: 0.8827 (mmt) REVERT: I 5 MET cc_start: 0.9112 (ptm) cc_final: 0.8716 (ppp) REVERT: I 56 MET cc_start: 0.9207 (mpp) cc_final: 0.8955 (mpp) REVERT: I 184 ASN cc_start: 0.9639 (m-40) cc_final: 0.9433 (m110) REVERT: I 193 MET cc_start: 0.8983 (ttp) cc_final: 0.8280 (ttt) REVERT: J 31 MET cc_start: 0.9236 (mmp) cc_final: 0.9025 (mmm) REVERT: J 193 MET cc_start: 0.8945 (ttp) cc_final: 0.8362 (ttt) REVERT: J 226 MET cc_start: 0.9022 (mmt) cc_final: 0.8809 (mmt) REVERT: K 193 MET cc_start: 0.9164 (ttp) cc_final: 0.8500 (ttt) REVERT: L 5 MET cc_start: 0.9084 (ptm) cc_final: 0.8784 (ppp) REVERT: L 193 MET cc_start: 0.8523 (ttt) cc_final: 0.7824 (ttt) REVERT: M 193 MET cc_start: 0.9017 (ttp) cc_final: 0.8526 (ttt) REVERT: N 184 ASN cc_start: 0.9589 (m-40) cc_final: 0.9388 (m110) REVERT: N 193 MET cc_start: 0.8975 (ttp) cc_final: 0.8210 (ttt) REVERT: N 226 MET cc_start: 0.9178 (mmt) cc_final: 0.8950 (mmt) REVERT: O 31 MET cc_start: 0.9295 (mmp) cc_final: 0.9067 (mmm) REVERT: O 184 ASN cc_start: 0.9583 (m-40) cc_final: 0.9359 (m110) REVERT: O 193 MET cc_start: 0.9049 (ttp) cc_final: 0.8405 (ttt) REVERT: P 56 MET cc_start: 0.9233 (mpp) cc_final: 0.8991 (mpp) REVERT: P 158 MET cc_start: 0.9136 (ttp) cc_final: 0.8772 (ttm) REVERT: P 193 MET cc_start: 0.9033 (ttp) cc_final: 0.8391 (ttt) REVERT: Q 5 MET cc_start: 0.8721 (ppp) cc_final: 0.8485 (ppp) REVERT: Q 154 PHE cc_start: 0.9102 (m-10) cc_final: 0.8738 (m-10) REVERT: Q 193 MET cc_start: 0.8957 (ttp) cc_final: 0.8105 (ttt) REVERT: R 5 MET cc_start: 0.8553 (ppp) cc_final: 0.8329 (ppp) REVERT: R 193 MET cc_start: 0.8546 (ttp) cc_final: 0.8149 (ttt) REVERT: R 226 MET cc_start: 0.9119 (mmt) cc_final: 0.8725 (mmt) REVERT: S 31 MET cc_start: 0.9272 (mmp) cc_final: 0.9045 (mmm) REVERT: S 184 ASN cc_start: 0.9500 (m-40) cc_final: 0.9233 (m110) REVERT: S 193 MET cc_start: 0.9020 (ttp) cc_final: 0.8199 (ttt) REVERT: S 226 MET cc_start: 0.8958 (mmp) cc_final: 0.8729 (mmp) REVERT: T 154 PHE cc_start: 0.9171 (m-10) cc_final: 0.8799 (m-10) REVERT: T 184 ASN cc_start: 0.9385 (m-40) cc_final: 0.9130 (m110) REVERT: T 193 MET cc_start: 0.8652 (ttp) cc_final: 0.8046 (ttt) REVERT: V 56 MET cc_start: 0.9175 (mpp) cc_final: 0.8933 (mpp) REVERT: V 192 MET cc_start: 0.8926 (mmm) cc_final: 0.8646 (mmm) REVERT: V 193 MET cc_start: 0.8934 (ttp) cc_final: 0.8162 (ttt) REVERT: W 193 MET cc_start: 0.8829 (ttp) cc_final: 0.8390 (ttt) REVERT: W 226 MET cc_start: 0.9250 (mmt) cc_final: 0.8899 (mmt) REVERT: X 184 ASN cc_start: 0.9584 (m-40) cc_final: 0.9355 (m110) REVERT: X 193 MET cc_start: 0.8961 (ttp) cc_final: 0.8333 (ttt) REVERT: Y 56 MET cc_start: 0.9187 (mpp) cc_final: 0.8949 (mpp) REVERT: Y 193 MET cc_start: 0.8781 (ttp) cc_final: 0.8212 (ttt) outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.4691 time to fit residues: 308.6869 Evaluate side-chains 300 residues out of total 4608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 5.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 6.9990 chunk 361 optimal weight: 0.6980 chunk 249 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 229 optimal weight: 0.9990 chunk 322 optimal weight: 20.0000 chunk 482 optimal weight: 9.9990 chunk 510 optimal weight: 9.9990 chunk 251 optimal weight: 5.9990 chunk 456 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 18 ASN K 18 ASN W 18 ASN W 27 ASN X 18 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 42864 Z= 0.209 Angle : 0.580 6.077 57768 Z= 0.311 Chirality : 0.041 0.138 6888 Planarity : 0.003 0.021 7344 Dihedral : 5.345 21.556 5952 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.12), residues: 5424 helix: 1.69 (0.11), residues: 2136 sheet: -0.21 (0.14), residues: 1104 loop : 1.48 (0.16), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS K 174 PHE 0.013 0.002 PHE Q 154 TYR 0.012 0.001 TYR X 41 ARG 0.005 0.000 ARG F 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 4608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 4.868 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: B 193 MET cc_start: 0.8962 (ttp) cc_final: 0.8309 (ttt) REVERT: A 193 MET cc_start: 0.8844 (ttp) cc_final: 0.8641 (tmm) REVERT: D 56 MET cc_start: 0.9354 (mpp) cc_final: 0.9133 (mpp) REVERT: D 192 MET cc_start: 0.8859 (mmp) cc_final: 0.8624 (mmm) REVERT: D 193 MET cc_start: 0.8293 (ttt) cc_final: 0.7128 (ttt) REVERT: D 226 MET cc_start: 0.9114 (mmt) cc_final: 0.8787 (mpp) REVERT: E 184 ASN cc_start: 0.9535 (m-40) cc_final: 0.9301 (m110) REVERT: E 193 MET cc_start: 0.8759 (ttp) cc_final: 0.7998 (ttt) REVERT: E 226 MET cc_start: 0.9169 (mmt) cc_final: 0.8887 (mmt) REVERT: F 56 MET cc_start: 0.9331 (mpp) cc_final: 0.9114 (mpp) REVERT: F 193 MET cc_start: 0.9242 (ttp) cc_final: 0.8606 (ttt) REVERT: G 226 MET cc_start: 0.9200 (mmt) cc_final: 0.8917 (mmt) REVERT: H 192 MET cc_start: 0.8454 (mmm) cc_final: 0.8217 (mmm) REVERT: I 5 MET cc_start: 0.9162 (ptm) cc_final: 0.8841 (ppp) REVERT: I 56 MET cc_start: 0.9342 (mpp) cc_final: 0.9142 (mpp) REVERT: I 192 MET cc_start: 0.8467 (mmm) cc_final: 0.8211 (mmm) REVERT: J 193 MET cc_start: 0.9041 (ttp) cc_final: 0.8312 (ttt) REVERT: J 226 MET cc_start: 0.9139 (mmt) cc_final: 0.8888 (mmt) REVERT: K 193 MET cc_start: 0.9129 (ttp) cc_final: 0.8679 (ttt) REVERT: L 5 MET cc_start: 0.9220 (ptm) cc_final: 0.8891 (ppp) REVERT: L 193 MET cc_start: 0.8450 (ttt) cc_final: 0.7634 (ttt) REVERT: M 46 LEU cc_start: 0.9873 (tp) cc_final: 0.9658 (mt) REVERT: N 192 MET cc_start: 0.9146 (mmm) cc_final: 0.8915 (mmm) REVERT: N 193 MET cc_start: 0.8723 (ttp) cc_final: 0.7976 (ttt) REVERT: O 31 MET cc_start: 0.9272 (mmp) cc_final: 0.9041 (mmm) REVERT: O 193 MET cc_start: 0.9038 (ttp) cc_final: 0.8481 (tmm) REVERT: P 158 MET cc_start: 0.8997 (ttp) cc_final: 0.8748 (ttm) REVERT: Q 5 MET cc_start: 0.8737 (ppp) cc_final: 0.8527 (ppp) REVERT: Q 184 ASN cc_start: 0.9522 (m-40) cc_final: 0.9318 (m110) REVERT: Q 193 MET cc_start: 0.8731 (ttp) cc_final: 0.8504 (tmm) REVERT: R 193 MET cc_start: 0.8681 (ttp) cc_final: 0.8030 (ttt) REVERT: R 226 MET cc_start: 0.9079 (mmt) cc_final: 0.8714 (mpp) REVERT: S 31 MET cc_start: 0.9187 (mmp) cc_final: 0.8965 (mmm) REVERT: S 184 ASN cc_start: 0.9553 (m-40) cc_final: 0.9327 (m110) REVERT: S 193 MET cc_start: 0.8815 (ttp) cc_final: 0.8113 (ttt) REVERT: T 154 PHE cc_start: 0.9314 (m-10) cc_final: 0.8961 (m-10) REVERT: T 184 ASN cc_start: 0.9478 (m-40) cc_final: 0.9258 (m110) REVERT: T 193 MET cc_start: 0.8731 (ttp) cc_final: 0.8502 (tmm) REVERT: V 31 MET cc_start: 0.9244 (mmp) cc_final: 0.9029 (mmm) REVERT: V 192 MET cc_start: 0.8957 (mmm) cc_final: 0.8642 (mmm) REVERT: V 193 MET cc_start: 0.8930 (ttp) cc_final: 0.8143 (ttt) REVERT: W 193 MET cc_start: 0.8891 (ttp) cc_final: 0.8549 (tmm) REVERT: W 226 MET cc_start: 0.9193 (mmt) cc_final: 0.8867 (mmt) REVERT: X 184 ASN cc_start: 0.9579 (m-40) cc_final: 0.9367 (m110) REVERT: X 193 MET cc_start: 0.9131 (ttp) cc_final: 0.8430 (ttt) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.4768 time to fit residues: 298.3749 Evaluate side-chains 303 residues out of total 4608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 4.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 20.0000 chunk 289 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 380 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 435 optimal weight: 8.9990 chunk 352 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 260 optimal weight: 6.9990 chunk 458 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN I 27 ASN K 18 ASN S 18 ASN X 18 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 42864 Z= 0.176 Angle : 0.537 7.602 57768 Z= 0.286 Chirality : 0.040 0.141 6888 Planarity : 0.003 0.024 7344 Dihedral : 5.004 22.720 5952 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.80 (0.12), residues: 5424 helix: 1.90 (0.11), residues: 2136 sheet: -0.25 (0.14), residues: 1104 loop : 1.54 (0.16), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS I 174 PHE 0.008 0.001 PHE T 26 TYR 0.018 0.001 TYR Q 219 ARG 0.002 0.000 ARG F 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 4608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 5.283 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: B 193 MET cc_start: 0.8935 (ttp) cc_final: 0.8302 (ttt) REVERT: A 193 MET cc_start: 0.8815 (ttp) cc_final: 0.8607 (tmm) REVERT: C 46 LEU cc_start: 0.9873 (tp) cc_final: 0.9667 (mt) REVERT: C 193 MET cc_start: 0.8843 (tmm) cc_final: 0.7777 (tmm) REVERT: D 193 MET cc_start: 0.8381 (ttt) cc_final: 0.7293 (ttt) REVERT: D 226 MET cc_start: 0.9106 (mmt) cc_final: 0.8841 (mmt) REVERT: E 193 MET cc_start: 0.8795 (ttp) cc_final: 0.8552 (tmm) REVERT: E 226 MET cc_start: 0.9152 (mmt) cc_final: 0.8824 (mmt) REVERT: F 192 MET cc_start: 0.8383 (mmm) cc_final: 0.8161 (mmm) REVERT: F 193 MET cc_start: 0.8733 (ttp) cc_final: 0.8094 (ttt) REVERT: G 193 MET cc_start: 0.8106 (tmm) cc_final: 0.7678 (tmm) REVERT: H 192 MET cc_start: 0.8618 (mmm) cc_final: 0.8396 (mmm) REVERT: I 192 MET cc_start: 0.8613 (mmm) cc_final: 0.8363 (mmm) REVERT: J 28 GLU cc_start: 0.9006 (pp20) cc_final: 0.8798 (pm20) REVERT: J 192 MET cc_start: 0.8082 (mmm) cc_final: 0.7853 (mmm) REVERT: J 193 MET cc_start: 0.8969 (ttp) cc_final: 0.8313 (ttt) REVERT: K 192 MET cc_start: 0.8462 (mmm) cc_final: 0.8220 (mmm) REVERT: K 193 MET cc_start: 0.9151 (ttp) cc_final: 0.8694 (ttt) REVERT: L 5 MET cc_start: 0.9185 (ptm) cc_final: 0.8869 (ppp) REVERT: L 193 MET cc_start: 0.8450 (ttt) cc_final: 0.7447 (ttt) REVERT: M 46 LEU cc_start: 0.9880 (tp) cc_final: 0.9676 (mp) REVERT: M 193 MET cc_start: 0.8675 (tmm) cc_final: 0.8442 (tmm) REVERT: N 192 MET cc_start: 0.9103 (mmm) cc_final: 0.8859 (mmm) REVERT: N 193 MET cc_start: 0.8581 (ttp) cc_final: 0.7905 (ttt) REVERT: O 31 MET cc_start: 0.9254 (mmp) cc_final: 0.9007 (mmm) REVERT: O 193 MET cc_start: 0.8745 (ttp) cc_final: 0.8336 (tmm) REVERT: P 158 MET cc_start: 0.8980 (ttp) cc_final: 0.8746 (ttm) REVERT: P 192 MET cc_start: 0.8502 (mmm) cc_final: 0.8276 (mmm) REVERT: Q 5 MET cc_start: 0.8736 (ppp) cc_final: 0.8527 (ppp) REVERT: Q 154 PHE cc_start: 0.9117 (m-10) cc_final: 0.8827 (m-10) REVERT: Q 226 MET cc_start: 0.9070 (mmp) cc_final: 0.8809 (mmp) REVERT: R 226 MET cc_start: 0.9018 (mmt) cc_final: 0.8788 (mmt) REVERT: S 184 ASN cc_start: 0.9572 (m-40) cc_final: 0.9365 (m110) REVERT: S 193 MET cc_start: 0.9055 (ttp) cc_final: 0.8605 (tmm) REVERT: T 184 ASN cc_start: 0.9505 (m-40) cc_final: 0.9299 (m110) REVERT: T 193 MET cc_start: 0.8712 (ttp) cc_final: 0.8474 (tmm) REVERT: W 28 GLU cc_start: 0.8805 (pp20) cc_final: 0.8597 (pp20) REVERT: W 193 MET cc_start: 0.8923 (ttp) cc_final: 0.8660 (tmm) REVERT: W 226 MET cc_start: 0.9198 (mmt) cc_final: 0.8968 (mmt) REVERT: X 184 ASN cc_start: 0.9618 (m-40) cc_final: 0.9411 (m110) REVERT: X 192 MET cc_start: 0.8118 (mmm) cc_final: 0.7874 (mmm) REVERT: X 193 MET cc_start: 0.8984 (ttp) cc_final: 0.8379 (ttt) REVERT: Y 192 MET cc_start: 0.8544 (mmm) cc_final: 0.8231 (mmm) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.4718 time to fit residues: 320.8271 Evaluate side-chains 315 residues out of total 4608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 4.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 0.9990 chunk 459 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 299 optimal weight: 0.0670 chunk 125 optimal weight: 9.9990 chunk 510 optimal weight: 0.0470 chunk 424 optimal weight: 3.9990 chunk 236 optimal weight: 9.9990 chunk 42 optimal weight: 0.5980 chunk 168 optimal weight: 10.0000 chunk 268 optimal weight: 3.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN I 27 ASN J 18 ASN S 18 ASN W 18 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 42864 Z= 0.120 Angle : 0.520 8.490 57768 Z= 0.275 Chirality : 0.041 0.139 6888 Planarity : 0.003 0.023 7344 Dihedral : 4.635 21.340 5952 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.12), residues: 5424 helix: 2.09 (0.11), residues: 2136 sheet: -0.12 (0.14), residues: 1104 loop : 1.67 (0.16), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS R 174 PHE 0.006 0.001 PHE X 59 TYR 0.017 0.001 TYR C 88 ARG 0.002 0.000 ARG W 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 4608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 451 time to evaluate : 4.856 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: A 192 MET cc_start: 0.8622 (mmm) cc_final: 0.8401 (mmm) REVERT: A 193 MET cc_start: 0.8783 (ttp) cc_final: 0.8545 (tmm) REVERT: A 195 LEU cc_start: 0.9602 (mt) cc_final: 0.9019 (mt) REVERT: C 226 MET cc_start: 0.8844 (mpp) cc_final: 0.8581 (mmt) REVERT: D 193 MET cc_start: 0.8122 (ttt) cc_final: 0.7085 (ttt) REVERT: D 226 MET cc_start: 0.9091 (mmt) cc_final: 0.8881 (mmt) REVERT: E 195 LEU cc_start: 0.9573 (mt) cc_final: 0.9294 (mp) REVERT: F 194 TYR cc_start: 0.8587 (m-10) cc_final: 0.8241 (m-10) REVERT: F 226 MET cc_start: 0.9196 (mpp) cc_final: 0.8990 (mmt) REVERT: I 158 MET cc_start: 0.9220 (ptm) cc_final: 0.9019 (tmm) REVERT: J 26 PHE cc_start: 0.8941 (m-80) cc_final: 0.8612 (m-80) REVERT: J 195 LEU cc_start: 0.9688 (mt) cc_final: 0.8940 (mt) REVERT: K 193 MET cc_start: 0.9015 (ttp) cc_final: 0.8724 (ttt) REVERT: K 194 TYR cc_start: 0.8572 (m-10) cc_final: 0.8245 (m-10) REVERT: L 192 MET cc_start: 0.8947 (mmp) cc_final: 0.8741 (mmm) REVERT: L 193 MET cc_start: 0.8466 (ttt) cc_final: 0.7310 (ttt) REVERT: M 26 PHE cc_start: 0.8864 (m-80) cc_final: 0.8537 (m-80) REVERT: M 46 LEU cc_start: 0.9882 (tp) cc_final: 0.9681 (mp) REVERT: N 158 MET cc_start: 0.8902 (ttm) cc_final: 0.8509 (ttm) REVERT: N 184 ASN cc_start: 0.9692 (m-40) cc_final: 0.9491 (m110) REVERT: N 193 MET cc_start: 0.8403 (ttp) cc_final: 0.8123 (ttt) REVERT: O 31 MET cc_start: 0.9261 (mmp) cc_final: 0.8998 (mmm) REVERT: O 184 ASN cc_start: 0.9685 (m-40) cc_final: 0.9481 (m-40) REVERT: O 195 LEU cc_start: 0.9572 (mt) cc_final: 0.8852 (mt) REVERT: Q 5 MET cc_start: 0.8716 (ppp) cc_final: 0.8499 (ppp) REVERT: Q 154 PHE cc_start: 0.9099 (m-10) cc_final: 0.8787 (m-10) REVERT: R 26 PHE cc_start: 0.8552 (m-80) cc_final: 0.7873 (m-80) REVERT: S 31 MET cc_start: 0.9123 (mmp) cc_final: 0.8914 (mmm) REVERT: S 192 MET cc_start: 0.9265 (mmm) cc_final: 0.8843 (mmm) REVERT: S 193 MET cc_start: 0.8885 (ttp) cc_final: 0.8599 (tmm) REVERT: S 195 LEU cc_start: 0.9627 (mt) cc_final: 0.8997 (mt) REVERT: T 154 PHE cc_start: 0.9387 (m-10) cc_final: 0.9031 (m-10) REVERT: T 195 LEU cc_start: 0.9575 (mt) cc_final: 0.9295 (mp) REVERT: V 26 PHE cc_start: 0.8964 (m-80) cc_final: 0.8593 (m-80) REVERT: V 158 MET cc_start: 0.8826 (ttm) cc_final: 0.8608 (ttt) REVERT: W 193 MET cc_start: 0.8606 (ttp) cc_final: 0.8274 (tmm) REVERT: W 195 LEU cc_start: 0.9582 (mt) cc_final: 0.8906 (mt) REVERT: X 26 PHE cc_start: 0.8800 (m-80) cc_final: 0.8513 (m-80) REVERT: X 158 MET cc_start: 0.9444 (ptm) cc_final: 0.9096 (ptm) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.4709 time to fit residues: 369.4899 Evaluate side-chains 339 residues out of total 4608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 4.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 3.9990 chunk 57 optimal weight: 0.0070 chunk 291 optimal weight: 6.9990 chunk 373 optimal weight: 8.9990 chunk 289 optimal weight: 6.9990 chunk 430 optimal weight: 5.9990 chunk 285 optimal weight: 9.9990 chunk 508 optimal weight: 6.9990 chunk 318 optimal weight: 6.9990 chunk 310 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 overall best weight: 4.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 ASN G 18 ASN H 201 HIS I 201 HIS J 18 ASN P 201 HIS Q 18 ASN R 18 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 42864 Z= 0.259 Angle : 0.611 14.165 57768 Z= 0.319 Chirality : 0.041 0.138 6888 Planarity : 0.004 0.026 7344 Dihedral : 4.946 23.326 5952 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.74 (0.12), residues: 5424 helix: 1.80 (0.11), residues: 2136 sheet: -0.31 (0.14), residues: 1104 loop : 1.59 (0.16), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS O 174 PHE 0.017 0.002 PHE C 26 TYR 0.021 0.002 TYR Q 194 ARG 0.003 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 4608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 5.205 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: B 193 MET cc_start: 0.8760 (tmm) cc_final: 0.8512 (tmm) REVERT: D 193 MET cc_start: 0.8609 (ttt) cc_final: 0.7751 (tmm) REVERT: H 193 MET cc_start: 0.8460 (tmm) cc_final: 0.7303 (tmm) REVERT: I 193 MET cc_start: 0.8456 (tmm) cc_final: 0.7286 (tmm) REVERT: J 158 MET cc_start: 0.9408 (ptm) cc_final: 0.9013 (ptm) REVERT: K 193 MET cc_start: 0.9127 (ttp) cc_final: 0.8837 (ttt) REVERT: M 26 PHE cc_start: 0.8752 (m-80) cc_final: 0.8154 (m-80) REVERT: M 192 MET cc_start: 0.8976 (mmp) cc_final: 0.8752 (mmm) REVERT: M 226 MET cc_start: 0.8581 (mpp) cc_final: 0.8319 (mpp) REVERT: N 193 MET cc_start: 0.8997 (ttp) cc_final: 0.8313 (ttt) REVERT: O 31 MET cc_start: 0.9232 (mmp) cc_final: 0.8991 (mmm) REVERT: O 193 MET cc_start: 0.8399 (tmm) cc_final: 0.8031 (tmm) REVERT: P 193 MET cc_start: 0.8411 (tmm) cc_final: 0.7222 (tmm) REVERT: P 226 MET cc_start: 0.8640 (mpp) cc_final: 0.8392 (mpp) REVERT: Q 5 MET cc_start: 0.8755 (ppp) cc_final: 0.8489 (ppp) REVERT: Q 226 MET cc_start: 0.9092 (mmp) cc_final: 0.8736 (mmp) REVERT: R 192 MET cc_start: 0.8216 (mmm) cc_final: 0.7996 (mmm) REVERT: R 226 MET cc_start: 0.8789 (mpp) cc_final: 0.8391 (mpp) REVERT: S 31 MET cc_start: 0.9177 (mmp) cc_final: 0.8917 (mmm) REVERT: S 193 MET cc_start: 0.8906 (ttp) cc_final: 0.8582 (tmm) REVERT: V 158 MET cc_start: 0.8912 (ttm) cc_final: 0.8362 (ttm) REVERT: V 192 MET cc_start: 0.8567 (mmm) cc_final: 0.8325 (mmm) REVERT: W 28 GLU cc_start: 0.8640 (pp20) cc_final: 0.8063 (pm20) REVERT: W 193 MET cc_start: 0.8934 (ttp) cc_final: 0.8208 (ttt) REVERT: X 158 MET cc_start: 0.9478 (ptm) cc_final: 0.8882 (tmm) REVERT: Y 193 MET cc_start: 0.8352 (tmm) cc_final: 0.7253 (tmm) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.4751 time to fit residues: 281.7947 Evaluate side-chains 300 residues out of total 4608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 4.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 20.0000 chunk 203 optimal weight: 5.9990 chunk 303 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 323 optimal weight: 9.9990 chunk 346 optimal weight: 20.0000 chunk 251 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 400 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 201 HIS K 18 ASN K 201 HIS L 201 HIS M 201 HIS N 201 HIS O 201 HIS S 201 HIS V 201 HIS W 18 ASN Y 201 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 42864 Z= 0.212 Angle : 0.580 13.644 57768 Z= 0.302 Chirality : 0.041 0.178 6888 Planarity : 0.003 0.027 7344 Dihedral : 4.855 22.281 5952 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.12), residues: 5424 helix: 1.78 (0.11), residues: 2136 sheet: -0.33 (0.14), residues: 1104 loop : 1.66 (0.16), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS W 174 PHE 0.019 0.002 PHE Q 154 TYR 0.018 0.001 TYR A 194 ARG 0.003 0.000 ARG D 224 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 4608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 4.872 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: A 26 PHE cc_start: 0.8787 (m-80) cc_final: 0.8391 (m-80) REVERT: A 192 MET cc_start: 0.8152 (mmm) cc_final: 0.7759 (mmm) REVERT: A 203 LEU cc_start: 0.9269 (tt) cc_final: 0.9031 (mm) REVERT: D 158 MET cc_start: 0.9384 (ptm) cc_final: 0.8807 (tmm) REVERT: D 192 MET cc_start: 0.8156 (mmm) cc_final: 0.7929 (mmm) REVERT: D 193 MET cc_start: 0.8548 (ttt) cc_final: 0.7820 (tmm) REVERT: D 226 MET cc_start: 0.8862 (mpp) cc_final: 0.8578 (mpp) REVERT: F 192 MET cc_start: 0.8222 (mmm) cc_final: 0.7892 (mmm) REVERT: H 193 MET cc_start: 0.8460 (tmm) cc_final: 0.7309 (tmm) REVERT: I 158 MET cc_start: 0.9382 (ptm) cc_final: 0.8820 (tmm) REVERT: I 192 MET cc_start: 0.8571 (mmm) cc_final: 0.8260 (mmm) REVERT: I 193 MET cc_start: 0.8513 (tmm) cc_final: 0.7290 (tmm) REVERT: J 158 MET cc_start: 0.9383 (ptm) cc_final: 0.8991 (ptm) REVERT: K 193 MET cc_start: 0.9224 (ttp) cc_final: 0.8980 (ttt) REVERT: L 193 MET cc_start: 0.7867 (ttt) cc_final: 0.7547 (ttt) REVERT: M 26 PHE cc_start: 0.8770 (m-80) cc_final: 0.8183 (m-80) REVERT: M 226 MET cc_start: 0.8674 (mpp) cc_final: 0.8390 (mpp) REVERT: N 192 MET cc_start: 0.8032 (mmm) cc_final: 0.7801 (mmm) REVERT: N 193 MET cc_start: 0.9077 (ttp) cc_final: 0.8825 (tmm) REVERT: O 31 MET cc_start: 0.9218 (mmp) cc_final: 0.8986 (mmm) REVERT: O 193 MET cc_start: 0.8470 (tmm) cc_final: 0.8244 (tmm) REVERT: P 193 MET cc_start: 0.8426 (tmm) cc_final: 0.7251 (tmm) REVERT: Q 5 MET cc_start: 0.8743 (ppp) cc_final: 0.8477 (ppp) REVERT: Q 226 MET cc_start: 0.9060 (mmp) cc_final: 0.8736 (mmp) REVERT: R 26 PHE cc_start: 0.8623 (m-80) cc_final: 0.7755 (m-80) REVERT: S 31 MET cc_start: 0.9173 (mmp) cc_final: 0.8935 (mmm) REVERT: S 193 MET cc_start: 0.8938 (ttp) cc_final: 0.8627 (tmm) REVERT: T 26 PHE cc_start: 0.8334 (m-80) cc_final: 0.7676 (m-80) REVERT: V 158 MET cc_start: 0.8961 (ttm) cc_final: 0.8394 (ttm) REVERT: V 192 MET cc_start: 0.8603 (mmm) cc_final: 0.8329 (mmm) REVERT: W 31 MET cc_start: 0.9168 (mmp) cc_final: 0.8943 (mmm) REVERT: W 192 MET cc_start: 0.8757 (mmm) cc_final: 0.7923 (mmm) REVERT: W 193 MET cc_start: 0.8986 (ttp) cc_final: 0.8595 (tmm) REVERT: X 192 MET cc_start: 0.8949 (mmp) cc_final: 0.8730 (mmm) REVERT: Y 158 MET cc_start: 0.8549 (mmp) cc_final: 0.8281 (mmm) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.4742 time to fit residues: 283.0302 Evaluate side-chains 300 residues out of total 4608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 5.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 4.9990 chunk 487 optimal weight: 3.9990 chunk 444 optimal weight: 3.9990 chunk 474 optimal weight: 3.9990 chunk 285 optimal weight: 5.9990 chunk 206 optimal weight: 9.9990 chunk 372 optimal weight: 0.2980 chunk 145 optimal weight: 8.9990 chunk 428 optimal weight: 0.8980 chunk 448 optimal weight: 6.9990 chunk 472 optimal weight: 9.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 HIS K 18 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 42864 Z= 0.175 Angle : 0.553 9.078 57768 Z= 0.291 Chirality : 0.041 0.160 6888 Planarity : 0.003 0.028 7344 Dihedral : 4.738 21.886 5952 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.80 (0.12), residues: 5424 helix: 1.85 (0.11), residues: 2136 sheet: -0.35 (0.14), residues: 1056 loop : 1.63 (0.16), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS W 174 PHE 0.019 0.001 PHE Q 154 TYR 0.011 0.001 TYR O 88 ARG 0.002 0.000 ARG I 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 4608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 5.056 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: B 26 PHE cc_start: 0.8764 (m-10) cc_final: 0.8453 (m-80) REVERT: B 141 MET cc_start: 0.8835 (tpp) cc_final: 0.8306 (tpp) REVERT: A 26 PHE cc_start: 0.8755 (m-80) cc_final: 0.8380 (m-80) REVERT: A 192 MET cc_start: 0.8277 (mmm) cc_final: 0.8034 (mmm) REVERT: D 192 MET cc_start: 0.8242 (mmm) cc_final: 0.8012 (mmm) REVERT: E 158 MET cc_start: 0.9502 (ppp) cc_final: 0.8897 (ppp) REVERT: F 192 MET cc_start: 0.8221 (mmm) cc_final: 0.7926 (mmm) REVERT: H 193 MET cc_start: 0.8463 (tmm) cc_final: 0.7254 (tmm) REVERT: I 192 MET cc_start: 0.8552 (mmm) cc_final: 0.8326 (mmm) REVERT: I 193 MET cc_start: 0.8525 (tmm) cc_final: 0.7464 (tmm) REVERT: J 141 MET cc_start: 0.8804 (tpp) cc_final: 0.8342 (tpp) REVERT: J 194 TYR cc_start: 0.8812 (m-10) cc_final: 0.8606 (m-10) REVERT: L 193 MET cc_start: 0.7824 (ttt) cc_final: 0.7475 (ttt) REVERT: M 26 PHE cc_start: 0.8896 (m-80) cc_final: 0.8398 (m-80) REVERT: O 31 MET cc_start: 0.9213 (mmp) cc_final: 0.8986 (mmm) REVERT: P 193 MET cc_start: 0.8407 (tmm) cc_final: 0.7157 (tmm) REVERT: Q 5 MET cc_start: 0.8746 (ppp) cc_final: 0.8480 (ppp) REVERT: Q 226 MET cc_start: 0.9047 (mmp) cc_final: 0.8722 (mmp) REVERT: S 28 GLU cc_start: 0.9156 (pp20) cc_final: 0.8893 (pm20) REVERT: S 158 MET cc_start: 0.9545 (ppp) cc_final: 0.9038 (ppp) REVERT: S 193 MET cc_start: 0.8863 (ttp) cc_final: 0.8488 (tmm) REVERT: V 158 MET cc_start: 0.8803 (ttm) cc_final: 0.8244 (ttm) REVERT: V 192 MET cc_start: 0.8623 (mmm) cc_final: 0.8373 (mmm) REVERT: W 192 MET cc_start: 0.8681 (mmm) cc_final: 0.8231 (mmm) REVERT: W 193 MET cc_start: 0.8995 (ttp) cc_final: 0.8610 (tmm) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.4749 time to fit residues: 288.9067 Evaluate side-chains 301 residues out of total 4608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 4.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 6.9990 chunk 501 optimal weight: 9.9990 chunk 306 optimal weight: 0.7980 chunk 237 optimal weight: 0.1980 chunk 348 optimal weight: 0.9990 chunk 526 optimal weight: 0.1980 chunk 484 optimal weight: 0.9980 chunk 418 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 323 optimal weight: 4.9990 chunk 256 optimal weight: 9.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 27 ASN R 201 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 42864 Z= 0.129 Angle : 0.558 16.326 57768 Z= 0.286 Chirality : 0.042 0.232 6888 Planarity : 0.003 0.029 7344 Dihedral : 4.523 20.845 5952 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.12), residues: 5424 helix: 2.10 (0.11), residues: 2136 sheet: -0.28 (0.14), residues: 1056 loop : 1.71 (0.16), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 174 PHE 0.011 0.001 PHE A 26 TYR 0.030 0.001 TYR Q 194 ARG 0.004 0.000 ARG X 6 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 4608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 4.762 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: B 141 MET cc_start: 0.8823 (tpp) cc_final: 0.8268 (tpp) REVERT: A 26 PHE cc_start: 0.8713 (m-80) cc_final: 0.7998 (m-80) REVERT: A 203 LEU cc_start: 0.9222 (tt) cc_final: 0.8959 (mm) REVERT: C 226 MET cc_start: 0.8868 (mpp) cc_final: 0.8548 (mmt) REVERT: E 158 MET cc_start: 0.9466 (ppp) cc_final: 0.8959 (ppp) REVERT: G 26 PHE cc_start: 0.8930 (m-80) cc_final: 0.7245 (m-80) REVERT: H 193 MET cc_start: 0.8474 (tmm) cc_final: 0.6925 (tmm) REVERT: I 193 MET cc_start: 0.8398 (tmm) cc_final: 0.7800 (tmm) REVERT: I 226 MET cc_start: 0.8934 (mpp) cc_final: 0.8663 (mmt) REVERT: J 141 MET cc_start: 0.8789 (tpp) cc_final: 0.8295 (tpp) REVERT: J 194 TYR cc_start: 0.8768 (m-10) cc_final: 0.8526 (m-10) REVERT: L 193 MET cc_start: 0.7830 (ttt) cc_final: 0.7446 (ttt) REVERT: M 26 PHE cc_start: 0.8937 (m-80) cc_final: 0.8361 (m-80) REVERT: M 158 MET cc_start: 0.8744 (mmm) cc_final: 0.8507 (mmm) REVERT: O 31 MET cc_start: 0.9236 (mmp) cc_final: 0.9023 (mmm) REVERT: P 26 PHE cc_start: 0.8867 (m-80) cc_final: 0.8504 (m-80) REVERT: P 193 MET cc_start: 0.8429 (tmm) cc_final: 0.6782 (tmm) REVERT: Q 5 MET cc_start: 0.8738 (ppp) cc_final: 0.8450 (ppp) REVERT: Q 26 PHE cc_start: 0.8605 (m-80) cc_final: 0.8403 (m-80) REVERT: Q 226 MET cc_start: 0.9065 (mmp) cc_final: 0.8756 (mmp) REVERT: R 193 MET cc_start: 0.8993 (tmm) cc_final: 0.7612 (tmm) REVERT: S 158 MET cc_start: 0.9475 (ppp) cc_final: 0.9079 (ppp) REVERT: S 193 MET cc_start: 0.8927 (ttp) cc_final: 0.8565 (tmm) REVERT: T 26 PHE cc_start: 0.8460 (m-80) cc_final: 0.7808 (m-80) REVERT: T 78 GLU cc_start: 0.9236 (mt-10) cc_final: 0.9019 (mp0) REVERT: V 26 PHE cc_start: 0.8880 (m-80) cc_final: 0.8637 (m-80) REVERT: V 192 MET cc_start: 0.8541 (mmm) cc_final: 0.8300 (mmm) REVERT: W 192 MET cc_start: 0.8592 (mmm) cc_final: 0.8147 (mmm) REVERT: W 193 MET cc_start: 0.9039 (ttp) cc_final: 0.8653 (tmm) REVERT: X 158 MET cc_start: 0.9320 (ptm) cc_final: 0.9035 (ttp) REVERT: X 203 LEU cc_start: 0.9181 (tt) cc_final: 0.8776 (mm) REVERT: Y 192 MET cc_start: 0.7883 (mmm) cc_final: 0.7576 (mmm) REVERT: Y 193 MET cc_start: 0.9001 (tmm) cc_final: 0.7184 (tmm) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.5204 time to fit residues: 337.5226 Evaluate side-chains 308 residues out of total 4608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 5.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 0.9990 chunk 446 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 386 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 116 optimal weight: 0.9990 chunk 419 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 430 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.041060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.032599 restraints weight = 305657.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.033674 restraints weight = 190227.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.034453 restraints weight = 134929.301| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 42864 Z= 0.130 Angle : 0.541 15.245 57768 Z= 0.279 Chirality : 0.042 0.157 6888 Planarity : 0.003 0.035 7344 Dihedral : 4.453 24.351 5952 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.12), residues: 5424 helix: 2.30 (0.11), residues: 2136 sheet: -0.53 (0.13), residues: 1152 loop : 2.07 (0.17), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS N 174 PHE 0.027 0.001 PHE K 26 TYR 0.028 0.001 TYR Q 194 ARG 0.002 0.000 ARG W 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7133.16 seconds wall clock time: 133 minutes 13.05 seconds (7993.05 seconds total)