Starting phenix.real_space_refine on Mon Apr 8 08:27:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emh_28248/04_2024/8emh_28248.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emh_28248/04_2024/8emh_28248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emh_28248/04_2024/8emh_28248.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emh_28248/04_2024/8emh_28248.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emh_28248/04_2024/8emh_28248.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emh_28248/04_2024/8emh_28248.pdb" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 127 5.49 5 S 312 5.16 5 C 41517 2.51 5 N 11165 2.21 5 O 12557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A ASP 465": "OD1" <-> "OD2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B ASP 119": "OD1" <-> "OD2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 411": "OD1" <-> "OD2" Residue "B TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 542": "OE1" <-> "OE2" Residue "B TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 626": "OE1" <-> "OE2" Residue "C ASP 6": "OD1" <-> "OD2" Residue "C PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C ASP 95": "OD1" <-> "OD2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 312": "OE1" <-> "OE2" Residue "C TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 462": "OE1" <-> "OE2" Residue "C TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 494": "OE1" <-> "OE2" Residue "C TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 622": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D ASP 95": "OD1" <-> "OD2" Residue "D ASP 119": "OD1" <-> "OD2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 185": "OD1" <-> "OD2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "D ASP 279": "OD1" <-> "OD2" Residue "D GLU 312": "OE1" <-> "OE2" Residue "D TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D ASP 411": "OD1" <-> "OD2" Residue "D TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 453": "OE1" <-> "OE2" Residue "D PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 474": "OD1" <-> "OD2" Residue "E ASP 6": "OD1" <-> "OD2" Residue "E TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 52": "OD1" <-> "OD2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 279": "OD1" <-> "OD2" Residue "E ASP 297": "OD1" <-> "OD2" Residue "E GLU 312": "OE1" <-> "OE2" Residue "E PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 383": "OE1" <-> "OE2" Residue "E GLU 462": "OE1" <-> "OE2" Residue "E TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 485": "OE1" <-> "OE2" Residue "E TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F GLU 87": "OE1" <-> "OE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 185": "OD1" <-> "OD2" Residue "F PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 219": "OE1" <-> "OE2" Residue "F TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F GLU 240": "OE1" <-> "OE2" Residue "F PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 309": "OE1" <-> "OE2" Residue "F GLU 312": "OE1" <-> "OE2" Residue "F TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 383": "OE1" <-> "OE2" Residue "F TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 474": "OD1" <-> "OD2" Residue "F TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G ASP 95": "OD1" <-> "OD2" Residue "G PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "G PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 219": "OE1" <-> "OE2" Residue "G PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 648": "OD1" <-> "OD2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "H TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 79": "OE1" <-> "OE2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 205": "OD1" <-> "OD2" Residue "H PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 219": "OE1" <-> "OE2" Residue "H TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 226": "OE1" <-> "OE2" Residue "H GLU 240": "OE1" <-> "OE2" Residue "H PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 312": "OE1" <-> "OE2" Residue "H PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 453": "OE1" <-> "OE2" Residue "H TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 485": "OE1" <-> "OE2" Residue "H TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 519": "OE1" <-> "OE2" Residue "H TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 622": "OE1" <-> "OE2" Residue "H PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 129": "OE1" <-> "OE2" Residue "I TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 205": "OD1" <-> "OD2" Residue "I PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 297": "OD1" <-> "OD2" Residue "I GLU 309": "OE1" <-> "OE2" Residue "I TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 383": "OE1" <-> "OE2" Residue "I GLU 387": "OE1" <-> "OE2" Residue "I GLU 398": "OE1" <-> "OE2" Residue "I TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 462": "OE1" <-> "OE2" Residue "I TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 519": "OE1" <-> "OE2" Residue "I ASP 648": "OD1" <-> "OD2" Residue "J PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 70": "OE1" <-> "OE2" Residue "J ASP 95": "OD1" <-> "OD2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J GLU 131": "OE1" <-> "OE2" Residue "J PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 204": "OE1" <-> "OE2" Residue "J PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 290": "OD1" <-> "OD2" Residue "J ASP 297": "OD1" <-> "OD2" Residue "J GLU 309": "OE1" <-> "OE2" Residue "J ASP 346": "OD1" <-> "OD2" Residue "J TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 383": "OE1" <-> "OE2" Residue "J GLU 398": "OE1" <-> "OE2" Residue "J GLU 453": "OE1" <-> "OE2" Residue "J GLU 485": "OE1" <-> "OE2" Residue "J GLU 494": "OE1" <-> "OE2" Residue "J GLU 519": "OE1" <-> "OE2" Residue "J PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 648": "OD1" <-> "OD2" Residue "K GLU 87": "OE1" <-> "OE2" Residue "K GLU 103": "OE1" <-> "OE2" Residue "K GLU 121": "OE1" <-> "OE2" Residue "K PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 174": "OE1" <-> "OE2" Residue "K GLU 204": "OE1" <-> "OE2" Residue "K PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 297": "OD1" <-> "OD2" Residue "K GLU 312": "OE1" <-> "OE2" Residue "K PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 42": "OE1" <-> "OE2" Residue "L GLU 77": "OE1" <-> "OE2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "L GLU 103": "OE1" <-> "OE2" Residue "L PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 205": "OD1" <-> "OD2" Residue "L TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 328": "OE1" <-> "OE2" Residue "L GLU 342": "OE1" <-> "OE2" Residue "L TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 398": "OE1" <-> "OE2" Residue "L PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 462": "OE1" <-> "OE2" Residue "L ASP 474": "OD1" <-> "OD2" Residue "L PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 65678 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 5282 Classifications: {'peptide': 672} Link IDs: {'PTRANS': 27, 'TRANS': 644} Chain breaks: 1 Chain: "B" Number of atoms: 5298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5298 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 27, 'TRANS': 648} Chain: "C" Number of atoms: 5282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5282 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 27, 'TRANS': 645} Chain breaks: 1 Chain: "D" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5245 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 27, 'TRANS': 639} Chain breaks: 1 Chain: "E" Number of atoms: 5210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5210 Classifications: {'peptide': 662} Link IDs: {'PTRANS': 25, 'TRANS': 636} Chain breaks: 1 Chain: "F" Number of atoms: 5238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5238 Classifications: {'peptide': 666} Link IDs: {'PTRANS': 25, 'TRANS': 640} Chain breaks: 1 Chain: "G" Number of atoms: 5271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5271 Classifications: {'peptide': 671} Link IDs: {'PTRANS': 27, 'TRANS': 643} Chain breaks: 1 Chain: "H" Number of atoms: 5269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5269 Classifications: {'peptide': 671} Link IDs: {'PTRANS': 27, 'TRANS': 643} Chain breaks: 1 Chain: "I" Number of atoms: 5282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 5282 Classifications: {'peptide': 672} Link IDs: {'PTRANS': 27, 'TRANS': 644} Chain breaks: 1 Chain: "J" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5267 Classifications: {'peptide': 670} Link IDs: {'PTRANS': 27, 'TRANS': 642} Chain breaks: 1 Chain: "K" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5222 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 26, 'TRANS': 637} Chain breaks: 1 Chain: "L" Number of atoms: 5206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5206 Classifications: {'peptide': 661} Link IDs: {'PTRANS': 25, 'TRANS': 635} Chain breaks: 1 Chain: "O" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1310 Classifications: {'DNA': 64} Link IDs: {'rna3p': 63} Chain: "P" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1296 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Time building chain proxies: 25.63, per 1000 atoms: 0.39 Number of scatterers: 65678 At special positions: 0 Unit cell: (153.994, 160.41, 223.505, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 312 16.00 P 127 15.00 O 12557 8.00 N 11165 7.00 C 41517 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.45 Conformation dependent library (CDL) restraints added in 9.1 seconds 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14816 Finding SS restraints... Secondary structure from input PDB file: 402 helices and 96 sheets defined 49.8% alpha, 18.2% beta 46 base pairs and 103 stacking pairs defined. Time for finding SS restraints: 18.68 Creating SS restraints... Processing helix chain 'A' and resid 2 through 17 Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.750A pdb=" N LEU A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 49 Processing helix chain 'A' and resid 53 through 72 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 77 through 89 removed outlier: 3.503A pdb=" N VAL A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 171 through 181 Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.820A pdb=" N ILE A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 203 through 219 Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 269 through 272 Processing helix chain 'A' and resid 290 through 302 Processing helix chain 'A' and resid 326 through 334 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 377 through 389 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 408 through 427 Processing helix chain 'A' and resid 433 through 460 removed outlier: 3.548A pdb=" N VAL A 437 " --> pdb=" O ASN A 433 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 451 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 464 removed outlier: 3.611A pdb=" N TYR A 464 " --> pdb=" O MET A 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 461 through 464' Processing helix chain 'A' and resid 537 through 554 Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 563 through 565 No H-bonds generated for 'chain 'A' and resid 563 through 565' Processing helix chain 'A' and resid 585 through 599 Processing helix chain 'A' and resid 623 through 635 Processing helix chain 'A' and resid 644 through 649 removed outlier: 4.118A pdb=" N ALA A 647 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 658 Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'B' and resid 3 through 17 removed outlier: 3.537A pdb=" N HIS B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 31 removed outlier: 3.603A pdb=" N LYS B 28 " --> pdb=" O LYS B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 48 Processing helix chain 'B' and resid 53 through 72 Processing helix chain 'B' and resid 77 through 89 Processing helix chain 'B' and resid 123 through 130 removed outlier: 3.645A pdb=" N VAL B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 134 Processing helix chain 'B' and resid 171 through 181 removed outlier: 3.596A pdb=" N LEU B 175 " --> pdb=" O ASN B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 195 removed outlier: 3.739A pdb=" N ILE B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 203 through 215 Processing helix chain 'B' and resid 216 through 218 No H-bonds generated for 'chain 'B' and resid 216 through 218' Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.602A pdb=" N LYS B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 269 through 272 Processing helix chain 'B' and resid 290 through 302 Processing helix chain 'B' and resid 326 through 334 Processing helix chain 'B' and resid 341 through 345 Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 377 through 390 removed outlier: 4.090A pdb=" N LYS B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 removed outlier: 3.800A pdb=" N LYS B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 395 through 400' Processing helix chain 'B' and resid 408 through 427 Processing helix chain 'B' and resid 433 through 460 removed outlier: 3.656A pdb=" N VAL B 451 " --> pdb=" O VAL B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 464 removed outlier: 4.047A pdb=" N TYR B 464 " --> pdb=" O MET B 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 461 through 464' Processing helix chain 'B' and resid 537 through 554 Processing helix chain 'B' and resid 554 through 560 Processing helix chain 'B' and resid 563 through 565 No H-bonds generated for 'chain 'B' and resid 563 through 565' Processing helix chain 'B' and resid 585 through 599 Processing helix chain 'B' and resid 623 through 635 Processing helix chain 'B' and resid 644 through 649 removed outlier: 3.910A pdb=" N ALA B 647 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 658 Processing helix chain 'B' and resid 667 through 677 Processing helix chain 'C' and resid 3 through 17 Processing helix chain 'C' and resid 24 through 32 removed outlier: 3.950A pdb=" N LYS C 28 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU C 32 " --> pdb=" O LYS C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 49 removed outlier: 3.567A pdb=" N LEU C 41 " --> pdb=" O PRO C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 72 Processing helix chain 'C' and resid 77 through 89 Processing helix chain 'C' and resid 123 through 130 Processing helix chain 'C' and resid 131 through 134 Processing helix chain 'C' and resid 171 through 181 Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 198 through 202 Processing helix chain 'C' and resid 203 through 215 Processing helix chain 'C' and resid 216 through 218 No H-bonds generated for 'chain 'C' and resid 216 through 218' Processing helix chain 'C' and resid 233 through 240 removed outlier: 4.546A pdb=" N ILE C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TYR C 238 " --> pdb=" O LYS C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 269 through 272 Processing helix chain 'C' and resid 280 through 284 Processing helix chain 'C' and resid 289 through 302 removed outlier: 4.264A pdb=" N GLN C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 332 Processing helix chain 'C' and resid 341 through 345 Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 360 through 362 No H-bonds generated for 'chain 'C' and resid 360 through 362' Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 377 through 389 Processing helix chain 'C' and resid 393 through 395 No H-bonds generated for 'chain 'C' and resid 393 through 395' Processing helix chain 'C' and resid 396 through 400 removed outlier: 4.003A pdb=" N TYR C 400 " --> pdb=" O SER C 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 396 through 400' Processing helix chain 'C' and resid 408 through 427 Processing helix chain 'C' and resid 433 through 460 removed outlier: 3.688A pdb=" N VAL C 437 " --> pdb=" O ASN C 433 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 451 " --> pdb=" O VAL C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 554 Processing helix chain 'C' and resid 554 through 560 removed outlier: 3.592A pdb=" N ILE C 558 " --> pdb=" O ASN C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 565 No H-bonds generated for 'chain 'C' and resid 563 through 565' Processing helix chain 'C' and resid 585 through 599 Processing helix chain 'C' and resid 623 through 635 Processing helix chain 'C' and resid 644 through 652 Proline residue: C 650 - end of helix Processing helix chain 'C' and resid 653 through 658 Processing helix chain 'C' and resid 667 through 677 Processing helix chain 'D' and resid 6 through 17 Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.969A pdb=" N LYS D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 29' Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.684A pdb=" N TYR D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 123 through 130 removed outlier: 3.569A pdb=" N VAL D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 134 Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 183 through 196 removed outlier: 3.647A pdb=" N ILE D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 Processing helix chain 'D' and resid 203 through 215 Processing helix chain 'D' and resid 216 through 218 No H-bonds generated for 'chain 'D' and resid 216 through 218' Processing helix chain 'D' and resid 235 through 241 Processing helix chain 'D' and resid 254 through 259 Processing helix chain 'D' and resid 269 through 272 Processing helix chain 'D' and resid 280 through 284 Processing helix chain 'D' and resid 290 through 302 Processing helix chain 'D' and resid 326 through 334 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 346 through 351 Processing helix chain 'D' and resid 360 through 362 No H-bonds generated for 'chain 'D' and resid 360 through 362' Processing helix chain 'D' and resid 366 through 370 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 395 through 400 removed outlier: 4.281A pdb=" N LYS D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR D 400 " --> pdb=" O SER D 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 395 through 400' Processing helix chain 'D' and resid 408 through 427 Processing helix chain 'D' and resid 433 through 460 removed outlier: 3.532A pdb=" N VAL D 437 " --> pdb=" O ASN D 433 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL D 451 " --> pdb=" O VAL D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 464 Processing helix chain 'D' and resid 540 through 554 Processing helix chain 'D' and resid 554 through 560 Processing helix chain 'D' and resid 563 through 565 No H-bonds generated for 'chain 'D' and resid 563 through 565' Processing helix chain 'D' and resid 585 through 599 Processing helix chain 'D' and resid 623 through 635 Processing helix chain 'D' and resid 644 through 652 removed outlier: 3.808A pdb=" N ALA D 647 " --> pdb=" O SER D 644 " (cutoff:3.500A) Proline residue: D 650 - end of helix Processing helix chain 'D' and resid 653 through 658 Processing helix chain 'D' and resid 667 through 677 Processing helix chain 'E' and resid 6 through 18 Processing helix chain 'E' and resid 24 through 31 removed outlier: 3.917A pdb=" N LYS E 28 " --> pdb=" O LYS E 24 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 48 removed outlier: 3.557A pdb=" N LEU E 41 " --> pdb=" O PRO E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 3.594A pdb=" N ASN E 71 " --> pdb=" O VAL E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 123 through 130 removed outlier: 3.572A pdb=" N VAL E 127 " --> pdb=" O SER E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 136 removed outlier: 3.806A pdb=" N VAL E 135 " --> pdb=" O GLU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 182 removed outlier: 3.670A pdb=" N LEU E 175 " --> pdb=" O ASN E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 195 Processing helix chain 'E' and resid 198 through 202 Processing helix chain 'E' and resid 203 through 215 Processing helix chain 'E' and resid 216 through 219 removed outlier: 3.925A pdb=" N GLU E 219 " --> pdb=" O PRO E 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 216 through 219' Processing helix chain 'E' and resid 235 through 241 Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 269 through 272 Processing helix chain 'E' and resid 281 through 284 Processing helix chain 'E' and resid 290 through 302 Processing helix chain 'E' and resid 326 through 334 Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 346 through 352 removed outlier: 3.661A pdb=" N ARG E 352 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 389 Processing helix chain 'E' and resid 393 through 397 removed outlier: 3.672A pdb=" N SER E 396 " --> pdb=" O PHE E 393 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE E 397 " --> pdb=" O ALA E 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 393 through 397' Processing helix chain 'E' and resid 408 through 427 Processing helix chain 'E' and resid 433 through 460 removed outlier: 3.534A pdb=" N VAL E 451 " --> pdb=" O VAL E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 554 Processing helix chain 'E' and resid 554 through 560 Processing helix chain 'E' and resid 563 through 565 No H-bonds generated for 'chain 'E' and resid 563 through 565' Processing helix chain 'E' and resid 585 through 599 Processing helix chain 'E' and resid 623 through 635 Processing helix chain 'E' and resid 644 through 649 removed outlier: 3.793A pdb=" N ALA E 647 " --> pdb=" O SER E 644 " (cutoff:3.500A) Processing helix chain 'E' and resid 653 through 659 removed outlier: 3.922A pdb=" N LYS E 659 " --> pdb=" O GLU E 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 667 through 677 Processing helix chain 'F' and resid 3 through 17 Processing helix chain 'F' and resid 25 through 31 Processing helix chain 'F' and resid 37 through 49 removed outlier: 3.505A pdb=" N LEU F 41 " --> pdb=" O PRO F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 72 removed outlier: 3.745A pdb=" N ASN F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR F 72 " --> pdb=" O LEU F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 77 through 89 Processing helix chain 'F' and resid 123 through 130 removed outlier: 3.619A pdb=" N VAL F 127 " --> pdb=" O SER F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 134 Processing helix chain 'F' and resid 171 through 181 Processing helix chain 'F' and resid 183 through 196 removed outlier: 3.743A pdb=" N ILE F 195 " --> pdb=" O LEU F 191 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY F 196 " --> pdb=" O ILE F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 202 Processing helix chain 'F' and resid 203 through 219 Proline residue: F 216 - end of helix Processing helix chain 'F' and resid 234 through 240 removed outlier: 4.440A pdb=" N TYR F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 269 through 272 Processing helix chain 'F' and resid 289 through 302 removed outlier: 4.592A pdb=" N GLN F 293 " --> pdb=" O LYS F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 334 Processing helix chain 'F' and resid 341 through 345 Processing helix chain 'F' and resid 346 through 352 removed outlier: 3.620A pdb=" N ARG F 352 " --> pdb=" O ALA F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 362 No H-bonds generated for 'chain 'F' and resid 360 through 362' Processing helix chain 'F' and resid 366 through 370 Processing helix chain 'F' and resid 377 through 389 Processing helix chain 'F' and resid 395 through 400 removed outlier: 3.838A pdb=" N LYS F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR F 400 " --> pdb=" O SER F 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 395 through 400' Processing helix chain 'F' and resid 408 through 427 Processing helix chain 'F' and resid 433 through 460 removed outlier: 3.503A pdb=" N VAL F 437 " --> pdb=" O ASN F 433 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL F 451 " --> pdb=" O VAL F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 464 Processing helix chain 'F' and resid 537 through 554 Processing helix chain 'F' and resid 554 through 560 Processing helix chain 'F' and resid 585 through 599 Processing helix chain 'F' and resid 623 through 635 Processing helix chain 'F' and resid 644 through 649 removed outlier: 3.687A pdb=" N ALA F 647 " --> pdb=" O SER F 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 659 removed outlier: 3.716A pdb=" N LYS F 659 " --> pdb=" O GLU F 655 " (cutoff:3.500A) Processing helix chain 'F' and resid 667 through 677 Processing helix chain 'G' and resid 5 through 17 Processing helix chain 'G' and resid 24 through 32 removed outlier: 3.679A pdb=" N LYS G 28 " --> pdb=" O LYS G 24 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 48 Processing helix chain 'G' and resid 53 through 72 Processing helix chain 'G' and resid 77 through 89 Processing helix chain 'G' and resid 123 through 130 removed outlier: 3.530A pdb=" N VAL G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 135 Processing helix chain 'G' and resid 173 through 182 Processing helix chain 'G' and resid 183 through 196 Processing helix chain 'G' and resid 203 through 215 Processing helix chain 'G' and resid 216 through 218 No H-bonds generated for 'chain 'G' and resid 216 through 218' Processing helix chain 'G' and resid 235 through 241 Processing helix chain 'G' and resid 254 through 259 Processing helix chain 'G' and resid 269 through 272 Processing helix chain 'G' and resid 281 through 284 Processing helix chain 'G' and resid 289 through 302 removed outlier: 4.576A pdb=" N GLN G 293 " --> pdb=" O LYS G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 334 Processing helix chain 'G' and resid 341 through 345 Processing helix chain 'G' and resid 346 through 351 Processing helix chain 'G' and resid 377 through 389 Processing helix chain 'G' and resid 393 through 397 removed outlier: 4.152A pdb=" N ILE G 397 " --> pdb=" O ALA G 394 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 427 Processing helix chain 'G' and resid 433 through 460 removed outlier: 3.578A pdb=" N VAL G 451 " --> pdb=" O VAL G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 554 Processing helix chain 'G' and resid 554 through 559 Processing helix chain 'G' and resid 563 through 565 No H-bonds generated for 'chain 'G' and resid 563 through 565' Processing helix chain 'G' and resid 585 through 599 Processing helix chain 'G' and resid 623 through 634 Processing helix chain 'G' and resid 643 through 649 removed outlier: 3.513A pdb=" N ALA G 647 " --> pdb=" O SER G 644 " (cutoff:3.500A) Processing helix chain 'G' and resid 653 through 658 Processing helix chain 'G' and resid 667 through 677 Processing helix chain 'H' and resid 4 through 16 Processing helix chain 'H' and resid 17 through 19 No H-bonds generated for 'chain 'H' and resid 17 through 19' Processing helix chain 'H' and resid 25 through 32 removed outlier: 4.439A pdb=" N GLU H 32 " --> pdb=" O LYS H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 48 Processing helix chain 'H' and resid 53 through 72 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 77 through 89 Processing helix chain 'H' and resid 123 through 130 Processing helix chain 'H' and resid 131 through 135 Processing helix chain 'H' and resid 171 through 181 Processing helix chain 'H' and resid 183 through 195 Processing helix chain 'H' and resid 198 through 202 Processing helix chain 'H' and resid 203 through 215 Processing helix chain 'H' and resid 216 through 218 No H-bonds generated for 'chain 'H' and resid 216 through 218' Processing helix chain 'H' and resid 235 through 240 Processing helix chain 'H' and resid 254 through 259 Processing helix chain 'H' and resid 269 through 272 Processing helix chain 'H' and resid 280 through 284 Processing helix chain 'H' and resid 289 through 302 removed outlier: 3.645A pdb=" N GLN H 293 " --> pdb=" O LYS H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 334 Processing helix chain 'H' and resid 341 through 345 Processing helix chain 'H' and resid 346 through 351 Processing helix chain 'H' and resid 360 through 362 No H-bonds generated for 'chain 'H' and resid 360 through 362' Processing helix chain 'H' and resid 366 through 370 Processing helix chain 'H' and resid 377 through 389 Processing helix chain 'H' and resid 395 through 400 removed outlier: 3.936A pdb=" N LYS H 399 " --> pdb=" O ASP H 395 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR H 400 " --> pdb=" O SER H 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 395 through 400' Processing helix chain 'H' and resid 408 through 427 Processing helix chain 'H' and resid 433 through 460 removed outlier: 3.610A pdb=" N VAL H 437 " --> pdb=" O ASN H 433 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL H 451 " --> pdb=" O VAL H 447 " (cutoff:3.500A) Processing helix chain 'H' and resid 461 through 464 Processing helix chain 'H' and resid 537 through 554 Processing helix chain 'H' and resid 554 through 560 Processing helix chain 'H' and resid 563 through 565 No H-bonds generated for 'chain 'H' and resid 563 through 565' Processing helix chain 'H' and resid 585 through 599 Processing helix chain 'H' and resid 623 through 635 Processing helix chain 'H' and resid 644 through 652 Proline residue: H 650 - end of helix Processing helix chain 'H' and resid 653 through 658 Processing helix chain 'H' and resid 667 through 677 Processing helix chain 'I' and resid 3 through 17 Processing helix chain 'I' and resid 25 through 31 Processing helix chain 'I' and resid 37 through 49 Processing helix chain 'I' and resid 53 through 72 Processing helix chain 'I' and resid 77 through 89 Processing helix chain 'I' and resid 123 through 130 removed outlier: 3.526A pdb=" N TYR I 130 " --> pdb=" O ILE I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 134 Processing helix chain 'I' and resid 171 through 181 Processing helix chain 'I' and resid 183 through 195 Processing helix chain 'I' and resid 198 through 202 Processing helix chain 'I' and resid 203 through 219 Proline residue: I 216 - end of helix Processing helix chain 'I' and resid 235 through 240 Processing helix chain 'I' and resid 254 through 259 Processing helix chain 'I' and resid 269 through 272 Processing helix chain 'I' and resid 280 through 284 Processing helix chain 'I' and resid 289 through 302 removed outlier: 4.159A pdb=" N GLN I 293 " --> pdb=" O LYS I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 334 Processing helix chain 'I' and resid 341 through 345 Processing helix chain 'I' and resid 346 through 351 Processing helix chain 'I' and resid 366 through 370 Processing helix chain 'I' and resid 377 through 389 Processing helix chain 'I' and resid 396 through 400 removed outlier: 4.286A pdb=" N TYR I 400 " --> pdb=" O SER I 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 396 through 400' Processing helix chain 'I' and resid 408 through 427 Processing helix chain 'I' and resid 433 through 460 removed outlier: 3.538A pdb=" N VAL I 437 " --> pdb=" O ASN I 433 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL I 451 " --> pdb=" O VAL I 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 461 through 464 removed outlier: 3.940A pdb=" N TYR I 464 " --> pdb=" O MET I 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 461 through 464' Processing helix chain 'I' and resid 537 through 554 Processing helix chain 'I' and resid 554 through 560 removed outlier: 3.859A pdb=" N ILE I 558 " --> pdb=" O ASN I 554 " (cutoff:3.500A) Processing helix chain 'I' and resid 563 through 565 No H-bonds generated for 'chain 'I' and resid 563 through 565' Processing helix chain 'I' and resid 585 through 599 Processing helix chain 'I' and resid 623 through 635 Processing helix chain 'I' and resid 644 through 652 removed outlier: 3.792A pdb=" N ALA I 647 " --> pdb=" O SER I 644 " (cutoff:3.500A) Proline residue: I 650 - end of helix Processing helix chain 'I' and resid 653 through 658 Processing helix chain 'I' and resid 667 through 677 Processing helix chain 'J' and resid 5 through 17 Processing helix chain 'J' and resid 24 through 32 removed outlier: 3.705A pdb=" N LYS J 28 " --> pdb=" O LYS J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 49 removed outlier: 3.601A pdb=" N LEU J 41 " --> pdb=" O PRO J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 71 removed outlier: 3.544A pdb=" N ASN J 71 " --> pdb=" O VAL J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 89 removed outlier: 3.521A pdb=" N LYS J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 130 removed outlier: 3.586A pdb=" N VAL J 127 " --> pdb=" O SER J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 136 removed outlier: 3.896A pdb=" N VAL J 135 " --> pdb=" O GLU J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 181 Processing helix chain 'J' and resid 183 through 195 removed outlier: 3.577A pdb=" N ILE J 195 " --> pdb=" O LEU J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 202 Processing helix chain 'J' and resid 203 through 219 Proline residue: J 216 - end of helix Processing helix chain 'J' and resid 235 through 241 removed outlier: 3.530A pdb=" N LYS J 239 " --> pdb=" O SER J 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 259 Processing helix chain 'J' and resid 269 through 272 Processing helix chain 'J' and resid 289 through 302 removed outlier: 4.244A pdb=" N GLN J 293 " --> pdb=" O LYS J 289 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 334 Processing helix chain 'J' and resid 341 through 345 Processing helix chain 'J' and resid 346 through 352 removed outlier: 3.761A pdb=" N ARG J 352 " --> pdb=" O ALA J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 360 through 362 No H-bonds generated for 'chain 'J' and resid 360 through 362' Processing helix chain 'J' and resid 366 through 370 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 396 through 399 Processing helix chain 'J' and resid 408 through 427 Processing helix chain 'J' and resid 433 through 460 removed outlier: 3.576A pdb=" N VAL J 451 " --> pdb=" O VAL J 447 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 464 removed outlier: 3.673A pdb=" N TYR J 464 " --> pdb=" O MET J 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 461 through 464' Processing helix chain 'J' and resid 537 through 554 Processing helix chain 'J' and resid 554 through 560 Processing helix chain 'J' and resid 585 through 599 Processing helix chain 'J' and resid 623 through 634 Processing helix chain 'J' and resid 644 through 649 removed outlier: 3.703A pdb=" N ALA J 647 " --> pdb=" O SER J 644 " (cutoff:3.500A) Processing helix chain 'J' and resid 653 through 658 Processing helix chain 'J' and resid 667 through 677 Processing helix chain 'K' and resid 5 through 17 Processing helix chain 'K' and resid 24 through 32 removed outlier: 3.502A pdb=" N LYS K 28 " --> pdb=" O LYS K 24 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU K 32 " --> pdb=" O LYS K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 49 Processing helix chain 'K' and resid 53 through 71 Processing helix chain 'K' and resid 74 through 76 No H-bonds generated for 'chain 'K' and resid 74 through 76' Processing helix chain 'K' and resid 77 through 89 removed outlier: 3.503A pdb=" N VAL K 81 " --> pdb=" O GLU K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 130 Processing helix chain 'K' and resid 131 through 135 Processing helix chain 'K' and resid 171 through 181 Processing helix chain 'K' and resid 183 through 195 Processing helix chain 'K' and resid 198 through 202 Processing helix chain 'K' and resid 203 through 219 Proline residue: K 216 - end of helix Processing helix chain 'K' and resid 235 through 240 Processing helix chain 'K' and resid 254 through 259 Processing helix chain 'K' and resid 269 through 272 Processing helix chain 'K' and resid 280 through 284 Processing helix chain 'K' and resid 290 through 302 Processing helix chain 'K' and resid 326 through 334 Processing helix chain 'K' and resid 341 through 345 Processing helix chain 'K' and resid 346 through 352 Processing helix chain 'K' and resid 360 through 362 No H-bonds generated for 'chain 'K' and resid 360 through 362' Processing helix chain 'K' and resid 377 through 389 Processing helix chain 'K' and resid 393 through 399 removed outlier: 3.944A pdb=" N ILE K 397 " --> pdb=" O ALA K 394 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS K 399 " --> pdb=" O SER K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 408 through 427 Processing helix chain 'K' and resid 433 through 460 Processing helix chain 'K' and resid 461 through 464 Processing helix chain 'K' and resid 537 through 554 Processing helix chain 'K' and resid 554 through 560 Processing helix chain 'K' and resid 585 through 599 Processing helix chain 'K' and resid 623 through 634 Processing helix chain 'K' and resid 644 through 646 No H-bonds generated for 'chain 'K' and resid 644 through 646' Processing helix chain 'K' and resid 648 through 652 Processing helix chain 'K' and resid 653 through 658 removed outlier: 3.622A pdb=" N PHE K 657 " --> pdb=" O PRO K 653 " (cutoff:3.500A) Processing helix chain 'K' and resid 667 through 677 Processing helix chain 'L' and resid 7 through 17 Processing helix chain 'L' and resid 24 through 32 removed outlier: 4.470A pdb=" N GLU L 32 " --> pdb=" O LYS L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 49 Processing helix chain 'L' and resid 53 through 71 removed outlier: 3.514A pdb=" N ALA L 69 " --> pdb=" O LYS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 76 No H-bonds generated for 'chain 'L' and resid 74 through 76' Processing helix chain 'L' and resid 77 through 89 removed outlier: 3.741A pdb=" N VAL L 81 " --> pdb=" O GLU L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 130 removed outlier: 3.691A pdb=" N VAL L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 134 Processing helix chain 'L' and resid 171 through 182 Processing helix chain 'L' and resid 183 through 196 Processing helix chain 'L' and resid 203 through 215 Processing helix chain 'L' and resid 216 through 218 No H-bonds generated for 'chain 'L' and resid 216 through 218' Processing helix chain 'L' and resid 235 through 240 Processing helix chain 'L' and resid 254 through 259 Processing helix chain 'L' and resid 268 through 272 Processing helix chain 'L' and resid 281 through 284 Processing helix chain 'L' and resid 289 through 302 removed outlier: 4.362A pdb=" N GLN L 293 " --> pdb=" O LYS L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 326 through 334 Processing helix chain 'L' and resid 341 through 345 Processing helix chain 'L' and resid 346 through 352 removed outlier: 3.884A pdb=" N ARG L 352 " --> pdb=" O ALA L 348 " (cutoff:3.500A) Processing helix chain 'L' and resid 377 through 389 Processing helix chain 'L' and resid 393 through 397 removed outlier: 3.520A pdb=" N SER L 396 " --> pdb=" O PHE L 393 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE L 397 " --> pdb=" O ALA L 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 393 through 397' Processing helix chain 'L' and resid 408 through 427 Processing helix chain 'L' and resid 433 through 460 removed outlier: 3.551A pdb=" N VAL L 437 " --> pdb=" O ASN L 433 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL L 451 " --> pdb=" O VAL L 447 " (cutoff:3.500A) Processing helix chain 'L' and resid 461 through 464 Processing helix chain 'L' and resid 537 through 554 Processing helix chain 'L' and resid 554 through 560 removed outlier: 3.711A pdb=" N ILE L 558 " --> pdb=" O ASN L 554 " (cutoff:3.500A) Processing helix chain 'L' and resid 585 through 599 Processing helix chain 'L' and resid 623 through 635 Processing helix chain 'L' and resid 644 through 649 Processing helix chain 'L' and resid 667 through 677 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 102 removed outlier: 4.185A pdb=" N TYR A 108 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU A 121 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N LEU A 161 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR A 143 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU A 162 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE A 141 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N TRP A 139 " --> pdb=" O PRO A 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 245 through 248 removed outlier: 6.375A pdb=" N ILE A 246 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N CYS A 225 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.615A pdb=" N ARG A 266 " --> pdb=" O ASN A 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 303 through 306 removed outlier: 3.551A pdb=" N GLU A 309 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 403 Processing sheet with id=AA7, first strand: chain 'A' and resid 501 through 507 removed outlier: 6.469A pdb=" N ALA A 530 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL A 573 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N SER A 532 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N GLU A 575 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 606 through 608 removed outlier: 6.477A pdb=" N VAL A 607 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL A 639 " --> pdb=" O SER A 663 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N TYR A 665 " --> pdb=" O VAL A 639 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 641 " --> pdb=" O TYR A 665 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 611 through 612 removed outlier: 4.051A pdb=" N ASP A 611 " --> pdb=" O THR A 619 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 21 through 23 Processing sheet with id=AB2, first strand: chain 'B' and resid 90 through 102 removed outlier: 4.083A pdb=" N TYR B 108 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR B 143 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU B 162 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE B 141 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N TRP B 139 " --> pdb=" O PRO B 164 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 245 through 248 removed outlier: 6.501A pdb=" N ILE B 246 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N CYS B 225 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 260 through 261 removed outlier: 3.558A pdb=" N ARG B 266 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 303 through 306 removed outlier: 3.931A pdb=" N GLU B 309 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 401 through 403 Processing sheet with id=AB7, first strand: chain 'B' and resid 529 through 532 removed outlier: 6.544A pdb=" N ALA B 530 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N VAL B 573 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER B 532 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLU B 575 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N PHE B 501 " --> pdb=" O MET B 606 " (cutoff:3.500A) removed outlier: 9.485A pdb=" N VAL B 608 " --> pdb=" O PHE B 501 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR B 503 " --> pdb=" O VAL B 608 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 639 " --> pdb=" O GLN B 661 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 611 through 612 removed outlier: 4.100A pdb=" N ASP B 611 " --> pdb=" O THR B 619 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AC1, first strand: chain 'C' and resid 90 through 102 removed outlier: 4.239A pdb=" N TYR C 108 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLU C 121 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N LEU C 161 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR C 143 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU C 162 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE C 141 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N TRP C 139 " --> pdb=" O PRO C 164 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 245 through 248 removed outlier: 6.390A pdb=" N ILE C 246 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N CYS C 225 " --> pdb=" O ILE C 357 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 260 through 261 Processing sheet with id=AC4, first strand: chain 'C' and resid 303 through 306 removed outlier: 3.512A pdb=" N GLU C 309 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 401 through 403 Processing sheet with id=AC6, first strand: chain 'C' and resid 529 through 532 removed outlier: 6.496A pdb=" N ALA C 530 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N VAL C 573 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N SER C 532 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N GLU C 575 " --> pdb=" O SER C 532 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N PHE C 501 " --> pdb=" O MET C 606 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N VAL C 608 " --> pdb=" O PHE C 501 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR C 503 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL C 607 " --> pdb=" O ALA C 640 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 611 through 612 removed outlier: 3.858A pdb=" N ASP C 611 " --> pdb=" O THR C 619 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 90 through 102 removed outlier: 4.336A pdb=" N TYR D 108 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLU D 121 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N LEU D 161 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR D 143 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU D 162 " --> pdb=" O ILE D 141 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE D 141 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TRP D 139 " --> pdb=" O PRO D 164 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 245 through 248 removed outlier: 6.632A pdb=" N ILE D 246 " --> pdb=" O ALA D 277 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL D 276 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL D 320 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE D 278 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N ASN D 322 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N CYS D 225 " --> pdb=" O ILE D 357 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 260 through 261 removed outlier: 3.521A pdb=" N ARG D 266 " --> pdb=" O ASN D 261 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 303 through 306 Processing sheet with id=AD3, first strand: chain 'D' and resid 401 through 403 Processing sheet with id=AD4, first strand: chain 'D' and resid 503 through 507 removed outlier: 6.346A pdb=" N ALA D 530 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL D 573 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER D 532 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N GLU D 575 " --> pdb=" O SER D 532 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 611 through 612 removed outlier: 3.765A pdb=" N ASP D 611 " --> pdb=" O THR D 619 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 638 through 642 removed outlier: 6.973A pdb=" N VAL D 639 " --> pdb=" O SER D 663 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N TYR D 665 " --> pdb=" O VAL D 639 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU D 641 " --> pdb=" O TYR D 665 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'E' and resid 21 through 23 Processing sheet with id=AD8, first strand: chain 'E' and resid 90 through 102 removed outlier: 4.222A pdb=" N TYR E 108 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLU E 121 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N LEU E 161 " --> pdb=" O GLU E 121 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL E 159 " --> pdb=" O SER E 145 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER E 145 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU E 161 " --> pdb=" O THR E 143 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 245 through 248 removed outlier: 7.147A pdb=" N CYS E 225 " --> pdb=" O ILE E 357 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 260 through 261 removed outlier: 3.627A pdb=" N ASN E 261 " --> pdb=" O ARG E 266 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG E 266 " --> pdb=" O ASN E 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 303 through 306 Processing sheet with id=AE3, first strand: chain 'E' and resid 401 through 403 Processing sheet with id=AE4, first strand: chain 'E' and resid 503 through 507 removed outlier: 6.594A pdb=" N ALA E 530 " --> pdb=" O LEU E 571 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL E 573 " --> pdb=" O ALA E 530 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N SER E 532 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N GLU E 575 " --> pdb=" O SER E 532 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 606 through 608 removed outlier: 6.755A pdb=" N VAL E 607 " --> pdb=" O ALA E 640 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL E 639 " --> pdb=" O SER E 663 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N TYR E 665 " --> pdb=" O VAL E 639 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU E 641 " --> pdb=" O TYR E 665 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 611 through 612 removed outlier: 3.930A pdb=" N ASP E 611 " --> pdb=" O THR E 619 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 21 through 23 Processing sheet with id=AE8, first strand: chain 'F' and resid 90 through 102 removed outlier: 4.338A pdb=" N TYR F 108 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLU F 121 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N LEU F 161 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR F 143 " --> pdb=" O SER F 160 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU F 162 " --> pdb=" O ILE F 141 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE F 141 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N TRP F 139 " --> pdb=" O PRO F 164 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 245 through 248 removed outlier: 6.719A pdb=" N ILE F 246 " --> pdb=" O ALA F 277 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU F 227 " --> pdb=" O ILE F 357 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 260 through 261 removed outlier: 3.611A pdb=" N ARG F 266 " --> pdb=" O ASN F 261 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 303 through 306 Processing sheet with id=AF3, first strand: chain 'F' and resid 401 through 403 Processing sheet with id=AF4, first strand: chain 'F' and resid 529 through 532 removed outlier: 6.477A pdb=" N ALA F 530 " --> pdb=" O LEU F 571 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL F 573 " --> pdb=" O ALA F 530 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER F 532 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N GLU F 575 " --> pdb=" O SER F 532 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N PHE F 501 " --> pdb=" O MET F 606 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N VAL F 608 " --> pdb=" O PHE F 501 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR F 503 " --> pdb=" O VAL F 608 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL F 607 " --> pdb=" O ALA F 640 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL F 639 " --> pdb=" O GLN F 661 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 21 through 23 Processing sheet with id=AF6, first strand: chain 'G' and resid 90 through 102 removed outlier: 4.083A pdb=" N TYR G 108 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR G 143 " --> pdb=" O SER G 160 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU G 162 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE G 141 " --> pdb=" O LEU G 162 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N TRP G 139 " --> pdb=" O PRO G 164 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 245 through 247 removed outlier: 6.567A pdb=" N ILE G 246 " --> pdb=" O ALA G 277 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASP G 279 " --> pdb=" O ILE G 246 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU G 227 " --> pdb=" O ILE G 357 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 260 through 261 Processing sheet with id=AF9, first strand: chain 'G' and resid 303 through 306 Processing sheet with id=AG1, first strand: chain 'G' and resid 401 through 403 Processing sheet with id=AG2, first strand: chain 'G' and resid 529 through 532 removed outlier: 6.377A pdb=" N ALA G 530 " --> pdb=" O LEU G 571 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL G 573 " --> pdb=" O ALA G 530 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER G 532 " --> pdb=" O VAL G 573 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N GLU G 575 " --> pdb=" O SER G 532 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR G 503 " --> pdb=" O VAL G 608 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 611 through 612 removed outlier: 4.119A pdb=" N ASP G 611 " --> pdb=" O THR G 619 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AG5, first strand: chain 'H' and resid 90 through 102 removed outlier: 4.340A pdb=" N TYR H 108 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU H 121 " --> pdb=" O VAL H 159 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N LEU H 161 " --> pdb=" O GLU H 121 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR H 143 " --> pdb=" O SER H 160 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU H 162 " --> pdb=" O ILE H 141 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE H 141 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N TRP H 139 " --> pdb=" O PRO H 164 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 245 through 248 removed outlier: 6.501A pdb=" N ILE H 246 " --> pdb=" O ALA H 277 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N CYS H 225 " --> pdb=" O ILE H 357 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 260 through 261 Processing sheet with id=AG8, first strand: chain 'H' and resid 303 through 306 Processing sheet with id=AG9, first strand: chain 'H' and resid 401 through 403 removed outlier: 4.398A pdb=" N PHE H 468 " --> pdb=" O VAL H 481 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 529 through 532 removed outlier: 6.314A pdb=" N ALA H 530 " --> pdb=" O LEU H 571 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL H 573 " --> pdb=" O ALA H 530 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N SER H 532 " --> pdb=" O VAL H 573 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N GLU H 575 " --> pdb=" O SER H 532 " (cutoff:3.500A) removed outlier: 9.786A pdb=" N PHE H 501 " --> pdb=" O MET H 606 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N VAL H 608 " --> pdb=" O PHE H 501 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TYR H 503 " --> pdb=" O VAL H 608 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 611 through 612 removed outlier: 3.854A pdb=" N ASP H 611 " --> pdb=" O THR H 619 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 21 through 23 Processing sheet with id=AH4, first strand: chain 'I' and resid 90 through 102 removed outlier: 4.311A pdb=" N TYR I 108 " --> pdb=" O ILE I 122 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLU I 121 " --> pdb=" O VAL I 159 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N LEU I 161 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR I 143 " --> pdb=" O SER I 160 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU I 162 " --> pdb=" O ILE I 141 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE I 141 " --> pdb=" O LEU I 162 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TRP I 139 " --> pdb=" O PRO I 164 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 245 through 248 removed outlier: 6.526A pdb=" N ILE I 246 " --> pdb=" O ALA I 277 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N CYS I 225 " --> pdb=" O ILE I 357 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 260 through 261 Processing sheet with id=AH7, first strand: chain 'I' and resid 303 through 306 Processing sheet with id=AH8, first strand: chain 'I' and resid 401 through 403 Processing sheet with id=AH9, first strand: chain 'I' and resid 529 through 532 removed outlier: 6.405A pdb=" N ALA I 530 " --> pdb=" O LEU I 571 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL I 573 " --> pdb=" O ALA I 530 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER I 532 " --> pdb=" O VAL I 573 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N GLU I 575 " --> pdb=" O SER I 532 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N PHE I 501 " --> pdb=" O MET I 606 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N VAL I 608 " --> pdb=" O PHE I 501 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR I 503 " --> pdb=" O VAL I 608 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA I 640 " --> pdb=" O VAL I 607 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 611 through 612 removed outlier: 3.850A pdb=" N ASP I 611 " --> pdb=" O THR I 619 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 21 through 23 Processing sheet with id=AI3, first strand: chain 'J' and resid 90 through 102 removed outlier: 4.218A pdb=" N TYR J 108 " --> pdb=" O ILE J 122 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLU J 121 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N LEU J 161 " --> pdb=" O GLU J 121 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR J 143 " --> pdb=" O SER J 160 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU J 162 " --> pdb=" O ILE J 141 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE J 141 " --> pdb=" O LEU J 162 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N TRP J 139 " --> pdb=" O PRO J 164 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 245 through 248 removed outlier: 6.589A pdb=" N ILE J 246 " --> pdb=" O ALA J 277 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASP J 279 " --> pdb=" O ILE J 246 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL J 248 " --> pdb=" O ASP J 279 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N CYS J 225 " --> pdb=" O ILE J 357 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 260 through 261 removed outlier: 3.512A pdb=" N ARG J 266 " --> pdb=" O ASN J 261 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 303 through 306 Processing sheet with id=AI7, first strand: chain 'J' and resid 401 through 403 Processing sheet with id=AI8, first strand: chain 'J' and resid 529 through 532 removed outlier: 6.486A pdb=" N ALA J 530 " --> pdb=" O LEU J 571 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N VAL J 573 " --> pdb=" O ALA J 530 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N SER J 532 " --> pdb=" O VAL J 573 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N GLU J 575 " --> pdb=" O SER J 532 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N PHE J 501 " --> pdb=" O MET J 606 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N VAL J 608 " --> pdb=" O PHE J 501 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR J 503 " --> pdb=" O VAL J 608 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL J 607 " --> pdb=" O ALA J 640 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL J 639 " --> pdb=" O GLN J 661 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'J' and resid 611 through 612 removed outlier: 3.885A pdb=" N ASP J 611 " --> pdb=" O THR J 619 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 21 through 23 Processing sheet with id=AJ2, first strand: chain 'K' and resid 90 through 102 removed outlier: 4.244A pdb=" N TYR K 108 " --> pdb=" O ILE K 122 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR K 143 " --> pdb=" O SER K 160 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU K 162 " --> pdb=" O ILE K 141 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE K 141 " --> pdb=" O LEU K 162 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N TRP K 139 " --> pdb=" O PRO K 164 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'K' and resid 245 through 248 removed outlier: 8.395A pdb=" N ILE K 357 " --> pdb=" O ASN K 223 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N CYS K 225 " --> pdb=" O ILE K 357 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'K' and resid 260 through 261 Processing sheet with id=AJ5, first strand: chain 'K' and resid 303 through 306 Processing sheet with id=AJ6, first strand: chain 'K' and resid 401 through 403 Processing sheet with id=AJ7, first strand: chain 'K' and resid 529 through 532 removed outlier: 6.516A pdb=" N ALA K 530 " --> pdb=" O LEU K 571 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N VAL K 573 " --> pdb=" O ALA K 530 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N SER K 532 " --> pdb=" O VAL K 573 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N GLU K 575 " --> pdb=" O SER K 532 " (cutoff:3.500A) removed outlier: 9.650A pdb=" N PHE K 501 " --> pdb=" O MET K 606 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N VAL K 608 " --> pdb=" O PHE K 501 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR K 503 " --> pdb=" O VAL K 608 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL K 607 " --> pdb=" O ALA K 640 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL K 639 " --> pdb=" O SER K 663 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N TYR K 665 " --> pdb=" O VAL K 639 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU K 641 " --> pdb=" O TYR K 665 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'K' and resid 611 through 612 removed outlier: 3.985A pdb=" N ASP K 611 " --> pdb=" O THR K 619 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'L' and resid 21 through 23 Processing sheet with id=AK1, first strand: chain 'L' and resid 90 through 102 removed outlier: 4.118A pdb=" N TYR L 108 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU L 121 " --> pdb=" O VAL L 159 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N LEU L 161 " --> pdb=" O GLU L 121 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR L 143 " --> pdb=" O SER L 160 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU L 162 " --> pdb=" O ILE L 141 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE L 141 " --> pdb=" O LEU L 162 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N TRP L 139 " --> pdb=" O PRO L 164 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'L' and resid 245 through 248 removed outlier: 3.768A pdb=" N LEU L 227 " --> pdb=" O ILE L 357 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'L' and resid 303 through 306 Processing sheet with id=AK4, first strand: chain 'L' and resid 401 through 403 Processing sheet with id=AK5, first strand: chain 'L' and resid 529 through 532 removed outlier: 6.626A pdb=" N ALA L 530 " --> pdb=" O LEU L 571 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N VAL L 573 " --> pdb=" O ALA L 530 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER L 532 " --> pdb=" O VAL L 573 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N GLU L 575 " --> pdb=" O SER L 532 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR L 504 " --> pdb=" O TYR L 516 " (cutoff:3.500A) removed outlier: 9.936A pdb=" N PHE L 501 " --> pdb=" O MET L 606 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N VAL L 608 " --> pdb=" O PHE L 501 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N TYR L 503 " --> pdb=" O VAL L 608 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL L 607 " --> pdb=" O ALA L 640 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'L' and resid 611 through 612 removed outlier: 3.717A pdb=" N ASP L 611 " --> pdb=" O THR L 619 " (cutoff:3.500A) 3061 hydrogen bonds defined for protein. 8583 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 108 hydrogen bonds 206 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 103 stacking parallelities Total time for adding SS restraints: 31.18 Time building geometry restraints manager: 23.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 20180 1.34 - 1.46: 11698 1.46 - 1.58: 34603 1.58 - 1.70: 252 1.70 - 1.82: 564 Bond restraints: 67297 Sorted by residual: bond pdb=" C ALA C 338 " pdb=" N PRO C 339 " ideal model delta sigma weight residual 1.333 1.361 -0.028 1.44e-02 4.82e+03 3.82e+00 bond pdb=" C3' DT P 12 " pdb=" O3' DT P 12 " ideal model delta sigma weight residual 1.422 1.476 -0.054 3.00e-02 1.11e+03 3.19e+00 bond pdb=" CG PRO H 513 " pdb=" CD PRO H 513 " ideal model delta sigma weight residual 1.503 1.446 0.057 3.40e-02 8.65e+02 2.77e+00 bond pdb=" C3' DG O 14 " pdb=" O3' DG O 14 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.70e+00 bond pdb=" N ASN I 578 " pdb=" CA ASN I 578 " ideal model delta sigma weight residual 1.457 1.479 -0.021 1.29e-02 6.01e+03 2.69e+00 ... (remaining 67292 not shown) Histogram of bond angle deviations from ideal: 96.61 - 104.09: 1316 104.09 - 111.58: 30102 111.58 - 119.06: 24116 119.06 - 126.55: 34723 126.55 - 134.03: 1110 Bond angle restraints: 91367 Sorted by residual: angle pdb=" CA ARG E 74 " pdb=" CB ARG E 74 " pdb=" CG ARG E 74 " ideal model delta sigma weight residual 114.10 125.96 -11.86 2.00e+00 2.50e-01 3.52e+01 angle pdb=" N ILE E 165 " pdb=" CA ILE E 165 " pdb=" C ILE E 165 " ideal model delta sigma weight residual 112.90 107.36 5.54 9.60e-01 1.09e+00 3.33e+01 angle pdb=" N ILE J 165 " pdb=" CA ILE J 165 " pdb=" C ILE J 165 " ideal model delta sigma weight residual 113.10 107.87 5.23 9.70e-01 1.06e+00 2.91e+01 angle pdb=" N ILE G 165 " pdb=" CA ILE G 165 " pdb=" C ILE G 165 " ideal model delta sigma weight residual 112.43 107.90 4.53 9.20e-01 1.18e+00 2.43e+01 angle pdb=" CA PRO H 513 " pdb=" N PRO H 513 " pdb=" CD PRO H 513 " ideal model delta sigma weight residual 112.00 105.71 6.29 1.40e+00 5.10e-01 2.02e+01 ... (remaining 91362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.41: 39049 35.41 - 70.82: 1064 70.82 - 106.23: 74 106.23 - 141.64: 9 141.64 - 177.05: 5 Dihedral angle restraints: 40201 sinusoidal: 17083 harmonic: 23118 Sorted by residual: dihedral pdb=" CA ARG E 74 " pdb=" C ARG E 74 " pdb=" N PRO E 75 " pdb=" CA PRO E 75 " ideal model delta harmonic sigma weight residual 180.00 -148.33 -31.67 0 5.00e+00 4.00e-02 4.01e+01 dihedral pdb=" CA MET D 365 " pdb=" C MET D 365 " pdb=" N ARG D 366 " pdb=" CA ARG D 366 " ideal model delta harmonic sigma weight residual 180.00 155.12 24.88 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ARG F 23 " pdb=" C ARG F 23 " pdb=" N LYS F 24 " pdb=" CA LYS F 24 " ideal model delta harmonic sigma weight residual -180.00 -155.40 -24.60 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 40198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 6954 0.040 - 0.080: 2306 0.080 - 0.120: 677 0.120 - 0.160: 80 0.160 - 0.200: 12 Chirality restraints: 10029 Sorted by residual: chirality pdb=" CA PRO E 75 " pdb=" N PRO E 75 " pdb=" C PRO E 75 " pdb=" CB PRO E 75 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.99e-01 chirality pdb=" CA PRO K 367 " pdb=" N PRO K 367 " pdb=" C PRO K 367 " pdb=" CB PRO K 367 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CB ILE L 237 " pdb=" CA ILE L 237 " pdb=" CG1 ILE L 237 " pdb=" CG2 ILE L 237 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.50e-01 ... (remaining 10026 not shown) Planarity restraints: 11346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 228 " -0.048 5.00e-02 4.00e+02 7.30e-02 8.52e+00 pdb=" N PRO E 229 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 229 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 229 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET H 512 " 0.046 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO H 513 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO H 513 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO H 513 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 74 " 0.041 5.00e-02 4.00e+02 6.30e-02 6.36e+00 pdb=" N PRO E 75 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " 0.034 5.00e-02 4.00e+02 ... (remaining 11343 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 1013 2.65 - 3.21: 63296 3.21 - 3.77: 106493 3.77 - 4.34: 147587 4.34 - 4.90: 233282 Nonbonded interactions: 551671 Sorted by model distance: nonbonded pdb=" NH1 ARG E 230 " pdb=" OD1 ASN E 322 " model vdw 2.084 2.520 nonbonded pdb=" OG SER F 242 " pdb=" OG SER F 245 " model vdw 2.110 2.440 nonbonded pdb=" O GLU G 129 " pdb=" ND2 ASN G 169 " model vdw 2.111 2.520 nonbonded pdb=" OD2 ASP G 52 " pdb=" OH TYR G 374 " model vdw 2.117 2.440 nonbonded pdb=" OD1 ASP A 297 " pdb=" NZ LYS B 239 " model vdw 2.125 2.520 ... (remaining 551666 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 6 through 485 or resid 498 through 677)) selection = (chain 'B' and (resid 6 through 485 or resid 498 through 677)) selection = (chain 'C' and (resid 6 through 485 or resid 498 through 677)) selection = (chain 'D' and (resid 6 through 485 or resid 498 through 677)) selection = (chain 'E' and (resid 6 through 485 or resid 498 through 677)) selection = (chain 'F' and (resid 6 through 485 or resid 498 through 677)) selection = (chain 'G' and (resid 6 through 485 or resid 498 through 677)) selection = (chain 'H' and (resid 6 through 485 or resid 498 through 677)) selection = (chain 'I' and (resid 6 through 485 or resid 498 through 677)) selection = (chain 'J' and (resid 6 through 485 or resid 498 through 677)) selection = (chain 'K' and (resid 6 through 485 or resid 498 through 677)) selection = (chain 'L' and (resid 6 through 485 or resid 498 through 677)) } 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: 3.170 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: 0.060 Extract box with map and model: 11.910 Check model and map are aligned: 0.760 Set scattering table: 0.470 Process input model: 156.530 Find NCS groups from input model: 4.650 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.004 0.071 67297 Z= 0.227 Angle : 0.678 11.863 91367 Z= 0.391 Chirality : 0.043 0.200 10029 Planarity : 0.005 0.073 11346 Dihedral : 15.524 177.053 25385 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.81 % Favored : 97.08 % Rotamer: Outliers : 0.01 % Allowed : 0.28 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.10), residues: 7979 helix: 1.11 (0.09), residues: 3188 sheet: 0.45 (0.14), residues: 1288 loop : 0.03 (0.11), residues: 3503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 187 HIS 0.014 0.001 HIS C 335 PHE 0.035 0.001 PHE D 593 TYR 0.021 0.001 TYR E 72 ARG 0.016 0.001 ARG G 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 6849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 429 time to evaluate : 5.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 MET cc_start: 0.7945 (mmt) cc_final: 0.7580 (mmt) REVERT: A 606 MET cc_start: 0.5331 (mtm) cc_final: 0.3607 (mpp) REVERT: B 197 MET cc_start: 0.8286 (mmt) cc_final: 0.7917 (mmt) REVERT: B 606 MET cc_start: 0.7053 (ttt) cc_final: 0.6502 (ttt) REVERT: B 612 MET cc_start: 0.8355 (ppp) cc_final: 0.7800 (ppp) REVERT: C 170 MET cc_start: 0.7758 (tpp) cc_final: 0.7549 (tpp) REVERT: C 197 MET cc_start: 0.8020 (mmt) cc_final: 0.7680 (mmt) REVERT: C 461 MET cc_start: 0.7061 (tpp) cc_final: 0.6758 (tpp) REVERT: C 612 MET cc_start: 0.7816 (ptt) cc_final: 0.7409 (ptt) REVERT: D 365 MET cc_start: 0.8547 (tpp) cc_final: 0.7889 (mmm) REVERT: D 565 MET cc_start: 0.6192 (mmm) cc_final: 0.5721 (mmp) REVERT: D 606 MET cc_start: 0.5871 (mmp) cc_final: 0.5586 (mmm) REVERT: E 197 MET cc_start: 0.8486 (mmt) cc_final: 0.7952 (mmm) REVERT: E 299 MET cc_start: 0.8625 (mtm) cc_final: 0.8386 (mpp) REVERT: E 365 MET cc_start: 0.8206 (mmt) cc_final: 0.7369 (mmm) REVERT: G 197 MET cc_start: 0.8446 (mmt) cc_final: 0.8013 (mmm) REVERT: G 423 MET cc_start: 0.8833 (mmp) cc_final: 0.8593 (mmm) REVERT: G 606 MET cc_start: 0.6857 (tpt) cc_final: 0.6644 (tpt) REVERT: I 170 MET cc_start: 0.7920 (tpp) cc_final: 0.7675 (tpp) REVERT: I 606 MET cc_start: 0.7945 (mtt) cc_final: 0.7423 (mtt) REVERT: J 170 MET cc_start: 0.7731 (tpt) cc_final: 0.7339 (tpt) REVERT: J 299 MET cc_start: 0.7117 (mtp) cc_final: 0.6892 (mtp) REVERT: K 567 HIS cc_start: 0.9163 (m-70) cc_final: 0.8561 (m-70) REVERT: K 606 MET cc_start: 0.5489 (mtt) cc_final: 0.5267 (mtt) REVERT: L 388 MET cc_start: 0.8342 (mmp) cc_final: 0.7717 (mmp) REVERT: L 512 MET cc_start: 0.8808 (ttt) cc_final: 0.8482 (ptp) outliers start: 1 outliers final: 0 residues processed: 430 average time/residue: 0.6548 time to fit residues: 475.0482 Evaluate side-chains 304 residues out of total 6849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 5.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 684 optimal weight: 20.0000 chunk 614 optimal weight: 7.9990 chunk 341 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 414 optimal weight: 30.0000 chunk 328 optimal weight: 6.9990 chunk 635 optimal weight: 6.9990 chunk 245 optimal weight: 9.9990 chunk 386 optimal weight: 20.0000 chunk 473 optimal weight: 6.9990 chunk 736 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 ASN ** C 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 521 GLN ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 661 GLN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 310 GLN K 252 GLN ** K 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 310 GLN ** L 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 67297 Z= 0.365 Angle : 0.670 13.684 91367 Z= 0.353 Chirality : 0.043 0.202 10029 Planarity : 0.005 0.061 11346 Dihedral : 15.302 171.296 10082 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.70 % Favored : 96.19 % Rotamer: Outliers : 0.50 % Allowed : 5.12 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.10), residues: 7979 helix: 1.34 (0.09), residues: 3252 sheet: 0.38 (0.14), residues: 1314 loop : 0.03 (0.11), residues: 3413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 187 HIS 0.008 0.002 HIS C 335 PHE 0.028 0.002 PHE D 593 TYR 0.024 0.002 TYR E 72 ARG 0.010 0.001 ARG B 600 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 6849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 315 time to evaluate : 5.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 MET cc_start: 0.6361 (tmm) cc_final: 0.5985 (tmm) REVERT: A 606 MET cc_start: 0.5916 (mtm) cc_final: 0.5008 (mtt) REVERT: B 197 MET cc_start: 0.8327 (mmt) cc_final: 0.8096 (mmt) REVERT: B 365 MET cc_start: 0.8082 (mmt) cc_final: 0.7851 (mmt) REVERT: B 606 MET cc_start: 0.7186 (ttt) cc_final: 0.6637 (ttt) REVERT: B 612 MET cc_start: 0.8261 (ppp) cc_final: 0.7512 (ppp) REVERT: C 461 MET cc_start: 0.7510 (tpp) cc_final: 0.7288 (tpp) REVERT: C 606 MET cc_start: 0.8466 (ptm) cc_final: 0.7950 (ptm) REVERT: C 612 MET cc_start: 0.7949 (ptt) cc_final: 0.7574 (ptt) REVERT: D 365 MET cc_start: 0.8371 (tpp) cc_final: 0.8001 (mmm) REVERT: D 565 MET cc_start: 0.6778 (mmm) cc_final: 0.6085 (mmt) REVERT: D 606 MET cc_start: 0.6224 (mmp) cc_final: 0.6012 (mmm) REVERT: D 628 LEU cc_start: 0.8470 (mt) cc_final: 0.8143 (tp) REVERT: E 197 MET cc_start: 0.8520 (mmt) cc_final: 0.7959 (mmm) REVERT: E 299 MET cc_start: 0.8744 (mtm) cc_final: 0.8404 (mpp) REVERT: E 365 MET cc_start: 0.8267 (mmt) cc_final: 0.7442 (mmm) REVERT: E 606 MET cc_start: 0.4787 (tpp) cc_final: 0.4387 (mmm) REVERT: G 197 MET cc_start: 0.8535 (mmt) cc_final: 0.8132 (mmm) REVERT: G 365 MET cc_start: 0.8377 (tpp) cc_final: 0.8174 (tpp) REVERT: G 388 MET cc_start: 0.8804 (mmm) cc_final: 0.8541 (mmm) REVERT: G 423 MET cc_start: 0.8711 (mmp) cc_final: 0.8495 (mmm) REVERT: G 512 MET cc_start: 0.6911 (tpt) cc_final: 0.6358 (mpp) REVERT: H 344 MET cc_start: 0.8748 (ppp) cc_final: 0.7284 (ppp) REVERT: I 365 MET cc_start: 0.8165 (mmt) cc_final: 0.7879 (mmt) REVERT: K 606 MET cc_start: 0.5499 (mtt) cc_final: 0.4879 (mmm) REVERT: L 299 MET cc_start: 0.9002 (ptm) cc_final: 0.8798 (ptm) REVERT: L 388 MET cc_start: 0.8639 (mmp) cc_final: 0.8096 (mmm) REVERT: L 512 MET cc_start: 0.8872 (ttt) cc_final: 0.8534 (ptp) outliers start: 34 outliers final: 18 residues processed: 337 average time/residue: 0.6221 time to fit residues: 364.6622 Evaluate side-chains 312 residues out of total 6849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 294 time to evaluate : 6.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 600 ARG Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain F residue 221 ASN Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 474 ASP Chi-restraints excluded: chain J residue 11 GLN Chi-restraints excluded: chain K residue 376 LEU Chi-restraints excluded: chain K residue 565 MET Chi-restraints excluded: chain L residue 287 LYS Chi-restraints excluded: chain L residue 474 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 409 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 chunk 612 optimal weight: 5.9990 chunk 501 optimal weight: 0.3980 chunk 203 optimal weight: 3.9990 chunk 737 optimal weight: 20.0000 chunk 797 optimal weight: 10.0000 chunk 657 optimal weight: 30.0000 chunk 731 optimal weight: 8.9990 chunk 251 optimal weight: 7.9990 chunk 591 optimal weight: 5.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 ASN ** D 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 439 GLN ** F 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 ASN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 ASN ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 63 ASN ** J 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 67297 Z= 0.258 Angle : 0.587 14.940 91367 Z= 0.310 Chirality : 0.041 0.182 10029 Planarity : 0.004 0.063 11346 Dihedral : 15.160 174.066 10082 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.27 % Favored : 96.63 % Rotamer: Outliers : 0.77 % Allowed : 7.17 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.10), residues: 7979 helix: 1.59 (0.09), residues: 3238 sheet: 0.46 (0.14), residues: 1261 loop : 0.07 (0.11), residues: 3480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 273 HIS 0.007 0.001 HIS C 335 PHE 0.022 0.001 PHE B 501 TYR 0.023 0.001 TYR E 72 ARG 0.009 0.000 ARG J 557 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 6849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 304 time to evaluate : 5.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7254 (ppp) cc_final: 0.6812 (ppp) REVERT: A 365 MET cc_start: 0.7922 (mmt) cc_final: 0.7444 (mmt) REVERT: A 512 MET cc_start: 0.6288 (tmm) cc_final: 0.5776 (tmm) REVERT: A 606 MET cc_start: 0.6164 (mtm) cc_final: 0.5300 (mtt) REVERT: B 606 MET cc_start: 0.7051 (ttt) cc_final: 0.6484 (ttt) REVERT: B 612 MET cc_start: 0.8161 (ppp) cc_final: 0.7402 (ppp) REVERT: C 170 MET cc_start: 0.7990 (tpp) cc_final: 0.7710 (tpp) REVERT: C 606 MET cc_start: 0.8505 (ptm) cc_final: 0.7953 (ptm) REVERT: C 612 MET cc_start: 0.7879 (ptt) cc_final: 0.7485 (ptt) REVERT: D 167 MET cc_start: 0.8144 (tpp) cc_final: 0.7923 (tpp) REVERT: D 197 MET cc_start: 0.8483 (mmp) cc_final: 0.8129 (mmt) REVERT: D 365 MET cc_start: 0.8515 (tpp) cc_final: 0.8188 (mmm) REVERT: D 565 MET cc_start: 0.6746 (mmm) cc_final: 0.6099 (mmt) REVERT: D 606 MET cc_start: 0.6243 (mmp) cc_final: 0.5919 (mmm) REVERT: D 628 LEU cc_start: 0.8428 (mt) cc_final: 0.8017 (tp) REVERT: E 197 MET cc_start: 0.8543 (mmt) cc_final: 0.7941 (mmm) REVERT: E 299 MET cc_start: 0.8727 (mtm) cc_final: 0.8398 (mpp) REVERT: E 365 MET cc_start: 0.8208 (mmt) cc_final: 0.7365 (mmm) REVERT: G 197 MET cc_start: 0.8514 (mmt) cc_final: 0.8093 (mmm) REVERT: G 344 MET cc_start: 0.7250 (ptp) cc_final: 0.6454 (ptm) REVERT: G 365 MET cc_start: 0.8252 (tpp) cc_final: 0.8051 (tpp) REVERT: I 365 MET cc_start: 0.8277 (mmt) cc_final: 0.7998 (mmt) REVERT: K 565 MET cc_start: 0.4666 (OUTLIER) cc_final: 0.4448 (mmt) REVERT: K 606 MET cc_start: 0.5889 (mtt) cc_final: 0.5564 (mmm) REVERT: L 299 MET cc_start: 0.8938 (ptm) cc_final: 0.8679 (ptm) REVERT: L 388 MET cc_start: 0.8719 (mmp) cc_final: 0.8023 (mmp) REVERT: L 512 MET cc_start: 0.8851 (ttt) cc_final: 0.8535 (ptp) REVERT: L 606 MET cc_start: 0.5706 (tmm) cc_final: 0.5100 (tpt) outliers start: 53 outliers final: 33 residues processed: 337 average time/residue: 0.6299 time to fit residues: 368.5900 Evaluate side-chains 327 residues out of total 6849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 293 time to evaluate : 5.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 436 ASP Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 169 ASN Chi-restraints excluded: chain G residue 262 MET Chi-restraints excluded: chain G residue 299 MET Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 317 MET Chi-restraints excluded: chain H residue 440 CYS Chi-restraints excluded: chain I residue 48 TYR Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 474 ASP Chi-restraints excluded: chain J residue 557 ARG Chi-restraints excluded: chain K residue 48 TYR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 172 MET Chi-restraints excluded: chain K residue 376 LEU Chi-restraints excluded: chain K residue 565 MET Chi-restraints excluded: chain K residue 643 MET Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 287 LYS Chi-restraints excluded: chain L residue 474 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 728 optimal weight: 20.0000 chunk 554 optimal weight: 0.9980 chunk 382 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 352 optimal weight: 1.9990 chunk 495 optimal weight: 8.9990 chunk 740 optimal weight: 0.9990 chunk 783 optimal weight: 20.0000 chunk 386 optimal weight: 30.0000 chunk 701 optimal weight: 8.9990 chunk 211 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN C 629 GLN ** D 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 603 GLN ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 GLN ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN I 14 ASN ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 521 GLN J 71 ASN ** J 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 67297 Z= 0.176 Angle : 0.553 13.380 91367 Z= 0.288 Chirality : 0.041 0.179 10029 Planarity : 0.004 0.064 11346 Dihedral : 15.055 174.014 10082 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.01 % Favored : 96.88 % Rotamer: Outliers : 0.92 % Allowed : 8.63 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: 1.24 (0.10), residues: 7979 helix: 1.78 (0.09), residues: 3239 sheet: 0.48 (0.14), residues: 1261 loop : 0.14 (0.11), residues: 3479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 187 HIS 0.006 0.001 HIS G 429 PHE 0.015 0.001 PHE D 593 TYR 0.020 0.001 TYR E 72 ARG 0.004 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 6849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 302 time to evaluate : 5.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7336 (ppp) cc_final: 0.6934 (ppp) REVERT: A 365 MET cc_start: 0.7840 (mmt) cc_final: 0.7389 (mmt) REVERT: A 512 MET cc_start: 0.6255 (tmm) cc_final: 0.5779 (tmm) REVERT: B 606 MET cc_start: 0.7045 (ttt) cc_final: 0.6481 (ttt) REVERT: B 612 MET cc_start: 0.8116 (ppp) cc_final: 0.7319 (ppp) REVERT: C 606 MET cc_start: 0.8402 (ptm) cc_final: 0.7922 (ptm) REVERT: C 612 MET cc_start: 0.7787 (ptt) cc_final: 0.7399 (ptt) REVERT: D 197 MET cc_start: 0.8410 (mmp) cc_final: 0.8144 (mmt) REVERT: D 365 MET cc_start: 0.8483 (tpp) cc_final: 0.8118 (mmm) REVERT: D 461 MET cc_start: 0.7922 (ttm) cc_final: 0.7355 (tpp) REVERT: D 565 MET cc_start: 0.6637 (mmm) cc_final: 0.6130 (mmt) REVERT: D 606 MET cc_start: 0.6422 (mmp) cc_final: 0.6000 (mmm) REVERT: D 612 MET cc_start: 0.3907 (ppp) cc_final: 0.3552 (ppp) REVERT: D 628 LEU cc_start: 0.8317 (mt) cc_final: 0.7989 (tp) REVERT: E 197 MET cc_start: 0.8546 (mmt) cc_final: 0.8022 (mmm) REVERT: E 365 MET cc_start: 0.8221 (mmt) cc_final: 0.7492 (mmm) REVERT: F 606 MET cc_start: 0.6032 (ptt) cc_final: 0.3905 (ttm) REVERT: G 171 ASN cc_start: 0.8293 (p0) cc_final: 0.7822 (p0) REVERT: G 197 MET cc_start: 0.8486 (mmt) cc_final: 0.8073 (mmm) REVERT: G 344 MET cc_start: 0.7269 (ptp) cc_final: 0.6330 (ppp) REVERT: G 388 MET cc_start: 0.8711 (mmm) cc_final: 0.8407 (mmm) REVERT: G 606 MET cc_start: 0.7736 (tpt) cc_final: 0.7009 (tpt) REVERT: H 344 MET cc_start: 0.8814 (ppp) cc_final: 0.7589 (ppp) REVERT: I 365 MET cc_start: 0.8296 (mmt) cc_final: 0.7929 (mmt) REVERT: J 557 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6261 (ptt90) REVERT: K 461 MET cc_start: 0.8991 (tpt) cc_final: 0.8677 (tpt) REVERT: K 565 MET cc_start: 0.4768 (OUTLIER) cc_final: 0.4497 (mmt) REVERT: K 567 HIS cc_start: 0.9186 (OUTLIER) cc_final: 0.8935 (t-90) REVERT: K 606 MET cc_start: 0.5850 (mtt) cc_final: 0.5589 (mmm) REVERT: L 197 MET cc_start: 0.7837 (mmm) cc_final: 0.7620 (mmm) REVERT: L 299 MET cc_start: 0.8918 (ptm) cc_final: 0.8649 (ptm) REVERT: L 388 MET cc_start: 0.8715 (mmp) cc_final: 0.8193 (mmm) REVERT: L 512 MET cc_start: 0.8832 (ttt) cc_final: 0.8549 (ptp) REVERT: L 606 MET cc_start: 0.5550 (tmm) cc_final: 0.4964 (tpt) outliers start: 63 outliers final: 29 residues processed: 345 average time/residue: 0.6224 time to fit residues: 374.2973 Evaluate side-chains 322 residues out of total 6849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 290 time to evaluate : 5.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 436 ASP Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 262 MET Chi-restraints excluded: chain G residue 299 MET Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 317 MET Chi-restraints excluded: chain H residue 440 CYS Chi-restraints excluded: chain I residue 474 ASP Chi-restraints excluded: chain J residue 557 ARG Chi-restraints excluded: chain K residue 48 TYR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 172 MET Chi-restraints excluded: chain K residue 237 ILE Chi-restraints excluded: chain K residue 565 MET Chi-restraints excluded: chain K residue 567 HIS Chi-restraints excluded: chain K residue 643 MET Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 287 LYS Chi-restraints excluded: chain L residue 474 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 652 optimal weight: 8.9990 chunk 444 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 583 optimal weight: 50.0000 chunk 323 optimal weight: 30.0000 chunk 668 optimal weight: 20.0000 chunk 541 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 400 optimal weight: 20.0000 chunk 703 optimal weight: 1.9990 chunk 197 optimal weight: 8.9990 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 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** C 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 446 GLN E 603 GLN ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 252 GLN ** G 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 ASN ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 67297 Z= 0.255 Angle : 0.578 13.345 91367 Z= 0.302 Chirality : 0.041 0.218 10029 Planarity : 0.004 0.063 11346 Dihedral : 15.035 173.788 10082 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.57 % Favored : 96.33 % Rotamer: Outliers : 1.17 % Allowed : 9.53 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: 1.25 (0.10), residues: 7979 helix: 1.83 (0.09), residues: 3210 sheet: 0.45 (0.15), residues: 1241 loop : 0.14 (0.11), residues: 3528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 273 HIS 0.006 0.001 HIS G 429 PHE 0.015 0.001 PHE F 286 TYR 0.022 0.001 TYR E 72 ARG 0.004 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 6849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 297 time to evaluate : 5.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7441 (ppp) cc_final: 0.7015 (ppp) REVERT: A 365 MET cc_start: 0.7884 (mmt) cc_final: 0.7432 (mmt) REVERT: A 512 MET cc_start: 0.6389 (tmm) cc_final: 0.6029 (tmm) REVERT: B 606 MET cc_start: 0.7112 (ttt) cc_final: 0.6527 (ttt) REVERT: B 612 MET cc_start: 0.8098 (ppp) cc_final: 0.7297 (ppp) REVERT: C 197 MET cc_start: 0.8028 (mmt) cc_final: 0.7457 (mmt) REVERT: C 206 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8157 (p) REVERT: C 365 MET cc_start: 0.7339 (mmt) cc_final: 0.6737 (mmt) REVERT: C 512 MET cc_start: 0.8881 (tmm) cc_final: 0.8526 (tmm) REVERT: C 606 MET cc_start: 0.8444 (ptm) cc_final: 0.7881 (ptm) REVERT: C 612 MET cc_start: 0.7897 (ptt) cc_final: 0.7400 (ptt) REVERT: D 365 MET cc_start: 0.8409 (tpp) cc_final: 0.8043 (mmm) REVERT: D 565 MET cc_start: 0.6564 (mmm) cc_final: 0.6077 (mmt) REVERT: D 606 MET cc_start: 0.6441 (mmp) cc_final: 0.5922 (mmm) REVERT: D 612 MET cc_start: 0.4310 (ppp) cc_final: 0.3980 (ppp) REVERT: D 628 LEU cc_start: 0.8444 (mt) cc_final: 0.8140 (tp) REVERT: E 197 MET cc_start: 0.8616 (mmt) cc_final: 0.8147 (mmm) REVERT: E 365 MET cc_start: 0.8304 (mmt) cc_final: 0.7848 (mmm) REVERT: E 606 MET cc_start: 0.3408 (mmm) cc_final: 0.2501 (mmm) REVERT: F 606 MET cc_start: 0.6188 (ptt) cc_final: 0.4147 (ttm) REVERT: G 197 MET cc_start: 0.8587 (mmt) cc_final: 0.8172 (mmm) REVERT: G 344 MET cc_start: 0.7389 (ptp) cc_final: 0.6480 (ppp) REVERT: G 388 MET cc_start: 0.8805 (mmm) cc_final: 0.8567 (mmm) REVERT: G 606 MET cc_start: 0.7821 (tpt) cc_final: 0.7003 (tpt) REVERT: H 47 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8400 (mtm) REVERT: H 344 MET cc_start: 0.8727 (ppp) cc_final: 0.7573 (ppp) REVERT: I 365 MET cc_start: 0.8375 (mmt) cc_final: 0.8070 (mmt) REVERT: J 557 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6443 (ptm160) REVERT: J 612 MET cc_start: 0.7693 (ppp) cc_final: 0.7220 (ppp) REVERT: J 662 THR cc_start: 0.6297 (OUTLIER) cc_final: 0.6010 (m) REVERT: K 565 MET cc_start: 0.4769 (OUTLIER) cc_final: 0.4324 (mmp) REVERT: K 567 HIS cc_start: 0.9213 (OUTLIER) cc_final: 0.8952 (t-90) REVERT: K 606 MET cc_start: 0.6036 (mtt) cc_final: 0.5765 (mmm) REVERT: L 47 MET cc_start: 0.8376 (mpp) cc_final: 0.7835 (mpp) REVERT: L 197 MET cc_start: 0.7864 (mmm) cc_final: 0.7663 (mmm) REVERT: L 299 MET cc_start: 0.8935 (ptm) cc_final: 0.8702 (ptm) REVERT: L 388 MET cc_start: 0.8778 (mmp) cc_final: 0.8072 (mmm) REVERT: L 512 MET cc_start: 0.8819 (ttt) cc_final: 0.8540 (ptp) REVERT: L 606 MET cc_start: 0.5759 (tmm) cc_final: 0.5212 (tpt) outliers start: 80 outliers final: 44 residues processed: 357 average time/residue: 0.6091 time to fit residues: 379.9563 Evaluate side-chains 338 residues out of total 6849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 288 time to evaluate : 5.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 643 MET Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 436 ASP Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 169 ASN Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 474 ASP Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 262 MET Chi-restraints excluded: chain G residue 299 MET Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 317 MET Chi-restraints excluded: chain H residue 440 CYS Chi-restraints excluded: chain I residue 451 VAL Chi-restraints excluded: chain I residue 474 ASP Chi-restraints excluded: chain J residue 557 ARG Chi-restraints excluded: chain J residue 643 MET Chi-restraints excluded: chain J residue 662 THR Chi-restraints excluded: chain K residue 48 TYR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 172 MET Chi-restraints excluded: chain K residue 237 ILE Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 376 LEU Chi-restraints excluded: chain K residue 565 MET Chi-restraints excluded: chain K residue 567 HIS Chi-restraints excluded: chain K residue 643 MET Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 287 LYS Chi-restraints excluded: chain L residue 474 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 263 optimal weight: 6.9990 chunk 705 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 460 optimal weight: 40.0000 chunk 193 optimal weight: 20.0000 chunk 784 optimal weight: 50.0000 chunk 651 optimal weight: 30.0000 chunk 363 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 259 optimal weight: 10.0000 chunk 411 optimal weight: 7.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN ** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 HIS ** E 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN ** E 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 HIS ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 325 GLN I 63 ASN ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 629 GLN ** L 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 67297 Z= 0.403 Angle : 0.686 13.667 91367 Z= 0.359 Chirality : 0.043 0.248 10029 Planarity : 0.004 0.083 11346 Dihedral : 15.125 175.431 10082 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.31 % Favored : 95.58 % Rotamer: Outliers : 1.43 % Allowed : 10.78 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.10), residues: 7979 helix: 1.45 (0.09), residues: 3254 sheet: 0.27 (0.14), residues: 1223 loop : -0.05 (0.11), residues: 3502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 273 HIS 0.008 0.002 HIS G 429 PHE 0.017 0.002 PHE F 286 TYR 0.026 0.002 TYR E 72 ARG 0.006 0.001 ARG H 266 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 6849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 302 time to evaluate : 5.827 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: A 47 MET cc_start: 0.7458 (ppp) cc_final: 0.6980 (ppp) REVERT: A 512 MET cc_start: 0.6504 (OUTLIER) cc_final: 0.6147 (tmm) REVERT: A 606 MET cc_start: 0.7087 (mtm) cc_final: 0.6224 (mtm) REVERT: B 606 MET cc_start: 0.7235 (ttt) cc_final: 0.6655 (ttt) REVERT: B 612 MET cc_start: 0.8213 (ppp) cc_final: 0.7358 (ppp) REVERT: C 365 MET cc_start: 0.7553 (mmt) cc_final: 0.7064 (mmt) REVERT: C 512 MET cc_start: 0.9044 (tmm) cc_final: 0.8631 (tmm) REVERT: C 606 MET cc_start: 0.8506 (ptm) cc_final: 0.8112 (ptm) REVERT: C 612 MET cc_start: 0.8139 (ptt) cc_final: 0.7662 (ptt) REVERT: D 365 MET cc_start: 0.8687 (tpp) cc_final: 0.7992 (tpp) REVERT: D 606 MET cc_start: 0.6673 (mmp) cc_final: 0.6261 (mmm) REVERT: D 628 LEU cc_start: 0.8459 (mt) cc_final: 0.8110 (tp) REVERT: E 197 MET cc_start: 0.8724 (mmt) cc_final: 0.8279 (mmm) REVERT: E 299 MET cc_start: 0.8964 (mtm) cc_final: 0.8677 (mtm) REVERT: E 365 MET cc_start: 0.8078 (mmt) cc_final: 0.7469 (mmm) REVERT: E 606 MET cc_start: 0.3931 (mmm) cc_final: 0.3069 (mmm) REVERT: G 197 MET cc_start: 0.8709 (mmt) cc_final: 0.8290 (mmm) REVERT: G 344 MET cc_start: 0.7505 (ptp) cc_final: 0.6515 (ppp) REVERT: G 606 MET cc_start: 0.8092 (tpt) cc_final: 0.7207 (tpt) REVERT: H 214 MET cc_start: 0.7634 (mmm) cc_final: 0.7175 (mmm) REVERT: H 344 MET cc_start: 0.8724 (ppp) cc_final: 0.8209 (ppp) REVERT: I 365 MET cc_start: 0.8408 (mmt) cc_final: 0.7329 (mmt) REVERT: I 528 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8546 (mmmt) REVERT: J 557 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6612 (ptm160) REVERT: J 662 THR cc_start: 0.6460 (OUTLIER) cc_final: 0.6201 (m) REVERT: K 565 MET cc_start: 0.4993 (OUTLIER) cc_final: 0.4431 (mmp) REVERT: K 567 HIS cc_start: 0.9262 (OUTLIER) cc_final: 0.9051 (t-90) REVERT: L 47 MET cc_start: 0.8454 (mpp) cc_final: 0.7709 (mpp) REVERT: L 299 MET cc_start: 0.8928 (ptm) cc_final: 0.8708 (ptm) REVERT: L 388 MET cc_start: 0.8864 (mmp) cc_final: 0.8077 (mmp) REVERT: L 512 MET cc_start: 0.8916 (ttt) cc_final: 0.8520 (tpp) REVERT: L 606 MET cc_start: 0.6090 (tmm) cc_final: 0.5603 (tpt) outliers start: 98 outliers final: 57 residues processed: 375 average time/residue: 0.6402 time to fit residues: 416.8794 Evaluate side-chains 351 residues out of total 6849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 289 time to evaluate : 5.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 643 MET Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 436 ASP Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 643 MET Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 169 ASN Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 221 ASN Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 474 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 262 MET Chi-restraints excluded: chain G residue 299 MET Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 440 CYS Chi-restraints excluded: chain H residue 643 MET Chi-restraints excluded: chain I residue 474 ASP Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 557 ARG Chi-restraints excluded: chain J residue 565 MET Chi-restraints excluded: chain J residue 643 MET Chi-restraints excluded: chain J residue 662 THR Chi-restraints excluded: chain K residue 48 TYR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 172 MET Chi-restraints excluded: chain K residue 237 ILE Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 565 MET Chi-restraints excluded: chain K residue 567 HIS Chi-restraints excluded: chain K residue 643 MET Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 287 LYS Chi-restraints excluded: chain L residue 474 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 756 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 447 optimal weight: 50.0000 chunk 573 optimal weight: 6.9990 chunk 443 optimal weight: 3.9990 chunk 660 optimal weight: 7.9990 chunk 438 optimal weight: 10.0000 chunk 781 optimal weight: 20.0000 chunk 489 optimal weight: 5.9990 chunk 476 optimal weight: 0.5980 chunk 360 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN ** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 ASN ** E 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 406 ASN ** G 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 629 GLN ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 67297 Z= 0.221 Angle : 0.597 16.432 91367 Z= 0.307 Chirality : 0.041 0.196 10029 Planarity : 0.004 0.062 11346 Dihedral : 15.023 173.957 10082 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.57 % Favored : 96.35 % Rotamer: Outliers : 1.20 % Allowed : 11.86 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.10), residues: 7979 helix: 1.73 (0.09), residues: 3224 sheet: 0.26 (0.14), residues: 1246 loop : 0.06 (0.11), residues: 3509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 273 HIS 0.007 0.001 HIS G 429 PHE 0.020 0.001 PHE F 673 TYR 0.031 0.001 TYR E 72 ARG 0.004 0.000 ARG K 450 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 6849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 298 time to evaluate : 5.826 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: A 47 MET cc_start: 0.7419 (ppp) cc_final: 0.6913 (ppp) REVERT: A 365 MET cc_start: 0.7764 (mmt) cc_final: 0.7396 (mmt) REVERT: A 512 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.6077 (tmm) REVERT: A 606 MET cc_start: 0.7078 (mtm) cc_final: 0.6268 (mtm) REVERT: B 606 MET cc_start: 0.7335 (ttt) cc_final: 0.6782 (ttt) REVERT: B 612 MET cc_start: 0.8164 (ppp) cc_final: 0.7328 (ppp) REVERT: C 197 MET cc_start: 0.8040 (mmt) cc_final: 0.7569 (mmm) REVERT: C 365 MET cc_start: 0.7479 (mmt) cc_final: 0.6995 (mmt) REVERT: C 512 MET cc_start: 0.8996 (tmm) cc_final: 0.8606 (tmm) REVERT: C 606 MET cc_start: 0.8478 (ptm) cc_final: 0.8057 (ptm) REVERT: C 612 MET cc_start: 0.7981 (ptt) cc_final: 0.7504 (ptt) REVERT: D 365 MET cc_start: 0.8536 (tpp) cc_final: 0.7840 (tpp) REVERT: D 606 MET cc_start: 0.6773 (mmp) cc_final: 0.6380 (mmm) REVERT: D 612 MET cc_start: 0.4200 (ppp) cc_final: 0.3616 (ptm) REVERT: D 628 LEU cc_start: 0.8445 (mt) cc_final: 0.8098 (tp) REVERT: E 197 MET cc_start: 0.8766 (mmt) cc_final: 0.8318 (mmm) REVERT: E 317 MET cc_start: 0.7684 (mpp) cc_final: 0.7457 (pmm) REVERT: E 365 MET cc_start: 0.8042 (mmt) cc_final: 0.7441 (mmm) REVERT: E 606 MET cc_start: 0.3715 (mmm) cc_final: 0.2972 (mmm) REVERT: G 197 MET cc_start: 0.8713 (mmt) cc_final: 0.8287 (mmm) REVERT: G 344 MET cc_start: 0.7411 (ptp) cc_final: 0.6447 (ppp) REVERT: G 388 MET cc_start: 0.8701 (mmm) cc_final: 0.8334 (mmm) REVERT: G 606 MET cc_start: 0.8012 (tpt) cc_final: 0.7185 (tpt) REVERT: H 214 MET cc_start: 0.7511 (mmm) cc_final: 0.7114 (mmm) REVERT: H 344 MET cc_start: 0.8771 (ppp) cc_final: 0.8272 (ppp) REVERT: H 365 MET cc_start: 0.7326 (mmt) cc_final: 0.6964 (mmt) REVERT: I 365 MET cc_start: 0.8446 (mmt) cc_final: 0.8142 (mmt) REVERT: I 528 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8559 (mmmt) REVERT: J 344 MET cc_start: 0.8318 (pmm) cc_final: 0.7963 (pmm) REVERT: J 662 THR cc_start: 0.6470 (OUTLIER) cc_final: 0.6204 (m) REVERT: K 565 MET cc_start: 0.5002 (OUTLIER) cc_final: 0.4456 (mmp) REVERT: K 567 HIS cc_start: 0.9223 (OUTLIER) cc_final: 0.8974 (t-90) REVERT: L 299 MET cc_start: 0.8933 (ptm) cc_final: 0.8659 (ptm) REVERT: L 388 MET cc_start: 0.8844 (mmp) cc_final: 0.8153 (mmm) REVERT: L 606 MET cc_start: 0.5969 (tmm) cc_final: 0.5478 (tpt) outliers start: 82 outliers final: 59 residues processed: 357 average time/residue: 0.6167 time to fit residues: 387.3423 Evaluate side-chains 352 residues out of total 6849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 289 time to evaluate : 5.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 643 MET Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 436 ASP Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 169 ASN Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 474 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 171 ASN Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 262 MET Chi-restraints excluded: chain G residue 299 MET Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 440 CYS Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 474 ASP Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain I residue 607 VAL Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 327 VAL Chi-restraints excluded: chain J residue 643 MET Chi-restraints excluded: chain J residue 662 THR Chi-restraints excluded: chain K residue 48 TYR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 172 MET Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 237 ILE Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 474 ASP Chi-restraints excluded: chain K residue 565 MET Chi-restraints excluded: chain K residue 567 HIS Chi-restraints excluded: chain K residue 643 MET Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 287 LYS Chi-restraints excluded: chain L residue 474 ASP Chi-restraints excluded: chain L residue 672 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 483 optimal weight: 5.9990 chunk 312 optimal weight: 10.0000 chunk 466 optimal weight: 5.9990 chunk 235 optimal weight: 0.2980 chunk 153 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 496 optimal weight: 9.9990 chunk 532 optimal weight: 1.9990 chunk 386 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 614 optimal weight: 7.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN ** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 ASN ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 ASN ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 67297 Z= 0.265 Angle : 0.618 12.684 91367 Z= 0.317 Chirality : 0.041 0.229 10029 Planarity : 0.004 0.063 11346 Dihedral : 15.008 174.826 10082 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 1.37 % Allowed : 12.03 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: 1.05 (0.10), residues: 7979 helix: 1.70 (0.09), residues: 3231 sheet: 0.22 (0.14), residues: 1255 loop : 0.02 (0.11), residues: 3493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 273 HIS 0.007 0.001 HIS G 429 PHE 0.021 0.001 PHE F 673 TYR 0.026 0.001 TYR E 72 ARG 0.004 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 6849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 296 time to evaluate : 5.847 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 47 MET cc_start: 0.7437 (ppp) cc_final: 0.6937 (ppp) REVERT: A 512 MET cc_start: 0.6408 (OUTLIER) cc_final: 0.6062 (tmm) REVERT: A 606 MET cc_start: 0.7133 (mtm) cc_final: 0.6316 (mtm) REVERT: B 606 MET cc_start: 0.7283 (ttt) cc_final: 0.6692 (ttt) REVERT: B 612 MET cc_start: 0.8168 (ppp) cc_final: 0.7333 (ppp) REVERT: C 47 MET cc_start: 0.8343 (ppp) cc_final: 0.7755 (ppp) REVERT: C 365 MET cc_start: 0.7511 (mmt) cc_final: 0.7092 (mmt) REVERT: C 512 MET cc_start: 0.9029 (tmm) cc_final: 0.8634 (tmm) REVERT: C 606 MET cc_start: 0.8481 (ptm) cc_final: 0.8056 (ptm) REVERT: C 612 MET cc_start: 0.8023 (ptt) cc_final: 0.7561 (ptt) REVERT: D 365 MET cc_start: 0.8480 (tpp) cc_final: 0.7799 (tpp) REVERT: D 606 MET cc_start: 0.7087 (mmp) cc_final: 0.6558 (mmm) REVERT: D 612 MET cc_start: 0.4344 (ppp) cc_final: 0.4122 (ptm) REVERT: D 628 LEU cc_start: 0.8464 (mt) cc_final: 0.8074 (tp) REVERT: E 197 MET cc_start: 0.8820 (mmt) cc_final: 0.8374 (mmm) REVERT: E 365 MET cc_start: 0.8058 (mmt) cc_final: 0.7421 (mmm) REVERT: E 606 MET cc_start: 0.3765 (mmm) cc_final: 0.3019 (mmm) REVERT: F 170 MET cc_start: 0.7941 (tpp) cc_final: 0.7693 (tpp) REVERT: F 565 MET cc_start: 0.6477 (mmm) cc_final: 0.4852 (mmt) REVERT: G 170 MET cc_start: 0.6908 (ppp) cc_final: 0.5902 (ppp) REVERT: G 197 MET cc_start: 0.8766 (mmt) cc_final: 0.8338 (mmm) REVERT: G 344 MET cc_start: 0.7544 (ptp) cc_final: 0.6579 (ppp) REVERT: G 388 MET cc_start: 0.8741 (mmm) cc_final: 0.8514 (mmm) REVERT: G 606 MET cc_start: 0.8085 (tpt) cc_final: 0.7217 (tpt) REVERT: H 214 MET cc_start: 0.7530 (mmm) cc_final: 0.7106 (mmm) REVERT: H 344 MET cc_start: 0.8777 (ppp) cc_final: 0.8320 (ppp) REVERT: H 365 MET cc_start: 0.7363 (mmt) cc_final: 0.6955 (mmt) REVERT: I 365 MET cc_start: 0.8460 (mmt) cc_final: 0.8095 (mmt) REVERT: I 528 LYS cc_start: 0.8809 (mmmt) cc_final: 0.8554 (mmmt) REVERT: I 606 MET cc_start: 0.8704 (mtt) cc_final: 0.7993 (mtp) REVERT: J 344 MET cc_start: 0.8258 (pmm) cc_final: 0.8034 (pmm) REVERT: J 557 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6949 (ptm160) REVERT: J 606 MET cc_start: 0.5431 (OUTLIER) cc_final: 0.4553 (mtp) REVERT: J 662 THR cc_start: 0.6528 (OUTLIER) cc_final: 0.6256 (m) REVERT: K 567 HIS cc_start: 0.9228 (OUTLIER) cc_final: 0.8962 (t-90) REVERT: L 388 MET cc_start: 0.8890 (mmp) cc_final: 0.8257 (mmm) REVERT: L 512 MET cc_start: 0.8851 (ttt) cc_final: 0.8648 (tpp) REVERT: L 606 MET cc_start: 0.6055 (tmm) cc_final: 0.5582 (tpt) outliers start: 94 outliers final: 70 residues processed: 368 average time/residue: 0.6250 time to fit residues: 400.0386 Evaluate side-chains 365 residues out of total 6849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 290 time to evaluate : 5.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 643 MET Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 436 ASP Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 629 GLN Chi-restraints excluded: chain D residue 648 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 169 ASN Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 474 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 171 ASN Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 262 MET Chi-restraints excluded: chain G residue 299 MET Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 440 CYS Chi-restraints excluded: chain H residue 643 MET Chi-restraints excluded: chain I residue 474 ASP Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain I residue 607 VAL Chi-restraints excluded: chain I residue 632 PHE Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 327 VAL Chi-restraints excluded: chain J residue 557 ARG Chi-restraints excluded: chain J residue 606 MET Chi-restraints excluded: chain J residue 643 MET Chi-restraints excluded: chain J residue 662 THR Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 48 TYR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 172 MET Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 237 ILE Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 474 ASP Chi-restraints excluded: chain K residue 567 HIS Chi-restraints excluded: chain K residue 606 MET Chi-restraints excluded: chain K residue 612 MET Chi-restraints excluded: chain K residue 643 MET Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 287 LYS Chi-restraints excluded: chain L residue 474 ASP Chi-restraints excluded: chain L residue 672 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 711 optimal weight: 10.0000 chunk 748 optimal weight: 20.0000 chunk 683 optimal weight: 9.9990 chunk 728 optimal weight: 10.0000 chunk 438 optimal weight: 20.0000 chunk 317 optimal weight: 5.9990 chunk 571 optimal weight: 4.9990 chunk 223 optimal weight: 20.0000 chunk 658 optimal weight: 0.9990 chunk 688 optimal weight: 4.9990 chunk 725 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 257 ASN ** J 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 ASN ** K 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 67297 Z= 0.303 Angle : 0.646 12.917 91367 Z= 0.331 Chirality : 0.042 0.220 10029 Planarity : 0.004 0.062 11346 Dihedral : 15.046 174.599 10082 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.19 % Favored : 95.75 % Rotamer: Outliers : 1.31 % Allowed : 12.34 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.10), residues: 7979 helix: 1.59 (0.09), residues: 3255 sheet: 0.24 (0.14), residues: 1233 loop : -0.05 (0.11), residues: 3491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 273 HIS 0.008 0.001 HIS G 429 PHE 0.016 0.001 PHE E 286 TYR 0.026 0.001 TYR E 72 ARG 0.004 0.000 ARG G 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 6849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 297 time to evaluate : 5.888 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 47 MET cc_start: 0.7489 (ppp) cc_final: 0.7008 (ppp) REVERT: A 512 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.6130 (tmm) REVERT: A 606 MET cc_start: 0.7243 (mtm) cc_final: 0.6449 (mtm) REVERT: B 606 MET cc_start: 0.7264 (ttt) cc_final: 0.6681 (ttt) REVERT: B 612 MET cc_start: 0.8225 (ppp) cc_final: 0.7401 (ppp) REVERT: C 47 MET cc_start: 0.8251 (ppp) cc_final: 0.7713 (ppp) REVERT: C 365 MET cc_start: 0.7590 (mmt) cc_final: 0.7170 (mmt) REVERT: C 512 MET cc_start: 0.9077 (tmm) cc_final: 0.8671 (tmm) REVERT: C 606 MET cc_start: 0.8484 (ptm) cc_final: 0.8056 (ptm) REVERT: C 612 MET cc_start: 0.8086 (ptt) cc_final: 0.7611 (ptt) REVERT: D 365 MET cc_start: 0.8489 (tpp) cc_final: 0.7860 (tpp) REVERT: D 606 MET cc_start: 0.7470 (mmp) cc_final: 0.6972 (mmm) REVERT: D 612 MET cc_start: 0.4362 (ppp) cc_final: 0.4047 (ptm) REVERT: D 628 LEU cc_start: 0.8489 (mt) cc_final: 0.8111 (tp) REVERT: E 172 MET cc_start: 0.7641 (mmt) cc_final: 0.7439 (mpp) REVERT: E 197 MET cc_start: 0.8837 (mmt) cc_final: 0.8389 (mmm) REVERT: E 365 MET cc_start: 0.8152 (mmt) cc_final: 0.7417 (mmm) REVERT: E 606 MET cc_start: 0.3870 (mmm) cc_final: 0.3126 (mmm) REVERT: G 170 MET cc_start: 0.7260 (ppp) cc_final: 0.6112 (ppp) REVERT: G 171 ASN cc_start: 0.8384 (p0) cc_final: 0.8133 (p0) REVERT: G 197 MET cc_start: 0.8842 (mmt) cc_final: 0.8410 (mmm) REVERT: G 295 MET cc_start: 0.9380 (ptp) cc_final: 0.9070 (ptp) REVERT: G 344 MET cc_start: 0.7488 (ptp) cc_final: 0.6509 (ppp) REVERT: G 388 MET cc_start: 0.8767 (mmm) cc_final: 0.8504 (mmm) REVERT: H 214 MET cc_start: 0.7538 (mmm) cc_final: 0.7114 (mmm) REVERT: H 344 MET cc_start: 0.8768 (ppp) cc_final: 0.8310 (ppp) REVERT: H 612 MET cc_start: 0.7728 (tmm) cc_final: 0.7525 (tmm) REVERT: I 262 MET cc_start: 0.8115 (mpp) cc_final: 0.7736 (ptp) REVERT: I 365 MET cc_start: 0.8471 (mmt) cc_final: 0.7376 (mmt) REVERT: I 528 LYS cc_start: 0.8843 (mmmt) cc_final: 0.8600 (mmmt) REVERT: I 606 MET cc_start: 0.8683 (mtt) cc_final: 0.7989 (mtp) REVERT: J 365 MET cc_start: 0.7739 (mmm) cc_final: 0.7458 (mmm) REVERT: J 557 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6922 (ptm160) REVERT: J 606 MET cc_start: 0.5479 (OUTLIER) cc_final: 0.4559 (mtp) REVERT: J 662 THR cc_start: 0.6623 (OUTLIER) cc_final: 0.6358 (m) REVERT: K 512 MET cc_start: 0.6242 (ppp) cc_final: 0.5932 (ppp) REVERT: K 567 HIS cc_start: 0.9251 (OUTLIER) cc_final: 0.8994 (t-90) REVERT: L 388 MET cc_start: 0.8964 (mmp) cc_final: 0.8374 (mmm) REVERT: L 606 MET cc_start: 0.6191 (tmm) cc_final: 0.5738 (tpt) outliers start: 90 outliers final: 74 residues processed: 361 average time/residue: 0.6462 time to fit residues: 412.3813 Evaluate side-chains 370 residues out of total 6849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 291 time to evaluate : 5.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 643 MET Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 436 ASP Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 436 ASP Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 629 GLN Chi-restraints excluded: chain D residue 648 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 169 ASN Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 474 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 262 MET Chi-restraints excluded: chain G residue 299 MET Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 440 CYS Chi-restraints excluded: chain H residue 643 MET Chi-restraints excluded: chain I residue 436 ASP Chi-restraints excluded: chain I residue 474 ASP Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain I residue 607 VAL Chi-restraints excluded: chain I residue 632 PHE Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 299 MET Chi-restraints excluded: chain J residue 327 VAL Chi-restraints excluded: chain J residue 557 ARG Chi-restraints excluded: chain J residue 565 MET Chi-restraints excluded: chain J residue 606 MET Chi-restraints excluded: chain J residue 643 MET Chi-restraints excluded: chain J residue 662 THR Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 48 TYR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 172 MET Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 237 ILE Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 474 ASP Chi-restraints excluded: chain K residue 567 HIS Chi-restraints excluded: chain K residue 606 MET Chi-restraints excluded: chain K residue 612 MET Chi-restraints excluded: chain K residue 643 MET Chi-restraints excluded: chain L residue 25 ASP Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 287 LYS Chi-restraints excluded: chain L residue 474 ASP Chi-restraints excluded: chain L residue 672 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 478 optimal weight: 6.9990 chunk 770 optimal weight: 3.9990 chunk 470 optimal weight: 20.0000 chunk 365 optimal weight: 0.0570 chunk 535 optimal weight: 5.9990 chunk 807 optimal weight: 10.0000 chunk 743 optimal weight: 5.9990 chunk 643 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 496 optimal weight: 7.9990 chunk 394 optimal weight: 9.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 GLN I 577 GLN ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 166 GLN ** K 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 67297 Z= 0.215 Angle : 0.617 13.170 91367 Z= 0.313 Chirality : 0.041 0.249 10029 Planarity : 0.004 0.061 11346 Dihedral : 14.990 174.253 10082 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.78 % Favored : 96.16 % Rotamer: Outliers : 1.17 % Allowed : 12.54 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: 1.05 (0.10), residues: 7979 helix: 1.67 (0.09), residues: 3277 sheet: 0.29 (0.15), residues: 1215 loop : 0.00 (0.11), residues: 3487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP K 139 HIS 0.007 0.001 HIS G 429 PHE 0.019 0.001 PHE E 286 TYR 0.024 0.001 TYR E 72 ARG 0.003 0.000 ARG K 450 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 6849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 293 time to evaluate : 5.864 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: A 47 MET cc_start: 0.7425 (ppp) cc_final: 0.6919 (ppp) REVERT: A 512 MET cc_start: 0.6395 (OUTLIER) cc_final: 0.6049 (tmm) REVERT: A 606 MET cc_start: 0.7160 (mtm) cc_final: 0.6353 (mtm) REVERT: B 606 MET cc_start: 0.7219 (ttt) cc_final: 0.6721 (ttt) REVERT: B 612 MET cc_start: 0.8180 (ppp) cc_final: 0.7320 (ppp) REVERT: C 47 MET cc_start: 0.8173 (ppp) cc_final: 0.7623 (ppp) REVERT: C 197 MET cc_start: 0.8051 (mmt) cc_final: 0.7583 (mmm) REVERT: C 365 MET cc_start: 0.7560 (mmt) cc_final: 0.7070 (mmt) REVERT: C 512 MET cc_start: 0.9012 (tmm) cc_final: 0.8617 (tmm) REVERT: C 606 MET cc_start: 0.8465 (ptm) cc_final: 0.8034 (ptm) REVERT: C 612 MET cc_start: 0.8089 (ptt) cc_final: 0.7589 (ptt) REVERT: D 461 MET cc_start: 0.8077 (tpp) cc_final: 0.7688 (tpp) REVERT: D 606 MET cc_start: 0.7581 (mmp) cc_final: 0.7009 (mmm) REVERT: D 612 MET cc_start: 0.4521 (ppp) cc_final: 0.4219 (ptm) REVERT: D 628 LEU cc_start: 0.8480 (mt) cc_final: 0.8098 (tp) REVERT: E 172 MET cc_start: 0.7556 (mmt) cc_final: 0.7353 (mpp) REVERT: E 197 MET cc_start: 0.8817 (mmt) cc_final: 0.8377 (mmm) REVERT: E 365 MET cc_start: 0.8075 (mmt) cc_final: 0.7348 (mmm) REVERT: E 606 MET cc_start: 0.3698 (mmm) cc_final: 0.3008 (mmm) REVERT: F 565 MET cc_start: 0.6365 (mmm) cc_final: 0.4889 (mmt) REVERT: F 606 MET cc_start: 0.6597 (ptt) cc_final: 0.4750 (ttp) REVERT: G 170 MET cc_start: 0.7114 (ppp) cc_final: 0.5914 (ppp) REVERT: G 171 ASN cc_start: 0.8408 (p0) cc_final: 0.8127 (p0) REVERT: G 197 MET cc_start: 0.8818 (mmt) cc_final: 0.8380 (mmm) REVERT: G 295 MET cc_start: 0.9330 (ptp) cc_final: 0.8986 (ptp) REVERT: G 299 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8902 (ptp) REVERT: G 344 MET cc_start: 0.7597 (ptp) cc_final: 0.6621 (ppp) REVERT: G 388 MET cc_start: 0.8732 (mmm) cc_final: 0.8473 (mmm) REVERT: H 214 MET cc_start: 0.7531 (mmm) cc_final: 0.7150 (mmm) REVERT: H 344 MET cc_start: 0.8762 (ppp) cc_final: 0.8286 (ppp) REVERT: H 612 MET cc_start: 0.7744 (tmm) cc_final: 0.7523 (tmm) REVERT: I 262 MET cc_start: 0.8202 (mpp) cc_final: 0.7855 (ptp) REVERT: I 365 MET cc_start: 0.8474 (mmt) cc_final: 0.8120 (mmt) REVERT: I 528 LYS cc_start: 0.8838 (mmmt) cc_final: 0.8581 (mmmt) REVERT: I 606 MET cc_start: 0.8673 (mtt) cc_final: 0.7922 (mtt) REVERT: J 512 MET cc_start: 0.7845 (tmm) cc_final: 0.7588 (tmm) REVERT: J 557 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6838 (ptm160) REVERT: J 606 MET cc_start: 0.5209 (OUTLIER) cc_final: 0.4340 (mtp) REVERT: J 612 MET cc_start: 0.7749 (ppp) cc_final: 0.7401 (ppp) REVERT: J 662 THR cc_start: 0.6659 (OUTLIER) cc_final: 0.6382 (m) REVERT: K 567 HIS cc_start: 0.9213 (OUTLIER) cc_final: 0.8923 (t-90) REVERT: L 388 MET cc_start: 0.8950 (mmp) cc_final: 0.8385 (mmm) REVERT: L 606 MET cc_start: 0.6057 (tmm) cc_final: 0.5598 (tpt) outliers start: 80 outliers final: 65 residues processed: 349 average time/residue: 0.6428 time to fit residues: 392.3101 Evaluate side-chains 360 residues out of total 6849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 289 time to evaluate : 6.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 643 MET Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 436 ASP Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 436 ASP Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 629 GLN Chi-restraints excluded: chain D residue 648 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 169 ASN Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 474 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 299 MET Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 440 CYS Chi-restraints excluded: chain H residue 643 MET Chi-restraints excluded: chain I residue 436 ASP Chi-restraints excluded: chain I residue 474 ASP Chi-restraints excluded: chain I residue 607 VAL Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 299 MET Chi-restraints excluded: chain J residue 327 VAL Chi-restraints excluded: chain J residue 557 ARG Chi-restraints excluded: chain J residue 606 MET Chi-restraints excluded: chain J residue 643 MET Chi-restraints excluded: chain J residue 662 THR Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 172 MET Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 237 ILE Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 474 ASP Chi-restraints excluded: chain K residue 567 HIS Chi-restraints excluded: chain K residue 606 MET Chi-restraints excluded: chain K residue 612 MET Chi-restraints excluded: chain K residue 643 MET Chi-restraints excluded: chain L residue 25 ASP Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 287 LYS Chi-restraints excluded: chain L residue 474 ASP Chi-restraints excluded: chain L residue 672 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 511 optimal weight: 20.0000 chunk 685 optimal weight: 0.6980 chunk 197 optimal weight: 10.0000 chunk 593 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 chunk 644 optimal weight: 10.0000 chunk 269 optimal weight: 5.9990 chunk 661 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 63 ASN ** J 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 293 GLN ** K 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.048908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.033296 restraints weight = 511144.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.034467 restraints weight = 266096.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.035181 restraints weight = 178293.408| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 67297 Z= 0.228 Angle : 0.625 13.686 91367 Z= 0.316 Chirality : 0.041 0.240 10029 Planarity : 0.004 0.061 11346 Dihedral : 14.947 174.979 10082 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.85 % Favored : 96.10 % Rotamer: Outliers : 1.15 % Allowed : 12.78 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.10), residues: 7979 helix: 1.72 (0.09), residues: 3265 sheet: 0.31 (0.15), residues: 1195 loop : -0.01 (0.11), residues: 3519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 139 HIS 0.009 0.001 HIS I 570 PHE 0.016 0.001 PHE A 349 TYR 0.024 0.001 TYR E 72 ARG 0.004 0.000 ARG A 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9700.11 seconds wall clock time: 175 minutes 27.18 seconds (10527.18 seconds total)