Starting phenix.real_space_refine on Fri Mar 22 14:15:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s12_10078/03_2024/6s12_10078.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s12_10078/03_2024/6s12_10078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s12_10078/03_2024/6s12_10078.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s12_10078/03_2024/6s12_10078.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s12_10078/03_2024/6s12_10078.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s12_10078/03_2024/6s12_10078.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 6 Type Number sf(0) Gaussians P 3019 5.49 5 S 63 5.16 5 C 43890 2.51 5 N 16399 2.21 5 O 25294 1.98 5 H 57352 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 84": "OD1" <-> "OD2" Residue "C ARG 243": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 274": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 89": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 54": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 168": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 54": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 152": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 163": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 2": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 103": "OE1" <-> "OE2" Residue "I ARG 17": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 115": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 11": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 11": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 28": "OD1" <-> "OD2" Residue "R PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ASP 31": "OD1" <-> "OD2" Residue "S ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y ASP 16": "OD1" <-> "OD2" Residue "Z ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 146017 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 93573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2905, 93573 Classifications: {'RNA': 2905} Modifications used: {'3*END': 1, 'rna2p_pur': 313, 'rna2p_pyr': 170, 'rna3p_pur': 1352, 'rna3p_pyr': 1070} Link IDs: {'rna2p': 483, 'rna3p': 2421} Chain breaks: 8 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' G%rna3p_pur:plan': 1, ' A%rna3p_pur:plan2': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 3685 Classifications: {'RNA': 115} Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 9, 'rna3p_pur': 54, 'rna3p_pyr': 47} Link IDs: {'rna2p': 14, 'rna3p': 100} Chain: "C" Number of atoms: 4291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 4291 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 17, 'TRANS': 256} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3294 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 8, 'TRANS': 206} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3192 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 2667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 2667 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 6, 'TRANS': 168} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "G" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 2488 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 7, 'TRANS': 167} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 68 Chain: "H" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2277 Classifications: {'peptide': 145} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1899 Classifications: {'peptide': 122} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2211 Classifications: {'peptide': 146} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2194 Classifications: {'peptide': 137} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 129} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1915 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "M" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1816 Classifications: {'peptide': 119} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "N" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1826 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "O" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1956 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1620 Classifications: {'peptide': 102} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1724 Classifications: {'peptide': 110} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1463 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "S" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1579 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "T" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1488 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "U" Number of atoms: 1265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1265 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 911 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1104 Classifications: {'peptide': 67} Link IDs: {'TRANS': 66} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 940 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Y" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 613 Classifications: {'peptide': 59} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 55} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "Z" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 718 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 17 Chain: "1" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 784 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 782 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "3" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1107 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "4" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 635 Classifications: {'peptide': 37} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 47.77, per 1000 atoms: 0.33 Number of scatterers: 146017 At special positions: 0 Unit cell: (218.735, 232.606, 196.328, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 3019 15.00 O 25294 8.00 N 16399 7.00 C 43890 6.00 H 57352 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS 1 9 " - pdb=" SG CYS 1 12 " distance=2.03 Simple disulfide: pdb=" SG CYS 1 12 " - pdb=" SG CYS 1 36 " distance=2.04 Simple disulfide: pdb=" SG CYS 4 14 " - pdb=" SG CYS 4 27 " 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 Time building additional restraints: 114.22 Conformation dependent library (CDL) restraints added in 5.3 seconds 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5698 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 45 sheets defined 25.7% alpha, 16.6% beta 893 base pairs and 1371 stacking pairs defined. Time for finding SS restraints: 60.16 Creating SS restraints... Processing helix chain 'C' and resid 131 through 135 removed outlier: 3.965A pdb=" N ILE C 135 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 202 removed outlier: 3.759A pdb=" N GLU C 201 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 70 through 80 removed outlier: 4.118A pdb=" N ALA D 80 " --> pdb=" O HIS D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 110 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 29 through 43 Processing helix chain 'E' and resid 102 through 120 removed outlier: 4.104A pdb=" N LEU E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 146 Processing helix chain 'E' and resid 160 through 167 Processing helix chain 'E' and resid 183 through 189 Processing helix chain 'E' and resid 196 through 207 Processing helix chain 'F' and resid 3 through 20 removed outlier: 4.420A pdb=" N LYS F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N MET F 17 " --> pdb=" O THR F 13 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LYS F 18 " --> pdb=" O GLU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 28 removed outlier: 3.554A pdb=" N VAL F 28 " --> pdb=" O VAL F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 61 removed outlier: 3.523A pdb=" N LEU F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU F 59 " --> pdb=" O GLU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 112 removed outlier: 4.644A pdb=" N LEU F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix removed outlier: 3.593A pdb=" N ARG F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 171 removed outlier: 3.573A pdb=" N GLU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 58 through 80 removed outlier: 4.030A pdb=" N GLY G 78 " --> pdb=" O ASN G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 149 removed outlier: 3.720A pdb=" N ARG G 149 " --> pdb=" O ALA G 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 39 removed outlier: 4.767A pdb=" N GLU H 32 " --> pdb=" O ARG H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 96 Processing helix chain 'H' and resid 97 through 106 removed outlier: 3.949A pdb=" N LEU H 101 " --> pdb=" O ASN H 97 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE H 102 " --> pdb=" O PRO H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 121 Processing helix chain 'I' and resid 111 through 118 Processing helix chain 'J' and resid 22 through 26 removed outlier: 3.785A pdb=" N THR J 25 " --> pdb=" O GLY J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'J' and resid 92 through 100 Processing helix chain 'J' and resid 129 through 140 removed outlier: 3.798A pdb=" N LYS J 139 " --> pdb=" O ALA J 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 59 Processing helix chain 'K' and resid 110 through 124 removed outlier: 3.576A pdb=" N HIS K 123 " --> pdb=" O ARG K 119 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS K 124 " --> pdb=" O LEU K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 28 Processing helix chain 'L' and resid 33 through 52 removed outlier: 3.908A pdb=" N ALA L 37 " --> pdb=" O THR L 33 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER L 42 " --> pdb=" O LYS L 38 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL L 43 " --> pdb=" O GLU L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 66 removed outlier: 3.500A pdb=" N LYS L 64 " --> pdb=" O ARG L 60 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR L 65 " --> pdb=" O ASN L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 89 removed outlier: 3.843A pdb=" N ILE L 89 " --> pdb=" O LEU L 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 20 Processing helix chain 'M' and resid 70 through 87 removed outlier: 3.572A pdb=" N ASP M 86 " --> pdb=" O LYS M 82 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS M 87 " --> pdb=" O LYS M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 115 Processing helix chain 'N' and resid 5 through 12 Processing helix chain 'N' and resid 55 through 58 removed outlier: 3.553A pdb=" N SER N 58 " --> pdb=" O GLY N 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 55 through 58' Processing helix chain 'N' and resid 99 through 103 removed outlier: 3.527A pdb=" N ARG N 103 " --> pdb=" O TYR N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 111 removed outlier: 4.327A pdb=" N ALA N 109 " --> pdb=" O ARG N 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 19 removed outlier: 3.998A pdb=" N THR O 17 " --> pdb=" O ARG O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 22 No H-bonds generated for 'chain 'O' and resid 20 through 22' Processing helix chain 'O' and resid 31 through 71 removed outlier: 4.659A pdb=" N GLN O 37 " --> pdb=" O LYS O 33 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG O 51 " --> pdb=" O PHE O 47 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG O 55 " --> pdb=" O ARG O 51 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG O 58 " --> pdb=" O LYS O 54 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG O 70 " --> pdb=" O ASN O 66 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN O 71 " --> pdb=" O ALA O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 87 Processing helix chain 'O' and resid 91 through 101 Processing helix chain 'O' and resid 102 through 115 Processing helix chain 'Q' and resid 13 through 22 removed outlier: 4.560A pdb=" N LEU Q 19 " --> pdb=" O ARG Q 15 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N VAL Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 39 Processing helix chain 'Q' and resid 42 through 61 removed outlier: 4.525A pdb=" N VAL Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 21 Processing helix chain 'R' and resid 34 through 46 Processing helix chain 'T' and resid 14 through 24 Processing helix chain 'T' and resid 45 through 56 Processing helix chain 'W' and resid 3 through 9 Processing helix chain 'W' and resid 13 through 34 Processing helix chain 'W' and resid 40 through 66 removed outlier: 4.234A pdb=" N ARG W 44 " --> pdb=" O THR W 40 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR W 45 " --> pdb=" O ALA W 41 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL W 46 " --> pdb=" O ARG W 42 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA W 57 " --> pdb=" O LEU W 53 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU W 61 " --> pdb=" O ALA W 57 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN W 64 " --> pdb=" O ARG W 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 16 through 27 Processing helix chain 'X' and resid 40 through 49 removed outlier: 3.646A pdb=" N GLN X 46 " --> pdb=" O ALA X 42 " (cutoff:3.500A) Processing helix chain 'X' and resid 50 through 52 No H-bonds generated for 'chain 'X' and resid 50 through 52' Processing helix chain 'Z' and resid 9 through 17 Processing helix chain '2' and resid 9 through 17 Processing helix chain '2' and resid 18 through 23 Processing helix chain '2' and resid 25 through 39 removed outlier: 4.654A pdb=" N VAL 2 31 " --> pdb=" O ASN 2 27 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU 2 32 " --> pdb=" O GLY 2 28 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA 2 33 " --> pdb=" O ARG 2 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG 2 34 " --> pdb=" O LYS 2 30 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 12 Processing helix chain '3' and resid 38 through 43 Processing helix chain '3' and resid 51 through 59 Processing helix chain '3' and resid 60 through 62 No H-bonds generated for 'chain '3' and resid 60 through 62' Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 83 removed outlier: 6.943A pdb=" N LEU C 93 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE C 81 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AA5, first strand: chain 'C' and resid 172 through 175 Processing sheet with id=AA6, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.530A pdb=" N ARG D 212 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 9 through 16 removed outlier: 6.320A pdb=" N LYS D 9 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU D 29 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL D 194 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N VAL D 188 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU D 196 " --> pdb=" O VAL D 186 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 34 through 38 removed outlier: 6.767A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 119 through 121 Processing sheet with id=AB1, first strand: chain 'D' and resid 126 through 128 Processing sheet with id=AB2, first strand: chain 'E' and resid 13 through 18 removed outlier: 11.255A pdb=" N LEU E 123 " --> pdb=" O ASN E 3 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ASP E 5 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL E 125 " --> pdb=" O ASP E 5 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU E 153 " --> pdb=" O VAL E 193 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 90 through 91 removed outlier: 6.831A pdb=" N VAL F 157 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE F 34 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL F 155 " --> pdb=" O ILE F 34 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 69 through 70 Processing sheet with id=AB5, first strand: chain 'G' and resid 16 through 20 removed outlier: 3.781A pdb=" N HIS G 23 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 43 through 45 Processing sheet with id=AB7, first strand: chain 'G' and resid 122 through 125 Processing sheet with id=AB8, first strand: chain 'G' and resid 97 through 98 Processing sheet with id=AB9, first strand: chain 'H' and resid 123 through 125 removed outlier: 6.627A pdb=" N VAL H 55 " --> pdb=" O PHE H 124 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP H 16 " --> pdb=" O GLU H 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 75 through 78 Processing sheet with id=AC2, first strand: chain 'I' and resid 7 through 9 removed outlier: 6.427A pdb=" N ALA I 16 " --> pdb=" O ALA I 46 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA I 46 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLU I 18 " --> pdb=" O LYS I 44 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL I 40 " --> pdb=" O ILE I 22 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL I 24 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL I 38 " --> pdb=" O VAL I 24 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 76 through 79 removed outlier: 6.306A pdb=" N THR N 60 " --> pdb=" O ARG N 52 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG N 52 " --> pdb=" O THR N 60 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR N 62 " --> pdb=" O ILE N 50 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE N 66 " --> pdb=" O GLU N 46 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N GLU N 46 " --> pdb=" O ILE N 66 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR N 27 " --> pdb=" O LYS N 89 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG N 33 " --> pdb=" O ILE N 83 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE N 83 " --> pdb=" O ARG N 33 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 75 through 77 removed outlier: 6.078A pdb=" N ALA J 75 " --> pdb=" O LYS J 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'K' and resid 63 through 66 removed outlier: 3.714A pdb=" N PHE K 104 " --> pdb=" O LEU K 34 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 72 through 75 removed outlier: 4.306A pdb=" N GLY K 92 " --> pdb=" O TYR K 74 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 29 through 32 Processing sheet with id=AC8, first strand: chain 'L' and resid 70 through 73 Processing sheet with id=AC9, first strand: chain 'M' and resid 56 through 57 Processing sheet with id=AD1, first strand: chain 'P' and resid 10 through 14 removed outlier: 3.786A pdb=" N PHE P 40 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU P 6 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL P 38 " --> pdb=" O GLU P 6 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 19 through 23 removed outlier: 3.532A pdb=" N VAL P 22 " --> pdb=" O THR P 93 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LYS P 64 " --> pdb=" O LYS P 94 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR P 96 " --> pdb=" O VAL P 62 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL P 62 " --> pdb=" O THR P 96 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASP P 98 " --> pdb=" O ALA P 60 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA P 60 " --> pdb=" O ASP P 98 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE P 100 " --> pdb=" O VAL P 58 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL P 58 " --> pdb=" O ILE P 100 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 71 through 77 removed outlier: 4.631A pdb=" N SER P 82 " --> pdb=" O LYS P 77 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 2 through 7 removed outlier: 5.723A pdb=" N SER Q 106 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N VAL Q 71 " --> pdb=" O SER Q 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 82 through 85 Processing sheet with id=AD6, first strand: chain 'R' and resid 7 through 10 removed outlier: 4.240A pdb=" N ARG R 76 " --> pdb=" O VAL R 29 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 62 through 64 Processing sheet with id=AD8, first strand: chain 'S' and resid 63 through 64 removed outlier: 7.191A pdb=" N VAL S 34 " --> pdb=" O ILE S 24 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 82 through 86 Processing sheet with id=AE1, first strand: chain 'T' and resid 3 through 5 removed outlier: 7.148A pdb=" N LEU T 4 " --> pdb=" O GLY T 64 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP T 90 " --> pdb=" O ALA T 75 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TYR T 77 " --> pdb=" O HIS T 88 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N HIS T 88 " --> pdb=" O TYR T 77 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE T 79 " --> pdb=" O ILE T 86 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE T 86 " --> pdb=" O PHE T 79 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N LYS T 26 " --> pdb=" O GLN T 85 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR T 87 " --> pdb=" O LYS T 26 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 30 through 31 removed outlier: 6.392A pdb=" N ILE U 44 " --> pdb=" O ALA U 69 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA U 69 " --> pdb=" O ILE U 44 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR U 46 " --> pdb=" O LEU U 67 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'U' and resid 54 through 57 removed outlier: 6.756A pdb=" N VAL U 89 " --> pdb=" O GLY U 56 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 13 through 17 Processing sheet with id=AE5, first strand: chain 'V' and resid 33 through 38 Processing sheet with id=AE6, first strand: chain 'X' and resid 34 through 38 Processing sheet with id=AE7, first strand: chain '1' and resid 18 through 19 removed outlier: 3.535A pdb=" N VAL 1 5 " --> pdb=" O THR 1 19 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG 1 46 " --> pdb=" O ALA 1 8 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '3' and resid 14 through 16 Processing sheet with id=AE9, first strand: chain '4' and resid 15 through 19 removed outlier: 3.532A pdb=" N LYS 4 15 " --> pdb=" O ILE 4 26 " (cutoff:3.500A) 780 hydrogen bonds defined for protein. 2145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2216 hydrogen bonds 3516 hydrogen bond angles 0 basepair planarities 893 basepair parallelities 1371 stacking parallelities Total time for adding SS restraints: 150.08 Time building geometry restraints manager: 119.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.15: 57347 1.15 - 1.49: 69061 1.49 - 1.82: 27658 1.82 - 2.16: 2 2.16 - 2.49: 6 Bond restraints: 154074 Sorted by residual: bond pdb=" C1' G A 393 " pdb=" N9 G A 393 " ideal model delta sigma weight residual 1.475 2.492 -1.017 1.50e-02 4.44e+03 4.59e+03 bond pdb=" C2 C A 333 " pdb=" N3 C A 333 " ideal model delta sigma weight residual 1.353 2.220 -0.867 2.00e-02 2.50e+03 1.88e+03 bond pdb=" N3 C A 333 " pdb=" C4 C A 333 " ideal model delta sigma weight residual 1.334 2.160 -0.826 2.00e-02 2.50e+03 1.71e+03 bond pdb=" N1 C A 333 " pdb=" C6 C A 333 " ideal model delta sigma weight residual 1.367 2.192 -0.825 2.00e-02 2.50e+03 1.70e+03 bond pdb=" N1 C A 333 " pdb=" C2 C A 333 " ideal model delta sigma weight residual 1.397 2.207 -0.810 2.00e-02 2.50e+03 1.64e+03 ... (remaining 154069 not shown) Histogram of bond angle deviations from ideal: 65.85 - 82.39: 1 82.39 - 98.93: 16 98.93 - 115.46: 188689 115.46 - 132.00: 87624 132.00 - 148.54: 524 Bond angle restraints: 276854 Sorted by residual: angle pdb=" C8 G A 393 " pdb=" N9 G A 393 " pdb=" C4 G A 393 " ideal model delta sigma weight residual 106.40 65.85 40.55 3.00e+00 1.11e-01 1.83e+02 angle pdb=" C2' G A 393 " pdb=" C1' G A 393 " pdb=" N9 G A 393 " ideal model delta sigma weight residual 112.00 131.09 -19.09 1.50e+00 4.44e-01 1.62e+02 angle pdb=" N9 G A 393 " pdb=" C8 G A 393 " pdb=" N7 G A 393 " ideal model delta sigma weight residual 113.10 145.09 -31.99 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C2' G A 393 " pdb=" C1' G A 393 " pdb=" H1' G A 393 " ideal model delta sigma weight residual 109.00 84.12 24.88 3.00e+00 1.11e-01 6.88e+01 angle pdb=" O4' G A 393 " pdb=" C1' G A 393 " pdb=" N9 G A 393 " ideal model delta sigma weight residual 108.50 120.67 -12.17 1.50e+00 4.44e-01 6.58e+01 ... (remaining 276849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 63106 35.94 - 71.88: 11439 71.88 - 107.81: 1371 107.81 - 143.75: 39 143.75 - 179.69: 34 Dihedral angle restraints: 75989 sinusoidal: 66218 harmonic: 9771 Sorted by residual: dihedral pdb=" O4' U A1804 " pdb=" C1' U A1804 " pdb=" N1 U A1804 " pdb=" C2 U A1804 " ideal model delta sinusoidal sigma weight residual -160.00 19.69 -179.69 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A1343 " pdb=" C1' U A1343 " pdb=" N1 U A1343 " pdb=" C2 U A1343 " ideal model delta sinusoidal sigma weight residual 200.00 20.83 179.17 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1692 " pdb=" C1' C A1692 " pdb=" N1 C A1692 " pdb=" C2 C A1692 " ideal model delta sinusoidal sigma weight residual -160.00 19.10 -179.10 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 75986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 15905 0.083 - 0.166: 2560 0.166 - 0.249: 301 0.249 - 0.332: 24 0.332 - 0.415: 2 Chirality restraints: 18792 Sorted by residual: chirality pdb=" C1' U A 759 " pdb=" O4' U A 759 " pdb=" C2' U A 759 " pdb=" N1 U A 759 " both_signs ideal model delta sigma weight residual False 2.47 2.05 0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" C1' A A1626 " pdb=" O4' A A1626 " pdb=" C2' A A1626 " pdb=" N9 A A1626 " both_signs ideal model delta sigma weight residual False 2.46 2.10 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C1' C A1452 " pdb=" O4' C A1452 " pdb=" C2' C A1452 " pdb=" N1 C A1452 " both_signs ideal model delta sigma weight residual False 2.47 2.15 0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 18789 not shown) Planarity restraints: 12519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 402 " 0.007 2.00e-02 2.50e+03 3.87e-02 4.13e+01 pdb=" N1 C A 402 " -0.016 2.00e-02 2.50e+03 pdb=" C2 C A 402 " 0.107 2.00e-02 2.50e+03 pdb=" O2 C A 402 " -0.045 2.00e-02 2.50e+03 pdb=" N3 C A 402 " -0.041 2.00e-02 2.50e+03 pdb=" C4 C A 402 " -0.001 2.00e-02 2.50e+03 pdb=" N4 C A 402 " 0.012 2.00e-02 2.50e+03 pdb=" C5 C A 402 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C A 402 " -0.029 2.00e-02 2.50e+03 pdb=" H5 C A 402 " -0.001 2.00e-02 2.50e+03 pdb=" H6 C A 402 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 333 " -0.021 2.00e-02 2.50e+03 3.46e-02 3.29e+01 pdb=" N1 C A 333 " -0.004 2.00e-02 2.50e+03 pdb=" C2 C A 333 " 0.056 2.00e-02 2.50e+03 pdb=" O2 C A 333 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C A 333 " -0.017 2.00e-02 2.50e+03 pdb=" C4 C A 333 " -0.035 2.00e-02 2.50e+03 pdb=" N4 C A 333 " -0.015 2.00e-02 2.50e+03 pdb=" C5 C A 333 " 0.078 2.00e-02 2.50e+03 pdb=" C6 C A 333 " -0.041 2.00e-02 2.50e+03 pdb=" H5 C A 333 " 0.001 2.00e-02 2.50e+03 pdb=" H6 C A 333 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 4 " 0.046 2.00e-02 2.50e+03 2.37e-02 1.97e+01 pdb=" N9 G B 4 " -0.040 2.00e-02 2.50e+03 pdb=" C8 G B 4 " -0.029 2.00e-02 2.50e+03 pdb=" N7 G B 4 " 0.006 2.00e-02 2.50e+03 pdb=" C5 G B 4 " 0.038 2.00e-02 2.50e+03 pdb=" C6 G B 4 " 0.022 2.00e-02 2.50e+03 pdb=" O6 G B 4 " 0.002 2.00e-02 2.50e+03 pdb=" N1 G B 4 " -0.033 2.00e-02 2.50e+03 pdb=" C2 G B 4 " 0.009 2.00e-02 2.50e+03 pdb=" N2 G B 4 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 4 " -0.012 2.00e-02 2.50e+03 pdb=" C4 G B 4 " -0.005 2.00e-02 2.50e+03 pdb=" H8 G B 4 " -0.005 2.00e-02 2.50e+03 pdb=" H1 G B 4 " 0.004 2.00e-02 2.50e+03 ... (remaining 12516 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 3577 2.07 - 2.70: 205018 2.70 - 3.34: 403903 3.34 - 3.97: 576107 3.97 - 4.60: 839660 Nonbonded interactions: 2028265 Sorted by model distance: nonbonded pdb=" H3 U A 159 " pdb=" O6 G A 169 " model vdw 1.439 1.850 nonbonded pdb=" H42 C A 608 " pdb=" O4 U A 619 " model vdw 1.498 1.850 nonbonded pdb=" H21 G A1494 " pdb=" O2 C A1506 " model vdw 1.560 1.850 nonbonded pdb=" OP2 A A1053 " pdb=" HZ1 LYS H 40 " model vdw 1.594 1.850 nonbonded pdb=" O VAL E 142 " pdb=" HG1 THR E 145 " model vdw 1.595 1.850 ... (remaining 2028260 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.270 Extract box with map and model: 17.590 Check model and map are aligned: 1.580 Set scattering table: 1.000 Process input model: 505.110 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 534.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 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 : 0.015 1.017 96722 Z= 0.908 Angle : 1.206 40.549 145523 Z= 0.591 Chirality : 0.062 0.415 18792 Planarity : 0.008 0.087 7188 Dihedral : 25.736 179.690 56118 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.14 % Favored : 85.76 % Rotamer: Outliers : 15.92 % Allowed : 16.41 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.17 % 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: -5.24 (0.11), residues: 3069 helix: -3.19 (0.13), residues: 751 sheet: -3.39 (0.19), residues: 522 loop : -3.80 (0.11), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP E 65 HIS 0.013 0.002 HIS O 29 PHE 0.027 0.003 PHE P 21 TYR 0.023 0.003 TYR D 46 ARG 0.014 0.001 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. Residue LYS 16 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Evaluate side-chains 1103 residues out of total 2635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 397 poor density : 706 time to evaluate : 4.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 171 TYR cc_start: 0.6023 (m-10) cc_final: 0.5817 (m-80) REVERT: C 175 ARG cc_start: 0.5940 (ttm110) cc_final: 0.5678 (ttm170) REVERT: C 183 MET cc_start: 0.6045 (mtt) cc_final: 0.5090 (mtp) REVERT: C 187 THR cc_start: 0.6491 (OUTLIER) cc_final: 0.6272 (p) REVERT: C 252 LYS cc_start: 0.2331 (OUTLIER) cc_final: 0.1905 (mttt) REVERT: D 37 GLN cc_start: 0.7526 (mt0) cc_final: 0.7113 (mt0) REVERT: D 42 GLU cc_start: 0.6652 (pt0) cc_final: 0.6439 (pt0) REVERT: D 61 LYS cc_start: 0.5848 (OUTLIER) cc_final: 0.5540 (mtmm) REVERT: D 93 ASN cc_start: 0.7444 (p0) cc_final: 0.6982 (p0) REVERT: D 99 TYR cc_start: 0.7015 (m-80) cc_final: 0.6552 (m-80) REVERT: D 205 LYS cc_start: 0.7651 (mtmm) cc_final: 0.7367 (mttp) REVERT: D 210 GLU cc_start: 0.6684 (mt-10) cc_final: 0.6479 (mt-10) REVERT: E 66 LYS cc_start: 0.6541 (mtmm) cc_final: 0.6172 (mmmt) REVERT: E 114 LEU cc_start: 0.5612 (OUTLIER) cc_final: 0.5351 (pp) REVERT: E 140 LYS cc_start: 0.5983 (OUTLIER) cc_final: 0.5592 (tmtt) REVERT: E 159 GLU cc_start: 0.7012 (tp30) cc_final: 0.6771 (mm-30) REVERT: E 203 GLU cc_start: 0.6963 (tt0) cc_final: 0.6699 (tt0) REVERT: E 204 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6054 (mm-30) REVERT: F 4 LEU cc_start: 0.0659 (OUTLIER) cc_final: -0.0616 (tt) REVERT: F 17 MET cc_start: 0.2721 (mmm) cc_final: 0.2113 (ttt) REVERT: F 25 VAL cc_start: 0.4114 (p) cc_final: 0.3853 (t) REVERT: F 71 LYS cc_start: 0.3115 (OUTLIER) cc_final: 0.2487 (mmmt) REVERT: G 111 HIS cc_start: 0.4235 (OUTLIER) cc_final: 0.3721 (p90) REVERT: H 20 ASP cc_start: 0.6636 (p0) cc_final: 0.5881 (p0) REVERT: H 53 ASP cc_start: 0.7877 (m-30) cc_final: 0.7635 (m-30) REVERT: H 64 GLU cc_start: 0.6529 (mm-30) cc_final: 0.6228 (tt0) REVERT: H 92 GLU cc_start: 0.6281 (tp30) cc_final: 0.5771 (tp30) REVERT: I 1 MET cc_start: 0.1976 (tpp) cc_final: 0.0894 (tpp) REVERT: I 113 LYS cc_start: 0.6216 (tptt) cc_final: 0.5926 (tttt) REVERT: I 117 LEU cc_start: 0.7218 (mt) cc_final: 0.6806 (mt) REVERT: J 64 ARG cc_start: 0.6102 (ptm160) cc_final: 0.5889 (ptm160) REVERT: J 68 ASN cc_start: 0.6380 (t0) cc_final: 0.6112 (t0) REVERT: J 72 LYS cc_start: 0.5406 (mptt) cc_final: 0.5159 (mtpt) REVERT: J 73 GLU cc_start: 0.6601 (mt-10) cc_final: 0.6118 (pm20) REVERT: J 83 ASN cc_start: 0.5532 (m110) cc_final: 0.5037 (p0) REVERT: J 98 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6333 (tp30) REVERT: J 127 LYS cc_start: 0.6260 (OUTLIER) cc_final: 0.5746 (mttm) REVERT: K 1 MET cc_start: 0.3571 (ttm) cc_final: 0.2570 (tpt) REVERT: K 2 LEU cc_start: -0.2106 (OUTLIER) cc_final: -0.2478 (mp) REVERT: K 18 THR cc_start: 0.4691 (p) cc_final: 0.4479 (p) REVERT: K 69 PHE cc_start: 0.4897 (t80) cc_final: 0.4672 (t80) REVERT: K 109 VAL cc_start: 0.5306 (p) cc_final: 0.4325 (p) REVERT: L 28 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6953 (tt0) REVERT: L 31 GLU cc_start: 0.7878 (tt0) cc_final: 0.7273 (pt0) REVERT: L 79 GLN cc_start: 0.6553 (OUTLIER) cc_final: 0.5956 (pt0) REVERT: M 1 MET cc_start: 0.4195 (OUTLIER) cc_final: 0.3360 (ptt) REVERT: M 2 ILE cc_start: 0.1806 (OUTLIER) cc_final: 0.1510 (tp) REVERT: M 7 LYS cc_start: 0.6343 (OUTLIER) cc_final: 0.5657 (tppt) REVERT: M 22 LEU cc_start: 0.4107 (OUTLIER) cc_final: 0.3848 (tp) REVERT: M 87 LYS cc_start: 0.3049 (OUTLIER) cc_final: 0.2668 (tmtt) REVERT: N 93 LYS cc_start: 0.7650 (tttt) cc_final: 0.6754 (tptt) REVERT: N 98 LYS cc_start: 0.6952 (OUTLIER) cc_final: 0.6685 (mmtm) REVERT: N 100 TYR cc_start: 0.7126 (m-80) cc_final: 0.6783 (m-80) REVERT: O 16 LYS cc_start: 0.7610 (ptpt) cc_final: 0.6804 (ptmm) REVERT: O 78 ARG cc_start: 0.6913 (mtp-110) cc_final: 0.6676 (mtm-85) REVERT: P 6 GLU cc_start: 0.6568 (tt0) cc_final: 0.6150 (tt0) REVERT: P 16 GLU cc_start: 0.5690 (pt0) cc_final: 0.4972 (pm20) REVERT: P 21 PHE cc_start: 0.6407 (OUTLIER) cc_final: 0.6161 (m-80) REVERT: P 28 ASN cc_start: 0.7324 (m-40) cc_final: 0.7007 (m-40) REVERT: P 64 LYS cc_start: 0.5996 (tptt) cc_final: 0.5789 (tppt) REVERT: P 75 THR cc_start: 0.6307 (OUTLIER) cc_final: 0.5999 (p) REVERT: Q 4 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6825 (mmtm) REVERT: Q 28 ASN cc_start: 0.6659 (OUTLIER) cc_final: 0.6421 (m110) REVERT: Q 65 ASN cc_start: 0.5492 (OUTLIER) cc_final: 0.4918 (p0) REVERT: Q 88 GLN cc_start: 0.1018 (OUTLIER) cc_final: 0.0421 (tt0) REVERT: Q 96 LYS cc_start: 0.6659 (mttm) cc_final: 0.6314 (mmpt) REVERT: R 32 ARG cc_start: 0.6426 (mtm180) cc_final: 0.5558 (mmm160) REVERT: R 53 VAL cc_start: 0.6602 (OUTLIER) cc_final: 0.6260 (p) REVERT: R 75 ARG cc_start: 0.6227 (ptt90) cc_final: 0.5799 (ptm-80) REVERT: R 84 GLU cc_start: 0.5346 (OUTLIER) cc_final: 0.4729 (tp30) REVERT: S 41 MET cc_start: 0.5861 (ptt) cc_final: 0.4934 (mmt) REVERT: S 69 GLN cc_start: 0.6032 (tt0) cc_final: 0.5538 (tt0) REVERT: S 100 GLU cc_start: 0.6381 (pt0) cc_final: 0.6042 (pm20) REVERT: T 54 GLU cc_start: 0.5710 (OUTLIER) cc_final: 0.5376 (mm-30) REVERT: U 25 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7345 (tp30) REVERT: U 72 ASP cc_start: 0.6259 (OUTLIER) cc_final: 0.5908 (m-30) REVERT: U 79 ARG cc_start: 0.3592 (OUTLIER) cc_final: 0.3119 (ptm-80) REVERT: U 86 GLN cc_start: 0.6098 (pt0) cc_final: 0.5636 (pt0) REVERT: V 3 LYS cc_start: 0.3520 (OUTLIER) cc_final: 0.2352 (mtmm) REVERT: W 12 SER cc_start: 0.5336 (p) cc_final: 0.4577 (t) REVERT: W 16 GLU cc_start: 0.4945 (OUTLIER) cc_final: 0.4132 (tt0) REVERT: W 19 LYS cc_start: 0.7206 (ptmm) cc_final: 0.6715 (tptt) REVERT: W 42 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.5871 (tpp-160) REVERT: W 59 GLU cc_start: 0.7276 (pt0) cc_final: 0.6502 (mm-30) REVERT: W 61 GLU cc_start: 0.5926 (mp0) cc_final: 0.5649 (tm-30) REVERT: X 3 LYS cc_start: 0.4858 (OUTLIER) cc_final: 0.4504 (mmtm) REVERT: X 29 LYS cc_start: 0.6688 (OUTLIER) cc_final: 0.5912 (mmtt) REVERT: X 48 ASN cc_start: 0.7736 (OUTLIER) cc_final: 0.7484 (t0) REVERT: Z 22 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6852 (tp) REVERT: 2 37 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6494 (mtm-85) REVERT: 2 41 LYS cc_start: 0.6583 (tttp) cc_final: 0.6172 (tttt) REVERT: 3 32 LEU cc_start: 0.5185 (OUTLIER) cc_final: 0.4448 (tp) REVERT: 3 43 GLN cc_start: 0.7148 (mt0) cc_final: 0.6633 (mt0) REVERT: 3 59 LYS cc_start: 0.7422 (ttmp) cc_final: 0.6767 (mmtt) REVERT: 4 24 MET cc_start: 0.1488 (mmt) cc_final: 0.1183 (mmt) outliers start: 397 outliers final: 104 residues processed: 978 average time/residue: 1.9190 time to fit residues: 2993.9748 Evaluate side-chains 578 residues out of total 2635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 435 time to evaluate : 4.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 49 HIS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 8 PHE Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 112 PRO Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 112 MET Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 114 ASN Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain K residue 2 LEU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 46 ASP Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 98 LYS Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain P residue 21 PHE Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 4 LYS Chi-restraints excluded: chain Q residue 28 ASN Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 88 GLN Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 84 GLU Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 13 LYS Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 58 ASN Chi-restraints excluded: chain U residue 72 ASP Chi-restraints excluded: chain U residue 79 ARG Chi-restraints excluded: chain V residue 3 LYS Chi-restraints excluded: chain V residue 29 TRP Chi-restraints excluded: chain V residue 32 ASN Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain W residue 16 GLU Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 42 ARG Chi-restraints excluded: chain X residue 3 LYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 29 LYS Chi-restraints excluded: chain X residue 48 ASN Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain Z residue 37 LYS Chi-restraints excluded: chain 1 residue 3 VAL Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 22 ASN Chi-restraints excluded: chain 1 residue 34 LYS Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 11 ARG Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 37 ARG Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 35 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 599 random chunks: chunk 505 optimal weight: 0.7980 chunk 454 optimal weight: 4.9990 chunk 251 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 306 optimal weight: 0.8980 chunk 242 optimal weight: 4.9990 chunk 469 optimal weight: 7.9990 chunk 181 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 chunk 349 optimal weight: 0.9980 chunk 543 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN D 128 GLN D 148 HIS E 46 GLN E 148 GLN E 162 ASN ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 119 GLN I 3 GLN I 82 ASN ** J 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 114 ASN K 71 HIS L 106 GLN ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 16 ASN V 23 ASN 3 43 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.560 96722 Z= 0.298 Angle : 0.726 32.749 145523 Z= 0.362 Chirality : 0.038 0.320 18792 Planarity : 0.005 0.080 7188 Dihedral : 25.996 179.912 50462 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 7.58 % Allowed : 20.54 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: -4.18 (0.13), residues: 3069 helix: -1.82 (0.17), residues: 756 sheet: -2.98 (0.19), residues: 580 loop : -3.26 (0.13), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 83 HIS 0.010 0.001 HIS N 79 PHE 0.011 0.001 PHE O 57 TYR 0.011 0.002 TYR I 76 ARG 0.009 0.001 ARG Q 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. Residue LYS 16 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Evaluate side-chains 680 residues out of total 2635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 491 time to evaluate : 4.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 LYS cc_start: 0.5147 (pttt) cc_final: 0.4947 (pttt) REVERT: C 115 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7796 (mm) REVERT: C 171 TYR cc_start: 0.5963 (m-10) cc_final: 0.5684 (m-80) REVERT: C 183 MET cc_start: 0.5934 (mtt) cc_final: 0.4893 (mtp) REVERT: C 204 ASN cc_start: 0.5725 (t0) cc_final: 0.5455 (t0) REVERT: D 24 PRO cc_start: 0.7806 (Cg_endo) cc_final: 0.7587 (Cg_exo) REVERT: D 61 LYS cc_start: 0.5731 (OUTLIER) cc_final: 0.5445 (mtmm) REVERT: D 62 ASP cc_start: 0.6098 (m-30) cc_final: 0.5812 (m-30) REVERT: D 84 PRO cc_start: 0.5437 (Cg_exo) cc_final: 0.5215 (Cg_endo) REVERT: D 99 TYR cc_start: 0.6945 (m-80) cc_final: 0.6548 (m-80) REVERT: D 119 THR cc_start: 0.6537 (m) cc_final: 0.6126 (m) REVERT: D 191 GLU cc_start: 0.7610 (mp0) cc_final: 0.7026 (pm20) REVERT: D 205 LYS cc_start: 0.7530 (mtmm) cc_final: 0.7276 (mttm) REVERT: E 66 LYS cc_start: 0.6584 (mtmm) cc_final: 0.6172 (mmmt) REVERT: E 114 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5988 (pp) REVERT: E 140 LYS cc_start: 0.5902 (OUTLIER) cc_final: 0.5411 (tmtt) REVERT: E 145 THR cc_start: 0.5892 (p) cc_final: 0.5564 (p) REVERT: F 17 MET cc_start: 0.2806 (mmm) cc_final: 0.2074 (ttt) REVERT: F 51 ASP cc_start: 0.2231 (OUTLIER) cc_final: 0.1817 (m-30) REVERT: F 71 LYS cc_start: 0.2986 (OUTLIER) cc_final: 0.2284 (mmtm) REVERT: G 111 HIS cc_start: 0.4393 (OUTLIER) cc_final: 0.3767 (p90) REVERT: H 20 ASP cc_start: 0.6292 (p0) cc_final: 0.5913 (p0) REVERT: H 64 GLU cc_start: 0.6433 (mm-30) cc_final: 0.6072 (tt0) REVERT: H 118 LYS cc_start: 0.7083 (mttt) cc_final: 0.6569 (tttt) REVERT: I 1 MET cc_start: 0.1566 (tpp) cc_final: 0.0527 (tpp) REVERT: I 113 LYS cc_start: 0.6396 (tptt) cc_final: 0.6195 (ttmt) REVERT: I 117 LEU cc_start: 0.7204 (mt) cc_final: 0.6983 (mt) REVERT: I 120 GLU cc_start: 0.6215 (pp20) cc_final: 0.5881 (pp20) REVERT: J 73 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6195 (pm20) REVERT: J 83 ASN cc_start: 0.5648 (m110) cc_final: 0.5175 (p0) REVERT: J 98 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.6076 (tp30) REVERT: J 127 LYS cc_start: 0.6434 (OUTLIER) cc_final: 0.6197 (mmtt) REVERT: K 1 MET cc_start: 0.3528 (ttm) cc_final: 0.2657 (tpt) REVERT: K 2 LEU cc_start: -0.2448 (OUTLIER) cc_final: -0.2909 (mp) REVERT: K 83 MET cc_start: 0.7662 (mmm) cc_final: 0.7047 (mmm) REVERT: L 28 GLU cc_start: 0.6753 (mt-10) cc_final: 0.6517 (tm-30) REVERT: L 29 ARG cc_start: 0.7269 (ptp-110) cc_final: 0.6875 (ptp-110) REVERT: L 31 GLU cc_start: 0.7853 (tt0) cc_final: 0.7410 (pt0) REVERT: M 1 MET cc_start: 0.4060 (OUTLIER) cc_final: 0.3223 (ptt) REVERT: M 2 ILE cc_start: 0.2249 (OUTLIER) cc_final: 0.1971 (tp) REVERT: M 7 LYS cc_start: 0.6018 (OUTLIER) cc_final: 0.5472 (tppt) REVERT: M 87 LYS cc_start: 0.3394 (OUTLIER) cc_final: 0.2771 (tmtt) REVERT: N 59 GLU cc_start: 0.5776 (tp30) cc_final: 0.5253 (tp30) REVERT: N 82 LYS cc_start: 0.6646 (mtpp) cc_final: 0.6330 (mttt) REVERT: N 93 LYS cc_start: 0.7746 (tttt) cc_final: 0.7019 (tptt) REVERT: O 16 LYS cc_start: 0.7820 (ptpt) cc_final: 0.7066 (ptmm) REVERT: O 19 LYS cc_start: 0.7524 (ptmt) cc_final: 0.6734 (pttp) REVERT: O 48 ARG cc_start: 0.6024 (ttp-110) cc_final: 0.5655 (ttp-110) REVERT: O 78 ARG cc_start: 0.7078 (mtp-110) cc_final: 0.6713 (mtm-85) REVERT: P 75 THR cc_start: 0.6636 (OUTLIER) cc_final: 0.6337 (p) REVERT: Q 4 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6895 (mmtp) REVERT: Q 52 MET cc_start: 0.6465 (mmm) cc_final: 0.6227 (mmp) REVERT: Q 65 ASN cc_start: 0.5712 (OUTLIER) cc_final: 0.5132 (p0) REVERT: Q 96 LYS cc_start: 0.6891 (mttm) cc_final: 0.6229 (mmpt) REVERT: R 32 ARG cc_start: 0.6396 (mtm180) cc_final: 0.5447 (mmm160) REVERT: R 53 VAL cc_start: 0.7009 (OUTLIER) cc_final: 0.6792 (p) REVERT: R 84 GLU cc_start: 0.5457 (OUTLIER) cc_final: 0.4769 (tp30) REVERT: S 41 MET cc_start: 0.6408 (ptt) cc_final: 0.5076 (mmt) REVERT: S 69 GLN cc_start: 0.6581 (tt0) cc_final: 0.6132 (tt0) REVERT: S 100 GLU cc_start: 0.6459 (pt0) cc_final: 0.6059 (pm20) REVERT: T 54 GLU cc_start: 0.5862 (OUTLIER) cc_final: 0.5415 (mm-30) REVERT: U 25 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7281 (tp30) REVERT: U 79 ARG cc_start: 0.3991 (OUTLIER) cc_final: 0.3492 (ptt-90) REVERT: V 3 LYS cc_start: 0.3495 (OUTLIER) cc_final: 0.2862 (mtmm) REVERT: V 37 ARG cc_start: 0.6600 (ptm160) cc_final: 0.5867 (ptt-90) REVERT: W 16 GLU cc_start: 0.5159 (OUTLIER) cc_final: 0.4941 (tp30) REVERT: W 19 LYS cc_start: 0.7218 (ptmm) cc_final: 0.6702 (tptt) REVERT: W 42 ARG cc_start: 0.6513 (OUTLIER) cc_final: 0.5723 (tpp-160) REVERT: W 59 GLU cc_start: 0.7244 (pt0) cc_final: 0.6579 (mm-30) REVERT: W 60 ARG cc_start: 0.5253 (mmp80) cc_final: 0.4863 (mmp80) REVERT: W 61 GLU cc_start: 0.5840 (OUTLIER) cc_final: 0.5506 (tm-30) REVERT: X 3 LYS cc_start: 0.5574 (OUTLIER) cc_final: 0.5052 (mmtm) REVERT: X 29 LYS cc_start: 0.6641 (OUTLIER) cc_final: 0.6214 (mmtt) REVERT: Z 22 ILE cc_start: 0.7109 (OUTLIER) cc_final: 0.6785 (tp) REVERT: 3 59 LYS cc_start: 0.7343 (ttmp) cc_final: 0.6792 (tptt) REVERT: 4 24 MET cc_start: 0.1336 (mmt) cc_final: 0.1060 (mmt) outliers start: 189 outliers final: 115 residues processed: 636 average time/residue: 1.7316 time to fit residues: 1828.2113 Evaluate side-chains 564 residues out of total 2635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 421 time to evaluate : 4.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 213 TRP Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 49 HIS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 116 PHE Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 8 PHE Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 112 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain K residue 2 LEU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 4 LYS Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain R residue 84 GLU Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 13 LYS Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 58 ASN Chi-restraints excluded: chain U residue 79 ARG Chi-restraints excluded: chain U residue 88 SER Chi-restraints excluded: chain V residue 3 LYS Chi-restraints excluded: chain V residue 29 TRP Chi-restraints excluded: chain V residue 32 ASN Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain W residue 16 GLU Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 42 ARG Chi-restraints excluded: chain W residue 54 LYS Chi-restraints excluded: chain W residue 61 GLU Chi-restraints excluded: chain X residue 3 LYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 29 LYS Chi-restraints excluded: chain X residue 32 ASN Chi-restraints excluded: chain X residue 43 ILE Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 22 ASN Chi-restraints excluded: chain 1 residue 34 LYS Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 35 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 599 random chunks: chunk 302 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 452 optimal weight: 0.7980 chunk 370 optimal weight: 4.9990 chunk 150 optimal weight: 20.0000 chunk 544 optimal weight: 9.9990 chunk 588 optimal weight: 2.9990 chunk 485 optimal weight: 2.9990 chunk 540 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 chunk 437 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** J 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 71 HIS P 18 GLN P 28 ASN Q 65 ASN Q 88 GLN Q 95 ASN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.532 96722 Z= 0.315 Angle : 0.674 31.931 145523 Z= 0.341 Chirality : 0.038 0.305 18792 Planarity : 0.005 0.067 7188 Dihedral : 25.471 179.667 50373 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 7.54 % Allowed : 21.02 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.56 (0.13), residues: 3069 helix: -1.02 (0.18), residues: 753 sheet: -2.60 (0.19), residues: 580 loop : -3.00 (0.13), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 83 HIS 0.024 0.002 HIS C 142 PHE 0.016 0.002 PHE O 57 TYR 0.046 0.002 TYR I 76 ARG 0.011 0.001 ARG I 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. Residue LYS 16 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Evaluate side-chains 649 residues out of total 2635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 461 time to evaluate : 4.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 GLU cc_start: 0.6642 (pm20) cc_final: 0.6212 (pt0) REVERT: C 115 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7750 (mm) REVERT: C 171 TYR cc_start: 0.5977 (m-10) cc_final: 0.5556 (m-80) REVERT: C 175 ARG cc_start: 0.6401 (ttm170) cc_final: 0.5847 (ttm170) REVERT: C 183 MET cc_start: 0.6031 (mtt) cc_final: 0.5254 (mtp) REVERT: D 61 LYS cc_start: 0.5892 (OUTLIER) cc_final: 0.5393 (mtmm) REVERT: D 62 ASP cc_start: 0.6175 (m-30) cc_final: 0.5341 (t0) REVERT: D 84 PRO cc_start: 0.5729 (Cg_exo) cc_final: 0.5480 (Cg_endo) REVERT: D 99 TYR cc_start: 0.7044 (m-80) cc_final: 0.6552 (m-80) REVERT: D 119 THR cc_start: 0.6742 (m) cc_final: 0.6493 (m) REVERT: D 191 GLU cc_start: 0.7653 (mp0) cc_final: 0.6983 (pm20) REVERT: D 205 LYS cc_start: 0.7572 (mtmm) cc_final: 0.7235 (mttm) REVERT: E 66 LYS cc_start: 0.6844 (mtmm) cc_final: 0.6253 (mmmt) REVERT: E 140 LYS cc_start: 0.6182 (OUTLIER) cc_final: 0.5865 (tmtt) REVERT: E 201 LYS cc_start: 0.6727 (mtpp) cc_final: 0.6519 (mtpp) REVERT: E 204 GLU cc_start: 0.7665 (pt0) cc_final: 0.7040 (pp20) REVERT: F 17 MET cc_start: 0.2513 (mmm) cc_final: 0.2087 (ttm) REVERT: F 51 ASP cc_start: 0.2137 (OUTLIER) cc_final: 0.1736 (m-30) REVERT: F 71 LYS cc_start: 0.2731 (OUTLIER) cc_final: 0.1829 (mmtm) REVERT: F 98 GLU cc_start: 0.3245 (OUTLIER) cc_final: 0.2921 (pt0) REVERT: G 111 HIS cc_start: 0.4385 (OUTLIER) cc_final: 0.3693 (p90) REVERT: H 118 LYS cc_start: 0.7241 (mttt) cc_final: 0.6653 (tttt) REVERT: I 1 MET cc_start: 0.2343 (tpp) cc_final: 0.1170 (tpp) REVERT: I 117 LEU cc_start: 0.7482 (mt) cc_final: 0.7270 (mt) REVERT: J 71 ARG cc_start: 0.5880 (ttt180) cc_final: 0.5568 (ttp80) REVERT: J 73 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6599 (mp0) REVERT: J 83 ASN cc_start: 0.5591 (m110) cc_final: 0.5168 (p0) REVERT: J 98 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.6072 (tp30) REVERT: J 127 LYS cc_start: 0.6418 (OUTLIER) cc_final: 0.6009 (mmtt) REVERT: K 1 MET cc_start: 0.3152 (ttm) cc_final: 0.2420 (tpt) REVERT: K 2 LEU cc_start: -0.2746 (OUTLIER) cc_final: -0.3024 (mp) REVERT: K 83 MET cc_start: 0.7500 (mmm) cc_final: 0.6984 (mmm) REVERT: L 31 GLU cc_start: 0.7665 (tt0) cc_final: 0.7188 (pt0) REVERT: L 59 ARG cc_start: 0.6675 (ttt90) cc_final: 0.6287 (mtt180) REVERT: M 18 VAL cc_start: 0.7799 (t) cc_final: 0.7540 (p) REVERT: M 35 ARG cc_start: 0.4082 (OUTLIER) cc_final: 0.3772 (ppt-90) REVERT: M 87 LYS cc_start: 0.3718 (OUTLIER) cc_final: 0.3081 (tmtt) REVERT: N 59 GLU cc_start: 0.6086 (tp30) cc_final: 0.5351 (tp30) REVERT: N 82 LYS cc_start: 0.6889 (mtpp) cc_final: 0.6574 (mttt) REVERT: N 93 LYS cc_start: 0.7914 (tttt) cc_final: 0.7286 (tptt) REVERT: O 19 LYS cc_start: 0.7607 (ptmt) cc_final: 0.6907 (pttp) REVERT: O 48 ARG cc_start: 0.6415 (ttp-110) cc_final: 0.6146 (ttp-110) REVERT: O 78 ARG cc_start: 0.7274 (mtp-110) cc_final: 0.6889 (mtm-85) REVERT: P 1 MET cc_start: 0.5161 (OUTLIER) cc_final: 0.4943 (tpt) REVERT: P 75 THR cc_start: 0.7030 (OUTLIER) cc_final: 0.6727 (p) REVERT: Q 4 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6901 (mmtp) REVERT: Q 96 LYS cc_start: 0.6941 (mttm) cc_final: 0.6296 (mmtm) REVERT: R 32 ARG cc_start: 0.6168 (mtm180) cc_final: 0.5369 (mmm160) REVERT: R 84 GLU cc_start: 0.5324 (OUTLIER) cc_final: 0.4753 (tp30) REVERT: S 41 MET cc_start: 0.6726 (ptt) cc_final: 0.5259 (mmt) REVERT: S 69 GLN cc_start: 0.6917 (tt0) cc_final: 0.6602 (tt0) REVERT: S 100 GLU cc_start: 0.6402 (pt0) cc_final: 0.5847 (pm20) REVERT: T 54 GLU cc_start: 0.5825 (OUTLIER) cc_final: 0.5243 (mm-30) REVERT: U 25 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7181 (tp30) REVERT: U 65 ASP cc_start: 0.6868 (m-30) cc_final: 0.6653 (m-30) REVERT: U 79 ARG cc_start: 0.4461 (OUTLIER) cc_final: 0.3735 (ptm-80) REVERT: V 37 ARG cc_start: 0.6810 (ptm160) cc_final: 0.6149 (ptp90) REVERT: W 16 GLU cc_start: 0.5284 (OUTLIER) cc_final: 0.5029 (tp30) REVERT: W 19 LYS cc_start: 0.7171 (ptmm) cc_final: 0.6894 (tptt) REVERT: W 42 ARG cc_start: 0.6446 (mmm160) cc_final: 0.5665 (tpp-160) REVERT: W 43 ILE cc_start: 0.5294 (OUTLIER) cc_final: 0.5071 (pt) REVERT: W 59 GLU cc_start: 0.6939 (pt0) cc_final: 0.6303 (mm-30) REVERT: X 3 LYS cc_start: 0.5803 (OUTLIER) cc_final: 0.5426 (mmtm) REVERT: X 20 ARG cc_start: 0.5993 (mmm-85) cc_final: 0.5649 (mtt180) REVERT: Z 22 ILE cc_start: 0.7012 (OUTLIER) cc_final: 0.6766 (tp) REVERT: 3 32 LEU cc_start: 0.5294 (pt) cc_final: 0.5061 (tp) REVERT: 3 43 GLN cc_start: 0.6895 (mt0) cc_final: 0.6417 (mt0) REVERT: 3 59 LYS cc_start: 0.7345 (ttmp) cc_final: 0.6795 (tptt) REVERT: 4 24 MET cc_start: 0.1779 (mmt) cc_final: 0.1504 (mmt) outliers start: 188 outliers final: 120 residues processed: 602 average time/residue: 1.7405 time to fit residues: 1730.4893 Evaluate side-chains 548 residues out of total 2635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 406 time to evaluate : 4.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 213 TRP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 49 HIS Chi-restraints excluded: chain E residue 116 PHE Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 8 PHE Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 112 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain K residue 2 LEU Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 35 ARG Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 4 LYS Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 95 ASN Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 84 GLU Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 26 THR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 44 ASP Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 13 LYS Chi-restraints excluded: chain U residue 58 ASN Chi-restraints excluded: chain U residue 79 ARG Chi-restraints excluded: chain U residue 88 SER Chi-restraints excluded: chain V residue 29 TRP Chi-restraints excluded: chain V residue 32 ASN Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 16 GLU Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain X residue 3 LYS Chi-restraints excluded: chain X residue 11 SER Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 32 ASN Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 43 ILE Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain 1 residue 5 VAL Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 22 ASN Chi-restraints excluded: chain 1 residue 34 LYS Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 35 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 599 random chunks: chunk 538 optimal weight: 1.9990 chunk 409 optimal weight: 4.9990 chunk 282 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 260 optimal weight: 6.9990 chunk 365 optimal weight: 4.9990 chunk 546 optimal weight: 3.9990 chunk 578 optimal weight: 3.9990 chunk 285 optimal weight: 6.9990 chunk 518 optimal weight: 0.5980 chunk 156 optimal weight: 20.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN C 134 ASN D 37 GLN H 48 HIS ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 119 GLN I 3 GLN I 4 GLN ** J 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 23 ASN X 5 GLN ** 3 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.560 96722 Z= 0.354 Angle : 0.721 30.072 145523 Z= 0.363 Chirality : 0.041 0.342 18792 Planarity : 0.006 0.088 7188 Dihedral : 25.386 179.594 50336 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 7.70 % Allowed : 20.74 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.37 (0.13), residues: 3069 helix: -0.99 (0.18), residues: 754 sheet: -2.27 (0.20), residues: 575 loop : -2.91 (0.13), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 61 HIS 0.014 0.002 HIS H 48 PHE 0.034 0.002 PHE K 32 TYR 0.018 0.002 TYR L 100 ARG 0.010 0.001 ARG L 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. Residue LYS 16 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Evaluate side-chains 648 residues out of total 2635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 456 time to evaluate : 4.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 ARG cc_start: 0.7029 (mtp180) cc_final: 0.6778 (mtm-85) REVERT: C 71 LYS cc_start: 0.7046 (tppp) cc_final: 0.6560 (tttt) REVERT: C 171 TYR cc_start: 0.6238 (m-10) cc_final: 0.5943 (m-80) REVERT: C 183 MET cc_start: 0.5940 (mtt) cc_final: 0.5538 (mtt) REVERT: C 252 LYS cc_start: 0.4797 (mttt) cc_final: 0.4473 (mtmt) REVERT: D 61 LYS cc_start: 0.6270 (OUTLIER) cc_final: 0.5962 (mtmm) REVERT: D 84 PRO cc_start: 0.6539 (Cg_exo) cc_final: 0.6271 (Cg_endo) REVERT: D 99 TYR cc_start: 0.7417 (m-80) cc_final: 0.6980 (m-80) REVERT: D 169 MET cc_start: 0.8005 (mtt) cc_final: 0.7774 (mtt) REVERT: D 205 LYS cc_start: 0.7641 (mtmm) cc_final: 0.7313 (mttp) REVERT: E 10 ASP cc_start: 0.6780 (m-30) cc_final: 0.6395 (p0) REVERT: E 66 LYS cc_start: 0.6871 (mtmm) cc_final: 0.6237 (mttp) REVERT: E 129 PHE cc_start: 0.7066 (m-80) cc_final: 0.6704 (m-80) REVERT: E 140 LYS cc_start: 0.6303 (OUTLIER) cc_final: 0.6058 (tttm) REVERT: E 204 GLU cc_start: 0.7571 (pt0) cc_final: 0.7034 (pp20) REVERT: F 17 MET cc_start: 0.2413 (mmm) cc_final: 0.2126 (ttm) REVERT: F 51 ASP cc_start: 0.2080 (OUTLIER) cc_final: 0.1815 (m-30) REVERT: F 71 LYS cc_start: 0.2563 (OUTLIER) cc_final: 0.1677 (tmtt) REVERT: F 98 GLU cc_start: 0.3253 (OUTLIER) cc_final: 0.2889 (pt0) REVERT: G 111 HIS cc_start: 0.4572 (OUTLIER) cc_final: 0.3822 (p90) REVERT: H 64 GLU cc_start: 0.6352 (mm-30) cc_final: 0.5521 (tt0) REVERT: H 107 LYS cc_start: 0.7553 (mttm) cc_final: 0.6235 (tmtt) REVERT: H 112 SER cc_start: 0.8070 (m) cc_final: 0.7798 (t) REVERT: H 118 LYS cc_start: 0.7307 (mttt) cc_final: 0.6744 (tttt) REVERT: J 5 GLU cc_start: 0.7149 (tt0) cc_final: 0.6931 (mt-10) REVERT: J 13 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7249 (mmt180) REVERT: J 73 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6469 (mp0) REVERT: J 127 LYS cc_start: 0.6331 (OUTLIER) cc_final: 0.5917 (mmtt) REVERT: K 1 MET cc_start: 0.2521 (ttm) cc_final: 0.1700 (tpt) REVERT: K 2 LEU cc_start: -0.2941 (OUTLIER) cc_final: -0.3298 (mp) REVERT: K 58 MET cc_start: 0.7129 (tpp) cc_final: 0.6913 (tpp) REVERT: K 83 MET cc_start: 0.7100 (mmm) cc_final: 0.6562 (mmm) REVERT: L 31 GLU cc_start: 0.7699 (tt0) cc_final: 0.7250 (pt0) REVERT: M 7 LYS cc_start: 0.5764 (OUTLIER) cc_final: 0.5244 (tttt) REVERT: M 35 ARG cc_start: 0.4209 (OUTLIER) cc_final: 0.3758 (ppt-90) REVERT: M 87 LYS cc_start: 0.3567 (OUTLIER) cc_final: 0.2984 (tmtt) REVERT: N 6 LEU cc_start: 0.5841 (OUTLIER) cc_final: 0.5581 (mp) REVERT: N 42 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7392 (mt) REVERT: N 59 GLU cc_start: 0.5913 (tp30) cc_final: 0.5425 (tp30) REVERT: N 60 THR cc_start: 0.7724 (m) cc_final: 0.7512 (m) REVERT: N 82 LYS cc_start: 0.6850 (mtpp) cc_final: 0.6591 (mttt) REVERT: N 84 GLU cc_start: 0.7580 (tt0) cc_final: 0.7313 (tp30) REVERT: N 93 LYS cc_start: 0.7948 (tttt) cc_final: 0.7449 (tptt) REVERT: O 19 LYS cc_start: 0.7650 (ptmt) cc_final: 0.6993 (mmtt) REVERT: O 78 ARG cc_start: 0.7523 (mtp-110) cc_final: 0.7070 (mtm-85) REVERT: P 6 GLU cc_start: 0.6904 (tt0) cc_final: 0.6618 (tm-30) REVERT: Q 48 GLU cc_start: 0.6443 (tp30) cc_final: 0.6082 (tp30) REVERT: Q 84 ARG cc_start: 0.4363 (mmt-90) cc_final: 0.4117 (mmt180) REVERT: Q 95 ASN cc_start: 0.3568 (OUTLIER) cc_final: 0.2993 (p0) REVERT: Q 96 LYS cc_start: 0.7190 (mttm) cc_final: 0.6386 (mmpt) REVERT: R 84 GLU cc_start: 0.5470 (OUTLIER) cc_final: 0.4987 (tp30) REVERT: S 41 MET cc_start: 0.7062 (ptt) cc_final: 0.5599 (mmt) REVERT: U 25 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7276 (tp30) REVERT: U 53 ILE cc_start: 0.6528 (mp) cc_final: 0.6148 (mt) REVERT: U 65 ASP cc_start: 0.6784 (m-30) cc_final: 0.6259 (m-30) REVERT: V 37 ARG cc_start: 0.6897 (ptm160) cc_final: 0.6184 (ptp90) REVERT: W 16 GLU cc_start: 0.5299 (OUTLIER) cc_final: 0.5054 (tp30) REVERT: W 19 LYS cc_start: 0.7375 (ptmm) cc_final: 0.6950 (tptt) REVERT: W 42 ARG cc_start: 0.6343 (mmm160) cc_final: 0.5757 (tpp-160) REVERT: W 59 GLU cc_start: 0.6969 (pt0) cc_final: 0.6340 (mm-30) REVERT: X 3 LYS cc_start: 0.6043 (OUTLIER) cc_final: 0.5751 (mmtm) REVERT: X 6 ILE cc_start: 0.7533 (mt) cc_final: 0.7210 (pt) REVERT: X 20 ARG cc_start: 0.6026 (mmm-85) cc_final: 0.5729 (mtt180) REVERT: 1 32 MET cc_start: 0.4037 (mtm) cc_final: 0.3767 (ttm) REVERT: 2 37 ARG cc_start: 0.7326 (tpp-160) cc_final: 0.6970 (mtm180) REVERT: 3 43 GLN cc_start: 0.6796 (mt0) cc_final: 0.6374 (mt0) REVERT: 3 59 LYS cc_start: 0.7457 (ttmp) cc_final: 0.6866 (tptp) REVERT: 4 35 ARG cc_start: 0.4835 (OUTLIER) cc_final: 0.3449 (mmt180) outliers start: 192 outliers final: 134 residues processed: 608 average time/residue: 1.7719 time to fit residues: 1787.5515 Evaluate side-chains 560 residues out of total 2635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 407 time to evaluate : 4.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 213 TRP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 49 HIS Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain F residue 8 PHE Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 112 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 13 ARG Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain K residue 2 LEU Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 35 ARG Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 43 GLN Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain P residue 2 PHE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain Q residue 92 SER Chi-restraints excluded: chain Q residue 95 ASN Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 84 GLU Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain S residue 8 ASN Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 26 THR Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain T residue 90 ASP Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 13 LYS Chi-restraints excluded: chain U residue 58 ASN Chi-restraints excluded: chain U residue 88 SER Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 29 TRP Chi-restraints excluded: chain V residue 32 ASN Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain W residue 7 ARG Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 16 GLU Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain X residue 3 LYS Chi-restraints excluded: chain X residue 11 SER Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 32 ASN Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 43 ILE Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 3 VAL Chi-restraints excluded: chain 1 residue 5 VAL Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 22 ASN Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 4 residue 19 ARG Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 35 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 599 random chunks: chunk 482 optimal weight: 4.9990 chunk 328 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 431 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 494 optimal weight: 2.9990 chunk 400 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 295 optimal weight: 9.9990 chunk 519 optimal weight: 0.7980 chunk 146 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 HIS F 52 ASN H 104 ASN L 12 GLN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN ** 3 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.555 96722 Z= 0.339 Angle : 0.668 31.011 145523 Z= 0.340 Chirality : 0.039 0.280 18792 Planarity : 0.005 0.080 7188 Dihedral : 25.286 179.822 50302 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 6.78 % Allowed : 22.18 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.16 (0.14), residues: 3069 helix: -0.79 (0.18), residues: 761 sheet: -1.98 (0.20), residues: 585 loop : -2.86 (0.13), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 93 HIS 0.009 0.002 HIS D 148 PHE 0.017 0.002 PHE C 21 TYR 0.016 0.002 TYR L 100 ARG 0.011 0.001 ARG X 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. Residue LYS 16 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Evaluate side-chains 594 residues out of total 2635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 425 time to evaluate : 4.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 LYS cc_start: 0.6983 (tppp) cc_final: 0.6511 (tttt) REVERT: D 61 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6304 (mtmm) REVERT: D 84 PRO cc_start: 0.6716 (Cg_exo) cc_final: 0.6485 (Cg_endo) REVERT: D 93 ASN cc_start: 0.7503 (p0) cc_final: 0.6959 (p0) REVERT: D 169 MET cc_start: 0.7795 (mtt) cc_final: 0.7576 (mtt) REVERT: D 205 LYS cc_start: 0.7569 (mtmm) cc_final: 0.7325 (mttp) REVERT: E 10 ASP cc_start: 0.6659 (m-30) cc_final: 0.6187 (p0) REVERT: E 66 LYS cc_start: 0.6875 (mtmm) cc_final: 0.6323 (mtpp) REVERT: E 140 LYS cc_start: 0.6486 (OUTLIER) cc_final: 0.6071 (tttm) REVERT: E 204 GLU cc_start: 0.7676 (pt0) cc_final: 0.7089 (pp20) REVERT: F 17 MET cc_start: 0.2644 (mmm) cc_final: 0.2266 (ttm) REVERT: F 51 ASP cc_start: 0.2107 (OUTLIER) cc_final: 0.1820 (m-30) REVERT: F 71 LYS cc_start: 0.2318 (OUTLIER) cc_final: 0.1492 (tmtt) REVERT: F 98 GLU cc_start: 0.3314 (OUTLIER) cc_final: 0.3027 (pt0) REVERT: G 111 HIS cc_start: 0.4570 (OUTLIER) cc_final: 0.3789 (p90) REVERT: H 92 GLU cc_start: 0.6804 (tp30) cc_final: 0.6363 (tp30) REVERT: H 107 LYS cc_start: 0.7531 (mttm) cc_final: 0.6310 (tmtt) REVERT: H 112 SER cc_start: 0.8029 (m) cc_final: 0.7760 (t) REVERT: H 118 LYS cc_start: 0.7319 (mttt) cc_final: 0.6748 (tttt) REVERT: I 88 ARG cc_start: 0.4651 (ttm110) cc_final: 0.4226 (tpm170) REVERT: J 5 GLU cc_start: 0.7349 (tt0) cc_final: 0.7125 (mt-10) REVERT: J 73 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6561 (mp0) REVERT: J 127 LYS cc_start: 0.6301 (OUTLIER) cc_final: 0.5874 (mmtt) REVERT: J 134 GLU cc_start: 0.5656 (mm-30) cc_final: 0.5427 (mm-30) REVERT: K 1 MET cc_start: 0.2334 (ttm) cc_final: 0.1505 (tpt) REVERT: K 2 LEU cc_start: -0.3461 (OUTLIER) cc_final: -0.3871 (mp) REVERT: K 58 MET cc_start: 0.7112 (tpp) cc_final: 0.6895 (tpp) REVERT: K 83 MET cc_start: 0.7232 (mmm) cc_final: 0.6800 (mmm) REVERT: L 31 GLU cc_start: 0.7609 (tt0) cc_final: 0.7293 (pt0) REVERT: L 59 ARG cc_start: 0.6598 (ttt90) cc_final: 0.6330 (mtt180) REVERT: M 7 LYS cc_start: 0.5663 (OUTLIER) cc_final: 0.4892 (tttt) REVERT: M 35 ARG cc_start: 0.4170 (OUTLIER) cc_final: 0.3827 (ppt-90) REVERT: M 87 LYS cc_start: 0.3520 (OUTLIER) cc_final: 0.2936 (tmtt) REVERT: N 6 LEU cc_start: 0.6006 (OUTLIER) cc_final: 0.5741 (mp) REVERT: N 59 GLU cc_start: 0.6105 (tp30) cc_final: 0.5462 (tp30) REVERT: N 82 LYS cc_start: 0.6948 (mtpp) cc_final: 0.6643 (mttt) REVERT: N 93 LYS cc_start: 0.7956 (tttt) cc_final: 0.7455 (tptt) REVERT: O 74 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7042 (mtt) REVERT: O 78 ARG cc_start: 0.7485 (mtp-110) cc_final: 0.7126 (mtm-85) REVERT: P 6 GLU cc_start: 0.6911 (tt0) cc_final: 0.6694 (tm-30) REVERT: Q 48 GLU cc_start: 0.6543 (tp30) cc_final: 0.6153 (tp30) REVERT: Q 59 GLU cc_start: 0.6093 (tp30) cc_final: 0.5816 (mt-10) REVERT: Q 96 LYS cc_start: 0.7261 (mttm) cc_final: 0.6453 (mmtt) REVERT: R 84 GLU cc_start: 0.5417 (OUTLIER) cc_final: 0.5031 (tp30) REVERT: S 41 MET cc_start: 0.7165 (ptt) cc_final: 0.5659 (mmt) REVERT: T 54 GLU cc_start: 0.5890 (OUTLIER) cc_final: 0.5293 (mm-30) REVERT: U 25 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7325 (tp30) REVERT: U 53 ILE cc_start: 0.6579 (mp) cc_final: 0.6266 (mt) REVERT: U 65 ASP cc_start: 0.6898 (m-30) cc_final: 0.6388 (m-30) REVERT: V 37 ARG cc_start: 0.6948 (ptm160) cc_final: 0.6270 (ptp90) REVERT: W 16 GLU cc_start: 0.5273 (OUTLIER) cc_final: 0.5041 (tp30) REVERT: W 19 LYS cc_start: 0.7282 (ptmm) cc_final: 0.6863 (tptt) REVERT: W 59 GLU cc_start: 0.6868 (pt0) cc_final: 0.6302 (mm-30) REVERT: X 3 LYS cc_start: 0.6071 (OUTLIER) cc_final: 0.5663 (mmtm) REVERT: X 6 ILE cc_start: 0.7590 (mt) cc_final: 0.7320 (pt) REVERT: X 20 ARG cc_start: 0.5934 (mmm-85) cc_final: 0.5695 (mtt180) REVERT: 2 25 THR cc_start: 0.6937 (m) cc_final: 0.6404 (p) REVERT: 2 37 ARG cc_start: 0.7325 (tpp-160) cc_final: 0.6983 (ttm170) REVERT: 3 43 GLN cc_start: 0.6691 (mt0) cc_final: 0.6267 (mt0) REVERT: 3 59 LYS cc_start: 0.7477 (ttmp) cc_final: 0.6919 (tptp) REVERT: 4 35 ARG cc_start: 0.4977 (OUTLIER) cc_final: 0.3427 (mmm-85) outliers start: 169 outliers final: 123 residues processed: 564 average time/residue: 1.7524 time to fit residues: 1646.9271 Evaluate side-chains 547 residues out of total 2635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 406 time to evaluate : 4.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 213 TRP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 49 HIS Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 8 PHE Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 112 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain K residue 2 LEU Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 31 GLU Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 35 ARG Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 74 MET Chi-restraints excluded: chain P residue 2 PHE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 84 GLU Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 26 THR Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 51 VAL Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 90 ASP Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 13 LYS Chi-restraints excluded: chain U residue 58 ASN Chi-restraints excluded: chain U residue 88 SER Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 29 TRP Chi-restraints excluded: chain V residue 32 ASN Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain W residue 7 ARG Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 16 GLU Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 61 GLU Chi-restraints excluded: chain X residue 3 LYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 32 ASN Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 43 ILE Chi-restraints excluded: chain X residue 48 ASN Chi-restraints excluded: chain X residue 57 GLU Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 5 VAL Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 22 ASN Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 4 residue 19 ARG Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 35 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 599 random chunks: chunk 194 optimal weight: 10.0000 chunk 521 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 339 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 chunk 579 optimal weight: 2.9990 chunk 481 optimal weight: 3.9990 chunk 268 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 304 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN X 19 GLN ** 3 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.557 96722 Z= 0.335 Angle : 0.678 30.161 145523 Z= 0.343 Chirality : 0.039 0.272 18792 Planarity : 0.005 0.080 7188 Dihedral : 25.237 179.605 50293 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 6.94 % Allowed : 22.42 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.01 (0.14), residues: 3069 helix: -0.67 (0.18), residues: 763 sheet: -1.77 (0.21), residues: 559 loop : -2.81 (0.13), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 93 HIS 0.006 0.001 HIS Y 55 PHE 0.026 0.002 PHE O 106 TYR 0.016 0.002 TYR L 100 ARG 0.015 0.001 ARG K 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. Residue LYS 16 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Evaluate side-chains 597 residues out of total 2635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 424 time to evaluate : 4.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 ARG cc_start: 0.6641 (OUTLIER) cc_final: 0.6325 (ttt180) REVERT: C 71 LYS cc_start: 0.7092 (tppp) cc_final: 0.6557 (tttt) REVERT: D 40 THR cc_start: 0.7323 (OUTLIER) cc_final: 0.6841 (p) REVERT: D 61 LYS cc_start: 0.6853 (OUTLIER) cc_final: 0.6551 (mtmm) REVERT: D 169 MET cc_start: 0.7916 (mtt) cc_final: 0.7706 (mtt) REVERT: D 191 GLU cc_start: 0.7793 (mp0) cc_final: 0.7242 (pm20) REVERT: D 205 LYS cc_start: 0.7606 (mtmm) cc_final: 0.7394 (mtmm) REVERT: E 10 ASP cc_start: 0.6784 (m-30) cc_final: 0.6315 (p0) REVERT: E 140 LYS cc_start: 0.6540 (OUTLIER) cc_final: 0.6113 (tttm) REVERT: F 17 MET cc_start: 0.2509 (mmm) cc_final: 0.2158 (ttm) REVERT: F 51 ASP cc_start: 0.2578 (OUTLIER) cc_final: 0.2246 (m-30) REVERT: F 71 LYS cc_start: 0.1942 (OUTLIER) cc_final: 0.1238 (tmtt) REVERT: F 98 GLU cc_start: 0.3196 (OUTLIER) cc_final: 0.2907 (pt0) REVERT: G 111 HIS cc_start: 0.4826 (OUTLIER) cc_final: 0.4109 (p90) REVERT: H 20 ASP cc_start: 0.6384 (p0) cc_final: 0.5651 (p0) REVERT: H 92 GLU cc_start: 0.6706 (tp30) cc_final: 0.6386 (tp30) REVERT: H 107 LYS cc_start: 0.7655 (mttm) cc_final: 0.6598 (ttpp) REVERT: H 112 SER cc_start: 0.8129 (m) cc_final: 0.7887 (t) REVERT: H 118 LYS cc_start: 0.7337 (mttt) cc_final: 0.6749 (tttt) REVERT: I 88 ARG cc_start: 0.4861 (ttm110) cc_final: 0.4354 (tpm170) REVERT: I 112 MET cc_start: 0.6057 (OUTLIER) cc_final: 0.5602 (ptt) REVERT: J 5 GLU cc_start: 0.7356 (tt0) cc_final: 0.7108 (mt-10) REVERT: J 13 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7392 (mmt180) REVERT: J 71 ARG cc_start: 0.5982 (ttt180) cc_final: 0.5602 (ttp80) REVERT: J 73 GLU cc_start: 0.6827 (mt-10) cc_final: 0.6390 (mp0) REVERT: J 127 LYS cc_start: 0.6400 (OUTLIER) cc_final: 0.6087 (mmtt) REVERT: K 1 MET cc_start: 0.2310 (ttm) cc_final: 0.1416 (tpt) REVERT: M 35 ARG cc_start: 0.4086 (OUTLIER) cc_final: 0.3681 (ppt-90) REVERT: M 87 LYS cc_start: 0.3397 (OUTLIER) cc_final: 0.2813 (tmtt) REVERT: N 6 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5877 (mp) REVERT: N 82 LYS cc_start: 0.6945 (mtpp) cc_final: 0.6650 (mttt) REVERT: N 93 LYS cc_start: 0.7880 (tttt) cc_final: 0.7497 (tptt) REVERT: O 55 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.5625 (ptp-170) REVERT: O 74 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.6964 (mtt) REVERT: Q 48 GLU cc_start: 0.6466 (tp30) cc_final: 0.5956 (tp30) REVERT: Q 59 GLU cc_start: 0.6160 (tp30) cc_final: 0.5846 (mt-10) REVERT: Q 96 LYS cc_start: 0.7229 (mttm) cc_final: 0.6586 (mmpt) REVERT: R 72 THR cc_start: 0.7937 (m) cc_final: 0.7515 (p) REVERT: R 75 ARG cc_start: 0.6167 (ptt90) cc_final: 0.5898 (ptm-80) REVERT: R 84 GLU cc_start: 0.5470 (OUTLIER) cc_final: 0.5128 (tp30) REVERT: S 41 MET cc_start: 0.7156 (ptt) cc_final: 0.5750 (mmt) REVERT: S 58 GLU cc_start: 0.6233 (mp0) cc_final: 0.6032 (mp0) REVERT: T 54 GLU cc_start: 0.5793 (OUTLIER) cc_final: 0.5340 (mm-30) REVERT: U 25 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7402 (tp30) REVERT: U 53 ILE cc_start: 0.6582 (mp) cc_final: 0.6371 (mt) REVERT: U 65 ASP cc_start: 0.6817 (m-30) cc_final: 0.6384 (m-30) REVERT: V 37 ARG cc_start: 0.6705 (ptm160) cc_final: 0.6070 (ptp90) REVERT: W 16 GLU cc_start: 0.5535 (OUTLIER) cc_final: 0.5312 (tp30) REVERT: W 19 LYS cc_start: 0.7526 (ptmm) cc_final: 0.7047 (tptt) REVERT: W 42 ARG cc_start: 0.5937 (mmm-85) cc_final: 0.5228 (mmm160) REVERT: W 59 GLU cc_start: 0.6813 (pt0) cc_final: 0.6275 (mm-30) REVERT: X 3 LYS cc_start: 0.6216 (OUTLIER) cc_final: 0.5940 (mmtm) REVERT: X 20 ARG cc_start: 0.6067 (mmm-85) cc_final: 0.5819 (mtt180) REVERT: 2 25 THR cc_start: 0.6927 (m) cc_final: 0.6403 (p) REVERT: 2 37 ARG cc_start: 0.7314 (tpp-160) cc_final: 0.6943 (ttm170) REVERT: 3 43 GLN cc_start: 0.6596 (mt0) cc_final: 0.6339 (mt0) REVERT: 3 59 LYS cc_start: 0.7533 (ttmp) cc_final: 0.7002 (tptp) REVERT: 4 35 ARG cc_start: 0.5026 (OUTLIER) cc_final: 0.3731 (mmt180) outliers start: 173 outliers final: 122 residues processed: 559 average time/residue: 1.7594 time to fit residues: 1622.9220 Evaluate side-chains 540 residues out of total 2635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 397 time to evaluate : 4.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 213 TRP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 49 HIS Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 8 PHE Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 112 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 13 ARG Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain K residue 2 LEU Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 31 GLU Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 35 ARG Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 74 MET Chi-restraints excluded: chain P residue 2 PHE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 84 GLU Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 26 THR Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 51 VAL Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 90 ASP Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 13 LYS Chi-restraints excluded: chain U residue 58 ASN Chi-restraints excluded: chain U residue 88 SER Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 29 TRP Chi-restraints excluded: chain V residue 32 ASN Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain W residue 7 ARG Chi-restraints excluded: chain W residue 16 GLU Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 61 GLU Chi-restraints excluded: chain X residue 3 LYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 32 ASN Chi-restraints excluded: chain X residue 43 ILE Chi-restraints excluded: chain X residue 48 ASN Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 3 VAL Chi-restraints excluded: chain 1 residue 5 VAL Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 22 ASN Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 17 HIS Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 4 residue 19 ARG Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 35 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 599 random chunks: chunk 558 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 330 optimal weight: 2.9990 chunk 423 optimal weight: 2.9990 chunk 327 optimal weight: 5.9990 chunk 487 optimal weight: 4.9990 chunk 323 optimal weight: 3.9990 chunk 577 optimal weight: 50.0000 chunk 361 optimal weight: 2.9990 chunk 351 optimal weight: 0.3980 chunk 266 optimal weight: 10.0000 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN F 45 GLN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN ** 3 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.558 96722 Z= 0.332 Angle : 0.658 30.392 145523 Z= 0.334 Chirality : 0.038 0.275 18792 Planarity : 0.005 0.073 7188 Dihedral : 25.184 179.559 50289 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 6.34 % Allowed : 23.06 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.88 (0.14), residues: 3069 helix: -0.55 (0.18), residues: 758 sheet: -1.71 (0.21), residues: 574 loop : -2.73 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 93 HIS 0.006 0.001 HIS D 148 PHE 0.016 0.002 PHE U 77 TYR 0.014 0.002 TYR L 100 ARG 0.005 0.001 ARG R 4 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. Residue LYS 16 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Evaluate side-chains 585 residues out of total 2635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 427 time to evaluate : 4.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6487 (ttt180) REVERT: C 71 LYS cc_start: 0.7078 (tppp) cc_final: 0.6564 (tttt) REVERT: C 213 TRP cc_start: 0.6198 (OUTLIER) cc_final: 0.5923 (m-10) REVERT: D 61 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6765 (mtmm) REVERT: D 169 MET cc_start: 0.7741 (mtt) cc_final: 0.7522 (mtt) REVERT: D 205 LYS cc_start: 0.7667 (mtmm) cc_final: 0.7441 (mtmm) REVERT: E 10 ASP cc_start: 0.6701 (m-30) cc_final: 0.6217 (p0) REVERT: E 66 LYS cc_start: 0.6876 (mtmm) cc_final: 0.6332 (mtpp) REVERT: E 140 LYS cc_start: 0.6774 (OUTLIER) cc_final: 0.6223 (tttm) REVERT: F 17 MET cc_start: 0.2414 (mmm) cc_final: 0.2143 (ttm) REVERT: F 51 ASP cc_start: 0.2598 (OUTLIER) cc_final: 0.2320 (m-30) REVERT: F 71 LYS cc_start: 0.2046 (OUTLIER) cc_final: 0.1300 (tmtt) REVERT: F 98 GLU cc_start: 0.3113 (OUTLIER) cc_final: 0.2780 (pt0) REVERT: G 111 HIS cc_start: 0.4756 (OUTLIER) cc_final: 0.4026 (p90) REVERT: H 20 ASP cc_start: 0.6404 (p0) cc_final: 0.5739 (p0) REVERT: H 92 GLU cc_start: 0.6845 (tp30) cc_final: 0.6465 (tp30) REVERT: H 107 LYS cc_start: 0.7664 (mttm) cc_final: 0.6595 (ttpp) REVERT: H 118 LYS cc_start: 0.7346 (mttt) cc_final: 0.6738 (tttt) REVERT: I 112 MET cc_start: 0.5975 (OUTLIER) cc_final: 0.5560 (ptt) REVERT: J 71 ARG cc_start: 0.6052 (ttt180) cc_final: 0.5646 (ttp80) REVERT: J 73 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6410 (mp0) REVERT: J 127 LYS cc_start: 0.6488 (OUTLIER) cc_final: 0.6119 (mmtt) REVERT: K 1 MET cc_start: 0.2219 (ttm) cc_final: 0.1221 (tpt) REVERT: L 31 GLU cc_start: 0.7213 (tt0) cc_final: 0.6350 (tt0) REVERT: L 106 GLN cc_start: 0.6237 (mt0) cc_final: 0.5865 (mt0) REVERT: M 35 ARG cc_start: 0.4245 (OUTLIER) cc_final: 0.3835 (ppt-90) REVERT: M 87 LYS cc_start: 0.3429 (OUTLIER) cc_final: 0.2825 (tmtt) REVERT: N 5 LYS cc_start: 0.5602 (mmtt) cc_final: 0.5114 (mtmt) REVERT: N 6 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.6041 (mp) REVERT: N 59 GLU cc_start: 0.5911 (tp30) cc_final: 0.5387 (tp30) REVERT: N 82 LYS cc_start: 0.6962 (mtpp) cc_final: 0.6642 (mttt) REVERT: N 93 LYS cc_start: 0.7941 (tttt) cc_final: 0.7540 (tptt) REVERT: O 74 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.6940 (mtt) REVERT: Q 48 GLU cc_start: 0.6486 (tp30) cc_final: 0.5920 (tp30) REVERT: Q 59 GLU cc_start: 0.6284 (tp30) cc_final: 0.5727 (mt-10) REVERT: Q 96 LYS cc_start: 0.7113 (mtmm) cc_final: 0.6489 (mmpt) REVERT: R 72 THR cc_start: 0.8007 (m) cc_final: 0.7571 (p) REVERT: R 75 ARG cc_start: 0.6206 (ptt90) cc_final: 0.5907 (ptm-80) REVERT: R 84 GLU cc_start: 0.5441 (OUTLIER) cc_final: 0.5199 (tp30) REVERT: S 41 MET cc_start: 0.7181 (ptt) cc_final: 0.5775 (mmt) REVERT: T 54 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.5231 (mm-30) REVERT: U 25 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7375 (tp30) REVERT: U 65 ASP cc_start: 0.6787 (m-30) cc_final: 0.6360 (m-30) REVERT: V 37 ARG cc_start: 0.6684 (ptm160) cc_final: 0.6068 (ptp90) REVERT: W 16 GLU cc_start: 0.5566 (OUTLIER) cc_final: 0.5349 (tp30) REVERT: W 19 LYS cc_start: 0.7333 (ptmm) cc_final: 0.6918 (tptt) REVERT: W 42 ARG cc_start: 0.5929 (mmm-85) cc_final: 0.5255 (mmm160) REVERT: W 59 GLU cc_start: 0.6772 (pt0) cc_final: 0.6260 (mm-30) REVERT: X 3 LYS cc_start: 0.6320 (OUTLIER) cc_final: 0.6032 (mmtm) REVERT: X 20 ARG cc_start: 0.6125 (mmm-85) cc_final: 0.5867 (mtt180) REVERT: 2 25 THR cc_start: 0.6899 (m) cc_final: 0.6396 (p) REVERT: 2 37 ARG cc_start: 0.7384 (tpp-160) cc_final: 0.7032 (ttm170) REVERT: 3 59 LYS cc_start: 0.7592 (ttmp) cc_final: 0.7008 (tptp) REVERT: 4 35 ARG cc_start: 0.5007 (OUTLIER) cc_final: 0.3756 (mmt90) outliers start: 158 outliers final: 114 residues processed: 551 average time/residue: 1.7268 time to fit residues: 1587.2575 Evaluate side-chains 537 residues out of total 2635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 404 time to evaluate : 4.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 213 TRP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 49 HIS Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 8 PHE Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 112 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain K residue 2 LEU Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 31 GLU Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 35 ARG Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 74 MET Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain P residue 2 PHE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 84 GLU Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 26 THR Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 51 VAL Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 90 ASP Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 13 LYS Chi-restraints excluded: chain U residue 58 ASN Chi-restraints excluded: chain U residue 88 SER Chi-restraints excluded: chain V residue 32 ASN Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain W residue 7 ARG Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 16 GLU Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 61 GLU Chi-restraints excluded: chain X residue 3 LYS Chi-restraints excluded: chain X residue 6 ILE Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 32 ASN Chi-restraints excluded: chain X residue 43 ILE Chi-restraints excluded: chain X residue 48 ASN Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 5 VAL Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 22 ASN Chi-restraints excluded: chain 2 residue 17 HIS Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 4 residue 19 ARG Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 35 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 599 random chunks: chunk 357 optimal weight: 2.9990 chunk 230 optimal weight: 10.0000 chunk 344 optimal weight: 0.9980 chunk 173 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 111 optimal weight: 40.0000 chunk 367 optimal weight: 0.9980 chunk 393 optimal weight: 10.0000 chunk 285 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 453 optimal weight: 0.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 182 ASN S 44 HIS ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN ** 3 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.557 96722 Z= 0.313 Angle : 0.643 30.179 145523 Z= 0.327 Chirality : 0.037 0.278 18792 Planarity : 0.005 0.075 7188 Dihedral : 25.139 179.767 50278 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 6.14 % Allowed : 23.31 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.73 (0.14), residues: 3069 helix: -0.43 (0.18), residues: 760 sheet: -1.53 (0.21), residues: 550 loop : -2.65 (0.13), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 93 HIS 0.005 0.001 HIS Y 55 PHE 0.019 0.002 PHE O 106 TYR 0.021 0.002 TYR L 93 ARG 0.008 0.001 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. Residue LYS 16 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Evaluate side-chains 578 residues out of total 2635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 425 time to evaluate : 4.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6515 (ttt180) REVERT: C 71 LYS cc_start: 0.7214 (tppp) cc_final: 0.6638 (tttt) REVERT: C 213 TRP cc_start: 0.6194 (OUTLIER) cc_final: 0.5900 (m-10) REVERT: D 49 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7293 (tt) REVERT: D 169 MET cc_start: 0.7804 (mtt) cc_final: 0.7589 (mtt) REVERT: D 205 LYS cc_start: 0.7699 (mtmm) cc_final: 0.7466 (mtmm) REVERT: E 10 ASP cc_start: 0.6768 (m-30) cc_final: 0.6217 (p0) REVERT: E 66 LYS cc_start: 0.6867 (mtmm) cc_final: 0.6329 (mtpp) REVERT: E 140 LYS cc_start: 0.6818 (OUTLIER) cc_final: 0.6293 (tttm) REVERT: F 17 MET cc_start: 0.2203 (mmm) cc_final: 0.1823 (ttm) REVERT: F 51 ASP cc_start: 0.2595 (OUTLIER) cc_final: 0.2326 (m-30) REVERT: F 71 LYS cc_start: 0.1703 (OUTLIER) cc_final: 0.0953 (tmtt) REVERT: F 98 GLU cc_start: 0.3373 (OUTLIER) cc_final: 0.3055 (pt0) REVERT: G 111 HIS cc_start: 0.4938 (OUTLIER) cc_final: 0.4174 (p90) REVERT: H 20 ASP cc_start: 0.6394 (p0) cc_final: 0.5724 (p0) REVERT: H 92 GLU cc_start: 0.6820 (tp30) cc_final: 0.6431 (tp30) REVERT: H 107 LYS cc_start: 0.7671 (mttm) cc_final: 0.6614 (ttpp) REVERT: H 118 LYS cc_start: 0.7341 (mttt) cc_final: 0.6730 (tttt) REVERT: I 112 MET cc_start: 0.5924 (OUTLIER) cc_final: 0.5552 (ptt) REVERT: J 13 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7405 (mmt180) REVERT: J 71 ARG cc_start: 0.6040 (ttt180) cc_final: 0.5649 (ttp80) REVERT: J 73 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6478 (mp0) REVERT: J 127 LYS cc_start: 0.6506 (OUTLIER) cc_final: 0.6130 (mmtt) REVERT: K 1 MET cc_start: 0.2185 (ttm) cc_final: 0.1177 (tpt) REVERT: M 35 ARG cc_start: 0.4393 (OUTLIER) cc_final: 0.3862 (ppt-90) REVERT: M 87 LYS cc_start: 0.3559 (OUTLIER) cc_final: 0.2890 (tmtt) REVERT: N 5 LYS cc_start: 0.5670 (mmtt) cc_final: 0.5238 (mtmm) REVERT: N 6 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.6061 (mp) REVERT: N 59 GLU cc_start: 0.6055 (tp30) cc_final: 0.5709 (tp30) REVERT: N 82 LYS cc_start: 0.6857 (mtpp) cc_final: 0.6543 (mttt) REVERT: N 93 LYS cc_start: 0.7956 (tttt) cc_final: 0.7521 (tptt) REVERT: O 55 ARG cc_start: 0.6292 (OUTLIER) cc_final: 0.5724 (ptp-170) REVERT: O 74 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.6855 (mtt) REVERT: Q 59 GLU cc_start: 0.6276 (tp30) cc_final: 0.5725 (mt-10) REVERT: Q 96 LYS cc_start: 0.6875 (mtmm) cc_final: 0.6293 (mmpt) REVERT: R 72 THR cc_start: 0.7985 (m) cc_final: 0.7549 (p) REVERT: R 75 ARG cc_start: 0.6199 (ptt90) cc_final: 0.5897 (ptm-80) REVERT: R 84 GLU cc_start: 0.5454 (OUTLIER) cc_final: 0.5211 (tp30) REVERT: S 41 MET cc_start: 0.7190 (ptt) cc_final: 0.5808 (mmt) REVERT: T 54 GLU cc_start: 0.5794 (OUTLIER) cc_final: 0.5234 (mm-30) REVERT: U 25 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7356 (tp30) REVERT: U 65 ASP cc_start: 0.6811 (m-30) cc_final: 0.6389 (m-30) REVERT: V 37 ARG cc_start: 0.6902 (ptm160) cc_final: 0.6228 (ptp90) REVERT: W 16 GLU cc_start: 0.5565 (OUTLIER) cc_final: 0.5348 (tp30) REVERT: W 19 LYS cc_start: 0.7467 (ptmm) cc_final: 0.7108 (tptt) REVERT: W 42 ARG cc_start: 0.5985 (mmm-85) cc_final: 0.5265 (mmm160) REVERT: W 59 GLU cc_start: 0.6760 (pt0) cc_final: 0.6269 (mm-30) REVERT: X 3 LYS cc_start: 0.6257 (OUTLIER) cc_final: 0.5936 (mmtm) REVERT: X 20 ARG cc_start: 0.6148 (mmm-85) cc_final: 0.5867 (mtt180) REVERT: 2 25 THR cc_start: 0.6825 (m) cc_final: 0.6329 (p) REVERT: 2 37 ARG cc_start: 0.7413 (tpp-160) cc_final: 0.7091 (ttm170) REVERT: 3 59 LYS cc_start: 0.7588 (ttmp) cc_final: 0.6995 (tptp) REVERT: 4 35 ARG cc_start: 0.4955 (OUTLIER) cc_final: 0.3815 (mmt180) outliers start: 153 outliers final: 119 residues processed: 541 average time/residue: 1.7421 time to fit residues: 1553.0588 Evaluate side-chains 548 residues out of total 2635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 408 time to evaluate : 4.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 213 TRP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 49 HIS Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 8 PHE Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 112 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 13 ARG Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain K residue 2 LEU Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 31 GLU Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 35 ARG Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 43 GLN Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 74 MET Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain P residue 2 PHE Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 84 GLU Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain S residue 8 ASN Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 26 THR Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 51 VAL Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 82 LEU Chi-restraints excluded: chain T residue 90 ASP Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 13 LYS Chi-restraints excluded: chain U residue 58 ASN Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain U residue 88 SER Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 32 ASN Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain W residue 7 ARG Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 16 GLU Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 23 GLU Chi-restraints excluded: chain W residue 61 GLU Chi-restraints excluded: chain X residue 3 LYS Chi-restraints excluded: chain X residue 6 ILE Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 32 ASN Chi-restraints excluded: chain X residue 43 ILE Chi-restraints excluded: chain X residue 48 ASN Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 5 VAL Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 22 ASN Chi-restraints excluded: chain 2 residue 17 HIS Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 4 residue 19 ARG Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 35 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 599 random chunks: chunk 525 optimal weight: 0.4980 chunk 553 optimal weight: 1.9990 chunk 504 optimal weight: 3.9990 chunk 538 optimal weight: 0.0370 chunk 552 optimal weight: 0.6980 chunk 323 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 chunk 422 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 486 optimal weight: 2.9990 chunk 508 optimal weight: 2.9990 overall best weight: 1.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 61 ASN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN ** 3 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.6175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.558 96722 Z= 0.265 Angle : 0.583 30.313 145523 Z= 0.298 Chirality : 0.034 0.272 18792 Planarity : 0.004 0.069 7188 Dihedral : 25.003 179.454 50274 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 4.89 % Allowed : 24.35 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.48 (0.14), residues: 3069 helix: -0.12 (0.19), residues: 764 sheet: -1.49 (0.21), residues: 569 loop : -2.52 (0.13), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 61 HIS 0.005 0.001 HIS O 29 PHE 0.013 0.001 PHE F 138 TYR 0.010 0.001 TYR 2 6 ARG 0.007 0.000 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. Residue LYS 16 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Evaluate side-chains 556 residues out of total 2635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 434 time to evaluate : 4.754 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 TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 LYS cc_start: 0.7115 (tppp) cc_final: 0.6544 (tttt) REVERT: C 213 TRP cc_start: 0.6053 (OUTLIER) cc_final: 0.5757 (m-10) REVERT: D 49 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7225 (tt) REVERT: D 169 MET cc_start: 0.7733 (mtt) cc_final: 0.7487 (mtt) REVERT: D 205 LYS cc_start: 0.7629 (mtmm) cc_final: 0.7406 (mtmm) REVERT: E 66 LYS cc_start: 0.6876 (mtmm) cc_final: 0.6249 (mmtp) REVERT: E 140 LYS cc_start: 0.6825 (OUTLIER) cc_final: 0.6300 (tttm) REVERT: F 17 MET cc_start: 0.2110 (mmm) cc_final: 0.1763 (ttm) REVERT: F 71 LYS cc_start: 0.1861 (OUTLIER) cc_final: 0.1135 (tmtt) REVERT: F 98 GLU cc_start: 0.3292 (OUTLIER) cc_final: 0.3016 (pt0) REVERT: G 111 HIS cc_start: 0.4889 (OUTLIER) cc_final: 0.4601 (p90) REVERT: H 92 GLU cc_start: 0.6908 (tp30) cc_final: 0.6534 (tp30) REVERT: H 107 LYS cc_start: 0.7645 (mttm) cc_final: 0.6653 (ttpp) REVERT: H 118 LYS cc_start: 0.7313 (mttt) cc_final: 0.6710 (tttt) REVERT: I 112 MET cc_start: 0.5869 (OUTLIER) cc_final: 0.5532 (ptt) REVERT: J 10 GLU cc_start: 0.7569 (tp30) cc_final: 0.7338 (tp30) REVERT: J 71 ARG cc_start: 0.6027 (ttt180) cc_final: 0.5666 (ttp80) REVERT: J 73 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6402 (mp0) REVERT: J 127 LYS cc_start: 0.6488 (OUTLIER) cc_final: 0.6116 (mmtt) REVERT: K 1 MET cc_start: 0.2141 (ttm) cc_final: 0.1103 (tpt) REVERT: K 39 THR cc_start: 0.4914 (OUTLIER) cc_final: 0.4539 (t) REVERT: L 31 GLU cc_start: 0.7389 (tt0) cc_final: 0.6959 (tt0) REVERT: M 35 ARG cc_start: 0.4393 (OUTLIER) cc_final: 0.3915 (ppt-90) REVERT: M 87 LYS cc_start: 0.3547 (OUTLIER) cc_final: 0.2863 (tmtt) REVERT: N 5 LYS cc_start: 0.5628 (mmtt) cc_final: 0.5198 (mtmm) REVERT: N 6 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.6029 (mp) REVERT: N 59 GLU cc_start: 0.6034 (tp30) cc_final: 0.5789 (tp30) REVERT: N 82 LYS cc_start: 0.6804 (mtpp) cc_final: 0.6500 (mttt) REVERT: N 93 LYS cc_start: 0.7938 (tttt) cc_final: 0.7489 (tptt) REVERT: Q 59 GLU cc_start: 0.6319 (tp30) cc_final: 0.5805 (mt-10) REVERT: Q 96 LYS cc_start: 0.6796 (mtmm) cc_final: 0.6212 (mmtm) REVERT: R 55 ILE cc_start: 0.8128 (pt) cc_final: 0.7897 (tt) REVERT: R 72 THR cc_start: 0.7959 (m) cc_final: 0.7530 (p) REVERT: R 84 GLU cc_start: 0.5299 (OUTLIER) cc_final: 0.4940 (tp30) REVERT: S 41 MET cc_start: 0.7121 (ptt) cc_final: 0.5731 (mmt) REVERT: T 54 GLU cc_start: 0.5698 (OUTLIER) cc_final: 0.5161 (mm-30) REVERT: U 25 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7392 (tp30) REVERT: U 65 ASP cc_start: 0.7070 (m-30) cc_final: 0.6588 (m-30) REVERT: V 37 ARG cc_start: 0.6727 (ptm160) cc_final: 0.6003 (ptp90) REVERT: W 16 GLU cc_start: 0.5553 (OUTLIER) cc_final: 0.5338 (tp30) REVERT: W 19 LYS cc_start: 0.7521 (ptmm) cc_final: 0.7140 (tptt) REVERT: W 42 ARG cc_start: 0.6028 (mmm-85) cc_final: 0.5326 (mmm160) REVERT: W 59 GLU cc_start: 0.6750 (pt0) cc_final: 0.6302 (mm-30) REVERT: X 3 LYS cc_start: 0.6316 (OUTLIER) cc_final: 0.6065 (mmtm) REVERT: X 20 ARG cc_start: 0.6186 (mmm-85) cc_final: 0.5903 (mtt180) REVERT: 2 25 THR cc_start: 0.6724 (m) cc_final: 0.6248 (p) REVERT: 2 37 ARG cc_start: 0.7362 (tpp-160) cc_final: 0.7087 (ttm170) REVERT: 3 59 LYS cc_start: 0.7574 (ttmp) cc_final: 0.6979 (tptp) REVERT: 4 35 ARG cc_start: 0.4747 (OUTLIER) cc_final: 0.3679 (mtt-85) outliers start: 122 outliers final: 90 residues processed: 519 average time/residue: 1.7143 time to fit residues: 1470.6849 Evaluate side-chains 527 residues out of total 2635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 420 time to evaluate : 4.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 213 TRP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 49 HIS Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 112 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain K residue 2 LEU Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 31 GLU Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 35 ARG Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 43 GLN Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain P residue 2 PHE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 84 GLU Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 26 THR Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 51 VAL Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 13 LYS Chi-restraints excluded: chain U residue 58 ASN Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain U residue 88 SER Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 32 ASN Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain W residue 7 ARG Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 16 GLU Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain X residue 3 LYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 32 ASN Chi-restraints excluded: chain X residue 43 ILE Chi-restraints excluded: chain X residue 48 ASN Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 5 VAL Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 22 ASN Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 4 residue 19 ARG Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 35 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 599 random chunks: chunk 536 optimal weight: 0.8980 chunk 353 optimal weight: 3.9990 chunk 568 optimal weight: 2.9990 chunk 347 optimal weight: 4.9990 chunk 269 optimal weight: 4.9990 chunk 395 optimal weight: 7.9990 chunk 596 optimal weight: 1.9990 chunk 549 optimal weight: 2.9990 chunk 475 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 367 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 192 ASN Q 61 ASN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN ** 3 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 moved from start: 0.6309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.558 96722 Z= 0.290 Angle : 0.606 30.225 145523 Z= 0.309 Chirality : 0.036 0.271 18792 Planarity : 0.005 0.062 7188 Dihedral : 24.990 178.898 50270 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 4.85 % Allowed : 24.23 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.38 (0.14), residues: 3069 helix: -0.10 (0.19), residues: 761 sheet: -1.33 (0.22), residues: 542 loop : -2.44 (0.13), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 83 HIS 0.005 0.001 HIS O 29 PHE 0.030 0.002 PHE F 8 TYR 0.014 0.001 TYR L 100 ARG 0.006 0.000 ARG L 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. Residue LYS 16 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Evaluate side-chains 542 residues out of total 2635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 421 time to evaluate : 4.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 TRP cc_start: 0.6130 (OUTLIER) cc_final: 0.5856 (m-10) REVERT: D 49 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7244 (tt) REVERT: D 169 MET cc_start: 0.7746 (mtt) cc_final: 0.7539 (mtt) REVERT: D 205 LYS cc_start: 0.7683 (mtmm) cc_final: 0.7471 (mtmm) REVERT: E 10 ASP cc_start: 0.6671 (m-30) cc_final: 0.6151 (p0) REVERT: E 66 LYS cc_start: 0.6861 (mtmm) cc_final: 0.6248 (mmmt) REVERT: E 140 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6345 (tttm) REVERT: F 17 MET cc_start: 0.1769 (mmm) cc_final: 0.1455 (ttm) REVERT: F 71 LYS cc_start: 0.1772 (OUTLIER) cc_final: 0.0998 (tmtt) REVERT: F 98 GLU cc_start: 0.3333 (OUTLIER) cc_final: 0.3064 (pt0) REVERT: G 111 HIS cc_start: 0.4894 (OUTLIER) cc_final: 0.4625 (p90) REVERT: H 92 GLU cc_start: 0.6929 (tp30) cc_final: 0.6605 (tp30) REVERT: H 107 LYS cc_start: 0.7660 (mttm) cc_final: 0.6722 (ttpp) REVERT: H 118 LYS cc_start: 0.7290 (mttt) cc_final: 0.6702 (tttt) REVERT: I 112 MET cc_start: 0.6063 (OUTLIER) cc_final: 0.5269 (tmm) REVERT: J 71 ARG cc_start: 0.6033 (ttt180) cc_final: 0.5663 (ttp80) REVERT: J 73 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6467 (mp0) REVERT: J 127 LYS cc_start: 0.6552 (OUTLIER) cc_final: 0.6159 (mmtt) REVERT: K 39 THR cc_start: 0.4902 (OUTLIER) cc_final: 0.4521 (t) REVERT: M 35 ARG cc_start: 0.4409 (OUTLIER) cc_final: 0.4026 (ppt-90) REVERT: M 87 LYS cc_start: 0.3519 (OUTLIER) cc_final: 0.2845 (tmtt) REVERT: N 5 LYS cc_start: 0.5747 (mmtt) cc_final: 0.5267 (mtmm) REVERT: N 6 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.6093 (mp) REVERT: N 59 GLU cc_start: 0.6158 (tp30) cc_final: 0.5772 (tp30) REVERT: N 82 LYS cc_start: 0.6783 (mtpp) cc_final: 0.6474 (mttt) REVERT: N 93 LYS cc_start: 0.7935 (tttt) cc_final: 0.7547 (tptt) REVERT: Q 59 GLU cc_start: 0.6319 (tp30) cc_final: 0.5726 (mt-10) REVERT: Q 92 SER cc_start: -0.0821 (OUTLIER) cc_final: -0.1061 (t) REVERT: Q 96 LYS cc_start: 0.6801 (mtmm) cc_final: 0.6225 (mmtm) REVERT: R 55 ILE cc_start: 0.8150 (pt) cc_final: 0.7862 (tt) REVERT: R 72 THR cc_start: 0.8021 (m) cc_final: 0.7603 (p) REVERT: R 84 GLU cc_start: 0.5428 (OUTLIER) cc_final: 0.5208 (tp30) REVERT: S 41 MET cc_start: 0.7137 (ptt) cc_final: 0.5787 (mmt) REVERT: T 54 GLU cc_start: 0.5699 (OUTLIER) cc_final: 0.5158 (mm-30) REVERT: U 25 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7351 (tp30) REVERT: U 65 ASP cc_start: 0.6880 (m-30) cc_final: 0.6431 (m-30) REVERT: V 37 ARG cc_start: 0.7033 (ptm160) cc_final: 0.6331 (ptp90) REVERT: W 16 GLU cc_start: 0.5580 (OUTLIER) cc_final: 0.5355 (tp30) REVERT: W 19 LYS cc_start: 0.7472 (ptmm) cc_final: 0.7177 (tptt) REVERT: W 42 ARG cc_start: 0.6077 (mmm-85) cc_final: 0.5333 (mmm160) REVERT: W 58 ARG cc_start: 0.6446 (tpt170) cc_final: 0.6114 (tpt-90) REVERT: W 59 GLU cc_start: 0.6759 (pt0) cc_final: 0.6311 (mm-30) REVERT: X 3 LYS cc_start: 0.6227 (OUTLIER) cc_final: 0.5987 (mmtm) REVERT: X 20 ARG cc_start: 0.6167 (mmm-85) cc_final: 0.5890 (mtt180) REVERT: 2 25 THR cc_start: 0.6778 (m) cc_final: 0.6294 (p) REVERT: 2 37 ARG cc_start: 0.7363 (tpp-160) cc_final: 0.7039 (ttm170) REVERT: 3 59 LYS cc_start: 0.7581 (ttmp) cc_final: 0.6984 (tptp) REVERT: 4 35 ARG cc_start: 0.4827 (OUTLIER) cc_final: 0.3814 (mtt-85) outliers start: 121 outliers final: 98 residues processed: 508 average time/residue: 1.7042 time to fit residues: 1427.1584 Evaluate side-chains 522 residues out of total 2635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 406 time to evaluate : 4.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 213 TRP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 49 HIS Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 112 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain K residue 2 LEU Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 31 GLU Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 35 ARG Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 43 GLN Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain P residue 2 PHE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain Q residue 92 SER Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 84 GLU Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 26 THR Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 51 VAL Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 13 LYS Chi-restraints excluded: chain U residue 58 ASN Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain U residue 88 SER Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 32 ASN Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain W residue 7 ARG Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 16 GLU Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain X residue 3 LYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 32 ASN Chi-restraints excluded: chain X residue 43 ILE Chi-restraints excluded: chain X residue 48 ASN Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 5 VAL Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 22 ASN Chi-restraints excluded: chain 2 residue 17 HIS Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 4 residue 19 ARG Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 35 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 599 random chunks: chunk 291 optimal weight: 10.0000 chunk 377 optimal weight: 5.9990 chunk 506 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 chunk 438 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 475 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 488 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN ** F 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN X 46 GLN ** 3 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.185535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.162635 restraints weight = 312118.314| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 0.54 r_work: 0.3727 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.559 96722 Z= 0.358 Angle : 0.695 30.135 145523 Z= 0.353 Chirality : 0.040 0.280 18792 Planarity : 0.006 0.064 7188 Dihedral : 25.121 178.497 50270 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 5.42 % Allowed : 23.91 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.73 (0.14), residues: 3069 helix: -0.44 (0.18), residues: 760 sheet: -1.56 (0.21), residues: 562 loop : -2.64 (0.13), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 250 HIS 0.007 0.002 HIS D 148 PHE 0.022 0.002 PHE O 106 TYR 0.017 0.002 TYR L 100 ARG 0.007 0.001 ARG L 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 42858.45 seconds wall clock time: 738 minutes 17.70 seconds (44297.70 seconds total)