Starting phenix.real_space_refine on Fri Mar 22 22:56:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioj_35620/03_2024/8ioj_35620_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioj_35620/03_2024/8ioj_35620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioj_35620/03_2024/8ioj_35620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioj_35620/03_2024/8ioj_35620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioj_35620/03_2024/8ioj_35620_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioj_35620/03_2024/8ioj_35620_neut.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 150 5.16 5 C 22132 2.51 5 N 6122 2.21 5 O 6392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 30": "OD1" <-> "OD2" Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 265": "OD1" <-> "OD2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 299": "OD1" <-> "OD2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 394": "OD1" <-> "OD2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 30": "OD1" <-> "OD2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "C TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 245": "OE1" <-> "OE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 265": "OD1" <-> "OD2" Residue "C PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 349": "OD1" <-> "OD2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C GLU 430": "OE1" <-> "OE2" Residue "C ASP 440": "OD1" <-> "OD2" Residue "D TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 30": "OD1" <-> "OD2" Residue "D PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 75": "OD1" <-> "OD2" Residue "D TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 213": "OD1" <-> "OD2" Residue "D TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "E PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 214": "OD1" <-> "OD2" Residue "E TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 83": "OD1" <-> "OD2" Residue "F TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 111": "OD1" <-> "OD2" Residue "F PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 156": "OD1" <-> "OD2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "F ASP 193": "OD1" <-> "OD2" Residue "G TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 111": "OD1" <-> "OD2" Residue "G ASP 140": "OD1" <-> "OD2" Residue "G ASP 156": "OD1" <-> "OD2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 232": "OE1" <-> "OE2" Residue "H ASP 30": "OD1" <-> "OD2" Residue "H PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 265": "OD1" <-> "OD2" Residue "H PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 299": "OD1" <-> "OD2" Residue "H PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 394": "OD1" <-> "OD2" Residue "H PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 30": "OD1" <-> "OD2" Residue "I PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "I TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 106": "OE1" <-> "OE2" Residue "I PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 157": "OD1" <-> "OD2" Residue "I TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 195": "OD1" <-> "OD2" Residue "I PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 212": "NH1" <-> "NH2" Residue "I PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 106": "OE1" <-> "OE2" Residue "J PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 188": "OE1" <-> "OE2" Residue "J PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 245": "OE1" <-> "OE2" Residue "J PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 265": "OD1" <-> "OD2" Residue "J PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 349": "OD1" <-> "OD2" Residue "J PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 364": "OD1" <-> "OD2" Residue "J GLU 430": "OE1" <-> "OE2" Residue "J ASP 440": "OD1" <-> "OD2" Residue "K TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 30": "OD1" <-> "OD2" Residue "K PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 75": "OD1" <-> "OD2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 213": "OD1" <-> "OD2" Residue "K TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 325": "OE1" <-> "OE2" Residue "L ASP 331": "OD1" <-> "OD2" Residue "L PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 367": "OD1" <-> "OD2" Residue "L ASP 375": "OD1" <-> "OD2" Residue "L GLU 379": "OE1" <-> "OE2" Residue "L ARG 387": "NH1" <-> "NH2" Residue "L GLU 393": "OE1" <-> "OE2" Residue "L ASP 395": "OD1" <-> "OD2" Residue "L ASP 396": "OD1" <-> "OD2" Residue "L TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 414": "OD1" <-> "OD2" Residue "L GLU 419": "OE1" <-> "OE2" Residue "L GLU 422": "OE1" <-> "OE2" Residue "L ASP 437": "OD1" <-> "OD2" Residue "M GLU 297": "OE1" <-> "OE2" Residue "M GLU 313": "OE1" <-> "OE2" Residue "M GLU 314": "OE1" <-> "OE2" Residue "M ASP 331": "OD1" <-> "OD2" Residue "M PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 336": "OE1" <-> "OE2" Residue "M ARG 343": "NH1" <-> "NH2" Residue "M ARG 366": "NH1" <-> "NH2" Residue "M ASP 375": "OD1" <-> "OD2" Residue "M GLU 378": "OE1" <-> "OE2" Residue "M ARG 387": "NH1" <-> "NH2" Residue "M TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 435": "NH1" <-> "NH2" Residue "N GLU 325": "OE1" <-> "OE2" Residue "N ASP 331": "OD1" <-> "OD2" Residue "N PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 367": "OD1" <-> "OD2" Residue "N ASP 375": "OD1" <-> "OD2" Residue "N GLU 379": "OE1" <-> "OE2" Residue "N ARG 387": "NH1" <-> "NH2" Residue "N GLU 393": "OE1" <-> "OE2" Residue "N ASP 395": "OD1" <-> "OD2" Residue "N ASP 396": "OD1" <-> "OD2" Residue "N TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 414": "OD1" <-> "OD2" Residue "N GLU 419": "OE1" <-> "OE2" Residue "N GLU 422": "OE1" <-> "OE2" Residue "N ASP 437": "OD1" <-> "OD2" Residue "O GLU 297": "OE1" <-> "OE2" Residue "O GLU 313": "OE1" <-> "OE2" Residue "O GLU 314": "OE1" <-> "OE2" Residue "O ASP 331": "OD1" <-> "OD2" Residue "O PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 336": "OE1" <-> "OE2" Residue "O ARG 343": "NH1" <-> "NH2" Residue "O ARG 366": "NH1" <-> "NH2" Residue "O ASP 375": "OD1" <-> "OD2" Residue "O GLU 378": "OE1" <-> "OE2" Residue "O ARG 387": "NH1" <-> "NH2" Residue "O TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 435": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34796 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3257 Classifications: {'peptide': 415} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 393} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3217 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3245 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 392} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3229 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1562 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 12, 'TRANS': 184} Chain breaks: 6 Chain: "F" Number of atoms: 1216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1216 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain breaks: 1 Chain: "G" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1608 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 12, 'TRANS': 190} Chain: "H" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3257 Classifications: {'peptide': 415} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 393} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 3217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3217 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 3245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3245 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 392} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3229 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1133 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 138} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1124 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 140} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "N" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1133 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 138} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1124 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 140} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 18.33, per 1000 atoms: 0.53 Number of scatterers: 34796 At special positions: 0 Unit cell: (162.24, 170.56, 147.16, 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 150 16.00 O 6392 8.00 N 6122 7.00 C 22132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 189 " distance=2.04 Simple disulfide: pdb=" SG CYS I 169 " - pdb=" SG CYS I 189 " distance=2.04 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: 13.78 Conformation dependent library (CDL) restraints added in 6.5 seconds 8692 Ramachandran restraints generated. 4346 Oldfield, 0 Emsley, 4346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8158 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 40 sheets defined 45.5% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 removed outlier: 3.554A pdb=" N ALA A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.510A pdb=" N LYS A 78 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 138 through 145 removed outlier: 3.948A pdb=" N THR A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 removed outlier: 3.819A pdb=" N VAL A 154 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 192 removed outlier: 3.762A pdb=" N GLY A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 230 Processing helix chain 'A' and resid 243 through 257 removed outlier: 3.539A pdb=" N MET A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 285 removed outlier: 4.370A pdb=" N ALA A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.937A pdb=" N LEU A 311 " --> pdb=" O HIS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 348 removed outlier: 3.509A pdb=" N GLU A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 391 removed outlier: 4.065A pdb=" N GLU A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 422 Processing helix chain 'A' and resid 424 through 431 Processing helix chain 'A' and resid 433 through 442 removed outlier: 6.090A pdb=" N GLY A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASP A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 460 removed outlier: 4.145A pdb=" N LEU A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 109 through 118 removed outlier: 3.950A pdb=" N ILE B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 178 through 192 Processing helix chain 'B' and resid 210 through 228 Processing helix chain 'B' and resid 243 through 258 removed outlier: 3.766A pdb=" N MET B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 294 through 298 Processing helix chain 'B' and resid 307 through 319 removed outlier: 3.905A pdb=" N LEU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 348 Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.720A pdb=" N LEU B 387 " --> pdb=" O HIS B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 430 Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'C' and resid 46 through 58 Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 109 through 118 Processing helix chain 'C' and resid 150 through 159 removed outlier: 4.104A pdb=" N VAL C 154 " --> pdb=" O HIS C 150 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU C 155 " --> pdb=" O GLY C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 192 Processing helix chain 'C' and resid 210 through 228 Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 265 through 284 removed outlier: 6.083A pdb=" N PHE C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N THR C 272 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA C 273 " --> pdb=" O ALA C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 307 through 319 removed outlier: 3.966A pdb=" N LEU C 311 " --> pdb=" O HIS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 348 removed outlier: 3.846A pdb=" N MET C 346 " --> pdb=" O PHE C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 391 Processing helix chain 'C' and resid 410 through 418 Processing helix chain 'C' and resid 422 through 431 Processing helix chain 'C' and resid 437 through 442 removed outlier: 4.057A pdb=" N ILE C 441 " --> pdb=" O GLU C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 459 removed outlier: 4.300A pdb=" N TRP C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 57 Processing helix chain 'D' and resid 101 through 105 Processing helix chain 'D' and resid 110 through 119 Processing helix chain 'D' and resid 138 through 144 removed outlier: 3.892A pdb=" N THR D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 160 Processing helix chain 'D' and resid 178 through 192 removed outlier: 3.509A pdb=" N TYR D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 244 through 258 removed outlier: 3.776A pdb=" N GLY D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 285 Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.988A pdb=" N ILE D 298 " --> pdb=" O MET D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 319 removed outlier: 3.907A pdb=" N LEU D 311 " --> pdb=" O HIS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 346 Processing helix chain 'D' and resid 380 through 382 No H-bonds generated for 'chain 'D' and resid 380 through 382' Processing helix chain 'D' and resid 383 through 391 Processing helix chain 'D' and resid 409 through 422 removed outlier: 3.785A pdb=" N GLY D 413 " --> pdb=" O GLY D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 431 Processing helix chain 'D' and resid 433 through 442 removed outlier: 6.444A pdb=" N GLY D 439 " --> pdb=" O TYR D 435 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP D 440 " --> pdb=" O ARG D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 457 Processing helix chain 'E' and resid 83 through 94 Processing helix chain 'E' and resid 97 through 110 Proline residue: E 103 - end of helix removed outlier: 4.146A pdb=" N SER E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 123 Processing helix chain 'E' and resid 125 through 145 removed outlier: 3.645A pdb=" N GLN E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'E' and resid 160 through 167 Processing helix chain 'E' and resid 173 through 185 Processing helix chain 'E' and resid 189 through 204 Proline residue: E 202 - end of helix Processing helix chain 'E' and resid 217 through 231 Processing helix chain 'E' and resid 237 through 244 Processing helix chain 'E' and resid 253 through 263 Processing helix chain 'F' and resid 84 through 87 removed outlier: 3.898A pdb=" N LYS F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 84 through 87' Processing helix chain 'F' and resid 88 through 93 removed outlier: 4.576A pdb=" N GLY F 93 " --> pdb=" O GLU F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 111 removed outlier: 3.781A pdb=" N ASP F 111 " --> pdb=" O SER F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 123 removed outlier: 4.503A pdb=" N GLU F 120 " --> pdb=" O PRO F 116 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU F 121 " --> pdb=" O THR F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 144 Processing helix chain 'F' and resid 149 through 157 Processing helix chain 'F' and resid 160 through 164 removed outlier: 3.701A pdb=" N TYR F 164 " --> pdb=" O GLU F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 185 removed outlier: 3.517A pdb=" N ARG F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 199 removed outlier: 4.308A pdb=" N ALA F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 221 Processing helix chain 'G' and resid 83 through 94 Processing helix chain 'G' and resid 101 through 112 removed outlier: 3.609A pdb=" N GLY G 112 " --> pdb=" O LEU G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 123 Processing helix chain 'G' and resid 125 through 145 Processing helix chain 'G' and resid 149 through 154 Processing helix chain 'G' and resid 159 through 166 Processing helix chain 'G' and resid 170 through 185 removed outlier: 4.104A pdb=" N VAL G 175 " --> pdb=" O THR G 171 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA G 176 " --> pdb=" O THR G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 201 removed outlier: 3.539A pdb=" N ALA G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 233 removed outlier: 4.125A pdb=" N ASN G 233 " --> pdb=" O GLN G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 248 Processing helix chain 'G' and resid 253 through 263 Processing helix chain 'H' and resid 46 through 58 removed outlier: 3.553A pdb=" N ALA H 50 " --> pdb=" O PRO H 46 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER H 58 " --> pdb=" O ILE H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 78 removed outlier: 3.509A pdb=" N LYS H 78 " --> pdb=" O ASP H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'H' and resid 110 through 119 Processing helix chain 'H' and resid 139 through 144 removed outlier: 4.486A pdb=" N THR H 144 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 160 removed outlier: 3.819A pdb=" N VAL H 154 " --> pdb=" O HIS H 150 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU H 155 " --> pdb=" O GLY H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 192 removed outlier: 3.762A pdb=" N GLY H 192 " --> pdb=" O GLU H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 230 Processing helix chain 'H' and resid 243 through 257 removed outlier: 3.539A pdb=" N MET H 247 " --> pdb=" O THR H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 285 removed outlier: 4.369A pdb=" N ALA H 273 " --> pdb=" O ALA H 269 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN H 274 " --> pdb=" O GLY H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 298 Processing helix chain 'H' and resid 307 through 319 removed outlier: 3.937A pdb=" N LEU H 311 " --> pdb=" O HIS H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 348 removed outlier: 3.508A pdb=" N GLU H 348 " --> pdb=" O ASP H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 382 No H-bonds generated for 'chain 'H' and resid 380 through 382' Processing helix chain 'H' and resid 383 through 391 removed outlier: 4.066A pdb=" N GLU H 389 " --> pdb=" O PRO H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 410 through 422 Processing helix chain 'H' and resid 424 through 431 Processing helix chain 'H' and resid 433 through 442 removed outlier: 6.090A pdb=" N GLY H 439 " --> pdb=" O TYR H 435 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASP H 440 " --> pdb=" O ARG H 436 " (cutoff:3.500A) Processing helix chain 'H' and resid 450 through 460 removed outlier: 4.146A pdb=" N LEU H 456 " --> pdb=" O LEU H 452 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 58 Processing helix chain 'I' and resid 101 through 105 Processing helix chain 'I' and resid 109 through 118 removed outlier: 3.950A pdb=" N ILE I 113 " --> pdb=" O SER I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 143 Processing helix chain 'I' and resid 151 through 160 Processing helix chain 'I' and resid 178 through 192 Processing helix chain 'I' and resid 210 through 228 Processing helix chain 'I' and resid 243 through 258 removed outlier: 3.765A pdb=" N MET I 247 " --> pdb=" O THR I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 270 Processing helix chain 'I' and resid 270 through 285 Processing helix chain 'I' and resid 294 through 298 Processing helix chain 'I' and resid 307 through 319 removed outlier: 3.905A pdb=" N LEU I 311 " --> pdb=" O HIS I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 348 Processing helix chain 'I' and resid 380 through 382 No H-bonds generated for 'chain 'I' and resid 380 through 382' Processing helix chain 'I' and resid 383 through 391 removed outlier: 3.721A pdb=" N LEU I 387 " --> pdb=" O HIS I 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 409 through 430 Processing helix chain 'I' and resid 433 through 438 Processing helix chain 'I' and resid 448 through 453 Processing helix chain 'J' and resid 46 through 58 Processing helix chain 'J' and resid 101 through 105 Processing helix chain 'J' and resid 109 through 118 Processing helix chain 'J' and resid 150 through 159 removed outlier: 4.105A pdb=" N VAL J 154 " --> pdb=" O HIS J 150 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU J 155 " --> pdb=" O GLY J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 192 Processing helix chain 'J' and resid 210 through 228 Processing helix chain 'J' and resid 243 through 257 Processing helix chain 'J' and resid 265 through 284 removed outlier: 6.082A pdb=" N PHE J 271 " --> pdb=" O LEU J 267 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N THR J 272 " --> pdb=" O THR J 268 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA J 273 " --> pdb=" O ALA J 269 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 298 Processing helix chain 'J' and resid 307 through 319 removed outlier: 3.966A pdb=" N LEU J 311 " --> pdb=" O HIS J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 348 removed outlier: 3.847A pdb=" N MET J 346 " --> pdb=" O PHE J 342 " (cutoff:3.500A) Processing helix chain 'J' and resid 380 through 382 No H-bonds generated for 'chain 'J' and resid 380 through 382' Processing helix chain 'J' and resid 383 through 391 Processing helix chain 'J' and resid 410 through 419 Processing helix chain 'J' and resid 423 through 431 Processing helix chain 'J' and resid 437 through 442 removed outlier: 4.057A pdb=" N ILE J 441 " --> pdb=" O GLU J 437 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 459 removed outlier: 4.300A pdb=" N TRP J 459 " --> pdb=" O ALA J 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 57 Processing helix chain 'K' and resid 101 through 105 Processing helix chain 'K' and resid 110 through 119 Processing helix chain 'K' and resid 138 through 145 removed outlier: 3.664A pdb=" N PHE K 145 " --> pdb=" O LEU K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 160 Processing helix chain 'K' and resid 178 through 192 removed outlier: 3.509A pdb=" N TYR K 182 " --> pdb=" O SER K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 230 Processing helix chain 'K' and resid 244 through 258 removed outlier: 3.776A pdb=" N GLY K 258 " --> pdb=" O ALA K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 285 Processing helix chain 'K' and resid 294 through 299 removed outlier: 3.989A pdb=" N ILE K 298 " --> pdb=" O MET K 294 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 319 removed outlier: 3.906A pdb=" N LEU K 311 " --> pdb=" O HIS K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 346 Processing helix chain 'K' and resid 380 through 382 No H-bonds generated for 'chain 'K' and resid 380 through 382' Processing helix chain 'K' and resid 383 through 391 Processing helix chain 'K' and resid 409 through 422 removed outlier: 3.785A pdb=" N GLY K 413 " --> pdb=" O GLY K 409 " (cutoff:3.500A) Processing helix chain 'K' and resid 424 through 431 Processing helix chain 'K' and resid 433 through 442 removed outlier: 6.444A pdb=" N GLY K 439 " --> pdb=" O TYR K 435 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP K 440 " --> pdb=" O ARG K 436 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 457 Processing helix chain 'L' and resid 315 through 322 removed outlier: 3.653A pdb=" N ILE L 319 " --> pdb=" O GLY L 315 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 357 removed outlier: 4.218A pdb=" N GLY L 357 " --> pdb=" O VAL L 353 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 418 Processing helix chain 'M' and resid 315 through 322 removed outlier: 3.603A pdb=" N ILE M 319 " --> pdb=" O GLY M 315 " (cutoff:3.500A) Processing helix chain 'M' and resid 350 through 357 removed outlier: 3.552A pdb=" N ILE M 356 " --> pdb=" O PRO M 352 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY M 357 " --> pdb=" O VAL M 353 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 372 removed outlier: 4.262A pdb=" N VAL M 371 " --> pdb=" O ASP M 367 " (cutoff:3.500A) Processing helix chain 'M' and resid 388 through 390 No H-bonds generated for 'chain 'M' and resid 388 through 390' Processing helix chain 'M' and resid 412 through 418 Processing helix chain 'N' and resid 315 through 322 removed outlier: 3.654A pdb=" N ILE N 319 " --> pdb=" O GLY N 315 " (cutoff:3.500A) Processing helix chain 'N' and resid 350 through 357 removed outlier: 4.217A pdb=" N GLY N 357 " --> pdb=" O VAL N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 412 through 418 Processing helix chain 'O' and resid 315 through 322 removed outlier: 3.604A pdb=" N ILE O 319 " --> pdb=" O GLY O 315 " (cutoff:3.500A) Processing helix chain 'O' and resid 350 through 357 removed outlier: 3.553A pdb=" N ILE O 356 " --> pdb=" O PRO O 352 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY O 357 " --> pdb=" O VAL O 353 " (cutoff:3.500A) Processing helix chain 'O' and resid 367 through 372 removed outlier: 4.261A pdb=" N VAL O 371 " --> pdb=" O ASP O 367 " (cutoff:3.500A) Processing helix chain 'O' and resid 388 through 390 No H-bonds generated for 'chain 'O' and resid 388 through 390' Processing helix chain 'O' and resid 412 through 418 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 86 removed outlier: 6.126A pdb=" N CYS A 81 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA A 99 " --> pdb=" O CYS A 81 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG A 38 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU A 132 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N SER A 40 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU A 130 " --> pdb=" O SER A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 234 through 235 removed outlier: 6.705A pdb=" N LEU A 167 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LYS A 198 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N CYS A 169 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N MET A 166 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 261 through 265 removed outlier: 6.137A pdb=" N ILE A 262 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N HIS A 291 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N HIS A 264 " --> pdb=" O HIS A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 86 removed outlier: 6.322A pdb=" N PHE B 97 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE B 84 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE B 95 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA B 36 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 234 through 236 removed outlier: 7.625A pdb=" N THR B 197 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N MET B 166 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N PHE B 399 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY B 168 " --> pdb=" O PHE B 399 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 261 through 263 removed outlier: 5.870A pdb=" N ILE B 262 " --> pdb=" O HIS B 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 322 through 324 removed outlier: 5.974A pdb=" N LEU B 323 " --> pdb=" O VAL B 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 86 removed outlier: 6.525A pdb=" N PHE C 97 " --> pdb=" O TYR C 82 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE C 84 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE C 95 " --> pdb=" O ILE C 84 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 34 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE C 135 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA C 36 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 305 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 196 through 198 removed outlier: 7.520A pdb=" N GLN C 398 " --> pdb=" O PRO C 373 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA C 375 " --> pdb=" O GLN C 398 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU C 323 " --> pdb=" O VAL C 374 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 263 through 264 Processing sheet with id=AB3, first strand: chain 'D' and resid 80 through 86 removed outlier: 5.655A pdb=" N CYS D 81 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA D 99 " --> pdb=" O CYS D 81 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU D 34 " --> pdb=" O ILE D 135 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE D 135 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA D 36 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.753A pdb=" N LEU D 167 " --> pdb=" O PHE D 196 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N LYS D 198 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N CYS D 169 " --> pdb=" O LYS D 198 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N MET D 166 " --> pdb=" O LEU D 397 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLN D 398 " --> pdb=" O PRO D 373 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA D 375 " --> pdb=" O GLN D 398 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 261 through 265 removed outlier: 3.695A pdb=" N HIS D 291 " --> pdb=" O HIS D 264 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 350 through 351 Processing sheet with id=AB7, first strand: chain 'H' and resid 80 through 86 removed outlier: 6.125A pdb=" N CYS H 81 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA H 99 " --> pdb=" O CYS H 81 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG H 38 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LEU H 132 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N SER H 40 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU H 130 " --> pdb=" O SER H 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 234 through 235 removed outlier: 6.704A pdb=" N LEU H 167 " --> pdb=" O PHE H 196 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LYS H 198 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N CYS H 169 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N MET H 166 " --> pdb=" O LEU H 397 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 261 through 265 removed outlier: 6.137A pdb=" N ILE H 262 " --> pdb=" O HIS H 289 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N HIS H 291 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N HIS H 264 " --> pdb=" O HIS H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'H' and resid 350 through 351 Processing sheet with id=AC2, first strand: chain 'I' and resid 80 through 86 removed outlier: 6.322A pdb=" N PHE I 97 " --> pdb=" O TYR I 82 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE I 84 " --> pdb=" O PHE I 95 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE I 95 " --> pdb=" O ILE I 84 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA I 36 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 234 through 236 removed outlier: 7.624A pdb=" N THR I 197 " --> pdb=" O TYR I 236 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N MET I 166 " --> pdb=" O LEU I 397 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N PHE I 399 " --> pdb=" O MET I 166 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY I 168 " --> pdb=" O PHE I 399 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 261 through 263 removed outlier: 5.870A pdb=" N ILE I 262 " --> pdb=" O HIS I 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'I' and resid 322 through 324 removed outlier: 5.974A pdb=" N LEU I 323 " --> pdb=" O VAL I 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'J' and resid 80 through 86 removed outlier: 6.526A pdb=" N PHE J 97 " --> pdb=" O TYR J 82 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE J 84 " --> pdb=" O PHE J 95 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE J 95 " --> pdb=" O ILE J 84 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU J 34 " --> pdb=" O ILE J 135 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE J 135 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA J 36 " --> pdb=" O GLU J 133 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY J 305 " --> pdb=" O LEU J 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 196 through 198 removed outlier: 7.520A pdb=" N GLN J 398 " --> pdb=" O PRO J 373 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA J 375 " --> pdb=" O GLN J 398 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU J 323 " --> pdb=" O VAL J 374 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 263 through 264 Processing sheet with id=AC9, first strand: chain 'K' and resid 80 through 86 removed outlier: 5.655A pdb=" N CYS K 81 " --> pdb=" O ALA K 99 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA K 99 " --> pdb=" O CYS K 81 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU K 34 " --> pdb=" O ILE K 135 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE K 135 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA K 36 " --> pdb=" O GLU K 133 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 234 through 235 removed outlier: 6.752A pdb=" N LEU K 167 " --> pdb=" O PHE K 196 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N LYS K 198 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N CYS K 169 " --> pdb=" O LYS K 198 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N MET K 166 " --> pdb=" O LEU K 397 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLN K 398 " --> pdb=" O PRO K 373 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA K 375 " --> pdb=" O GLN K 398 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 261 through 265 removed outlier: 3.694A pdb=" N HIS K 291 " --> pdb=" O HIS K 264 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 350 through 351 Processing sheet with id=AD4, first strand: chain 'L' and resid 344 through 345 removed outlier: 3.721A pdb=" N GLY L 425 " --> pdb=" O LEU L 400 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TYR L 398 " --> pdb=" O VAL L 427 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 326 through 328 Processing sheet with id=AD6, first strand: chain 'M' and resid 290 through 292 removed outlier: 3.685A pdb=" N ARG M 432 " --> pdb=" O VAL M 291 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL M 427 " --> pdb=" O ASP M 386 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP M 386 " --> pdb=" O VAL M 427 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU M 429 " --> pdb=" O VAL M 384 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLY M 360 " --> pdb=" O VAL M 306 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 290 through 292 removed outlier: 3.685A pdb=" N ARG M 432 " --> pdb=" O VAL M 291 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY M 425 " --> pdb=" O LEU M 400 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N TYR M 398 " --> pdb=" O VAL M 427 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 326 through 328 Processing sheet with id=AD9, first strand: chain 'N' and resid 344 through 345 removed outlier: 3.721A pdb=" N GLY N 425 " --> pdb=" O LEU N 400 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N TYR N 398 " --> pdb=" O VAL N 427 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 326 through 328 Processing sheet with id=AE2, first strand: chain 'O' and resid 290 through 292 removed outlier: 3.685A pdb=" N ARG O 432 " --> pdb=" O VAL O 291 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL O 427 " --> pdb=" O ASP O 386 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP O 386 " --> pdb=" O VAL O 427 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU O 429 " --> pdb=" O VAL O 384 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLY O 360 " --> pdb=" O VAL O 306 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 290 through 292 removed outlier: 3.685A pdb=" N ARG O 432 " --> pdb=" O VAL O 291 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY O 425 " --> pdb=" O LEU O 400 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N TYR O 398 " --> pdb=" O VAL O 427 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 326 through 328 1459 hydrogen bonds defined for protein. 4152 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: 9.96 Time building geometry restraints manager: 14.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.52: 26155 1.52 - 1.85: 9444 1.85 - 2.18: 0 2.18 - 2.52: 0 2.52 - 2.85: 2 Bond restraints: 35601 Sorted by residual: bond pdb=" C ASP L 367 " pdb=" N ARG L 369 " ideal model delta sigma weight residual 1.329 2.848 -1.519 1.40e-02 5.10e+03 1.18e+04 bond pdb=" C ASP N 367 " pdb=" N ARG N 369 " ideal model delta sigma weight residual 1.329 2.848 -1.519 1.40e-02 5.10e+03 1.18e+04 bond pdb=" CA PRO L 433 " pdb=" C PRO L 433 " ideal model delta sigma weight residual 1.517 1.575 -0.058 9.30e-03 1.16e+04 3.86e+01 bond pdb=" CA PRO N 433 " pdb=" C PRO N 433 " ideal model delta sigma weight residual 1.517 1.574 -0.057 9.30e-03 1.16e+04 3.78e+01 bond pdb=" N VAL N 430 " pdb=" CA VAL N 430 " ideal model delta sigma weight residual 1.456 1.511 -0.056 1.11e-02 8.12e+03 2.51e+01 ... (remaining 35596 not shown) Histogram of bond angle deviations from ideal: 98.16 - 106.28: 1179 106.28 - 114.41: 20619 114.41 - 122.53: 22262 122.53 - 130.66: 3937 130.66 - 138.79: 227 Bond angle restraints: 48224 Sorted by residual: angle pdb=" N VAL L 431 " pdb=" CA VAL L 431 " pdb=" C VAL L 431 " ideal model delta sigma weight residual 110.74 138.79 -28.05 9.10e-01 1.21e+00 9.50e+02 angle pdb=" N VAL N 431 " pdb=" CA VAL N 431 " pdb=" C VAL N 431 " ideal model delta sigma weight residual 110.74 138.77 -28.03 9.10e-01 1.21e+00 9.49e+02 angle pdb=" O ASP N 367 " pdb=" C ASP N 367 " pdb=" N ARG N 369 " ideal model delta sigma weight residual 121.74 107.24 14.50 1.31e+00 5.83e-01 1.23e+02 angle pdb=" O ASP L 367 " pdb=" C ASP L 367 " pdb=" N ARG L 369 " ideal model delta sigma weight residual 121.74 107.26 14.48 1.31e+00 5.83e-01 1.22e+02 angle pdb=" N PRO N 433 " pdb=" CA PRO N 433 " pdb=" C PRO N 433 " ideal model delta sigma weight residual 110.70 123.72 -13.02 1.22e+00 6.72e-01 1.14e+02 ... (remaining 48219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 18550 17.96 - 35.91: 1931 35.91 - 53.87: 504 53.87 - 71.82: 145 71.82 - 89.78: 23 Dihedral angle restraints: 21153 sinusoidal: 8467 harmonic: 12686 Sorted by residual: dihedral pdb=" N ALA N 301 " pdb=" C ALA N 301 " pdb=" CA ALA N 301 " pdb=" CB ALA N 301 " ideal model delta harmonic sigma weight residual 122.90 154.15 -31.25 0 2.50e+00 1.60e-01 1.56e+02 dihedral pdb=" N ALA L 301 " pdb=" C ALA L 301 " pdb=" CA ALA L 301 " pdb=" CB ALA L 301 " ideal model delta harmonic sigma weight residual 122.90 154.14 -31.24 0 2.50e+00 1.60e-01 1.56e+02 dihedral pdb=" C ALA L 301 " pdb=" N ALA L 301 " pdb=" CA ALA L 301 " pdb=" CB ALA L 301 " ideal model delta harmonic sigma weight residual -122.60 -153.76 31.16 0 2.50e+00 1.60e-01 1.55e+02 ... (remaining 21150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.281: 5201 0.281 - 0.562: 25 0.562 - 0.843: 5 0.843 - 1.124: 0 1.124 - 1.405: 2 Chirality restraints: 5233 Sorted by residual: chirality pdb=" CA ALA N 301 " pdb=" N ALA N 301 " pdb=" C ALA N 301 " pdb=" CB ALA N 301 " both_signs ideal model delta sigma weight residual False 2.48 1.08 1.41 2.00e-01 2.50e+01 4.94e+01 chirality pdb=" CA ALA L 301 " pdb=" N ALA L 301 " pdb=" C ALA L 301 " pdb=" CB ALA L 301 " both_signs ideal model delta sigma weight residual False 2.48 1.08 1.40 2.00e-01 2.50e+01 4.92e+01 chirality pdb=" CA LYS M 377 " pdb=" N LYS M 377 " pdb=" C LYS M 377 " pdb=" CB LYS M 377 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.13e+01 ... (remaining 5230 not shown) Planarity restraints: 6307 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP N 367 " -0.116 2.00e-02 2.50e+03 1.80e-01 3.25e+02 pdb=" C ASP N 367 " 0.306 2.00e-02 2.50e+03 pdb=" O ASP N 367 " -0.144 2.00e-02 2.50e+03 pdb=" N ARG N 369 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP L 367 " 0.116 2.00e-02 2.50e+03 1.80e-01 3.24e+02 pdb=" C ASP L 367 " -0.306 2.00e-02 2.50e+03 pdb=" O ASP L 367 " 0.143 2.00e-02 2.50e+03 pdb=" N ARG L 369 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE O 326 " 0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C ILE O 326 " -0.058 2.00e-02 2.50e+03 pdb=" O ILE O 326 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE O 327 " 0.019 2.00e-02 2.50e+03 ... (remaining 6304 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 88 2.30 - 2.95: 17997 2.95 - 3.60: 51698 3.60 - 4.25: 80797 4.25 - 4.90: 131924 Nonbonded interactions: 282504 Sorted by model distance: nonbonded pdb=" NZ LYS H 143 " pdb=" CB ALA H 366 " model vdw 1.645 3.540 nonbonded pdb=" OG SER A 367 " pdb=" OD2 ASP K 103 " model vdw 1.901 2.440 nonbonded pdb=" CE LYS H 143 " pdb=" CB ALA H 366 " model vdw 1.955 3.860 nonbonded pdb=" OG SER J 129 " pdb=" O ASN J 303 " model vdw 2.089 2.440 nonbonded pdb=" OG SER C 129 " pdb=" O ASN C 303 " model vdw 2.089 2.440 ... (remaining 282499 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 21 through 59 or resid 76 through 173 or resid 177 through \ 399 or resid 406 through 458)) selection = (chain 'B' and (resid 21 through 328 or resid 335 through 399 or resid 406 throu \ gh 458)) selection = (chain 'C' and (resid 21 through 59 or resid 76 through 173 or resid 175 or resi \ d 178 through 328 or resid 335 through 399 or resid 406 through 458)) selection = (chain 'D' and (resid 21 through 59 or resid 76 through 328 or resid 335 through \ 458)) selection = (chain 'H' and (resid 21 through 59 or resid 76 through 173 or resid 177 through \ 399 or resid 406 through 458)) selection = (chain 'I' and (resid 21 through 328 or resid 335 through 399 or resid 406 throu \ gh 458)) selection = (chain 'J' and (resid 21 through 59 or resid 76 through 173 or resid 175 or resi \ d 178 through 328 or resid 335 through 399 or resid 406 through 458)) selection = (chain 'K' and (resid 21 through 59 or resid 76 through 328 or resid 335 through \ 458)) } ncs_group { reference = chain 'E' selection = (chain 'G' and (resid 62 through 152 or resid 154 through 186 or resid 188 throu \ gh 206 or resid 208 through 210 or resid 212 through 244 or resid 246 through 24 \ 7 or resid 249 through 264)) } ncs_group { reference = (chain 'L' and (resid 288 through 293 or (resid 294 and (name N or name CA or na \ me C or name O or name CB )) or resid 295 through 357 or (resid 358 and (name N \ or name CA or name C or name O or name CB )) or resid 359 through 369 or (resid \ 370 and (name N or name CA or name C or name O or name CB )) or resid 371 throug \ h 407 or (resid 408 and (name N or name CA or name C or name O or name CB )) or \ resid 409 through 418 or (resid 419 and (name N or name CA or name C or name O o \ r name CB )) or resid 420 through 435 or (resid 436 and (name N or name CA or na \ me C or name O or name CB )))) selection = (chain 'M' and (resid 288 through 316 or (resid 317 and (name N or name CA or na \ me C or name O or name CB )) or resid 318 through 367 or (resid 369 through 370 \ and (name N or name CA or name C or name O or name CB )) or resid 371 through 43 \ 6)) selection = (chain 'N' and (resid 288 through 293 or (resid 294 and (name N or name CA or na \ me C or name O or name CB )) or resid 295 through 357 or (resid 358 and (name N \ or name CA or name C or name O or name CB )) or resid 359 through 369 or (resid \ 370 and (name N or name CA or name C or name O or name CB )) or resid 371 throug \ h 407 or (resid 408 and (name N or name CA or name C or name O or name CB )) or \ resid 409 through 418 or (resid 419 and (name N or name CA or name C or name O o \ r name CB )) or resid 420 through 435 or (resid 436 and (name N or name CA or na \ me C or name O or name CB )))) selection = (chain 'O' and (resid 288 through 316 or (resid 317 and (name N or name CA or na \ me C or name O or name CB )) or resid 318 through 367 or (resid 369 through 370 \ and (name N or name CA or name C or name O or name CB )) or resid 371 through 43 \ 6)) } 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: 3.970 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: 16.590 Check model and map are aligned: 0.510 Set scattering table: 0.340 Process input model: 85.600 Find NCS groups from input model: 2.640 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 1.519 35601 Z= 0.727 Angle : 1.039 28.045 48224 Z= 0.654 Chirality : 0.070 1.405 5233 Planarity : 0.007 0.180 6307 Dihedral : 16.281 89.778 12989 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.93 % Favored : 88.86 % Rotamer: Outliers : 6.13 % Allowed : 10.44 % Favored : 83.43 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.11), residues: 4346 helix: -1.85 (0.11), residues: 1712 sheet: -2.38 (0.18), residues: 626 loop : -3.03 (0.12), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 382 HIS 0.007 0.001 HIS H 291 PHE 0.024 0.002 PHE I 266 TYR 0.015 0.002 TYR J 182 ARG 0.009 0.001 ARG K 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8692 Ramachandran restraints generated. 4346 Oldfield, 0 Emsley, 4346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8692 Ramachandran restraints generated. 4346 Oldfield, 0 Emsley, 4346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1046 time to evaluate : 4.054 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: A 25 ASP cc_start: 0.8261 (p0) cc_final: 0.7439 (t0) REVERT: A 42 GLN cc_start: 0.8278 (mm-40) cc_final: 0.8028 (tp40) REVERT: A 49 GLU cc_start: 0.7339 (tp30) cc_final: 0.6747 (tp30) REVERT: A 112 ASN cc_start: 0.7318 (t0) cc_final: 0.6985 (t0) REVERT: A 125 LYS cc_start: 0.7425 (pttt) cc_final: 0.7112 (tttt) REVERT: A 146 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7723 (tp40) REVERT: A 161 LYS cc_start: 0.7844 (mmtp) cc_final: 0.7511 (mmtt) REVERT: A 216 LEU cc_start: 0.8694 (mt) cc_final: 0.8476 (mt) REVERT: A 220 ASP cc_start: 0.7994 (t0) cc_final: 0.7608 (m-30) REVERT: A 283 ASP cc_start: 0.6869 (m-30) cc_final: 0.6377 (m-30) REVERT: A 304 HIS cc_start: 0.8358 (t-90) cc_final: 0.8114 (t-90) REVERT: A 315 LEU cc_start: 0.9210 (tt) cc_final: 0.8931 (tt) REVERT: A 426 GLN cc_start: 0.8131 (tt0) cc_final: 0.7683 (tt0) REVERT: A 452 LEU cc_start: 0.5825 (pt) cc_final: 0.5506 (tp) REVERT: B 34 LEU cc_start: 0.9112 (mm) cc_final: 0.8585 (mm) REVERT: B 103 ASP cc_start: 0.8111 (m-30) cc_final: 0.7580 (m-30) REVERT: B 122 PHE cc_start: 0.9019 (m-80) cc_final: 0.8689 (m-80) REVERT: B 172 LYS cc_start: 0.6360 (tttt) cc_final: 0.6026 (mmtt) REVERT: B 203 ILE cc_start: 0.7734 (mt) cc_final: 0.6981 (tt) REVERT: B 209 GLN cc_start: 0.8105 (mt0) cc_final: 0.7848 (mt0) REVERT: B 210 ARG cc_start: 0.5983 (mmt-90) cc_final: 0.5394 (mmt180) REVERT: B 224 LYS cc_start: 0.7570 (tttt) cc_final: 0.6931 (tttt) REVERT: B 231 GLU cc_start: 0.7251 (tt0) cc_final: 0.6942 (tt0) REVERT: B 261 ILE cc_start: 0.9109 (pt) cc_final: 0.8867 (tt) REVERT: B 297 VAL cc_start: 0.7942 (p) cc_final: 0.7741 (t) REVERT: B 302 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7308 (tpp80) REVERT: B 328 VAL cc_start: 0.7569 (t) cc_final: 0.7262 (p) REVERT: B 336 LYS cc_start: 0.5728 (pttt) cc_final: 0.4970 (ttpt) REVERT: B 350 HIS cc_start: 0.8074 (t-90) cc_final: 0.7769 (t-90) REVERT: B 390 ILE cc_start: 0.8726 (mm) cc_final: 0.8442 (pt) REVERT: B 417 ASN cc_start: 0.6362 (m110) cc_final: 0.5879 (m110) REVERT: C 90 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.6051 (tm-30) REVERT: C 120 ASN cc_start: 0.8618 (p0) cc_final: 0.8378 (p0) REVERT: C 128 ARG cc_start: 0.7066 (tpp80) cc_final: 0.6541 (ttt-90) REVERT: C 202 ASN cc_start: 0.7521 (p0) cc_final: 0.7283 (p0) REVERT: C 248 MET cc_start: 0.8763 (mmp) cc_final: 0.8547 (tpp) REVERT: C 390 ILE cc_start: 0.8726 (mm) cc_final: 0.8432 (mm) REVERT: C 428 ARG cc_start: 0.8890 (ttp-170) cc_final: 0.8597 (ttt-90) REVERT: C 432 ARG cc_start: 0.7711 (mmm-85) cc_final: 0.7137 (mtp85) REVERT: C 448 TRP cc_start: 0.5879 (m100) cc_final: 0.5641 (m100) REVERT: D 76 ARG cc_start: 0.6671 (ptt180) cc_final: 0.6234 (mtp180) REVERT: D 95 PHE cc_start: 0.7862 (m-80) cc_final: 0.7397 (m-80) REVERT: D 125 LYS cc_start: 0.6633 (pttt) cc_final: 0.5891 (tppt) REVERT: D 127 ILE cc_start: 0.8235 (mm) cc_final: 0.7988 (mt) REVERT: D 171 ILE cc_start: 0.8843 (tp) cc_final: 0.8576 (tt) REVERT: D 203 ILE cc_start: 0.6507 (mm) cc_final: 0.5833 (mm) REVERT: D 206 GLN cc_start: 0.6987 (mt0) cc_final: 0.6687 (mp10) REVERT: D 208 PHE cc_start: 0.7551 (p90) cc_final: 0.7053 (p90) REVERT: D 231 GLU cc_start: 0.6482 (mt-10) cc_final: 0.6248 (mm-30) REVERT: D 344 ASP cc_start: 0.8458 (m-30) cc_final: 0.8065 (t0) REVERT: D 357 ARG cc_start: 0.7371 (mtp85) cc_final: 0.6961 (mtp85) REVERT: D 359 VAL cc_start: 0.9239 (t) cc_final: 0.9031 (m) REVERT: D 363 GLN cc_start: 0.8224 (tp40) cc_final: 0.7668 (tm-30) REVERT: D 435 TYR cc_start: 0.6799 (t80) cc_final: 0.6472 (t80) REVERT: E 82 LEU cc_start: 0.6440 (mp) cc_final: 0.6172 (mm) REVERT: E 89 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8108 (mt-10) REVERT: E 119 GLU cc_start: 0.6514 (tt0) cc_final: 0.6096 (tt0) REVERT: E 164 TYR cc_start: 0.7130 (t80) cc_final: 0.6817 (t80) REVERT: E 171 THR cc_start: 0.8981 (t) cc_final: 0.8712 (m) REVERT: E 173 GLN cc_start: 0.7065 (mt0) cc_final: 0.6854 (tt0) REVERT: E 184 ARG cc_start: 0.6878 (mpt180) cc_final: 0.4730 (ttp80) REVERT: E 205 ARG cc_start: 0.7291 (mmt-90) cc_final: 0.6992 (mtp85) REVERT: E 226 TYR cc_start: 0.6904 (m-10) cc_final: 0.6531 (m-80) REVERT: E 228 ARG cc_start: 0.6674 (mmm-85) cc_final: 0.5416 (mmm160) REVERT: F 69 ARG cc_start: 0.4947 (OUTLIER) cc_final: 0.4382 (mtm180) REVERT: F 95 MET cc_start: 0.4844 (pmm) cc_final: 0.4303 (mpp) REVERT: G 68 PHE cc_start: 0.4898 (t80) cc_final: 0.4548 (t80) REVERT: G 117 THR cc_start: 0.7144 (p) cc_final: 0.6851 (t) REVERT: G 145 SER cc_start: 0.6383 (OUTLIER) cc_final: 0.5677 (m) REVERT: G 173 GLN cc_start: 0.7231 (mt0) cc_final: 0.6786 (mt0) REVERT: G 185 ASN cc_start: 0.7270 (t0) cc_final: 0.7033 (p0) REVERT: G 201 TYR cc_start: 0.6696 (t80) cc_final: 0.6013 (t80) REVERT: G 210 TRP cc_start: 0.6141 (t-100) cc_final: 0.5463 (t-100) REVERT: H 144 THR cc_start: 0.6279 (OUTLIER) cc_final: 0.5865 (t) REVERT: H 157 ASP cc_start: 0.7603 (m-30) cc_final: 0.6675 (m-30) REVERT: H 252 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7170 (mm-30) REVERT: H 339 THR cc_start: 0.8221 (m) cc_final: 0.7639 (t) REVERT: H 442 LEU cc_start: 0.5532 (OUTLIER) cc_final: 0.5269 (tp) REVERT: I 57 GLU cc_start: 0.5283 (tp30) cc_final: 0.4665 (tp30) REVERT: I 78 LYS cc_start: 0.6547 (pttp) cc_final: 0.5838 (mttm) REVERT: I 127 ILE cc_start: 0.7877 (mm) cc_final: 0.7168 (tp) REVERT: I 202 ASN cc_start: 0.7716 (p0) cc_final: 0.7000 (p0) REVERT: I 302 ARG cc_start: 0.6418 (ttm-80) cc_final: 0.6153 (tmm160) REVERT: I 307 HIS cc_start: 0.8591 (t-90) cc_final: 0.7992 (t-90) REVERT: I 315 LEU cc_start: 0.8550 (tt) cc_final: 0.7814 (tt) REVERT: I 336 LYS cc_start: 0.5070 (pttt) cc_final: 0.4283 (ptpp) REVERT: I 380 HIS cc_start: 0.6309 (p90) cc_final: 0.5733 (p90) REVERT: I 412 PRO cc_start: 0.7644 (Cg_exo) cc_final: 0.7341 (Cg_endo) REVERT: J 29 LYS cc_start: 0.5913 (mttt) cc_final: 0.5354 (ttpt) REVERT: J 83 HIS cc_start: 0.8230 (t-90) cc_final: 0.7813 (t-170) REVERT: J 94 TYR cc_start: 0.7446 (m-80) cc_final: 0.6968 (m-80) REVERT: J 95 PHE cc_start: 0.6966 (m-10) cc_final: 0.6386 (m-10) REVERT: J 107 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6788 (tt0) REVERT: J 210 ARG cc_start: 0.6617 (mmt180) cc_final: 0.6348 (mmt180) REVERT: J 224 LYS cc_start: 0.6421 (ttpt) cc_final: 0.6189 (mmmt) REVERT: J 255 LYS cc_start: 0.8598 (tmtt) cc_final: 0.8322 (tppt) REVERT: J 371 VAL cc_start: 0.8109 (m) cc_final: 0.7897 (m) REVERT: K 22 TYR cc_start: 0.6277 (t80) cc_final: 0.5954 (t80) REVERT: K 169 CYS cc_start: 0.7344 (t) cc_final: 0.6969 (p) REVERT: K 194 LEU cc_start: 0.7367 (mt) cc_final: 0.6863 (mt) REVERT: K 203 ILE cc_start: 0.6095 (mm) cc_final: 0.5841 (mt) REVERT: K 206 GLN cc_start: 0.7455 (mt0) cc_final: 0.6890 (mp10) REVERT: K 222 ILE cc_start: 0.8612 (mt) cc_final: 0.8200 (mm) REVERT: K 224 LYS cc_start: 0.7820 (mtpt) cc_final: 0.7460 (tppt) REVERT: K 279 LYS cc_start: 0.7472 (mmmt) cc_final: 0.6927 (mtpt) REVERT: K 303 ASN cc_start: 0.7851 (m-40) cc_final: 0.7527 (m-40) REVERT: K 324 HIS cc_start: 0.7559 (m170) cc_final: 0.7040 (m-70) REVERT: K 328 VAL cc_start: 0.7750 (t) cc_final: 0.7320 (m) REVERT: L 431 VAL cc_start: 0.0156 (OUTLIER) cc_final: -0.0447 (m) REVERT: M 316 GLU cc_start: 0.3976 (OUTLIER) cc_final: 0.2985 (tt0) REVERT: M 342 LYS cc_start: 0.1205 (OUTLIER) cc_final: 0.0591 (mmtm) REVERT: M 343 ARG cc_start: 0.0957 (OUTLIER) cc_final: -0.0218 (mmm160) REVERT: N 292 ARG cc_start: -0.0231 (OUTLIER) cc_final: -0.0622 (ttp-110) REVERT: N 361 VAL cc_start: 0.4082 (OUTLIER) cc_final: 0.3661 (p) REVERT: N 379 GLU cc_start: -0.1404 (OUTLIER) cc_final: -0.2184 (mp0) REVERT: N 396 ASP cc_start: 0.3731 (OUTLIER) cc_final: 0.2872 (m-30) REVERT: N 402 VAL cc_start: -0.1784 (OUTLIER) cc_final: -0.2013 (p) REVERT: N 413 SER cc_start: 0.2787 (OUTLIER) cc_final: 0.2480 (t) REVERT: O 341 TRP cc_start: 0.2457 (t-100) cc_final: 0.1354 (t-100) REVERT: O 342 LYS cc_start: 0.4020 (OUTLIER) cc_final: 0.2939 (tptp) REVERT: O 426 MET cc_start: -0.1096 (ttt) cc_final: -0.1331 (tmm) outliers start: 222 outliers final: 46 residues processed: 1239 average time/residue: 0.5077 time to fit residues: 970.0844 Evaluate side-chains 677 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 615 time to evaluate : 3.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 371 optimal weight: 5.9990 chunk 333 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 224 optimal weight: 8.9990 chunk 178 optimal weight: 20.0000 chunk 344 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 209 optimal weight: 7.9990 chunk 256 optimal weight: 10.0000 chunk 399 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 HIS A 383 HIS B 284 ASN B 301 GLN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 HIS B 383 HIS B 398 GLN B 417 ASN C 112 ASN C 209 GLN D 146 GLN D 181 ASN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 ASN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 GLN E 130 ASN E 233 ASN E 246 GLN F 173 GLN G 144 GLN G 173 GLN G 216 ASN ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 284 ASN ** I 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 380 HIS ** I 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 417 ASN J 112 ASN ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 ASN K 284 ASN K 291 HIS ** K 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 324 HIS K 380 HIS K 429 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 35601 Z= 0.389 Angle : 0.772 15.704 48224 Z= 0.401 Chirality : 0.049 0.250 5233 Planarity : 0.007 0.133 6307 Dihedral : 5.854 39.778 4819 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.53 % Favored : 91.36 % Rotamer: Outliers : 0.25 % Allowed : 6.52 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.47 (0.12), residues: 4350 helix: -0.56 (0.12), residues: 1727 sheet: -1.86 (0.18), residues: 596 loop : -2.55 (0.12), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP K 365 HIS 0.010 0.002 HIS J 380 PHE 0.045 0.003 PHE O 332 TYR 0.020 0.002 TYR I 236 ARG 0.012 0.001 ARG M 435 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 746 time to evaluate : 3.505 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: A 25 ASP cc_start: 0.8087 (p0) cc_final: 0.7457 (t0) REVERT: A 49 GLU cc_start: 0.7154 (tp30) cc_final: 0.6376 (tp30) REVERT: A 125 LYS cc_start: 0.7441 (pttt) cc_final: 0.6630 (ptpt) REVERT: A 172 LYS cc_start: 0.6272 (tptm) cc_final: 0.4618 (ptpt) REVERT: A 279 LYS cc_start: 0.7506 (tptp) cc_final: 0.6398 (mmtt) REVERT: A 315 LEU cc_start: 0.9005 (tt) cc_final: 0.8793 (tt) REVERT: A 384 MET cc_start: 0.8713 (tpp) cc_final: 0.8480 (ttm) REVERT: B 32 ASP cc_start: 0.8281 (m-30) cc_final: 0.7988 (m-30) REVERT: B 103 ASP cc_start: 0.8180 (m-30) cc_final: 0.7614 (m-30) REVERT: B 122 PHE cc_start: 0.8986 (m-80) cc_final: 0.8657 (m-80) REVERT: B 203 ILE cc_start: 0.7449 (mt) cc_final: 0.6926 (tt) REVERT: B 224 LYS cc_start: 0.7260 (tttt) cc_final: 0.6587 (ttpt) REVERT: B 261 ILE cc_start: 0.9065 (pt) cc_final: 0.8800 (tt) REVERT: B 302 ARG cc_start: 0.7837 (ttm-80) cc_final: 0.7589 (tpp80) REVERT: B 336 LYS cc_start: 0.5843 (pttt) cc_final: 0.4966 (ttpt) REVERT: B 350 HIS cc_start: 0.8015 (t-90) cc_final: 0.7648 (t-90) REVERT: B 372 LEU cc_start: 0.9025 (mt) cc_final: 0.8672 (mt) REVERT: B 385 PRO cc_start: 0.8809 (Cg_endo) cc_final: 0.8531 (Cg_exo) REVERT: B 390 ILE cc_start: 0.8850 (mm) cc_final: 0.8522 (pt) REVERT: C 48 ASP cc_start: 0.7938 (m-30) cc_final: 0.7547 (m-30) REVERT: C 120 ASN cc_start: 0.8540 (p0) cc_final: 0.8299 (p0) REVERT: C 128 ARG cc_start: 0.6997 (tpp80) cc_final: 0.6734 (ttt-90) REVERT: C 143 LYS cc_start: 0.8725 (mmmt) cc_final: 0.8383 (mmmm) REVERT: C 155 GLU cc_start: 0.8866 (pp20) cc_final: 0.8521 (pp20) REVERT: C 204 ASN cc_start: 0.7742 (p0) cc_final: 0.7454 (p0) REVERT: C 336 LYS cc_start: 0.6226 (mttt) cc_final: 0.5044 (mtmm) REVERT: C 428 ARG cc_start: 0.8874 (ttp-170) cc_final: 0.8582 (ttt-90) REVERT: C 432 ARG cc_start: 0.7726 (mmm-85) cc_final: 0.7272 (mtp85) REVERT: C 435 TYR cc_start: 0.3664 (t80) cc_final: 0.2870 (t80) REVERT: D 76 ARG cc_start: 0.6756 (ptt180) cc_final: 0.6279 (mtp180) REVERT: D 95 PHE cc_start: 0.7847 (m-80) cc_final: 0.7341 (m-80) REVERT: D 125 LYS cc_start: 0.6620 (pttt) cc_final: 0.5882 (tppt) REVERT: D 135 ILE cc_start: 0.8413 (mt) cc_final: 0.8043 (mm) REVERT: D 171 ILE cc_start: 0.8784 (tp) cc_final: 0.8480 (tt) REVERT: D 203 ILE cc_start: 0.6571 (mm) cc_final: 0.5836 (mm) REVERT: D 206 GLN cc_start: 0.6862 (mt0) cc_final: 0.6645 (mp10) REVERT: D 208 PHE cc_start: 0.7418 (p90) cc_final: 0.6752 (p90) REVERT: D 359 VAL cc_start: 0.9256 (t) cc_final: 0.9048 (m) REVERT: D 415 THR cc_start: 0.8239 (t) cc_final: 0.7958 (t) REVERT: D 460 LYS cc_start: 0.5075 (ptpp) cc_final: 0.4167 (tppt) REVERT: E 184 ARG cc_start: 0.6575 (mpt180) cc_final: 0.4687 (ttp80) REVERT: E 204 ARG cc_start: 0.6127 (mtt180) cc_final: 0.5861 (mmt90) REVERT: E 205 ARG cc_start: 0.7270 (mmt-90) cc_final: 0.7064 (mtp85) REVERT: E 228 ARG cc_start: 0.6656 (mmm-85) cc_final: 0.5255 (mmm160) REVERT: F 70 PRO cc_start: 0.5379 (Cg_exo) cc_final: 0.5051 (Cg_endo) REVERT: F 95 MET cc_start: 0.4960 (pmm) cc_final: 0.4431 (mpp) REVERT: F 143 LEU cc_start: 0.5920 (mt) cc_final: 0.5498 (tt) REVERT: G 117 THR cc_start: 0.7241 (p) cc_final: 0.7031 (t) REVERT: G 173 GLN cc_start: 0.7094 (mt0) cc_final: 0.6893 (mt0) REVERT: G 185 ASN cc_start: 0.7334 (t0) cc_final: 0.6820 (p0) REVERT: G 210 TRP cc_start: 0.6237 (t-100) cc_final: 0.5683 (t-100) REVERT: G 211 LEU cc_start: 0.8170 (mt) cc_final: 0.7969 (tt) REVERT: G 229 GLN cc_start: 0.7463 (mm110) cc_final: 0.7254 (mm-40) REVERT: H 252 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7172 (mm-30) REVERT: H 256 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7527 (tm-30) REVERT: H 259 MET cc_start: 0.8001 (mmt) cc_final: 0.7775 (mmt) REVERT: H 339 THR cc_start: 0.8285 (m) cc_final: 0.7870 (t) REVERT: I 49 GLU cc_start: 0.7075 (tt0) cc_final: 0.6687 (mm-30) REVERT: I 78 LYS cc_start: 0.6991 (pttp) cc_final: 0.5992 (mttm) REVERT: I 94 TYR cc_start: 0.8159 (m-80) cc_final: 0.7800 (m-80) REVERT: I 155 GLU cc_start: 0.7862 (tt0) cc_final: 0.7513 (tt0) REVERT: I 202 ASN cc_start: 0.7611 (p0) cc_final: 0.7298 (p0) REVERT: I 252 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7616 (mm-30) REVERT: I 266 PHE cc_start: 0.8393 (p90) cc_final: 0.8148 (p90) REVERT: I 336 LYS cc_start: 0.4638 (pttt) cc_final: 0.3720 (ptpp) REVERT: I 380 HIS cc_start: 0.6218 (p-80) cc_final: 0.5826 (p90) REVERT: I 412 PRO cc_start: 0.7662 (Cg_exo) cc_final: 0.7331 (Cg_endo) REVERT: J 22 TYR cc_start: 0.6870 (t80) cc_final: 0.6191 (t80) REVERT: J 29 LYS cc_start: 0.6157 (mttt) cc_final: 0.5709 (ttpt) REVERT: J 83 HIS cc_start: 0.8186 (t-90) cc_final: 0.7832 (t-170) REVERT: J 94 TYR cc_start: 0.7402 (m-80) cc_final: 0.6886 (m-80) REVERT: J 238 ASN cc_start: 0.8077 (t0) cc_final: 0.7867 (t0) REVERT: J 301 GLN cc_start: 0.7643 (pm20) cc_final: 0.7184 (mp10) REVERT: J 342 PHE cc_start: 0.7691 (p90) cc_final: 0.7429 (p90) REVERT: J 346 MET cc_start: 0.8007 (ptp) cc_final: 0.7805 (ptp) REVERT: K 109 SER cc_start: 0.8467 (t) cc_final: 0.8263 (p) REVERT: K 206 GLN cc_start: 0.7323 (mt0) cc_final: 0.7100 (mp10) REVERT: K 224 LYS cc_start: 0.7554 (mtpt) cc_final: 0.7280 (tppt) REVERT: K 281 CYS cc_start: 0.8347 (m) cc_final: 0.8088 (m) REVERT: K 303 ASN cc_start: 0.7928 (m-40) cc_final: 0.7595 (m-40) REVERT: K 336 LYS cc_start: 0.5619 (pttt) cc_final: 0.4612 (ptpt) outliers start: 9 outliers final: 3 residues processed: 753 average time/residue: 0.4570 time to fit residues: 556.2736 Evaluate side-chains 556 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 553 time to evaluate : 3.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 332 optimal weight: 6.9990 chunk 272 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 400 optimal weight: 7.9990 chunk 432 optimal weight: 20.0000 chunk 356 optimal weight: 8.9990 chunk 396 optimal weight: 20.0000 chunk 136 optimal weight: 7.9990 chunk 321 optimal weight: 0.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS A 426 GLN B 112 ASN B 181 ASN B 264 HIS ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN C 274 ASN D 112 ASN D 146 GLN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN E 130 ASN E 233 ASN G 173 GLN G 216 ASN ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN H 146 GLN H 153 GLN H 181 ASN H 202 ASN ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN ** H 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 301 GLN ** I 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 GLN ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 380 HIS K 429 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 35601 Z= 0.405 Angle : 0.764 16.061 48224 Z= 0.394 Chirality : 0.049 0.279 5233 Planarity : 0.006 0.087 6307 Dihedral : 5.922 33.650 4819 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.44 % Favored : 91.52 % Rotamer: Outliers : 0.08 % Allowed : 5.77 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.18 (0.12), residues: 4350 helix: -0.30 (0.12), residues: 1733 sheet: -1.67 (0.18), residues: 632 loop : -2.43 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP K 365 HIS 0.015 0.002 HIS I 295 PHE 0.039 0.003 PHE O 332 TYR 0.027 0.002 TYR I 236 ARG 0.017 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 701 time to evaluate : 3.796 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: A 25 ASP cc_start: 0.7972 (p0) cc_final: 0.7492 (t70) REVERT: A 125 LYS cc_start: 0.7160 (pttt) cc_final: 0.6692 (tttt) REVERT: A 184 ARG cc_start: 0.6816 (mmp-170) cc_final: 0.6525 (mmp-170) REVERT: A 224 LYS cc_start: 0.7901 (ttmm) cc_final: 0.7661 (mttp) REVERT: A 232 ILE cc_start: 0.8500 (mt) cc_final: 0.8167 (mp) REVERT: A 279 LYS cc_start: 0.7893 (tptp) cc_final: 0.6542 (mttt) REVERT: A 384 MET cc_start: 0.8761 (tpp) cc_final: 0.8454 (ttm) REVERT: A 447 LYS cc_start: 0.7092 (ttpp) cc_final: 0.6721 (ttmm) REVERT: B 103 ASP cc_start: 0.8233 (m-30) cc_final: 0.7703 (m-30) REVERT: B 122 PHE cc_start: 0.8891 (m-80) cc_final: 0.8625 (m-80) REVERT: B 203 ILE cc_start: 0.7103 (mt) cc_final: 0.6799 (tt) REVERT: B 224 LYS cc_start: 0.7108 (tttt) cc_final: 0.6395 (ttpt) REVERT: B 302 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7554 (tpp80) REVERT: B 336 LYS cc_start: 0.5944 (pttt) cc_final: 0.5042 (ttpt) REVERT: B 385 PRO cc_start: 0.8803 (Cg_endo) cc_final: 0.8555 (Cg_exo) REVERT: B 390 ILE cc_start: 0.8912 (mm) cc_final: 0.8604 (pt) REVERT: C 48 ASP cc_start: 0.7860 (m-30) cc_final: 0.7406 (m-30) REVERT: C 128 ARG cc_start: 0.7024 (tpp80) cc_final: 0.6587 (ttt-90) REVERT: C 155 GLU cc_start: 0.8763 (pp20) cc_final: 0.8460 (pp20) REVERT: C 336 LYS cc_start: 0.6257 (mttt) cc_final: 0.5242 (pttm) REVERT: C 357 ARG cc_start: 0.7824 (mtp85) cc_final: 0.7285 (ttp80) REVERT: C 432 ARG cc_start: 0.7841 (mmm-85) cc_final: 0.7265 (mtp85) REVERT: D 95 PHE cc_start: 0.7813 (m-80) cc_final: 0.7291 (m-80) REVERT: D 107 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7916 (mm-30) REVERT: D 125 LYS cc_start: 0.6548 (pttt) cc_final: 0.6093 (mmtt) REVERT: D 135 ILE cc_start: 0.8410 (mt) cc_final: 0.8154 (mm) REVERT: D 203 ILE cc_start: 0.6484 (mm) cc_final: 0.6242 (mm) REVERT: D 300 ARG cc_start: 0.6124 (tpt90) cc_final: 0.5634 (tpt170) REVERT: D 336 LYS cc_start: 0.5345 (tttt) cc_final: 0.4986 (ttpt) REVERT: D 359 VAL cc_start: 0.9277 (t) cc_final: 0.9070 (m) REVERT: D 363 GLN cc_start: 0.8262 (tp40) cc_final: 0.7759 (tm-30) REVERT: D 408 TRP cc_start: 0.6157 (m-10) cc_final: 0.5743 (m100) REVERT: E 95 MET cc_start: 0.7358 (mmp) cc_final: 0.7086 (mmt) REVERT: E 184 ARG cc_start: 0.6560 (mpt180) cc_final: 0.4618 (ttp80) REVERT: E 205 ARG cc_start: 0.7235 (mmt-90) cc_final: 0.6946 (mtp85) REVERT: E 228 ARG cc_start: 0.6789 (mmm-85) cc_final: 0.5238 (mmm160) REVERT: F 95 MET cc_start: 0.5226 (pmm) cc_final: 0.4625 (mpp) REVERT: G 120 GLU cc_start: 0.7395 (tt0) cc_final: 0.6701 (pt0) REVERT: H 146 GLN cc_start: 0.7333 (mm-40) cc_final: 0.6780 (mp10) REVERT: H 153 GLN cc_start: 0.7305 (tm130) cc_final: 0.7096 (tm-30) REVERT: H 252 GLU cc_start: 0.7566 (mm-30) cc_final: 0.6993 (mm-30) REVERT: H 256 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7557 (tm-30) REVERT: H 294 MET cc_start: 0.7462 (tpp) cc_final: 0.7217 (tpp) REVERT: H 339 THR cc_start: 0.8425 (m) cc_final: 0.8126 (p) REVERT: H 451 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6940 (mt-10) REVERT: I 49 GLU cc_start: 0.7202 (tt0) cc_final: 0.6864 (mm-30) REVERT: I 78 LYS cc_start: 0.7296 (pttp) cc_final: 0.6135 (mttt) REVERT: I 161 LYS cc_start: 0.7973 (mtpp) cc_final: 0.7654 (mtpp) REVERT: I 336 LYS cc_start: 0.4495 (pttt) cc_final: 0.3488 (ptpp) REVERT: I 363 GLN cc_start: 0.9195 (tp40) cc_final: 0.8630 (tp40) REVERT: I 380 HIS cc_start: 0.6170 (p-80) cc_final: 0.5829 (p90) REVERT: I 412 PRO cc_start: 0.7460 (Cg_exo) cc_final: 0.7106 (Cg_endo) REVERT: J 29 LYS cc_start: 0.6426 (mttt) cc_final: 0.5864 (ttpt) REVERT: J 83 HIS cc_start: 0.8082 (t-90) cc_final: 0.7776 (t70) REVERT: J 94 TYR cc_start: 0.7501 (m-80) cc_final: 0.7034 (m-80) REVERT: J 95 PHE cc_start: 0.7031 (m-80) cc_final: 0.6219 (m-10) REVERT: J 294 MET cc_start: 0.7457 (tpp) cc_final: 0.7205 (ttm) REVERT: J 342 PHE cc_start: 0.7525 (p90) cc_final: 0.7261 (p90) REVERT: J 415 THR cc_start: 0.7445 (m) cc_final: 0.7227 (p) REVERT: K 155 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8438 (tm-30) REVERT: K 224 LYS cc_start: 0.7405 (mtpt) cc_final: 0.6951 (tppt) REVERT: K 302 ARG cc_start: 0.7137 (ptm160) cc_final: 0.5896 (mtt90) REVERT: K 303 ASN cc_start: 0.7799 (m-40) cc_final: 0.7349 (m-40) REVERT: K 336 LYS cc_start: 0.5921 (pttt) cc_final: 0.4659 (ptpp) outliers start: 3 outliers final: 2 residues processed: 704 average time/residue: 0.4850 time to fit residues: 538.7033 Evaluate side-chains 514 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 512 time to evaluate : 3.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 395 optimal weight: 20.0000 chunk 300 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 268 optimal weight: 8.9990 chunk 401 optimal weight: 5.9990 chunk 425 optimal weight: 0.9990 chunk 209 optimal weight: 9.9990 chunk 380 optimal weight: 0.0870 chunk 114 optimal weight: 0.8980 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN B 264 HIS ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 HIS ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN D 146 GLN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 GLN E 130 ASN E 233 ASN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 GLN G 216 ASN ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 406 HIS ** I 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 383 HIS ** I 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 GLN ** K 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 295 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35601 Z= 0.196 Angle : 0.630 13.316 48224 Z= 0.321 Chirality : 0.045 0.219 5233 Planarity : 0.005 0.067 6307 Dihedral : 5.354 31.413 4819 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.92 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.60 (0.12), residues: 4350 helix: 0.27 (0.12), residues: 1757 sheet: -1.34 (0.19), residues: 630 loop : -2.23 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 350 HIS 0.008 0.001 HIS E 147 PHE 0.045 0.002 PHE O 332 TYR 0.025 0.001 TYR I 236 ARG 0.014 0.001 ARG K 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 737 time to evaluate : 3.708 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: A 22 TYR cc_start: 0.7268 (t80) cc_final: 0.7050 (t80) REVERT: A 125 LYS cc_start: 0.7147 (pttt) cc_final: 0.6636 (ptpt) REVERT: A 184 ARG cc_start: 0.6688 (mmp-170) cc_final: 0.6329 (mmp-170) REVERT: A 224 LYS cc_start: 0.7793 (ttmm) cc_final: 0.7545 (mttp) REVERT: A 232 ILE cc_start: 0.8456 (mt) cc_final: 0.8119 (mp) REVERT: A 301 GLN cc_start: 0.7786 (tp40) cc_final: 0.7253 (tp40) REVERT: A 384 MET cc_start: 0.8724 (tpp) cc_final: 0.8383 (ttm) REVERT: A 447 LYS cc_start: 0.7053 (ttpp) cc_final: 0.6781 (ttmm) REVERT: B 32 ASP cc_start: 0.8289 (m-30) cc_final: 0.8064 (m-30) REVERT: B 103 ASP cc_start: 0.8261 (m-30) cc_final: 0.7629 (m-30) REVERT: B 122 PHE cc_start: 0.8851 (m-80) cc_final: 0.8452 (m-80) REVERT: B 203 ILE cc_start: 0.7130 (mt) cc_final: 0.6773 (tt) REVERT: B 224 LYS cc_start: 0.7079 (tttt) cc_final: 0.6339 (ttpt) REVERT: B 302 ARG cc_start: 0.7807 (ttm-80) cc_final: 0.7516 (tpp80) REVERT: B 336 LYS cc_start: 0.5898 (pttt) cc_final: 0.5081 (ttpt) REVERT: B 385 PRO cc_start: 0.8809 (Cg_endo) cc_final: 0.8541 (Cg_exo) REVERT: B 390 ILE cc_start: 0.8898 (mm) cc_final: 0.8555 (pt) REVERT: C 48 ASP cc_start: 0.7771 (m-30) cc_final: 0.7270 (m-30) REVERT: C 120 ASN cc_start: 0.8337 (p0) cc_final: 0.8050 (p0) REVERT: C 128 ARG cc_start: 0.7009 (tpp80) cc_final: 0.6631 (ttt-90) REVERT: C 295 HIS cc_start: 0.7818 (p-80) cc_final: 0.7473 (p90) REVERT: C 432 ARG cc_start: 0.7718 (mmm-85) cc_final: 0.7191 (mtp85) REVERT: D 95 PHE cc_start: 0.7789 (m-80) cc_final: 0.7232 (m-80) REVERT: D 125 LYS cc_start: 0.6390 (pttt) cc_final: 0.5990 (mmtp) REVERT: D 135 ILE cc_start: 0.8496 (mt) cc_final: 0.8228 (mm) REVERT: D 203 ILE cc_start: 0.6295 (mm) cc_final: 0.5663 (mm) REVERT: D 206 GLN cc_start: 0.7048 (mt0) cc_final: 0.6756 (mp10) REVERT: D 208 PHE cc_start: 0.7045 (p90) cc_final: 0.6611 (p90) REVERT: D 359 VAL cc_start: 0.9252 (t) cc_final: 0.8986 (m) REVERT: D 363 GLN cc_start: 0.8273 (tp40) cc_final: 0.7787 (tm-30) REVERT: D 408 TRP cc_start: 0.6150 (m-10) cc_final: 0.5723 (m100) REVERT: D 415 THR cc_start: 0.8281 (t) cc_final: 0.7973 (t) REVERT: E 95 MET cc_start: 0.7347 (mmp) cc_final: 0.7057 (mmt) REVERT: E 205 ARG cc_start: 0.7226 (mmt-90) cc_final: 0.6914 (mtp85) REVERT: E 228 ARG cc_start: 0.6745 (mmm-85) cc_final: 0.5311 (mmm-85) REVERT: F 95 MET cc_start: 0.4813 (pmm) cc_final: 0.4550 (mpp) REVERT: H 133 GLU cc_start: 0.6873 (mp0) cc_final: 0.6622 (mp0) REVERT: H 252 GLU cc_start: 0.7532 (mm-30) cc_final: 0.6831 (mt-10) REVERT: H 256 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7452 (tm-30) REVERT: H 339 THR cc_start: 0.8395 (m) cc_final: 0.8032 (t) REVERT: H 451 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6920 (mt-10) REVERT: I 49 GLU cc_start: 0.7084 (tt0) cc_final: 0.6848 (mm-30) REVERT: I 78 LYS cc_start: 0.7186 (pttp) cc_final: 0.6079 (mttt) REVERT: I 124 PHE cc_start: 0.6884 (t80) cc_final: 0.6613 (t80) REVERT: I 336 LYS cc_start: 0.4458 (pttt) cc_final: 0.3435 (ptpp) REVERT: I 412 PRO cc_start: 0.7595 (Cg_exo) cc_final: 0.7237 (Cg_endo) REVERT: J 29 LYS cc_start: 0.6386 (mttt) cc_final: 0.5939 (ttpt) REVERT: J 83 HIS cc_start: 0.8065 (t-90) cc_final: 0.7856 (t70) REVERT: J 94 TYR cc_start: 0.7467 (m-80) cc_final: 0.7028 (m-80) REVERT: J 95 PHE cc_start: 0.7045 (m-80) cc_final: 0.6217 (m-10) REVERT: J 104 LEU cc_start: 0.7899 (mp) cc_final: 0.7143 (tp) REVERT: J 238 ASN cc_start: 0.8017 (t0) cc_final: 0.7812 (t0) REVERT: J 342 PHE cc_start: 0.7550 (p90) cc_final: 0.7175 (p90) REVERT: J 415 THR cc_start: 0.7417 (m) cc_final: 0.7147 (p) REVERT: K 94 TYR cc_start: 0.7591 (m-80) cc_final: 0.7190 (m-80) REVERT: K 186 VAL cc_start: 0.7918 (t) cc_final: 0.7653 (p) REVERT: K 224 LYS cc_start: 0.7517 (mtpt) cc_final: 0.7030 (tppt) REVERT: K 302 ARG cc_start: 0.6937 (ptm160) cc_final: 0.6132 (mtm-85) REVERT: K 336 LYS cc_start: 0.5875 (pttt) cc_final: 0.4722 (ptpt) REVERT: K 384 MET cc_start: 0.7834 (ttm) cc_final: 0.7620 (ttp) REVERT: K 437 GLU cc_start: 0.3900 (mp0) cc_final: 0.3371 (mm-30) outliers start: 0 outliers final: 0 residues processed: 737 average time/residue: 0.4655 time to fit residues: 551.9224 Evaluate side-chains 537 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 537 time to evaluate : 3.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 354 optimal weight: 10.0000 chunk 241 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 316 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 362 optimal weight: 3.9990 chunk 293 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 381 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 HIS B 112 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 HIS ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN E 130 ASN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN ** H 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 295 HIS I 383 HIS ** J 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 150 HIS ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 35601 Z= 0.330 Angle : 0.702 14.366 48224 Z= 0.360 Chirality : 0.047 0.257 5233 Planarity : 0.006 0.089 6307 Dihedral : 5.572 28.728 4819 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.14 % Favored : 91.82 % Rotamer: Outliers : 0.06 % Allowed : 3.90 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % 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 (0.12), residues: 4350 helix: 0.24 (0.12), residues: 1739 sheet: -1.23 (0.19), residues: 626 loop : -2.18 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 408 HIS 0.007 0.002 HIS H 380 PHE 0.046 0.002 PHE O 332 TYR 0.026 0.002 TYR I 236 ARG 0.016 0.001 ARG K 316 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 645 time to evaluate : 3.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7855 (p0) cc_final: 0.7481 (t70) REVERT: A 125 LYS cc_start: 0.7321 (pttt) cc_final: 0.6653 (ptpt) REVERT: A 184 ARG cc_start: 0.6699 (mmp-170) cc_final: 0.6411 (mmp-170) REVERT: A 224 LYS cc_start: 0.7856 (ttmm) cc_final: 0.7589 (mttp) REVERT: A 279 LYS cc_start: 0.7947 (tptp) cc_final: 0.6597 (mttt) REVERT: A 447 LYS cc_start: 0.7151 (ttpp) cc_final: 0.6898 (ttmm) REVERT: B 103 ASP cc_start: 0.8262 (m-30) cc_final: 0.7670 (m-30) REVERT: B 203 ILE cc_start: 0.7207 (mt) cc_final: 0.6865 (tt) REVERT: B 224 LYS cc_start: 0.6987 (tttt) cc_final: 0.6768 (mmtm) REVERT: B 302 ARG cc_start: 0.7877 (ttm-80) cc_final: 0.7493 (tpp80) REVERT: B 336 LYS cc_start: 0.6013 (pttt) cc_final: 0.5219 (ttpt) REVERT: B 390 ILE cc_start: 0.8908 (mm) cc_final: 0.8524 (pt) REVERT: C 128 ARG cc_start: 0.7044 (tpp80) cc_final: 0.6684 (ttt-90) REVERT: C 155 GLU cc_start: 0.8556 (pp20) cc_final: 0.8341 (pp20) REVERT: C 240 THR cc_start: 0.7917 (p) cc_final: 0.7669 (p) REVERT: C 432 ARG cc_start: 0.7733 (mmm-85) cc_final: 0.7277 (mtp85) REVERT: D 95 PHE cc_start: 0.7731 (m-80) cc_final: 0.7210 (m-80) REVERT: D 125 LYS cc_start: 0.6411 (pttt) cc_final: 0.6040 (mmtt) REVERT: D 135 ILE cc_start: 0.8434 (mt) cc_final: 0.8187 (mm) REVERT: D 206 GLN cc_start: 0.7082 (mt0) cc_final: 0.6748 (mp10) REVERT: D 256 GLU cc_start: 0.7893 (tp30) cc_final: 0.7656 (tp30) REVERT: D 359 VAL cc_start: 0.9286 (t) cc_final: 0.9033 (m) REVERT: D 363 GLN cc_start: 0.8294 (tp40) cc_final: 0.7874 (tm-30) REVERT: D 415 THR cc_start: 0.8358 (t) cc_final: 0.8037 (t) REVERT: E 95 MET cc_start: 0.7376 (mmp) cc_final: 0.7163 (mmt) REVERT: E 184 ARG cc_start: 0.6478 (mpt180) cc_final: 0.4506 (ttp80) REVERT: E 205 ARG cc_start: 0.7199 (mmt-90) cc_final: 0.6890 (mtp85) REVERT: E 228 ARG cc_start: 0.6730 (mmm-85) cc_final: 0.5298 (mmm-85) REVERT: F 95 MET cc_start: 0.4786 (pmm) cc_final: 0.4114 (mpp) REVERT: F 186 ILE cc_start: 0.5561 (tt) cc_final: 0.5116 (tp) REVERT: H 153 GLN cc_start: 0.7194 (tm130) cc_final: 0.6725 (tm-30) REVERT: H 252 GLU cc_start: 0.7503 (mm-30) cc_final: 0.6787 (mt-10) REVERT: H 256 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7529 (tm-30) REVERT: H 294 MET cc_start: 0.7322 (tpp) cc_final: 0.6992 (tpp) REVERT: I 49 GLU cc_start: 0.7235 (tt0) cc_final: 0.6999 (mm-30) REVERT: I 78 LYS cc_start: 0.7386 (pttp) cc_final: 0.6153 (mttm) REVERT: I 121 VAL cc_start: 0.7551 (t) cc_final: 0.7342 (t) REVERT: I 124 PHE cc_start: 0.6874 (t80) cc_final: 0.6564 (t80) REVERT: I 336 LYS cc_start: 0.4432 (pttt) cc_final: 0.3420 (ptpp) REVERT: I 412 PRO cc_start: 0.7463 (Cg_exo) cc_final: 0.7124 (Cg_endo) REVERT: J 29 LYS cc_start: 0.6443 (mttt) cc_final: 0.5822 (ttpt) REVERT: J 49 GLU cc_start: 0.5775 (tp30) cc_final: 0.4413 (mm-30) REVERT: J 90 GLU cc_start: 0.6756 (tm-30) cc_final: 0.6140 (tm-30) REVERT: J 94 TYR cc_start: 0.7586 (m-80) cc_final: 0.7092 (m-80) REVERT: J 95 PHE cc_start: 0.7165 (m-80) cc_final: 0.6224 (m-10) REVERT: J 236 TYR cc_start: 0.8079 (m-80) cc_final: 0.7836 (m-80) REVERT: J 342 PHE cc_start: 0.7449 (p90) cc_final: 0.7162 (p90) REVERT: J 415 THR cc_start: 0.7360 (m) cc_final: 0.7124 (p) REVERT: K 94 TYR cc_start: 0.7803 (m-80) cc_final: 0.7554 (m-80) REVERT: K 120 ASN cc_start: 0.6946 (p0) cc_final: 0.6632 (t0) REVERT: K 155 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8442 (tm-30) REVERT: K 171 ILE cc_start: 0.8192 (mp) cc_final: 0.7989 (mp) REVERT: K 224 LYS cc_start: 0.7445 (mtpt) cc_final: 0.6964 (tppt) REVERT: K 281 CYS cc_start: 0.8396 (m) cc_final: 0.8152 (m) REVERT: K 302 ARG cc_start: 0.6971 (ptm160) cc_final: 0.6096 (mtt90) REVERT: K 384 MET cc_start: 0.7771 (ttm) cc_final: 0.7554 (ttp) REVERT: N 427 VAL cc_start: 0.3335 (t) cc_final: 0.2995 (t) REVERT: O 324 MET cc_start: 0.0366 (tpp) cc_final: -0.1388 (mtm) outliers start: 2 outliers final: 0 residues processed: 645 average time/residue: 0.4717 time to fit residues: 491.3931 Evaluate side-chains 501 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 501 time to evaluate : 4.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 143 optimal weight: 6.9990 chunk 383 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 249 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 425 optimal weight: 5.9990 chunk 353 optimal weight: 0.6980 chunk 197 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 223 optimal weight: 0.0870 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 ASN ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 383 HIS J 83 HIS ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 ASN ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35601 Z= 0.202 Angle : 0.626 12.464 48224 Z= 0.318 Chirality : 0.045 0.224 5233 Planarity : 0.006 0.142 6307 Dihedral : 5.268 29.788 4819 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.97 % Favored : 93.01 % Rotamer: Outliers : 0.03 % Allowed : 2.40 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % 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: -1.28 (0.12), residues: 4350 helix: 0.47 (0.12), residues: 1753 sheet: -0.97 (0.19), residues: 644 loop : -2.07 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 408 HIS 0.018 0.001 HIS B 295 PHE 0.037 0.002 PHE O 332 TYR 0.023 0.002 TYR I 236 ARG 0.007 0.000 ARG M 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 679 time to evaluate : 3.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.7355 (pttt) cc_final: 0.6684 (ptpt) REVERT: A 184 ARG cc_start: 0.6673 (mmp-170) cc_final: 0.6339 (mmp-170) REVERT: A 224 LYS cc_start: 0.7798 (ttmm) cc_final: 0.7560 (mttp) REVERT: A 279 LYS cc_start: 0.7885 (tptp) cc_final: 0.6542 (mttt) REVERT: A 436 ARG cc_start: 0.6836 (mmt180) cc_final: 0.6448 (ptp-170) REVERT: A 447 LYS cc_start: 0.7150 (ttpp) cc_final: 0.6911 (ttmm) REVERT: B 32 ASP cc_start: 0.8402 (m-30) cc_final: 0.8134 (m-30) REVERT: B 103 ASP cc_start: 0.8263 (m-30) cc_final: 0.7635 (m-30) REVERT: B 122 PHE cc_start: 0.8833 (m-80) cc_final: 0.8452 (m-80) REVERT: B 203 ILE cc_start: 0.7079 (mt) cc_final: 0.6813 (tt) REVERT: B 224 LYS cc_start: 0.6965 (tttt) cc_final: 0.6155 (ttpt) REVERT: B 302 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7438 (tpp80) REVERT: B 336 LYS cc_start: 0.6056 (pttt) cc_final: 0.5213 (ttpt) REVERT: B 385 PRO cc_start: 0.8739 (Cg_endo) cc_final: 0.8431 (Cg_exo) REVERT: B 390 ILE cc_start: 0.8888 (mm) cc_final: 0.8501 (pt) REVERT: C 49 GLU cc_start: 0.7388 (tp30) cc_final: 0.6749 (mm-30) REVERT: C 128 ARG cc_start: 0.7068 (tpp80) cc_final: 0.6726 (ttt-90) REVERT: C 240 THR cc_start: 0.7799 (p) cc_final: 0.7544 (p) REVERT: C 432 ARG cc_start: 0.7771 (mmm-85) cc_final: 0.7280 (mtp85) REVERT: D 95 PHE cc_start: 0.7654 (m-80) cc_final: 0.7159 (m-80) REVERT: D 125 LYS cc_start: 0.6376 (pttt) cc_final: 0.6013 (mmtp) REVERT: D 135 ILE cc_start: 0.8470 (mt) cc_final: 0.8246 (mm) REVERT: D 203 ILE cc_start: 0.6308 (mm) cc_final: 0.5942 (mm) REVERT: D 256 GLU cc_start: 0.7906 (tp30) cc_final: 0.7706 (tp30) REVERT: D 359 VAL cc_start: 0.9239 (t) cc_final: 0.8987 (m) REVERT: D 363 GLN cc_start: 0.8311 (tp40) cc_final: 0.7938 (tm-30) REVERT: D 415 THR cc_start: 0.8314 (t) cc_final: 0.8015 (t) REVERT: E 205 ARG cc_start: 0.7183 (mmt-90) cc_final: 0.6847 (mtp85) REVERT: E 228 ARG cc_start: 0.6767 (mmm-85) cc_final: 0.5353 (mmm-85) REVERT: F 95 MET cc_start: 0.4828 (pmm) cc_final: 0.4140 (mpp) REVERT: F 186 ILE cc_start: 0.5435 (tt) cc_final: 0.4956 (tp) REVERT: G 173 GLN cc_start: 0.6989 (mt0) cc_final: 0.6759 (mt0) REVERT: H 128 ARG cc_start: 0.7208 (ttt180) cc_final: 0.6754 (tpt170) REVERT: H 252 GLU cc_start: 0.7492 (mm-30) cc_final: 0.6764 (mt-10) REVERT: H 300 ARG cc_start: 0.6101 (mmm160) cc_final: 0.5895 (mmm160) REVERT: H 349 ASP cc_start: 0.6632 (p0) cc_final: 0.6406 (t0) REVERT: I 49 GLU cc_start: 0.7205 (tt0) cc_final: 0.6804 (mm-30) REVERT: I 78 LYS cc_start: 0.7379 (pttp) cc_final: 0.6182 (mttm) REVERT: I 124 PHE cc_start: 0.6938 (t80) cc_final: 0.6579 (t80) REVERT: I 336 LYS cc_start: 0.4416 (pttt) cc_final: 0.3427 (ptpp) REVERT: I 412 PRO cc_start: 0.7514 (Cg_exo) cc_final: 0.7147 (Cg_endo) REVERT: J 29 LYS cc_start: 0.6388 (mttt) cc_final: 0.5783 (ttpt) REVERT: J 49 GLU cc_start: 0.5786 (tp30) cc_final: 0.4407 (mm-30) REVERT: J 90 GLU cc_start: 0.6899 (tm-30) cc_final: 0.6406 (tm-30) REVERT: J 94 TYR cc_start: 0.7534 (m-80) cc_final: 0.7041 (m-80) REVERT: J 95 PHE cc_start: 0.7094 (m-80) cc_final: 0.6246 (m-10) REVERT: J 104 LEU cc_start: 0.7998 (mp) cc_final: 0.7254 (tp) REVERT: J 236 TYR cc_start: 0.8016 (m-80) cc_final: 0.7745 (m-80) REVERT: J 237 LEU cc_start: 0.9185 (mt) cc_final: 0.8924 (mt) REVERT: J 238 ASN cc_start: 0.8041 (t0) cc_final: 0.7767 (t0) REVERT: J 415 THR cc_start: 0.7253 (m) cc_final: 0.7024 (p) REVERT: K 76 ARG cc_start: 0.5155 (mtm180) cc_final: 0.4894 (mtm180) REVERT: K 94 TYR cc_start: 0.7809 (m-80) cc_final: 0.7552 (m-80) REVERT: K 120 ASN cc_start: 0.6930 (p0) cc_final: 0.6653 (t0) REVERT: K 186 VAL cc_start: 0.7899 (t) cc_final: 0.7669 (p) REVERT: K 224 LYS cc_start: 0.7438 (mtpt) cc_final: 0.6915 (tppt) REVERT: K 302 ARG cc_start: 0.6787 (ptm160) cc_final: 0.5846 (mtt90) REVERT: M 426 MET cc_start: 0.3800 (ppp) cc_final: 0.3295 (ppp) REVERT: N 427 VAL cc_start: 0.3263 (t) cc_final: 0.2827 (t) outliers start: 1 outliers final: 0 residues processed: 679 average time/residue: 0.4827 time to fit residues: 532.9572 Evaluate side-chains 522 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 522 time to evaluate : 4.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 410 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 242 optimal weight: 10.0000 chunk 310 optimal weight: 8.9990 chunk 240 optimal weight: 2.9990 chunk 358 optimal weight: 9.9990 chunk 237 optimal weight: 10.0000 chunk 424 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 258 optimal weight: 0.0670 chunk 195 optimal weight: 30.0000 overall best weight: 5.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN B 274 ASN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN C 380 HIS D 146 GLN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN E 130 ASN E 137 GLN F 66 GLN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 380 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 35601 Z= 0.404 Angle : 0.751 14.849 48224 Z= 0.386 Chirality : 0.049 0.291 5233 Planarity : 0.006 0.134 6307 Dihedral : 5.758 36.320 4819 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.53 % Favored : 91.43 % Rotamer: Outliers : 0.03 % Allowed : 2.32 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.54 (0.12), residues: 4350 helix: 0.17 (0.12), residues: 1743 sheet: -1.01 (0.19), residues: 614 loop : -2.13 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 408 HIS 0.019 0.002 HIS C 295 PHE 0.051 0.003 PHE O 332 TYR 0.032 0.002 TYR H 77 ARG 0.016 0.001 ARG C 443 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 624 time to evaluate : 4.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7884 (p0) cc_final: 0.7411 (t70) REVERT: A 184 ARG cc_start: 0.6691 (mmp-170) cc_final: 0.6396 (mmp-170) REVERT: A 224 LYS cc_start: 0.7864 (ttmm) cc_final: 0.7632 (mttp) REVERT: A 436 ARG cc_start: 0.6958 (mmt180) cc_final: 0.6546 (ptp-170) REVERT: B 103 ASP cc_start: 0.8296 (m-30) cc_final: 0.7699 (m-30) REVERT: B 203 ILE cc_start: 0.7177 (mt) cc_final: 0.6933 (tt) REVERT: B 302 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7444 (tpp80) REVERT: B 336 LYS cc_start: 0.6198 (pttt) cc_final: 0.5375 (ttpt) REVERT: B 390 ILE cc_start: 0.8886 (mm) cc_final: 0.8496 (pt) REVERT: B 440 ASP cc_start: 0.6865 (p0) cc_final: 0.6613 (m-30) REVERT: C 128 ARG cc_start: 0.7140 (tpp80) cc_final: 0.6743 (ttt-90) REVERT: C 155 GLU cc_start: 0.8524 (pp20) cc_final: 0.8214 (pp20) REVERT: C 166 MET cc_start: 0.8327 (mpp) cc_final: 0.7917 (mpp) REVERT: C 295 HIS cc_start: 0.7402 (p90) cc_final: 0.7201 (p90) REVERT: C 315 LEU cc_start: 0.8640 (tt) cc_final: 0.8356 (tt) REVERT: C 432 ARG cc_start: 0.7777 (mmm-85) cc_final: 0.7315 (mtp85) REVERT: D 95 PHE cc_start: 0.7765 (m-80) cc_final: 0.7259 (m-80) REVERT: D 125 LYS cc_start: 0.6426 (pttt) cc_final: 0.6070 (mmtp) REVERT: D 135 ILE cc_start: 0.8399 (mt) cc_final: 0.8181 (mm) REVERT: D 203 ILE cc_start: 0.5969 (mm) cc_final: 0.5569 (tt) REVERT: D 206 GLN cc_start: 0.7586 (mp10) cc_final: 0.7199 (mp10) REVERT: D 256 GLU cc_start: 0.7912 (tp30) cc_final: 0.7683 (tp30) REVERT: D 359 VAL cc_start: 0.9277 (t) cc_final: 0.9046 (m) REVERT: D 363 GLN cc_start: 0.8369 (tp40) cc_final: 0.8085 (tm-30) REVERT: D 393 ASP cc_start: 0.7149 (m-30) cc_final: 0.6948 (m-30) REVERT: E 91 LEU cc_start: 0.7729 (tp) cc_final: 0.7419 (tt) REVERT: E 184 ARG cc_start: 0.6432 (mpt180) cc_final: 0.4470 (ttp80) REVERT: E 205 ARG cc_start: 0.7146 (mmt-90) cc_final: 0.6759 (mtp85) REVERT: E 228 ARG cc_start: 0.6757 (mmm-85) cc_final: 0.5293 (mmm-85) REVERT: F 70 PRO cc_start: 0.5133 (Cg_exo) cc_final: 0.4849 (Cg_endo) REVERT: F 95 MET cc_start: 0.4910 (pmm) cc_final: 0.4326 (mpp) REVERT: H 128 ARG cc_start: 0.7350 (ttt180) cc_final: 0.6588 (tpt170) REVERT: H 252 GLU cc_start: 0.7486 (mm-30) cc_final: 0.6761 (mt-10) REVERT: H 300 ARG cc_start: 0.6014 (mmm160) cc_final: 0.5798 (mmm160) REVERT: I 49 GLU cc_start: 0.7345 (tt0) cc_final: 0.7102 (mm-30) REVERT: I 78 LYS cc_start: 0.7507 (pttp) cc_final: 0.6194 (mttm) REVERT: I 124 PHE cc_start: 0.6832 (t80) cc_final: 0.6546 (t80) REVERT: I 194 LEU cc_start: 0.7157 (mt) cc_final: 0.6947 (mt) REVERT: J 29 LYS cc_start: 0.6488 (mttt) cc_final: 0.6014 (tttt) REVERT: J 49 GLU cc_start: 0.6102 (tp30) cc_final: 0.4571 (mm-30) REVERT: J 90 GLU cc_start: 0.6917 (tm-30) cc_final: 0.6575 (tm-30) REVERT: J 91 GLU cc_start: 0.7183 (pm20) cc_final: 0.6687 (pm20) REVERT: J 95 PHE cc_start: 0.7201 (m-80) cc_final: 0.6286 (m-10) REVERT: J 184 ARG cc_start: 0.5997 (mmt180) cc_final: 0.5677 (tpm170) REVERT: J 236 TYR cc_start: 0.8244 (m-80) cc_final: 0.7973 (m-80) REVERT: J 342 PHE cc_start: 0.7507 (p90) cc_final: 0.7273 (p90) REVERT: J 354 ASP cc_start: 0.7484 (t70) cc_final: 0.6658 (m-30) REVERT: K 94 TYR cc_start: 0.7943 (m-80) cc_final: 0.7740 (m-80) REVERT: K 155 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8464 (tm-30) REVERT: K 224 LYS cc_start: 0.7344 (mtpt) cc_final: 0.6861 (tppt) REVERT: K 288 LEU cc_start: 0.9309 (tp) cc_final: 0.9037 (tt) REVERT: K 302 ARG cc_start: 0.7059 (ptm160) cc_final: 0.6158 (mtt90) REVERT: M 426 MET cc_start: 0.3687 (ppp) cc_final: 0.3316 (ppp) outliers start: 1 outliers final: 0 residues processed: 625 average time/residue: 0.4640 time to fit residues: 465.9609 Evaluate side-chains 491 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 491 time to evaluate : 3.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 262 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 253 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 269 optimal weight: 7.9990 chunk 288 optimal weight: 20.0000 chunk 209 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 333 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 GLN ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN H 209 GLN ** J 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.5644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35601 Z= 0.210 Angle : 0.633 12.624 48224 Z= 0.323 Chirality : 0.045 0.298 5233 Planarity : 0.006 0.111 6307 Dihedral : 5.303 35.691 4819 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.83 % Favored : 93.15 % Rotamer: Outliers : 0.03 % Allowed : 1.16 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.12), residues: 4350 helix: 0.48 (0.13), residues: 1747 sheet: -0.82 (0.19), residues: 614 loop : -2.00 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 365 HIS 0.016 0.001 HIS D 304 PHE 0.046 0.002 PHE O 332 TYR 0.024 0.002 TYR H 77 ARG 0.010 0.001 ARG C 443 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 654 time to evaluate : 4.277 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: A 25 ASP cc_start: 0.7793 (p0) cc_final: 0.7414 (t70) REVERT: A 184 ARG cc_start: 0.6640 (mmp-170) cc_final: 0.6310 (mmp-170) REVERT: A 224 LYS cc_start: 0.7818 (ttmm) cc_final: 0.7560 (mttp) REVERT: A 384 MET cc_start: 0.8615 (tpp) cc_final: 0.8114 (ttm) REVERT: A 436 ARG cc_start: 0.6896 (mmt180) cc_final: 0.6465 (ptp-170) REVERT: B 32 ASP cc_start: 0.8411 (m-30) cc_final: 0.8169 (m-30) REVERT: B 103 ASP cc_start: 0.8220 (m-30) cc_final: 0.7593 (m-30) REVERT: B 203 ILE cc_start: 0.7072 (mt) cc_final: 0.6829 (tt) REVERT: B 302 ARG cc_start: 0.7862 (ttm-80) cc_final: 0.7391 (tpp80) REVERT: B 336 LYS cc_start: 0.6181 (pttt) cc_final: 0.5313 (ttmt) REVERT: B 354 ASP cc_start: 0.6604 (t70) cc_final: 0.6079 (t0) REVERT: B 390 ILE cc_start: 0.8874 (mm) cc_final: 0.8484 (pt) REVERT: C 128 ARG cc_start: 0.7106 (tpp80) cc_final: 0.6829 (ttt-90) REVERT: C 204 ASN cc_start: 0.7398 (p0) cc_final: 0.7174 (p0) REVERT: C 432 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7419 (mtp85) REVERT: D 125 LYS cc_start: 0.6314 (pttt) cc_final: 0.5999 (mmtp) REVERT: D 135 ILE cc_start: 0.8462 (mt) cc_final: 0.8214 (mm) REVERT: D 203 ILE cc_start: 0.5979 (mm) cc_final: 0.5584 (tt) REVERT: D 206 GLN cc_start: 0.7617 (mp10) cc_final: 0.7153 (mp10) REVERT: D 256 GLU cc_start: 0.7904 (tp30) cc_final: 0.7682 (tp30) REVERT: D 359 VAL cc_start: 0.9238 (t) cc_final: 0.8986 (m) REVERT: D 363 GLN cc_start: 0.8336 (tp40) cc_final: 0.8093 (tm-30) REVERT: D 393 ASP cc_start: 0.7124 (m-30) cc_final: 0.6917 (m-30) REVERT: D 415 THR cc_start: 0.8273 (t) cc_final: 0.7957 (t) REVERT: E 91 LEU cc_start: 0.7534 (tp) cc_final: 0.7250 (tt) REVERT: E 205 ARG cc_start: 0.7148 (mmt-90) cc_final: 0.6752 (mtp85) REVERT: E 208 VAL cc_start: 0.7358 (p) cc_final: 0.6892 (p) REVERT: E 228 ARG cc_start: 0.6777 (mmm-85) cc_final: 0.5364 (mmm-85) REVERT: F 70 PRO cc_start: 0.4990 (Cg_exo) cc_final: 0.4681 (Cg_endo) REVERT: H 128 ARG cc_start: 0.7210 (ttt180) cc_final: 0.6521 (tpt170) REVERT: H 248 MET cc_start: 0.8475 (tpp) cc_final: 0.8224 (mmp) REVERT: H 252 GLU cc_start: 0.7493 (mm-30) cc_final: 0.6785 (mt-10) REVERT: H 300 ARG cc_start: 0.5981 (mmm160) cc_final: 0.5776 (mmm160) REVERT: I 49 GLU cc_start: 0.7316 (tt0) cc_final: 0.7094 (mm-30) REVERT: I 78 LYS cc_start: 0.7458 (pttp) cc_final: 0.6167 (mttm) REVERT: I 94 TYR cc_start: 0.7785 (m-80) cc_final: 0.7464 (m-80) REVERT: I 124 PHE cc_start: 0.6866 (t80) cc_final: 0.6634 (t80) REVERT: I 194 LEU cc_start: 0.6909 (mt) cc_final: 0.6682 (mt) REVERT: I 363 GLN cc_start: 0.8769 (tp40) cc_final: 0.8565 (tp40) REVERT: I 422 GLU cc_start: 0.7163 (tm-30) cc_final: 0.6896 (tm-30) REVERT: J 29 LYS cc_start: 0.6462 (mttt) cc_final: 0.5921 (tttt) REVERT: J 49 GLU cc_start: 0.6075 (tp30) cc_final: 0.4535 (mm-30) REVERT: J 83 HIS cc_start: 0.7612 (t70) cc_final: 0.7360 (t70) REVERT: J 91 GLU cc_start: 0.7200 (pm20) cc_final: 0.6760 (pm20) REVERT: J 238 ASN cc_start: 0.7931 (t0) cc_final: 0.7679 (t0) REVERT: J 342 PHE cc_start: 0.7475 (p90) cc_final: 0.7250 (p90) REVERT: K 155 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8520 (tm-30) REVERT: K 186 VAL cc_start: 0.7943 (t) cc_final: 0.7736 (p) REVERT: K 224 LYS cc_start: 0.7295 (mtpt) cc_final: 0.6890 (tppt) REVERT: K 281 CYS cc_start: 0.8364 (m) cc_final: 0.8139 (m) REVERT: K 302 ARG cc_start: 0.6793 (ptm160) cc_final: 0.6300 (mtm-85) REVERT: K 348 GLU cc_start: 0.7423 (tt0) cc_final: 0.7133 (tp30) REVERT: M 426 MET cc_start: 0.3721 (ppp) cc_final: 0.3366 (ppp) REVERT: O 324 MET cc_start: 0.0094 (tpp) cc_final: -0.1350 (mtm) outliers start: 1 outliers final: 0 residues processed: 654 average time/residue: 0.4755 time to fit residues: 502.4081 Evaluate side-chains 506 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 4.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 385 optimal weight: 0.2980 chunk 406 optimal weight: 40.0000 chunk 370 optimal weight: 9.9990 chunk 395 optimal weight: 0.1980 chunk 237 optimal weight: 6.9990 chunk 172 optimal weight: 0.0030 chunk 310 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 357 optimal weight: 9.9990 chunk 373 optimal weight: 0.0570 chunk 393 optimal weight: 30.0000 overall best weight: 1.5110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 383 HIS ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35601 Z= 0.192 Angle : 0.619 14.676 48224 Z= 0.313 Chirality : 0.044 0.267 5233 Planarity : 0.005 0.093 6307 Dihedral : 5.057 33.929 4819 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.99 % Favored : 92.99 % Rotamer: Outliers : 0.03 % Allowed : 0.52 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.01 (0.13), residues: 4350 helix: 0.63 (0.13), residues: 1777 sheet: -0.69 (0.19), residues: 644 loop : -1.93 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 365 HIS 0.007 0.001 HIS E 147 PHE 0.043 0.002 PHE O 332 TYR 0.024 0.001 TYR J 236 ARG 0.009 0.000 ARG C 443 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 650 time to evaluate : 3.686 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: A 25 ASP cc_start: 0.7744 (p0) cc_final: 0.7345 (t70) REVERT: A 94 TYR cc_start: 0.7164 (m-10) cc_final: 0.6715 (m-80) REVERT: A 184 ARG cc_start: 0.6620 (mmp-170) cc_final: 0.6284 (mmp-170) REVERT: A 224 LYS cc_start: 0.7777 (ttmm) cc_final: 0.7531 (mttp) REVERT: A 384 MET cc_start: 0.8608 (tpp) cc_final: 0.8102 (ttm) REVERT: A 436 ARG cc_start: 0.6811 (mmt180) cc_final: 0.6439 (ptp-170) REVERT: B 32 ASP cc_start: 0.8375 (m-30) cc_final: 0.8014 (m-30) REVERT: B 103 ASP cc_start: 0.8208 (m-30) cc_final: 0.7563 (m-30) REVERT: B 162 TYR cc_start: 0.8179 (m-80) cc_final: 0.7710 (m-80) REVERT: B 302 ARG cc_start: 0.7855 (ttm-80) cc_final: 0.7394 (tpp80) REVERT: B 336 LYS cc_start: 0.6105 (pttt) cc_final: 0.5292 (ttpt) REVERT: B 390 ILE cc_start: 0.8862 (mm) cc_final: 0.8470 (pt) REVERT: C 128 ARG cc_start: 0.7123 (tpp80) cc_final: 0.6774 (ttt-90) REVERT: C 432 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7497 (mtp85) REVERT: D 125 LYS cc_start: 0.6325 (pttt) cc_final: 0.6066 (mmtp) REVERT: D 135 ILE cc_start: 0.8443 (mt) cc_final: 0.8056 (mm) REVERT: D 203 ILE cc_start: 0.5980 (mm) cc_final: 0.5565 (tt) REVERT: D 206 GLN cc_start: 0.7583 (mp10) cc_final: 0.7085 (mp10) REVERT: D 256 GLU cc_start: 0.7910 (tp30) cc_final: 0.7685 (tp30) REVERT: D 359 VAL cc_start: 0.9201 (t) cc_final: 0.8955 (m) REVERT: D 415 THR cc_start: 0.8297 (t) cc_final: 0.7972 (t) REVERT: D 435 TYR cc_start: 0.6198 (t80) cc_final: 0.5919 (t80) REVERT: E 91 LEU cc_start: 0.7492 (tp) cc_final: 0.7216 (tt) REVERT: E 205 ARG cc_start: 0.7154 (mmt-90) cc_final: 0.6735 (mtp85) REVERT: E 208 VAL cc_start: 0.7441 (p) cc_final: 0.6999 (p) REVERT: E 228 ARG cc_start: 0.6787 (mmm-85) cc_final: 0.5407 (mmm-85) REVERT: G 88 ILE cc_start: 0.7749 (mm) cc_final: 0.7479 (mm) REVERT: H 128 ARG cc_start: 0.7219 (ttt180) cc_final: 0.6560 (tpt170) REVERT: H 133 GLU cc_start: 0.6976 (mp0) cc_final: 0.6653 (mp0) REVERT: H 252 GLU cc_start: 0.7497 (mm-30) cc_final: 0.6723 (mt-10) REVERT: H 259 MET cc_start: 0.7755 (mmm) cc_final: 0.7521 (mmt) REVERT: H 300 ARG cc_start: 0.5999 (mmm160) cc_final: 0.5776 (mmm160) REVERT: H 349 ASP cc_start: 0.6895 (t70) cc_final: 0.6673 (t0) REVERT: I 49 GLU cc_start: 0.7317 (tt0) cc_final: 0.6890 (mm-30) REVERT: I 78 LYS cc_start: 0.7426 (pttp) cc_final: 0.6141 (mttm) REVERT: I 94 TYR cc_start: 0.7724 (m-80) cc_final: 0.7429 (m-80) REVERT: I 194 LEU cc_start: 0.6948 (mt) cc_final: 0.6674 (mt) REVERT: I 422 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6890 (tm-30) REVERT: J 29 LYS cc_start: 0.6284 (mttt) cc_final: 0.5787 (tttt) REVERT: J 49 GLU cc_start: 0.6050 (tp30) cc_final: 0.4531 (mm-30) REVERT: J 90 GLU cc_start: 0.7004 (tm-30) cc_final: 0.6728 (tm-30) REVERT: J 91 GLU cc_start: 0.7100 (pm20) cc_final: 0.6752 (pm20) REVERT: J 104 LEU cc_start: 0.7866 (mp) cc_final: 0.7460 (tp) REVERT: J 184 ARG cc_start: 0.5845 (mmt180) cc_final: 0.5537 (tpm170) REVERT: J 238 ASN cc_start: 0.7888 (t0) cc_final: 0.7529 (t0) REVERT: J 342 PHE cc_start: 0.7490 (p90) cc_final: 0.7218 (p90) REVERT: J 442 LEU cc_start: 0.7995 (tp) cc_final: 0.7089 (pp) REVERT: K 186 VAL cc_start: 0.7985 (t) cc_final: 0.7760 (p) REVERT: K 224 LYS cc_start: 0.7369 (mtpt) cc_final: 0.6885 (tppt) REVERT: K 281 CYS cc_start: 0.8318 (m) cc_final: 0.8081 (m) REVERT: K 302 ARG cc_start: 0.6734 (ptm160) cc_final: 0.6509 (mpt180) REVERT: K 348 GLU cc_start: 0.7364 (tt0) cc_final: 0.7039 (tp30) REVERT: M 426 MET cc_start: 0.3730 (ppp) cc_final: 0.3357 (ppp) REVERT: O 324 MET cc_start: -0.0129 (tpp) cc_final: -0.1363 (mtm) outliers start: 1 outliers final: 0 residues processed: 650 average time/residue: 0.4472 time to fit residues: 473.6834 Evaluate side-chains 506 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 4.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 259 optimal weight: 0.0770 chunk 417 optimal weight: 6.9990 chunk 255 optimal weight: 20.0000 chunk 198 optimal weight: 1.9990 chunk 290 optimal weight: 9.9990 chunk 438 optimal weight: 9.9990 chunk 403 optimal weight: 50.0000 chunk 349 optimal weight: 10.0000 chunk 36 optimal weight: 0.0470 chunk 269 optimal weight: 0.9980 chunk 214 optimal weight: 10.0000 overall best weight: 2.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN G 144 GLN ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35601 Z= 0.208 Angle : 0.627 13.540 48224 Z= 0.316 Chirality : 0.045 0.262 5233 Planarity : 0.005 0.084 6307 Dihedral : 5.015 34.748 4819 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.76 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.13), residues: 4350 helix: 0.71 (0.13), residues: 1773 sheet: -0.59 (0.19), residues: 644 loop : -1.91 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 459 HIS 0.007 0.001 HIS J 289 PHE 0.039 0.002 PHE O 332 TYR 0.023 0.001 TYR K 187 ARG 0.012 0.001 ARG H 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 637 time to evaluate : 4.259 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: A 25 ASP cc_start: 0.7727 (p0) cc_final: 0.7337 (t70) REVERT: A 94 TYR cc_start: 0.7180 (m-10) cc_final: 0.6749 (m-80) REVERT: A 184 ARG cc_start: 0.6589 (mmp-170) cc_final: 0.6284 (mmp-170) REVERT: A 224 LYS cc_start: 0.7753 (ttmm) cc_final: 0.7511 (mttp) REVERT: A 384 MET cc_start: 0.8609 (tpp) cc_final: 0.8135 (ttm) REVERT: A 436 ARG cc_start: 0.6815 (mmt180) cc_final: 0.6454 (ptp-170) REVERT: B 32 ASP cc_start: 0.8399 (m-30) cc_final: 0.8076 (m-30) REVERT: B 103 ASP cc_start: 0.8233 (m-30) cc_final: 0.7590 (m-30) REVERT: B 302 ARG cc_start: 0.7871 (ttm-80) cc_final: 0.7391 (tpp80) REVERT: B 336 LYS cc_start: 0.6108 (pttt) cc_final: 0.5303 (ttpt) REVERT: B 387 LEU cc_start: 0.8403 (mt) cc_final: 0.8172 (mt) REVERT: B 390 ILE cc_start: 0.8857 (mm) cc_final: 0.8461 (pt) REVERT: C 128 ARG cc_start: 0.7084 (tpp80) cc_final: 0.6760 (ttt-90) REVERT: C 432 ARG cc_start: 0.7824 (mmm-85) cc_final: 0.7526 (mtp85) REVERT: D 32 ASP cc_start: 0.8544 (m-30) cc_final: 0.7629 (t0) REVERT: D 38 ARG cc_start: 0.8063 (ttt-90) cc_final: 0.7757 (ttt90) REVERT: D 125 LYS cc_start: 0.6287 (pttt) cc_final: 0.6052 (mmtp) REVERT: D 135 ILE cc_start: 0.8398 (mt) cc_final: 0.8113 (mm) REVERT: D 203 ILE cc_start: 0.5967 (mm) cc_final: 0.5605 (tt) REVERT: D 206 GLN cc_start: 0.7667 (mp10) cc_final: 0.7109 (mp10) REVERT: D 256 GLU cc_start: 0.7881 (tp30) cc_final: 0.7648 (tp30) REVERT: D 359 VAL cc_start: 0.9190 (t) cc_final: 0.8943 (m) REVERT: D 393 ASP cc_start: 0.7242 (m-30) cc_final: 0.7019 (m-30) REVERT: D 415 THR cc_start: 0.8294 (t) cc_final: 0.7950 (t) REVERT: D 435 TYR cc_start: 0.6161 (t80) cc_final: 0.5891 (t80) REVERT: E 91 LEU cc_start: 0.7447 (tp) cc_final: 0.7180 (tt) REVERT: E 205 ARG cc_start: 0.7171 (mmt-90) cc_final: 0.6723 (mtp85) REVERT: E 208 VAL cc_start: 0.7432 (p) cc_final: 0.7015 (p) REVERT: E 228 ARG cc_start: 0.6773 (mmm-85) cc_final: 0.5397 (mmm-85) REVERT: E 263 GLU cc_start: 0.6375 (mm-30) cc_final: 0.6024 (mm-30) REVERT: H 128 ARG cc_start: 0.7156 (ttt180) cc_final: 0.6560 (tpt170) REVERT: H 133 GLU cc_start: 0.6965 (mp0) cc_final: 0.6429 (mp0) REVERT: H 252 GLU cc_start: 0.7446 (mm-30) cc_final: 0.6744 (mt-10) REVERT: H 294 MET cc_start: 0.7510 (tpt) cc_final: 0.7206 (tpp) REVERT: I 49 GLU cc_start: 0.7344 (tt0) cc_final: 0.6907 (mm-30) REVERT: I 78 LYS cc_start: 0.7456 (pttp) cc_final: 0.6177 (mttm) REVERT: I 94 TYR cc_start: 0.7707 (m-80) cc_final: 0.7371 (m-80) REVERT: I 155 GLU cc_start: 0.7884 (tt0) cc_final: 0.7622 (tt0) REVERT: I 194 LEU cc_start: 0.7037 (mt) cc_final: 0.6750 (mt) REVERT: I 422 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6897 (tm-30) REVERT: J 29 LYS cc_start: 0.6333 (mttt) cc_final: 0.5835 (tttp) REVERT: J 49 GLU cc_start: 0.6071 (tp30) cc_final: 0.4518 (mm-30) REVERT: J 104 LEU cc_start: 0.7867 (mp) cc_final: 0.7489 (tp) REVERT: J 184 ARG cc_start: 0.5870 (mmt180) cc_final: 0.5542 (tpm170) REVERT: J 238 ASN cc_start: 0.7898 (t0) cc_final: 0.7644 (t0) REVERT: J 259 MET cc_start: 0.8447 (mmm) cc_final: 0.8221 (mtt) REVERT: J 342 PHE cc_start: 0.7429 (p90) cc_final: 0.7209 (p90) REVERT: J 442 LEU cc_start: 0.7981 (tp) cc_final: 0.7156 (pp) REVERT: K 186 VAL cc_start: 0.7969 (t) cc_final: 0.7737 (p) REVERT: K 187 TYR cc_start: 0.6633 (t80) cc_final: 0.6366 (t80) REVERT: K 224 LYS cc_start: 0.7256 (mtpt) cc_final: 0.6867 (tppt) REVERT: K 281 CYS cc_start: 0.8359 (m) cc_final: 0.8154 (m) REVERT: K 348 GLU cc_start: 0.7341 (tt0) cc_final: 0.6970 (tp30) REVERT: M 426 MET cc_start: 0.3715 (ppp) cc_final: 0.3363 (ppp) REVERT: O 291 VAL cc_start: 0.6472 (p) cc_final: 0.6267 (m) outliers start: 0 outliers final: 0 residues processed: 637 average time/residue: 0.4660 time to fit residues: 481.9476 Evaluate side-chains 511 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 511 time to evaluate : 3.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 277 optimal weight: 8.9990 chunk 371 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 321 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 349 optimal weight: 0.0050 chunk 146 optimal weight: 6.9990 chunk 359 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 GLN ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 GLN ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 398 GLN ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.152834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.117996 restraints weight = 60943.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.116269 restraints weight = 45760.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.116208 restraints weight = 39637.960| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.5959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35601 Z= 0.204 Angle : 0.621 13.431 48224 Z= 0.314 Chirality : 0.045 0.323 5233 Planarity : 0.005 0.079 6307 Dihedral : 4.962 33.583 4819 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.97 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.13), residues: 4350 helix: 0.78 (0.13), residues: 1773 sheet: -0.49 (0.19), residues: 642 loop : -1.90 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 459 HIS 0.010 0.001 HIS K 295 PHE 0.041 0.002 PHE O 332 TYR 0.024 0.001 TYR A 22 ARG 0.009 0.000 ARG K 428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11292.25 seconds wall clock time: 200 minutes 57.17 seconds (12057.17 seconds total)