Starting phenix.real_space_refine on Tue Feb 20 21:57:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ohw_20070/02_2024/6ohw_20070.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ohw_20070/02_2024/6ohw_20070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ohw_20070/02_2024/6ohw_20070.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ohw_20070/02_2024/6ohw_20070.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ohw_20070/02_2024/6ohw_20070.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ohw_20070/02_2024/6ohw_20070.pdb" } resolution = 2.9 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= 0.003 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 183 5.16 5 C 18222 2.51 5 N 4593 2.21 5 O 5919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 538": "OD1" <-> "OD2" Residue "A TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 538": "OD1" <-> "OD2" Residue "B TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 160": "OE1" <-> "OE2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 538": "OD1" <-> "OD2" Residue "C TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28917 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "B" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "C" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Time building chain proxies: 14.61, per 1000 atoms: 0.51 Number of scatterers: 28917 At special positions: 0 Unit cell: (147, 155.4, 162.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 183 16.00 O 5919 8.00 N 4593 7.00 C 18222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=63, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 169 " distance=2.14 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 197 " distance=2.07 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 256 " distance=2.04 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 300 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 439 " distance=2.05 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 614 " distance=2.17 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 561 " distance=2.04 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 522 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 576 " distance=2.02 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 578 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 597 " distance=2.09 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 683 " distance=2.03 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 733 " distance=2.04 Simple disulfide: pdb=" SG CYS A 748 " - pdb=" SG CYS A 757 " distance=2.06 Simple disulfide: pdb=" SG CYS A 826 " - pdb=" SG CYS A 848 " distance=2.16 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS A 837 " distance=2.03 Simple disulfide: pdb=" SG CYS A 938 " - pdb=" SG CYS A 949 " distance=2.09 Simple disulfide: pdb=" SG CYS A1126 " - pdb=" SG CYS A1137 " distance=2.03 Simple disulfide: pdb=" SG CYS A1176 " - pdb=" SG CYS A1221 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 169 " distance=2.14 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 197 " distance=2.07 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 256 " distance=2.04 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 368 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 439 " distance=2.05 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 614 " distance=2.16 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 561 " distance=2.04 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 522 " distance=2.04 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 576 " distance=2.02 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 578 " distance=2.03 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 597 " distance=2.09 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 683 " distance=2.03 Simple disulfide: pdb=" SG CYS B 708 " - pdb=" SG CYS B 733 " distance=2.04 Simple disulfide: pdb=" SG CYS B 748 " - pdb=" SG CYS B 757 " distance=2.06 Simple disulfide: pdb=" SG CYS B 826 " - pdb=" SG CYS B 848 " distance=2.16 Simple disulfide: pdb=" SG CYS B 831 " - pdb=" SG CYS B 837 " distance=2.03 Simple disulfide: pdb=" SG CYS B 938 " - pdb=" SG CYS B 949 " distance=2.09 Simple disulfide: pdb=" SG CYS B1126 " - pdb=" SG CYS B1137 " distance=2.03 Simple disulfide: pdb=" SG CYS B1176 " - pdb=" SG CYS B1221 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 169 " distance=2.14 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 197 " distance=2.07 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 256 " distance=2.04 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 300 " distance=2.03 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 439 " distance=2.05 Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 614 " distance=2.16 Simple disulfide: pdb=" SG CYS C 491 " - pdb=" SG CYS C 561 " distance=2.04 Simple disulfide: pdb=" SG CYS C 499 " - pdb=" SG CYS C 522 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 576 " distance=2.02 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 548 " distance=2.03 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 578 " distance=2.03 Simple disulfide: pdb=" SG CYS C 591 " - pdb=" SG CYS C 597 " distance=2.09 Simple disulfide: pdb=" SG CYS C 630 " - pdb=" SG CYS C 683 " distance=2.03 Simple disulfide: pdb=" SG CYS C 708 " - pdb=" SG CYS C 733 " distance=2.04 Simple disulfide: pdb=" SG CYS C 748 " - pdb=" SG CYS C 757 " distance=2.06 Simple disulfide: pdb=" SG CYS C 826 " - pdb=" SG CYS C 848 " distance=2.16 Simple disulfide: pdb=" SG CYS C 831 " - pdb=" SG CYS C 837 " distance=2.03 Simple disulfide: pdb=" SG CYS C 938 " - pdb=" SG CYS C 949 " distance=2.09 Simple disulfide: pdb=" SG CYS C1126 " - pdb=" SG CYS C1137 " distance=2.03 Simple disulfide: pdb=" SG CYS C1176 " - pdb=" SG CYS C1221 " distance=2.03 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 Links applied ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA T 3 " - " MAN T 4 " " BMA d 3 " - " MAN d 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " NAG-ASN " NAG A1428 " - " ASN A 59 " " NAG A1429 " - " ASN A 146 " " NAG A1430 " - " ASN A 675 " " NAG A1431 " - " ASN A 695 " " NAG A1432 " - " ASN A 714 " " NAG B1428 " - " ASN B 59 " " NAG B1429 " - " ASN B 146 " " NAG B1430 " - " ASN B 675 " " NAG B1431 " - " ASN B 695 " " NAG B1432 " - " ASN B 714 " " NAG C1428 " - " ASN C 59 " " NAG C1429 " - " ASN C 146 " " NAG C1430 " - " ASN C 675 " " NAG C1431 " - " ASN C 695 " " NAG C1432 " - " ASN C 714 " " NAG D 1 " - " ASN A 133 " " NAG E 1 " - " ASN A 202 " " NAG F 1 " - " ASN A1224 " " NAG G 1 " - " ASN A 371 " " NAG H 1 " - " ASN A 449 " " NAG I 1 " - " ASN A 648 " " NAG J 1 " - " ASN A 739 " " NAG K 1 " - " ASN A 788 " " NAG L 1 " - " ASN A 937 " " NAG M 1 " - " ASN A1194 " " NAG N 1 " - " ASN B 133 " " NAG O 1 " - " ASN B 202 " " NAG P 1 " - " ASN B1224 " " NAG Q 1 " - " ASN B 371 " " NAG R 1 " - " ASN B 449 " " NAG S 1 " - " ASN B 648 " " NAG T 1 " - " ASN B 739 " " NAG U 1 " - " ASN B 788 " " NAG V 1 " - " ASN B 937 " " NAG W 1 " - " ASN B1194 " " NAG X 1 " - " ASN C 133 " " NAG Y 1 " - " ASN C 202 " " NAG Z 1 " - " ASN C1224 " " NAG a 1 " - " ASN C 371 " " NAG b 1 " - " ASN C 449 " " NAG c 1 " - " ASN C 648 " " NAG d 1 " - " ASN C 739 " " NAG e 1 " - " ASN C 788 " " NAG f 1 " - " ASN C 937 " " NAG g 1 " - " ASN C1194 " Time building additional restraints: 12.53 Conformation dependent library (CDL) restraints added in 5.0 seconds 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6588 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 66 sheets defined 25.3% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'A' and resid 89 through 92 Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 344 through 350 Processing helix chain 'A' and resid 371 through 379 removed outlier: 4.156A pdb=" N SER A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 removed outlier: 4.857A pdb=" N TYR A 395 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 423 through 429 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 458 through 464 Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 707 through 715 Processing helix chain 'A' and resid 825 through 831 Processing helix chain 'A' and resid 834 through 841 Processing helix chain 'A' and resid 844 through 874 removed outlier: 3.624A pdb=" N CYS A 848 " --> pdb=" O TYR A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 885 Processing helix chain 'A' and resid 914 through 923 removed outlier: 4.257A pdb=" N LYS A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 936 Processing helix chain 'A' and resid 946 through 954 Processing helix chain 'A' and resid 964 through 978 Processing helix chain 'A' and resid 984 through 988 Processing helix chain 'A' and resid 991 through 1002 Processing helix chain 'A' and resid 1006 through 1011 Processing helix chain 'A' and resid 1013 through 1031 Processing helix chain 'A' and resid 1036 through 1058 Processing helix chain 'A' and resid 1059 through 1062 Processing helix chain 'A' and resid 1070 through 1078 Processing helix chain 'A' and resid 1079 through 1126 removed outlier: 3.543A pdb=" N ALA A1085 " --> pdb=" O LEU A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1213 No H-bonds generated for 'chain 'A' and resid 1211 through 1213' Processing helix chain 'B' and resid 89 through 92 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 344 through 350 Processing helix chain 'B' and resid 371 through 379 removed outlier: 4.156A pdb=" N SER B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 396 removed outlier: 4.857A pdb=" N TYR B 395 " --> pdb=" O ALA B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 448 through 450 No H-bonds generated for 'chain 'B' and resid 448 through 450' Processing helix chain 'B' and resid 458 through 464 Processing helix chain 'B' and resid 467 through 472 Processing helix chain 'B' and resid 707 through 715 Processing helix chain 'B' and resid 825 through 831 Processing helix chain 'B' and resid 834 through 841 Processing helix chain 'B' and resid 844 through 874 removed outlier: 3.624A pdb=" N CYS B 848 " --> pdb=" O TYR B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 885 Processing helix chain 'B' and resid 914 through 923 removed outlier: 4.256A pdb=" N LYS B 923 " --> pdb=" O LEU B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 936 Processing helix chain 'B' and resid 946 through 954 Processing helix chain 'B' and resid 964 through 978 Processing helix chain 'B' and resid 984 through 988 Processing helix chain 'B' and resid 991 through 1002 Processing helix chain 'B' and resid 1006 through 1011 Processing helix chain 'B' and resid 1013 through 1031 Processing helix chain 'B' and resid 1036 through 1058 Processing helix chain 'B' and resid 1059 through 1062 Processing helix chain 'B' and resid 1070 through 1078 Processing helix chain 'B' and resid 1079 through 1126 removed outlier: 3.543A pdb=" N ALA B1085 " --> pdb=" O LEU B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1211 through 1213 No H-bonds generated for 'chain 'B' and resid 1211 through 1213' Processing helix chain 'C' and resid 89 through 92 Processing helix chain 'C' and resid 293 through 302 Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 371 through 379 removed outlier: 4.156A pdb=" N SER C 377 " --> pdb=" O SER C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 396 removed outlier: 4.857A pdb=" N TYR C 395 " --> pdb=" O ALA C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 458 through 464 Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 707 through 715 Processing helix chain 'C' and resid 825 through 831 Processing helix chain 'C' and resid 834 through 841 Processing helix chain 'C' and resid 844 through 874 removed outlier: 3.625A pdb=" N CYS C 848 " --> pdb=" O TYR C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 885 Processing helix chain 'C' and resid 914 through 923 removed outlier: 4.257A pdb=" N LYS C 923 " --> pdb=" O LEU C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 936 Processing helix chain 'C' and resid 946 through 954 Processing helix chain 'C' and resid 964 through 978 Processing helix chain 'C' and resid 984 through 988 Processing helix chain 'C' and resid 991 through 1002 Processing helix chain 'C' and resid 1006 through 1011 Processing helix chain 'C' and resid 1013 through 1031 Processing helix chain 'C' and resid 1036 through 1058 Processing helix chain 'C' and resid 1059 through 1062 Processing helix chain 'C' and resid 1070 through 1078 Processing helix chain 'C' and resid 1079 through 1126 removed outlier: 3.543A pdb=" N ALA C1085 " --> pdb=" O LEU C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1211 through 1213 No H-bonds generated for 'chain 'C' and resid 1211 through 1213' Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 40 removed outlier: 5.271A pdb=" N TYR A 75 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR A 74 " --> pdb=" O PRO A 268 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY A 102 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE A 223 " --> pdb=" O ASN A 239 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN A 239 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA A 225 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 69 Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 56 removed outlier: 6.976A pdb=" N ASP A 54 " --> pdb=" O GLN C 656 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ASN C 657 " --> pdb=" O PHE C 669 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE C 669 " --> pdb=" O ASN C 657 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU C 659 " --> pdb=" O TYR C 667 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N TYR C 667 " --> pdb=" O ILE C 680 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR C 677 " --> pdb=" O VAL C 647 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA C 331 " --> pdb=" O CYS C 630 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 8.218A pdb=" N THR A 255 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR A 174 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N TRP A 188 " --> pdb=" O CYS A 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.749A pdb=" N GLY A 157 " --> pdb=" O TYR A 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 326 removed outlier: 4.007A pdb=" N GLY A 316 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLY A 686 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG A 687 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ARG A 704 " --> pdb=" O ARG A 687 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 331 through 335 removed outlier: 4.005A pdb=" N ALA A 331 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR A 677 " --> pdb=" O VAL A 647 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 659 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE A 669 " --> pdb=" O ASN A 657 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ASN A 657 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLN A 656 " --> pdb=" O ASP B 54 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 56 " --> pdb=" O GLN A 656 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 658 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.836A pdb=" N VAL A 354 " --> pdb=" O SER A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 366 removed outlier: 6.521A pdb=" N PHE A 399 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A 608 " --> pdb=" O PHE A 399 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 380 through 387 removed outlier: 5.947A pdb=" N ALA A 381 " --> pdb=" O ASN A 444 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASN A 444 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A 608 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE A 399 " --> pdb=" O VAL A 608 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 484 through 488 Processing sheet with id=AB5, first strand: chain 'A' and resid 492 through 493 Processing sheet with id=AB6, first strand: chain 'A' and resid 565 through 566 Processing sheet with id=AB7, first strand: chain 'A' and resid 571 through 572 Processing sheet with id=AB8, first strand: chain 'A' and resid 738 through 745 removed outlier: 6.553A pdb=" N TYR A 738 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ASN A 778 " --> pdb=" O TYR A 738 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N SER A 740 " --> pdb=" O ASN A 778 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR A 756 " --> pdb=" O VAL A 752 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 750 " --> pdb=" O VAL A 758 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 785 through 787 removed outlier: 6.049A pdb=" N ASN A 785 " --> pdb=" O LEU B 879 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 798 through 816 removed outlier: 6.714A pdb=" N GLU A 799 " --> pdb=" O ARG A1170 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG A1170 " --> pdb=" O GLU A 799 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN A 801 " --> pdb=" O THR A1168 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR A1168 " --> pdb=" O GLN A 801 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N TYR A1166 " --> pdb=" O PRO A 803 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU A 805 " --> pdb=" O THR A1164 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE A1144 " --> pdb=" O PHE A1159 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N TYR A1161 " --> pdb=" O HIS A1142 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N HIS A1142 " --> pdb=" O TYR A1161 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 798 through 816 removed outlier: 6.714A pdb=" N GLU A 799 " --> pdb=" O ARG A1170 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG A1170 " --> pdb=" O GLU A 799 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN A 801 " --> pdb=" O THR A1168 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR A1168 " --> pdb=" O GLN A 801 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N TYR A1166 " --> pdb=" O PRO A 803 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU A 805 " --> pdb=" O THR A1164 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG A1170 " --> pdb=" O ASN A1192 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN A1192 " --> pdb=" O ARG A1170 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY A1201 " --> pdb=" O TYR A1206 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TYR A1206 " --> pdb=" O GLY A1201 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 821 through 824 removed outlier: 4.306A pdb=" N LYS A 821 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 878 through 880 Processing sheet with id=AC5, first strand: chain 'A' and resid 890 through 891 Processing sheet with id=AC6, first strand: chain 'A' and resid 1215 through 1218 Processing sheet with id=AC7, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AC8, first strand: chain 'B' and resid 36 through 40 removed outlier: 5.271A pdb=" N TYR B 75 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR B 74 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY B 102 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE B 223 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN B 239 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA B 225 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 60 through 69 Processing sheet with id=AD1, first strand: chain 'B' and resid 81 through 82 removed outlier: 8.219A pdb=" N THR B 255 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR B 174 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N TRP B 188 " --> pdb=" O CYS B 169 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.749A pdb=" N GLY B 157 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AD4, first strand: chain 'B' and resid 310 through 326 removed outlier: 4.007A pdb=" N GLY B 316 " --> pdb=" O GLY B 686 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY B 686 " --> pdb=" O GLY B 316 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG B 687 " --> pdb=" O ARG B 704 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ARG B 704 " --> pdb=" O ARG B 687 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 331 through 335 removed outlier: 4.005A pdb=" N ALA B 331 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU B 659 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE B 669 " --> pdb=" O ASN B 657 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ASN B 657 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLN B 656 " --> pdb=" O ASP C 54 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL C 56 " --> pdb=" O GLN B 656 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU B 658 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.837A pdb=" N VAL B 354 " --> pdb=" O SER B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 361 through 366 removed outlier: 6.521A pdb=" N PHE B 399 " --> pdb=" O VAL B 608 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 608 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASN B 444 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ALA B 381 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 369 through 370 removed outlier: 3.581A pdb=" N PHE B 370 " --> pdb=" O CYS B 614 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE B 399 " --> pdb=" O VAL B 608 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 608 " --> pdb=" O PHE B 399 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 484 through 488 Processing sheet with id=AE1, first strand: chain 'B' and resid 492 through 493 Processing sheet with id=AE2, first strand: chain 'B' and resid 565 through 566 Processing sheet with id=AE3, first strand: chain 'B' and resid 571 through 572 Processing sheet with id=AE4, first strand: chain 'B' and resid 738 through 745 removed outlier: 6.553A pdb=" N TYR B 738 " --> pdb=" O PHE B 776 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ASN B 778 " --> pdb=" O TYR B 738 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N SER B 740 " --> pdb=" O ASN B 778 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR B 756 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU B 750 " --> pdb=" O VAL B 758 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 785 through 787 removed outlier: 6.049A pdb=" N ASN B 785 " --> pdb=" O LEU C 879 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'B' and resid 798 through 816 removed outlier: 6.714A pdb=" N GLU B 799 " --> pdb=" O ARG B1170 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG B1170 " --> pdb=" O GLU B 799 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN B 801 " --> pdb=" O THR B1168 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR B1168 " --> pdb=" O GLN B 801 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR B1166 " --> pdb=" O PRO B 803 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU B 805 " --> pdb=" O THR B1164 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE B1144 " --> pdb=" O PHE B1159 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N TYR B1161 " --> pdb=" O HIS B1142 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N HIS B1142 " --> pdb=" O TYR B1161 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 798 through 816 removed outlier: 6.714A pdb=" N GLU B 799 " --> pdb=" O ARG B1170 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG B1170 " --> pdb=" O GLU B 799 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN B 801 " --> pdb=" O THR B1168 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR B1168 " --> pdb=" O GLN B 801 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR B1166 " --> pdb=" O PRO B 803 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU B 805 " --> pdb=" O THR B1164 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ARG B1170 " --> pdb=" O ASN B1192 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN B1192 " --> pdb=" O ARG B1170 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY B1201 " --> pdb=" O TYR B1206 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TYR B1206 " --> pdb=" O GLY B1201 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 821 through 824 removed outlier: 4.306A pdb=" N LYS B 821 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 890 through 891 Processing sheet with id=AF1, first strand: chain 'B' and resid 1215 through 1218 Processing sheet with id=AF2, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=AF3, first strand: chain 'C' and resid 36 through 40 removed outlier: 5.271A pdb=" N TYR C 75 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR C 74 " --> pdb=" O PRO C 268 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY C 102 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE C 223 " --> pdb=" O ASN C 239 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN C 239 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA C 225 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 60 through 69 Processing sheet with id=AF5, first strand: chain 'C' and resid 81 through 82 removed outlier: 8.218A pdb=" N THR C 255 " --> pdb=" O PRO C 172 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR C 174 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N TRP C 188 " --> pdb=" O CYS C 169 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.749A pdb=" N GLY C 157 " --> pdb=" O TYR C 205 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 110 through 114 Processing sheet with id=AF8, first strand: chain 'C' and resid 310 through 326 removed outlier: 4.007A pdb=" N GLY C 316 " --> pdb=" O GLY C 686 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY C 686 " --> pdb=" O GLY C 316 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG C 687 " --> pdb=" O ARG C 704 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ARG C 704 " --> pdb=" O ARG C 687 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 353 through 355 removed outlier: 6.836A pdb=" N VAL C 354 " --> pdb=" O SER C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'C' and resid 361 through 366 removed outlier: 6.520A pdb=" N PHE C 399 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL C 608 " --> pdb=" O PHE C 399 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASN C 444 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ALA C 381 " --> pdb=" O ASN C 444 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 369 through 370 removed outlier: 3.581A pdb=" N PHE C 370 " --> pdb=" O CYS C 614 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE C 399 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL C 608 " --> pdb=" O PHE C 399 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 484 through 488 Processing sheet with id=AG4, first strand: chain 'C' and resid 492 through 493 Processing sheet with id=AG5, first strand: chain 'C' and resid 565 through 566 Processing sheet with id=AG6, first strand: chain 'C' and resid 571 through 572 Processing sheet with id=AG7, first strand: chain 'C' and resid 738 through 745 removed outlier: 6.553A pdb=" N TYR C 738 " --> pdb=" O PHE C 776 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ASN C 778 " --> pdb=" O TYR C 738 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N SER C 740 " --> pdb=" O ASN C 778 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR C 756 " --> pdb=" O VAL C 752 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 750 " --> pdb=" O VAL C 758 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 798 through 816 removed outlier: 6.715A pdb=" N GLU C 799 " --> pdb=" O ARG C1170 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG C1170 " --> pdb=" O GLU C 799 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN C 801 " --> pdb=" O THR C1168 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR C1168 " --> pdb=" O GLN C 801 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N TYR C1166 " --> pdb=" O PRO C 803 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU C 805 " --> pdb=" O THR C1164 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE C1144 " --> pdb=" O PHE C1159 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N TYR C1161 " --> pdb=" O HIS C1142 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N HIS C1142 " --> pdb=" O TYR C1161 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 798 through 816 removed outlier: 6.715A pdb=" N GLU C 799 " --> pdb=" O ARG C1170 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG C1170 " --> pdb=" O GLU C 799 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN C 801 " --> pdb=" O THR C1168 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR C1168 " --> pdb=" O GLN C 801 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N TYR C1166 " --> pdb=" O PRO C 803 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU C 805 " --> pdb=" O THR C1164 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG C1170 " --> pdb=" O ASN C1192 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASN C1192 " --> pdb=" O ARG C1170 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY C1201 " --> pdb=" O TYR C1206 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TYR C1206 " --> pdb=" O GLY C1201 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 821 through 824 removed outlier: 4.306A pdb=" N LYS C 821 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 890 through 891 Processing sheet with id=AH3, first strand: chain 'C' and resid 1215 through 1218 1220 hydrogen bonds defined for protein. 3345 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.81 Time building geometry restraints manager: 13.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 9236 1.33 - 1.48: 9420 1.48 - 1.63: 10465 1.63 - 1.77: 101 1.77 - 1.92: 136 Bond restraints: 29358 Sorted by residual: bond pdb=" C HIS C 215 " pdb=" N PHE C 216 " ideal model delta sigma weight residual 1.331 1.204 0.128 1.29e-02 6.01e+03 9.83e+01 bond pdb=" C HIS B 215 " pdb=" N PHE B 216 " ideal model delta sigma weight residual 1.331 1.204 0.128 1.29e-02 6.01e+03 9.81e+01 bond pdb=" C HIS A 215 " pdb=" N PHE A 216 " ideal model delta sigma weight residual 1.331 1.204 0.128 1.29e-02 6.01e+03 9.78e+01 bond pdb=" CB HIS A 215 " pdb=" CG HIS A 215 " ideal model delta sigma weight residual 1.497 1.388 0.109 1.40e-02 5.10e+03 6.09e+01 bond pdb=" CB HIS C 215 " pdb=" CG HIS C 215 " ideal model delta sigma weight residual 1.497 1.388 0.109 1.40e-02 5.10e+03 6.09e+01 ... (remaining 29353 not shown) Histogram of bond angle deviations from ideal: 88.72 - 97.80: 10 97.80 - 106.87: 1401 106.87 - 115.94: 17870 115.94 - 125.02: 20253 125.02 - 134.09: 438 Bond angle restraints: 39972 Sorted by residual: angle pdb=" N PHE A 399 " pdb=" CA PHE A 399 " pdb=" CB PHE A 399 " ideal model delta sigma weight residual 111.05 88.72 22.33 1.50e+00 4.44e-01 2.22e+02 angle pdb=" N PHE B 399 " pdb=" CA PHE B 399 " pdb=" CB PHE B 399 " ideal model delta sigma weight residual 111.05 88.73 22.32 1.50e+00 4.44e-01 2.21e+02 angle pdb=" N PHE C 399 " pdb=" CA PHE C 399 " pdb=" CB PHE C 399 " ideal model delta sigma weight residual 111.05 88.74 22.31 1.50e+00 4.44e-01 2.21e+02 angle pdb=" N CYS C 614 " pdb=" CA CYS C 614 " pdb=" C CYS C 614 " ideal model delta sigma weight residual 109.59 124.65 -15.06 1.61e+00 3.86e-01 8.75e+01 angle pdb=" N CYS A 614 " pdb=" CA CYS A 614 " pdb=" C CYS A 614 " ideal model delta sigma weight residual 109.59 124.64 -15.05 1.61e+00 3.86e-01 8.74e+01 ... (remaining 39967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.00: 17898 22.00 - 43.99: 498 43.99 - 65.99: 117 65.99 - 87.99: 120 87.99 - 109.98: 75 Dihedral angle restraints: 18708 sinusoidal: 8403 harmonic: 10305 Sorted by residual: dihedral pdb=" N PHE B 399 " pdb=" C PHE B 399 " pdb=" CA PHE B 399 " pdb=" CB PHE B 399 " ideal model delta harmonic sigma weight residual 122.80 91.14 31.66 0 2.50e+00 1.60e-01 1.60e+02 dihedral pdb=" N PHE A 399 " pdb=" C PHE A 399 " pdb=" CA PHE A 399 " pdb=" CB PHE A 399 " ideal model delta harmonic sigma weight residual 122.80 91.14 31.66 0 2.50e+00 1.60e-01 1.60e+02 dihedral pdb=" N PHE C 399 " pdb=" C PHE C 399 " pdb=" CA PHE C 399 " pdb=" CB PHE C 399 " ideal model delta harmonic sigma weight residual 122.80 91.16 31.64 0 2.50e+00 1.60e-01 1.60e+02 ... (remaining 18705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 4002 0.155 - 0.310: 750 0.310 - 0.465: 39 0.465 - 0.620: 6 0.620 - 0.775: 3 Chirality restraints: 4800 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.33e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 ... (remaining 4797 not shown) Planarity restraints: 5058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 675 " -0.054 2.00e-02 2.50e+03 5.68e-02 4.03e+01 pdb=" CG ASN A 675 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 675 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 675 " 0.089 2.00e-02 2.50e+03 pdb=" C1 NAG A1430 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 675 " 0.054 2.00e-02 2.50e+03 5.68e-02 4.03e+01 pdb=" CG ASN B 675 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN B 675 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN B 675 " -0.089 2.00e-02 2.50e+03 pdb=" C1 NAG B1430 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 675 " -0.054 2.00e-02 2.50e+03 5.67e-02 4.02e+01 pdb=" CG ASN C 675 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN C 675 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C 675 " 0.089 2.00e-02 2.50e+03 pdb=" C1 NAG C1430 " -0.068 2.00e-02 2.50e+03 ... (remaining 5055 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 939 2.65 - 3.21: 26673 3.21 - 3.77: 47201 3.77 - 4.34: 65506 4.34 - 4.90: 106912 Nonbonded interactions: 247231 Sorted by model distance: nonbonded pdb=" O HOH A1508 " pdb=" O HOH B1516 " model vdw 2.085 2.440 nonbonded pdb=" O HOH A1516 " pdb=" O HOH C1508 " model vdw 2.085 2.440 nonbonded pdb=" O HOH B1508 " pdb=" O HOH C1516 " model vdw 2.086 2.440 nonbonded pdb=" O4 NAG I 2 " pdb=" O6 NAG I 2 " model vdw 2.368 2.440 nonbonded pdb=" O4 NAG c 2 " pdb=" O6 NAG c 2 " model vdw 2.368 2.440 ... (remaining 247226 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' } ncs_group { reference = chain 'J' selection = chain 'T' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.750 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: 0.020 Extract box with map and model: 14.130 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 79.540 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.440 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: 0.000 Load rotamer database and sin/cos tables:12.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 : 0.026 0.169 29358 Z= 1.699 Angle : 1.801 22.328 39972 Z= 1.180 Chirality : 0.115 0.775 4800 Planarity : 0.009 0.052 5013 Dihedral : 15.316 109.983 11931 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.39 % Allowed : 0.49 % Favored : 99.12 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.13), residues: 3489 helix: -0.56 (0.16), residues: 786 sheet: 1.12 (0.16), residues: 801 loop : 0.46 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.009 TRP B 655 HIS 0.009 0.003 HIS C1142 PHE 0.042 0.006 PHE C 713 TYR 0.066 0.009 TYR B 75 ARG 0.011 0.001 ARG C 999 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 522 time to evaluate : 3.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8749 (mmm) cc_final: 0.8329 (mmm) REVERT: A 376 MET cc_start: 0.8471 (mtm) cc_final: 0.8184 (mtm) REVERT: A 925 LYS cc_start: 0.7734 (tttt) cc_final: 0.7508 (mmpt) REVERT: B 168 MET cc_start: 0.8449 (mmm) cc_final: 0.8128 (mmt) REVERT: B 455 PHE cc_start: 0.8672 (m-80) cc_final: 0.8387 (m-80) REVERT: B 925 LYS cc_start: 0.7952 (tttt) cc_final: 0.7544 (mmpt) REVERT: C 78 MET cc_start: 0.8830 (mmm) cc_final: 0.8601 (mmp) REVERT: C 925 LYS cc_start: 0.7849 (tttt) cc_final: 0.7486 (mmpt) REVERT: C 1114 PHE cc_start: 0.8550 (t80) cc_final: 0.8289 (t80) outliers start: 12 outliers final: 3 residues processed: 526 average time/residue: 1.1002 time to fit residues: 705.3728 Evaluate side-chains 295 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 292 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain C residue 1224 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 0.9990 chunk 266 optimal weight: 0.6980 chunk 147 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 179 optimal weight: 0.6980 chunk 142 optimal weight: 0.7980 chunk 275 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 chunk 204 optimal weight: 0.5980 chunk 318 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 183 HIS ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 GLN A 951 GLN A1029 GLN A1036 ASN A1214 ASN B 167 ASN B 183 HIS B 286 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 GLN B 785 ASN B 895 ASN B1029 GLN B1036 ASN B1213 ASN B1214 ASN C 167 ASN C 183 HIS ** C 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 ASN C 746 GLN C 895 ASN C 951 GLN C1029 GLN C1214 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29358 Z= 0.248 Angle : 0.711 7.612 39972 Z= 0.369 Chirality : 0.053 0.597 4800 Planarity : 0.004 0.039 5013 Dihedral : 11.850 69.048 5799 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.74 % Allowed : 5.58 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.13), residues: 3489 helix: 0.97 (0.19), residues: 783 sheet: 0.80 (0.17), residues: 777 loop : 0.11 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 460 HIS 0.006 0.002 HIS B 183 PHE 0.027 0.002 PHE A 278 TYR 0.023 0.002 TYR C 738 ARG 0.006 0.001 ARG C 413 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 379 time to evaluate : 3.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8656 (mmm) cc_final: 0.8368 (mmm) REVERT: A 168 MET cc_start: 0.8564 (mmm) cc_final: 0.8203 (mmt) REVERT: A 185 LYS cc_start: 0.7637 (mmtm) cc_final: 0.6587 (mtpm) REVERT: A 252 MET cc_start: 0.8708 (mtt) cc_final: 0.8493 (mtt) REVERT: A 376 MET cc_start: 0.8331 (mtm) cc_final: 0.8082 (mtm) REVERT: A 593 GLN cc_start: 0.7658 (mt0) cc_final: 0.7439 (mm-40) REVERT: A 925 LYS cc_start: 0.7752 (tttt) cc_final: 0.7497 (mmpt) REVERT: A 944 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.6888 (pp) REVERT: A 1152 TYR cc_start: 0.8714 (m-80) cc_final: 0.7842 (m-80) REVERT: B 185 LYS cc_start: 0.7728 (mmtm) cc_final: 0.6865 (mtpm) REVERT: B 455 PHE cc_start: 0.8621 (m-80) cc_final: 0.8333 (m-80) REVERT: B 503 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7424 (tt) REVERT: B 579 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7107 (mpp-170) REVERT: B 593 GLN cc_start: 0.7905 (mt0) cc_final: 0.7574 (mm-40) REVERT: B 925 LYS cc_start: 0.7965 (tttt) cc_final: 0.7563 (mmpt) REVERT: B 1125 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: C 78 MET cc_start: 0.8616 (mmm) cc_final: 0.8327 (mmm) REVERT: C 185 LYS cc_start: 0.7678 (mmtm) cc_final: 0.6993 (mtpm) REVERT: C 240 VAL cc_start: 0.8864 (t) cc_final: 0.8626 (p) REVERT: C 747 THR cc_start: 0.8187 (t) cc_final: 0.7924 (p) REVERT: C 925 LYS cc_start: 0.7889 (tttt) cc_final: 0.7565 (mmpt) REVERT: C 1114 PHE cc_start: 0.8544 (t80) cc_final: 0.8324 (t80) outliers start: 84 outliers final: 37 residues processed: 439 average time/residue: 1.0149 time to fit residues: 550.4460 Evaluate side-chains 312 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 271 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 944 ILE Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1176 CYS Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 469 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 177 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 265 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 319 optimal weight: 3.9990 chunk 344 optimal weight: 0.4980 chunk 284 optimal weight: 2.9990 chunk 316 optimal weight: 0.1980 chunk 108 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN A 663 ASN A 746 GLN A 801 GLN A 951 GLN A1104 GLN A1214 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 GLN B 840 GLN B 850 ASN B1058 GLN B1104 GLN B1214 ASN C 328 GLN ** C 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 746 GLN ** C 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 ASN C 951 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29358 Z= 0.267 Angle : 0.638 7.610 39972 Z= 0.330 Chirality : 0.048 0.403 4800 Planarity : 0.004 0.050 5013 Dihedral : 8.227 47.951 5797 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.65 % Allowed : 7.37 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3489 helix: 1.20 (0.19), residues: 786 sheet: 0.41 (0.17), residues: 771 loop : -0.03 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 460 HIS 0.004 0.001 HIS B 490 PHE 0.019 0.002 PHE C 278 TYR 0.023 0.002 TYR B 738 ARG 0.006 0.001 ARG C 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 304 time to evaluate : 2.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8624 (mmm) cc_final: 0.8389 (mmm) REVERT: A 168 MET cc_start: 0.8592 (mmm) cc_final: 0.8161 (mmt) REVERT: A 185 LYS cc_start: 0.7721 (mmtm) cc_final: 0.6782 (mtpm) REVERT: A 376 MET cc_start: 0.8319 (mtm) cc_final: 0.8090 (mtm) REVERT: A 749 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7662 (p0) REVERT: A 923 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8383 (mttt) REVERT: A 925 LYS cc_start: 0.7732 (tttt) cc_final: 0.7483 (mmpt) REVERT: A 944 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.6879 (pp) REVERT: B 185 LYS cc_start: 0.7682 (mmtm) cc_final: 0.6987 (mtpm) REVERT: B 455 PHE cc_start: 0.8648 (m-80) cc_final: 0.8338 (m-80) REVERT: B 503 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7384 (tt) REVERT: B 925 LYS cc_start: 0.7959 (tttt) cc_final: 0.7561 (mmpt) REVERT: B 1125 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: C 185 LYS cc_start: 0.7797 (mmtm) cc_final: 0.7133 (mtpm) REVERT: C 219 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: C 244 MET cc_start: 0.6794 (OUTLIER) cc_final: 0.6445 (ttm) REVERT: C 747 THR cc_start: 0.8239 (t) cc_final: 0.8032 (p) REVERT: C 925 LYS cc_start: 0.7889 (tttt) cc_final: 0.7504 (mmpt) REVERT: C 1014 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: C 1114 PHE cc_start: 0.8639 (t80) cc_final: 0.8424 (t80) REVERT: C 1125 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7969 (mt-10) outliers start: 112 outliers final: 61 residues processed: 384 average time/residue: 1.0892 time to fit residues: 511.7001 Evaluate side-chains 334 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 264 time to evaluate : 2.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 923 LYS Chi-restraints excluded: chain A residue 944 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 840 GLN Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1176 CYS Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 1014 GLN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1132 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 315 optimal weight: 0.9980 chunk 240 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 320 optimal weight: 1.9990 chunk 339 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 303 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 GLN ** A 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 ASN A1214 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN ** B 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 GLN ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 GLN B1214 ASN C 328 GLN ** C 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 746 GLN ** C 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 GLN C1058 GLN C1104 GLN C1214 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 29358 Z= 0.238 Angle : 0.603 9.825 39972 Z= 0.312 Chirality : 0.047 0.546 4800 Planarity : 0.004 0.039 5013 Dihedral : 6.743 48.866 5797 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.08 % Allowed : 8.02 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.14), residues: 3489 helix: 1.31 (0.19), residues: 786 sheet: 0.28 (0.17), residues: 774 loop : -0.11 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 460 HIS 0.003 0.001 HIS B 215 PHE 0.021 0.002 PHE B 278 TYR 0.025 0.002 TYR C 738 ARG 0.004 0.000 ARG C 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 287 time to evaluate : 3.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 LYS cc_start: 0.7777 (mmtm) cc_final: 0.6830 (mtpm) REVERT: A 749 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7739 (p0) REVERT: A 866 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7942 (mt0) REVERT: A 893 ASP cc_start: 0.7922 (t70) cc_final: 0.7478 (t0) REVERT: A 929 VAL cc_start: 0.8353 (t) cc_final: 0.8151 (m) REVERT: A 944 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.6940 (pp) REVERT: B 118 MET cc_start: 0.6202 (OUTLIER) cc_final: 0.5976 (ttp) REVERT: B 185 LYS cc_start: 0.7797 (mmtm) cc_final: 0.7118 (mtpm) REVERT: B 455 PHE cc_start: 0.8635 (m-80) cc_final: 0.8317 (m-80) REVERT: B 503 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7161 (tt) REVERT: B 579 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7234 (mpp-170) REVERT: B 866 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: B 925 LYS cc_start: 0.7961 (tttt) cc_final: 0.7591 (mmpt) REVERT: B 1125 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8208 (mt-10) REVERT: C 185 LYS cc_start: 0.7791 (mmtm) cc_final: 0.7221 (mtpm) REVERT: C 190 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7385 (tm) REVERT: C 219 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7268 (tt0) REVERT: C 244 MET cc_start: 0.6677 (OUTLIER) cc_final: 0.6356 (ttm) REVERT: C 747 THR cc_start: 0.8285 (t) cc_final: 0.8048 (p) REVERT: C 811 MET cc_start: 0.8026 (ttp) cc_final: 0.7810 (ttp) REVERT: C 925 LYS cc_start: 0.7877 (tttt) cc_final: 0.7475 (mmpt) REVERT: C 1014 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: C 1125 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7974 (mt-10) outliers start: 125 outliers final: 63 residues processed: 379 average time/residue: 1.1157 time to fit residues: 529.4750 Evaluate side-chains 342 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 266 time to evaluate : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain A residue 944 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 866 GLN Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1176 CYS Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 1014 GLN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1224 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 282 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 234 optimal weight: 0.0070 chunk 0 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 304 optimal weight: 2.9990 chunk 85 optimal weight: 0.0980 overall best weight: 1.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 GLN ** A 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 GLN A1214 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1214 ASN C 328 GLN ** C 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 29358 Z= 0.376 Angle : 0.656 8.119 39972 Z= 0.338 Chirality : 0.049 0.503 4800 Planarity : 0.004 0.042 5013 Dihedral : 6.496 49.776 5795 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.31 % Allowed : 8.64 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3489 helix: 1.12 (0.19), residues: 786 sheet: 0.10 (0.17), residues: 792 loop : -0.29 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 460 HIS 0.005 0.002 HIS B 490 PHE 0.018 0.002 PHE B 278 TYR 0.023 0.002 TYR B 738 ARG 0.006 0.001 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 264 time to evaluate : 3.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.8515 (mtm) cc_final: 0.8230 (mtm) REVERT: A 749 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7738 (p0) REVERT: A 893 ASP cc_start: 0.7998 (t70) cc_final: 0.7536 (t0) REVERT: A 944 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.6971 (pp) REVERT: B 455 PHE cc_start: 0.8674 (m-80) cc_final: 0.8361 (m-80) REVERT: B 579 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7141 (mpp-170) REVERT: B 749 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7888 (p0) REVERT: B 925 LYS cc_start: 0.7915 (tttt) cc_final: 0.7539 (mmpt) REVERT: B 973 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8451 (tp) REVERT: B 1125 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8375 (mt-10) REVERT: B 1232 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6569 (mpp) REVERT: C 185 LYS cc_start: 0.7965 (mmtm) cc_final: 0.7370 (mtpm) REVERT: C 190 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7439 (tm) REVERT: C 219 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7296 (tt0) REVERT: C 559 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7840 (mm-30) REVERT: C 833 ASP cc_start: 0.7110 (t70) cc_final: 0.6904 (t0) REVERT: C 925 LYS cc_start: 0.7872 (tttt) cc_final: 0.7489 (mmpt) REVERT: C 1014 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7821 (tm-30) REVERT: C 1125 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8103 (mt-10) REVERT: C 1232 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6647 (mpp) outliers start: 132 outliers final: 72 residues processed: 363 average time/residue: 1.0962 time to fit residues: 487.7642 Evaluate side-chains 333 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 248 time to evaluate : 3.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 840 GLN Chi-restraints excluded: chain A residue 944 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1132 SER Chi-restraints excluded: chain B residue 1176 CYS Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1232 MET Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 874 MET Chi-restraints excluded: chain C residue 1014 GLN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1224 ASN Chi-restraints excluded: chain C residue 1232 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 114 optimal weight: 0.5980 chunk 305 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 339 optimal weight: 0.9980 chunk 281 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 28 optimal weight: 0.0670 chunk 112 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 GLN ** A 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 GLN A1058 GLN A1214 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 ASN B 850 ASN B1058 GLN B1214 ASN C 328 GLN ** C 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 ASN ** C 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29358 Z= 0.212 Angle : 0.576 7.886 39972 Z= 0.298 Chirality : 0.047 0.837 4800 Planarity : 0.004 0.045 5013 Dihedral : 6.025 50.349 5795 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.36 % Allowed : 10.05 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3489 helix: 1.35 (0.19), residues: 783 sheet: 0.31 (0.18), residues: 726 loop : -0.25 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 460 HIS 0.005 0.001 HIS B 483 PHE 0.021 0.002 PHE B 278 TYR 0.020 0.001 TYR C 738 ARG 0.004 0.000 ARG B 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 272 time to evaluate : 3.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8125 (mtt) REVERT: A 749 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7701 (p0) REVERT: A 893 ASP cc_start: 0.7899 (t70) cc_final: 0.7455 (t0) REVERT: A 944 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.6844 (pp) REVERT: B 455 PHE cc_start: 0.8633 (m-80) cc_final: 0.8350 (m-80) REVERT: B 579 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7117 (mpp-170) REVERT: B 749 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.7969 (p0) REVERT: B 925 LYS cc_start: 0.7952 (tttt) cc_final: 0.7558 (mmpt) REVERT: B 1030 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7052 (tm-30) REVERT: B 1125 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8385 (mt-10) REVERT: C 19 LEU cc_start: 0.7594 (mt) cc_final: 0.7346 (mp) REVERT: C 185 LYS cc_start: 0.7944 (mmtm) cc_final: 0.7398 (mtpm) REVERT: C 244 MET cc_start: 0.6683 (OUTLIER) cc_final: 0.6363 (ttm) REVERT: C 484 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7779 (m-30) REVERT: C 925 LYS cc_start: 0.7867 (tttt) cc_final: 0.7492 (mmpt) REVERT: C 1014 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: C 1125 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: C 1232 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6656 (mpp) outliers start: 103 outliers final: 59 residues processed: 350 average time/residue: 1.0595 time to fit residues: 457.5912 Evaluate side-chains 328 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 257 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 944 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 840 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1030 GLU Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1176 CYS Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 1014 GLN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1232 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 327 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 193 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 285 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 338 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 206 optimal weight: 0.1980 chunk 156 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 GLN ** A 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1214 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 ASN B1214 ASN C 109 ASN C 328 GLN ** C 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 ASN ** C 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 29358 Z= 0.313 Angle : 0.615 7.173 39972 Z= 0.317 Chirality : 0.047 0.605 4800 Planarity : 0.004 0.041 5013 Dihedral : 6.032 49.159 5795 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.62 % Allowed : 10.40 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3489 helix: 1.22 (0.19), residues: 783 sheet: 0.21 (0.18), residues: 741 loop : -0.35 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 460 HIS 0.004 0.001 HIS B 490 PHE 0.019 0.002 PHE B 278 TYR 0.016 0.002 TYR A 633 ARG 0.006 0.001 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 257 time to evaluate : 3.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8171 (mtt) REVERT: A 376 MET cc_start: 0.8603 (mtm) cc_final: 0.8286 (mtm) REVERT: A 749 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7734 (p0) REVERT: A 893 ASP cc_start: 0.7933 (t70) cc_final: 0.7477 (t0) REVERT: A 944 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.6837 (pp) REVERT: B 455 PHE cc_start: 0.8663 (m-80) cc_final: 0.8332 (m-80) REVERT: B 579 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7179 (mpp-170) REVERT: B 749 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.7997 (p0) REVERT: B 889 PHE cc_start: 0.7582 (p90) cc_final: 0.7119 (m-10) REVERT: B 925 LYS cc_start: 0.7899 (tttt) cc_final: 0.7524 (mmpt) REVERT: B 1125 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8439 (mt-10) REVERT: B 1232 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6537 (mpp) REVERT: C 60 THR cc_start: 0.8112 (p) cc_final: 0.7898 (p) REVERT: C 185 LYS cc_start: 0.7972 (mmtm) cc_final: 0.7480 (mtpm) REVERT: C 190 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7427 (tm) REVERT: C 484 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7828 (m-30) REVERT: C 925 LYS cc_start: 0.7863 (tttt) cc_final: 0.7483 (mmpt) REVERT: C 1014 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: C 1125 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8083 (mt-10) outliers start: 111 outliers final: 74 residues processed: 344 average time/residue: 1.0111 time to fit residues: 430.0028 Evaluate side-chains 330 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 245 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 490 HIS Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 944 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 683 CYS Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 840 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1132 SER Chi-restraints excluded: chain B residue 1176 CYS Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1232 MET Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 874 MET Chi-restraints excluded: chain C residue 1014 GLN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1137 CYS Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1224 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 209 optimal weight: 0.0970 chunk 135 optimal weight: 0.8980 chunk 202 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 230 optimal weight: 0.6980 chunk 167 optimal weight: 0.4980 chunk 31 optimal weight: 0.0570 chunk 265 optimal weight: 0.9980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 GLN ** A 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 GLN A1214 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 ASN ** B 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 ASN B1058 GLN B1214 ASN C 328 GLN ** C 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 ASN ** C 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29358 Z= 0.161 Angle : 0.553 13.763 39972 Z= 0.283 Chirality : 0.045 0.520 4800 Planarity : 0.004 0.046 5013 Dihedral : 5.684 48.349 5795 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.87 % Allowed : 11.90 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 3489 helix: 1.47 (0.19), residues: 783 sheet: 0.25 (0.18), residues: 726 loop : -0.30 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 460 HIS 0.003 0.001 HIS B 483 PHE 0.021 0.001 PHE B 278 TYR 0.015 0.001 TYR C 738 ARG 0.005 0.000 ARG B 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 268 time to evaluate : 3.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 749 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7745 (p0) REVERT: A 889 PHE cc_start: 0.7718 (p90) cc_final: 0.6971 (m-10) REVERT: A 893 ASP cc_start: 0.7834 (t70) cc_final: 0.7399 (t0) REVERT: A 944 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.6821 (pp) REVERT: B 244 MET cc_start: 0.7320 (pmm) cc_final: 0.7114 (mmm) REVERT: B 455 PHE cc_start: 0.8611 (m-80) cc_final: 0.8270 (m-80) REVERT: B 889 PHE cc_start: 0.7583 (p90) cc_final: 0.7083 (m-80) REVERT: B 925 LYS cc_start: 0.7931 (tttt) cc_final: 0.7549 (mmpt) REVERT: B 1125 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8305 (mt-10) REVERT: C 185 LYS cc_start: 0.7944 (mmtm) cc_final: 0.7456 (mtpm) REVERT: C 190 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7426 (tm) REVERT: C 484 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7765 (m-30) REVERT: C 925 LYS cc_start: 0.7860 (tttt) cc_final: 0.7480 (mmpt) REVERT: C 1014 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7838 (tm-30) REVERT: C 1125 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7993 (mt-10) outliers start: 88 outliers final: 47 residues processed: 335 average time/residue: 1.0689 time to fit residues: 443.1536 Evaluate side-chains 314 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 260 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 490 HIS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 944 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 683 CYS Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1176 CYS Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 1014 GLN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1137 CYS Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1224 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 307 optimal weight: 2.9990 chunk 324 optimal weight: 0.5980 chunk 295 optimal weight: 1.9990 chunk 315 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 247 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 284 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 chunk 314 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 GLN ** A 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1214 ASN B 109 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 ASN B1058 GLN C 328 GLN ** C 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 ASN ** C 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29358 Z= 0.230 Angle : 0.577 8.156 39972 Z= 0.298 Chirality : 0.045 0.458 4800 Planarity : 0.004 0.052 5013 Dihedral : 6.341 117.067 5795 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.58 % Allowed : 12.30 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.25 (0.14), residues: 3489 helix: 1.42 (0.19), residues: 783 sheet: 0.17 (0.18), residues: 741 loop : -0.30 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 460 HIS 0.004 0.001 HIS B 490 PHE 0.019 0.002 PHE B 278 TYR 0.015 0.001 TYR C1161 ARG 0.007 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 263 time to evaluate : 3.225 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: A 749 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7744 (p0) REVERT: A 889 PHE cc_start: 0.7636 (p90) cc_final: 0.6959 (m-10) REVERT: A 893 ASP cc_start: 0.7857 (t70) cc_final: 0.7436 (t0) REVERT: A 944 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.6870 (pp) REVERT: B 244 MET cc_start: 0.7369 (pmm) cc_final: 0.7159 (mmm) REVERT: B 455 PHE cc_start: 0.8667 (m-80) cc_final: 0.8318 (m-80) REVERT: B 889 PHE cc_start: 0.7611 (p90) cc_final: 0.7162 (m-80) REVERT: B 925 LYS cc_start: 0.7947 (tttt) cc_final: 0.7554 (mmpt) REVERT: B 1125 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8365 (mt-10) REVERT: B 1232 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6694 (mpp) REVERT: C 185 LYS cc_start: 0.7958 (mmtm) cc_final: 0.7555 (mtpm) REVERT: C 190 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7378 (tm) REVERT: C 484 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7775 (m-30) REVERT: C 805 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7717 (tt0) REVERT: C 889 PHE cc_start: 0.7708 (p90) cc_final: 0.6991 (m-80) REVERT: C 925 LYS cc_start: 0.7852 (tttt) cc_final: 0.7431 (mmpt) REVERT: C 1014 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7836 (tm-30) REVERT: C 1125 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8053 (mt-10) outliers start: 79 outliers final: 52 residues processed: 327 average time/residue: 1.0678 time to fit residues: 429.8040 Evaluate side-chains 314 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 253 time to evaluate : 3.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 490 HIS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 944 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 683 CYS Chi-restraints excluded: chain B residue 840 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1176 CYS Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1232 MET Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 805 GLU Chi-restraints excluded: chain C residue 944 ILE Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 1014 GLN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1137 CYS Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1224 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 207 optimal weight: 0.7980 chunk 333 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 231 optimal weight: 0.7980 chunk 349 optimal weight: 1.9990 chunk 321 optimal weight: 0.0470 chunk 278 optimal weight: 4.9990 chunk 28 optimal weight: 0.0050 chunk 215 optimal weight: 0.7980 chunk 170 optimal weight: 0.0980 overall best weight: 0.3492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 GLN ** A 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 ASN A1058 GLN A1214 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 ASN B1058 GLN C 328 GLN ** C 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29358 Z= 0.154 Angle : 0.540 9.485 39972 Z= 0.278 Chirality : 0.044 0.434 4800 Planarity : 0.003 0.045 5013 Dihedral : 6.167 118.214 5795 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.96 % Allowed : 13.05 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.14), residues: 3489 helix: 1.56 (0.19), residues: 783 sheet: 0.29 (0.18), residues: 696 loop : -0.28 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 460 HIS 0.003 0.001 HIS A 490 PHE 0.021 0.001 PHE B 278 TYR 0.014 0.001 TYR C 738 ARG 0.008 0.000 ARG B 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 274 time to evaluate : 3.298 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: A 749 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7778 (p0) REVERT: A 889 PHE cc_start: 0.7620 (p90) cc_final: 0.7012 (m-10) REVERT: A 893 ASP cc_start: 0.7759 (t70) cc_final: 0.7396 (t0) REVERT: B 244 MET cc_start: 0.7294 (pmm) cc_final: 0.7093 (mmm) REVERT: B 455 PHE cc_start: 0.8583 (m-80) cc_final: 0.8303 (m-80) REVERT: B 889 PHE cc_start: 0.7598 (p90) cc_final: 0.7190 (m-10) REVERT: B 925 LYS cc_start: 0.7925 (tttt) cc_final: 0.7548 (mmpt) REVERT: B 1125 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8240 (mt-10) REVERT: B 1232 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6657 (mpp) REVERT: C 60 THR cc_start: 0.7823 (p) cc_final: 0.7530 (p) REVERT: C 185 LYS cc_start: 0.7915 (mmtm) cc_final: 0.7509 (mtpm) REVERT: C 484 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7765 (m-30) REVERT: C 889 PHE cc_start: 0.7708 (p90) cc_final: 0.7033 (m-10) REVERT: C 925 LYS cc_start: 0.7845 (tttt) cc_final: 0.7426 (mmpt) REVERT: C 1125 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7944 (mm-30) outliers start: 60 outliers final: 40 residues processed: 320 average time/residue: 1.0518 time to fit residues: 413.6476 Evaluate side-chains 302 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 257 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 490 HIS Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 683 CYS Chi-restraints excluded: chain B residue 840 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1176 CYS Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1232 MET Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1224 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 221 optimal weight: 2.9990 chunk 296 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 256 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 278 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 286 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 GLN ** A 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 GLN A1214 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 ASN B1058 GLN C 328 GLN ** C 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.140630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.112885 restraints weight = 34361.565| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.04 r_work: 0.3146 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 29358 Z= 0.325 Angle : 0.620 11.399 39972 Z= 0.318 Chirality : 0.047 0.479 4800 Planarity : 0.004 0.039 5013 Dihedral : 6.001 75.867 5795 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.15 % Allowed : 13.21 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.19 (0.14), residues: 3489 helix: 1.28 (0.19), residues: 783 sheet: 0.18 (0.18), residues: 747 loop : -0.32 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 460 HIS 0.004 0.001 HIS A 490 PHE 0.019 0.002 PHE B 278 TYR 0.019 0.002 TYR A 633 ARG 0.010 0.001 ARG B 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8839.43 seconds wall clock time: 159 minutes 39.67 seconds (9579.67 seconds total)