Starting phenix.real_space_refine on Sun Apr 14 15:42:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug6_26485/04_2024/7ug6_26485_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug6_26485/04_2024/7ug6_26485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug6_26485/04_2024/7ug6_26485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug6_26485/04_2024/7ug6_26485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug6_26485/04_2024/7ug6_26485_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug6_26485/04_2024/7ug6_26485_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 sd= 0.032 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 3336 5.49 5 Mg 1 5.21 5 S 183 5.16 5 C 75848 2.51 5 N 25864 2.21 5 O 35718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "7 GLU 55": "OE1" <-> "OE2" Residue "7 GLU 57": "OE1" <-> "OE2" Residue "7 TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 36": "OE1" <-> "OE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 59": "OD1" <-> "OD2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B ASP 206": "OD1" <-> "OD2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 299": "OD1" <-> "OD2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C ASP 177": "OD1" <-> "OD2" Residue "C TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 259": "OD1" <-> "OD2" Residue "C ASP 285": "OD1" <-> "OD2" Residue "C PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E ASP 142": "OD1" <-> "OD2" Residue "F TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 83": "OD1" <-> "OD2" Residue "G TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H GLU 11": "OE1" <-> "OE2" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H ASP 42": "OD1" <-> "OD2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 143": "OE1" <-> "OE2" Residue "H GLU 189": "OE1" <-> "OE2" Residue "I TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 98": "OD1" <-> "OD2" Residue "L ASP 110": "OD1" <-> "OD2" Residue "L GLU 136": "OE1" <-> "OE2" Residue "L PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 16": "OE1" <-> "OE2" Residue "M GLU 92": "OE1" <-> "OE2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "M TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 103": "OE1" <-> "OE2" Residue "N TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 113": "OD1" <-> "OD2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "O GLU 157": "OE1" <-> "OE2" Residue "O GLU 166": "OE1" <-> "OE2" Residue "P TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 49": "OE1" <-> "OE2" Residue "P GLU 75": "OE1" <-> "OE2" Residue "P PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 154": "OE1" <-> "OE2" Residue "Q ASP 22": "OD1" <-> "OD2" Residue "Q TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "R TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 126": "OE1" <-> "OE2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "S TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 38": "OD1" <-> "OD2" Residue "T TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 107": "OE1" <-> "OE2" Residue "U GLU 24": "OE1" <-> "OE2" Residue "U TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 39": "OD1" <-> "OD2" Residue "U GLU 58": "OE1" <-> "OE2" Residue "V ASP 27": "OD1" <-> "OD2" Residue "V TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 96": "OE1" <-> "OE2" Residue "V ASP 97": "OD1" <-> "OD2" Residue "W PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 28": "OD1" <-> "OD2" Residue "W GLU 32": "OE1" <-> "OE2" Residue "W ASP 35": "OD1" <-> "OD2" Residue "W TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 152": "OE1" <-> "OE2" Residue "W GLU 170": "OE1" <-> "OE2" Residue "W ASP 196": "OD1" <-> "OD2" Residue "W GLU 212": "OE1" <-> "OE2" Residue "W PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 70": "OE1" <-> "OE2" Residue "X GLU 104": "OE1" <-> "OE2" Residue "X TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 83": "OD1" <-> "OD2" Residue "Y GLU 88": "OE1" <-> "OE2" Residue "Z PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 99": "OE1" <-> "OE2" Residue "Z GLU 119": "OE1" <-> "OE2" Residue "Z GLU 120": "OE1" <-> "OE2" Residue "Z PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 146": "OE1" <-> "OE2" Residue "b ASP 7": "OD1" <-> "OD2" Residue "b ASP 83": "OD1" <-> "OD2" Residue "b GLU 106": "OE1" <-> "OE2" Residue "b ASP 145": "OD1" <-> "OD2" Residue "b PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 210": "OD1" <-> "OD2" Residue "b TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 255": "OD1" <-> "OD2" Residue "b PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 311": "OE1" <-> "OE2" Residue "b ASP 371": "OD1" <-> "OD2" Residue "b ASP 392": "OD1" <-> "OD2" Residue "b GLU 405": "OE1" <-> "OE2" Residue "b TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 434": "OE1" <-> "OE2" Residue "b TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 443": "OD1" <-> "OD2" Residue "b PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 603": "OD1" <-> "OD2" Residue "b PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 98": "OE1" <-> "OE2" Residue "d ASP 48": "OD1" <-> "OD2" Residue "d TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 94": "OE1" <-> "OE2" Residue "e TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 83": "OE1" <-> "OE2" Residue "f PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 46": "OD1" <-> "OD2" Residue "g GLU 97": "OE1" <-> "OE2" Residue "h GLU 15": "OE1" <-> "OE2" Residue "h TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 96": "OE1" <-> "OE2" Residue "h TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 59": "OD1" <-> "OD2" Residue "i PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 89": "OE1" <-> "OE2" Residue "k PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 14": "OE1" <-> "OE2" Residue "m ASP 102": "OD1" <-> "OD2" Residue "m ASP 139": "OD1" <-> "OD2" Residue "m GLU 166": "OE1" <-> "OE2" Residue "m ASP 230": "OD1" <-> "OD2" Residue "m GLU 243": "OE1" <-> "OE2" Residue "m PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 413": "OE1" <-> "OE2" Residue "m GLU 429": "OE1" <-> "OE2" Residue "m ASP 456": "OD1" <-> "OD2" Residue "m PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 38": "OD1" <-> "OD2" Residue "p PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 28": "OE1" <-> "OE2" Residue "r GLU 31": "OE1" <-> "OE2" Residue "r TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 57": "OE1" <-> "OE2" Residue "r TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 132": "OE1" <-> "OE2" Residue "u TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 66": "OD1" <-> "OD2" Residue "u GLU 98": "OE1" <-> "OE2" Residue "u GLU 132": "OE1" <-> "OE2" Residue "v ASP 48": "OD1" <-> "OD2" Residue "v PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 71": "OD1" <-> "OD2" Residue "v GLU 76": "OE1" <-> "OE2" Residue "v TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 163": "OD1" <-> "OD2" Residue "v GLU 168": "OE1" <-> "OE2" Residue "v TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 225": "OE1" <-> "OE2" Residue "w ASP 56": "OD1" <-> "OD2" Residue "x GLU 61": "OE1" <-> "OE2" Residue "x GLU 62": "OE1" <-> "OE2" Residue "x TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 172": "OD1" <-> "OD2" Residue "x ASP 331": "OD1" <-> "OD2" Residue "x TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 361": "OE1" <-> "OE2" Residue "x PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 481": "OD1" <-> "OD2" Residue "x TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 493": "OD1" <-> "OD2" Residue "y ASP 112": "OD1" <-> "OD2" Residue "y ASP 120": "OD1" <-> "OD2" Residue "y TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 30": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 140950 Number of models: 1 Model: "" Number of chains: 53 Chain: "1" Number of atoms: 65424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3058, 65424 Classifications: {'RNA': 3058} Modifications used: {'5*END': 1, 'rna2p_pur': 359, 'rna2p_pyr': 249, 'rna3p_pur': 1342, 'rna3p_pyr': 1108} Link IDs: {'rna2p': 608, 'rna3p': 2449} Chain breaks: 9 Chain: "2" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3350 Classifications: {'RNA': 158} Modifications used: {'5*END': 1, 'rna2p_pur': 17, 'rna2p_pyr': 16, 'rna3p_pur': 61, 'rna3p_pyr': 64} Link IDs: {'rna2p': 32, 'rna3p': 125} Chain: "3" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2576 Classifications: {'RNA': 121} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 56, 'rna3p_pyr': 50} Link IDs: {'rna2p': 14, 'rna3p': 106} Chain: "7" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "A" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1634 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 201} Chain: "B" Number of atoms: 3082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3082 Classifications: {'peptide': 386} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Chain: "C" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2750 Classifications: {'peptide': 361} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Chain: "D" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2073 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "E" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1240 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Chain: "F" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1785 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "G" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1818 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain: "H" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1519 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 184} Chain: "I" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 905 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "J" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1354 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "L" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1499 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain: "M" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1060 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "N" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1721 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "O" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1556 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain: "P" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1443 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain: "Q" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1035 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "R" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1258 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "S" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1438 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "T" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 943 Classifications: {'peptide': 119} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "U" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 844 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "V" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1004 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "W" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1885 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain: "X" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1101 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "Y" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "Z" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1093 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "a" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 736 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain: "b" Number of atoms: 4169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4169 Classifications: {'peptide': 514} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 490} Chain breaks: 2 Chain: "c" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 743 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain breaks: 1 Chain: "d" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 873 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "e" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "f" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 851 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "g" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 881 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "h" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 970 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "i" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 772 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "j" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 682 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "k" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 613 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "l" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 437 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "m" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3774 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain breaks: 1 Chain: "p" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 695 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "q" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain breaks: 2 Chain: "r" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1861 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Chain: "s" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 573 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain breaks: 1 Chain: "u" Number of atoms: 1265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1265 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "v" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2318 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 273} Chain breaks: 1 Chain: "w" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1425 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 12, 'TRANS': 166} Chain breaks: 1 Chain: "x" Number of atoms: 3808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3808 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 462} Chain breaks: 5 Chain: "y" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1723 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "z" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 644 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "m" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 53.20, per 1000 atoms: 0.38 Number of scatterers: 140950 At special positions: 0 Unit cell: (226.8, 221.94, 264.87, 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 183 16.00 P 3336 15.00 Mg 1 11.99 O 35718 8.00 N 25864 7.00 C 75848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 57.17 Conformation dependent library (CDL) restraints added in 9.3 seconds 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16384 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 311 helices and 81 sheets defined 43.5% alpha, 14.3% beta 1042 base pairs and 1726 stacking pairs defined. Time for finding SS restraints: 75.80 Creating SS restraints... Processing helix chain '7' and resid 10 through 21 removed outlier: 4.035A pdb=" N LEU 7 16 " --> pdb=" O GLN 7 12 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL 7 17 " --> pdb=" O LYS 7 13 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE 7 18 " --> pdb=" O LEU 7 14 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS 7 19 " --> pdb=" O ALA 7 15 " (cutoff:3.500A) Processing helix chain '7' and resid 26 through 37 Processing helix chain '7' and resid 49 through 64 Processing helix chain '7' and resid 73 through 82 Processing helix chain '7' and resid 99 through 104 removed outlier: 3.673A pdb=" N THR 7 103 " --> pdb=" O ASP 7 99 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU 7 104 " --> pdb=" O ILE 7 100 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 99 through 104' Processing helix chain 'A' and resid 5 through 13 removed outlier: 4.695A pdb=" N GLY A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.019A pdb=" N VAL A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.525A pdb=" N ALA A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 4.072A pdb=" N MET A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 205' Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.603A pdb=" N LYS A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'B' and resid 13 through 18 removed outlier: 4.773A pdb=" N LEU B 17 " --> pdb=" O HIS B 13 " (cutoff:3.500A) Proline residue: B 18 - end of helix No H-bonds generated for 'chain 'B' and resid 13 through 18' Processing helix chain 'B' and resid 111 through 120 removed outlier: 3.657A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 removed outlier: 4.158A pdb=" N ALA B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASP B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 154 Processing helix chain 'B' and resid 165 through 170 removed outlier: 4.141A pdb=" N THR B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) Proline residue: B 170 - end of helix No H-bonds generated for 'chain 'B' and resid 165 through 170' Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.845A pdb=" N VAL B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 352 removed outlier: 4.052A pdb=" N LEU B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 228 through 234 removed outlier: 4.527A pdb=" N TRP B 233 " --> pdb=" O GLY B 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 29 removed outlier: 4.220A pdb=" N SER C 27 " --> pdb=" O PRO C 23 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Proline residue: C 29 - end of helix No H-bonds generated for 'chain 'C' and resid 23 through 29' Processing helix chain 'C' and resid 31 through 46 removed outlier: 4.438A pdb=" N LYS C 44 " --> pdb=" O THR C 40 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 132 removed outlier: 3.976A pdb=" N ALA C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 removed outlier: 3.820A pdb=" N GLY C 139 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 159 removed outlier: 4.678A pdb=" N GLU C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 159' Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 174 through 185 removed outlier: 3.931A pdb=" N LYS C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 196 removed outlier: 4.677A pdb=" N TYR C 194 " --> pdb=" O GLY C 190 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN C 196 " --> pdb=" O GLY C 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 190 through 196' Processing helix chain 'C' and resid 214 through 221 removed outlier: 4.678A pdb=" N ASN C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 240 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 251 through 262 removed outlier: 4.422A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 292 removed outlier: 3.769A pdb=" N ILE C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 300 removed outlier: 6.032A pdb=" N ARG C 300 " --> pdb=" O GLN C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 328 Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.565A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 361 Processing helix chain 'D' and resid 9 through 17 removed outlier: 5.697A pdb=" N GLN D 17 " --> pdb=" O SER D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 26 removed outlier: 4.744A pdb=" N GLY D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 Processing helix chain 'D' and resid 79 through 87 removed outlier: 4.356A pdb=" N LEU D 83 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 94 through 114 removed outlier: 3.691A pdb=" N GLY D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 170 Processing helix chain 'D' and resid 191 through 201 Processing helix chain 'D' and resid 202 through 215 Processing helix chain 'D' and resid 216 through 223 Processing helix chain 'D' and resid 224 through 230 Processing helix chain 'D' and resid 233 through 251 removed outlier: 4.916A pdb=" N GLU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASP D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Proline residue: D 251 - end of helix Processing helix chain 'D' and resid 261 through 274 removed outlier: 3.706A pdb=" N LYS D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLN D 274 " --> pdb=" O LYS D 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 85 removed outlier: 4.198A pdb=" N VAL E 84 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 80 through 85' Processing helix chain 'E' and resid 102 through 107 removed outlier: 3.858A pdb=" N PHE E 106 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 107 " --> pdb=" O VAL E 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 102 through 107' Processing helix chain 'E' and resid 131 through 150 removed outlier: 3.602A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLU E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 5.276A pdb=" N SER E 162 " --> pdb=" O TYR E 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 73 removed outlier: 4.440A pdb=" N ALA F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 107 Processing helix chain 'F' and resid 120 through 131 removed outlier: 4.098A pdb=" N GLU F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 150 Processing helix chain 'F' and resid 165 through 173 removed outlier: 4.100A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 191 removed outlier: 4.115A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 203 removed outlier: 4.884A pdb=" N TRP F 203 " --> pdb=" O ASN F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 244 removed outlier: 3.621A pdb=" N LEU F 239 " --> pdb=" O PHE F 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 69 Processing helix chain 'G' and resid 72 through 81 removed outlier: 5.058A pdb=" N PHE G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLN G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N THR G 81 " --> pdb=" O GLN G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 98 removed outlier: 4.043A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG G 98 " --> pdb=" O PHE G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 119 removed outlier: 3.618A pdb=" N GLU G 118 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY G 119 " --> pdb=" O ALA G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 146 Processing helix chain 'G' and resid 159 through 174 removed outlier: 4.840A pdb=" N VAL G 163 " --> pdb=" O PRO G 159 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LEU G 166 " --> pdb=" O LEU G 162 " (cutoff:3.500A) Proline residue: G 167 - end of helix Processing helix chain 'G' and resid 182 through 191 removed outlier: 4.037A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 222 removed outlier: 5.612A pdb=" N ALA G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 231 removed outlier: 5.711A pdb=" N LYS G 231 " --> pdb=" O ASP G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 256 removed outlier: 3.582A pdb=" N SER G 255 " --> pdb=" O LYS G 251 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA G 256 " --> pdb=" O ASN G 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 84 removed outlier: 3.560A pdb=" N ALA H 66 " --> pdb=" O ARG H 62 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG H 69 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 166 removed outlier: 3.581A pdb=" N CYS H 165 " --> pdb=" O LEU H 161 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 5.026A pdb=" N LEU H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 9 removed outlier: 4.918A pdb=" N VAL I 6 " --> pdb=" O GLY I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 27 removed outlier: 4.228A pdb=" N THR I 27 " --> pdb=" O ASN I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 37 removed outlier: 3.674A pdb=" N GLN I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 71 removed outlier: 3.742A pdb=" N LYS I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY I 70 " --> pdb=" O THR I 66 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LYS I 71 " --> pdb=" O HIS I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 82 removed outlier: 3.588A pdb=" N LEU I 80 " --> pdb=" O ARG I 76 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLY I 82 " --> pdb=" O LYS I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 95 removed outlier: 3.560A pdb=" N SER I 90 " --> pdb=" O THR I 86 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA I 94 " --> pdb=" O SER I 90 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY I 95 " --> pdb=" O ASP I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 111 Processing helix chain 'J' and resid 27 through 42 removed outlier: 3.853A pdb=" N THR J 31 " --> pdb=" O GLY J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 88 removed outlier: 3.543A pdb=" N LYS J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL J 86 " --> pdb=" O ARG J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 141 removed outlier: 3.885A pdb=" N ARG J 140 " --> pdb=" O ALA J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 167 Processing helix chain 'J' and resid 92 through 97 removed outlier: 5.179A pdb=" N SER J 97 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 22 removed outlier: 4.559A pdb=" N ARG L 21 " --> pdb=" O HIS L 17 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL L 22 " --> pdb=" O TRP L 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 17 through 22' Processing helix chain 'L' and resid 27 through 47 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 94 removed outlier: 3.886A pdb=" N THR L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 124 removed outlier: 3.516A pdb=" N ILE L 123 " --> pdb=" O TYR L 119 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE L 124 " --> pdb=" O GLN L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 146 removed outlier: 3.768A pdb=" N THR L 144 " --> pdb=" O SER L 140 " (cutoff:3.500A) Proline residue: L 146 - end of helix Processing helix chain 'L' and resid 165 through 180 Processing helix chain 'L' and resid 181 through 194 Processing helix chain 'M' and resid 59 through 64 removed outlier: 3.945A pdb=" N VAL M 63 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N VAL M 64 " --> pdb=" O LEU M 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 59 through 64' Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 90 through 98 removed outlier: 5.287A pdb=" N SER M 98 " --> pdb=" O TRP M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 112 Processing helix chain 'M' and resid 113 through 138 removed outlier: 4.361A pdb=" N ALA M 136 " --> pdb=" O LYS M 132 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS M 137 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA M 138 " --> pdb=" O ALA M 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 14 removed outlier: 3.605A pdb=" N LEU N 7 " --> pdb=" O ALA N 3 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 34 removed outlier: 4.827A pdb=" N ASN N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 97 through 111 Processing helix chain 'N' and resid 139 through 145 removed outlier: 3.988A pdb=" N ASP N 145 " --> pdb=" O ALA N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 153 removed outlier: 4.460A pdb=" N CYS N 152 " --> pdb=" O TYR N 148 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP N 153 " --> pdb=" O ASN N 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 148 through 153' Processing helix chain 'N' and resid 158 through 163 removed outlier: 3.571A pdb=" N ARG N 162 " --> pdb=" O HIS N 158 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 173 Processing helix chain 'N' and resid 177 through 182 removed outlier: 3.828A pdb=" N ASN N 181 " --> pdb=" O GLY N 177 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ASN N 182 " --> pdb=" O HIS N 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 177 through 182' Processing helix chain 'N' and resid 186 through 196 removed outlier: 3.504A pdb=" N THR N 196 " --> pdb=" O LYS N 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 30 Processing helix chain 'O' and resid 46 through 60 removed outlier: 4.104A pdb=" N LYS O 60 " --> pdb=" O ASP O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 70 removed outlier: 3.996A pdb=" N GLY O 69 " --> pdb=" O ASN O 65 " (cutoff:3.500A) Proline residue: O 70 - end of helix No H-bonds generated for 'chain 'O' and resid 65 through 70' Processing helix chain 'O' and resid 75 through 89 removed outlier: 4.117A pdb=" N MET O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL O 88 " --> pdb=" O LEU O 84 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SER O 89 " --> pdb=" O ARG O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 103 removed outlier: 3.603A pdb=" N ARG O 101 " --> pdb=" O ALA O 97 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LYS O 103 " --> pdb=" O LEU O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 116 removed outlier: 7.814A pdb=" N LYS O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LYS O 116 " --> pdb=" O TYR O 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 110 through 116' Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 137 through 146 Processing helix chain 'O' and resid 151 through 183 Processing helix chain 'O' and resid 188 through 198 Processing helix chain 'P' and resid 25 through 37 removed outlier: 3.728A pdb=" N ILE P 36 " --> pdb=" O THR P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 54 Processing helix chain 'P' and resid 70 through 75 removed outlier: 4.824A pdb=" N LYS P 74 " --> pdb=" O THR P 70 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLU P 75 " --> pdb=" O ALA P 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 70 through 75' Processing helix chain 'P' and resid 84 through 106 Processing helix chain 'P' and resid 108 through 113 removed outlier: 3.747A pdb=" N LEU P 112 " --> pdb=" O ASP P 108 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TYR P 113 " --> pdb=" O ALA P 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 108 through 113' Processing helix chain 'P' and resid 169 through 183 Processing helix chain 'Q' and resid 23 through 40 Processing helix chain 'Q' and resid 42 through 54 removed outlier: 3.848A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU Q 54 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 60 Proline residue: Q 60 - end of helix Processing helix chain 'Q' and resid 63 through 73 removed outlier: 3.951A pdb=" N GLN Q 73 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 118 removed outlier: 3.545A pdb=" N GLY Q 118 " --> pdb=" O ILE Q 114 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 23 removed outlier: 3.629A pdb=" N VAL R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TRP R 23 " --> pdb=" O LYS R 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 18 through 23' Processing helix chain 'R' and resid 28 through 36 removed outlier: 3.521A pdb=" N GLN R 34 " --> pdb=" O SER R 30 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASN R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 48 Processing helix chain 'R' and resid 60 through 73 Processing helix chain 'R' and resid 77 through 82 removed outlier: 5.996A pdb=" N LYS R 82 " --> pdb=" O TYR R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 113 Proline residue: R 90 - end of helix removed outlier: 6.171A pdb=" N VAL R 93 " --> pdb=" O LEU R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 130 Processing helix chain 'R' and resid 134 through 157 Processing helix chain 'S' and resid 33 through 49 Processing helix chain 'S' and resid 52 through 57 removed outlier: 5.023A pdb=" N GLU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 114 Processing helix chain 'S' and resid 117 through 122 removed outlier: 3.565A pdb=" N ILE S 121 " --> pdb=" O ARG S 117 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N HIS S 122 " --> pdb=" O PHE S 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 117 through 122' Processing helix chain 'S' and resid 137 through 145 removed outlier: 5.030A pdb=" N PHE S 143 " --> pdb=" O TYR S 139 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU S 144 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR S 145 " --> pdb=" O LYS S 141 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 97 removed outlier: 4.274A pdb=" N ILE T 96 " --> pdb=" O ARG T 92 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LYS T 97 " --> pdb=" O VAL T 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 92 through 97' Processing helix chain 'T' and resid 102 through 120 Processing helix chain 'U' and resid 19 through 26 removed outlier: 3.584A pdb=" N ASN U 25 " --> pdb=" O SER U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 40 Processing helix chain 'U' and resid 72 through 88 Processing helix chain 'V' and resid 66 through 71 removed outlier: 5.900A pdb=" N LYS V 71 " --> pdb=" O PRO V 67 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 127 removed outlier: 3.711A pdb=" N LEU V 125 " --> pdb=" O GLU V 121 " (cutoff:3.500A) Proline residue: V 127 - end of helix Processing helix chain 'V' and resid 128 through 133 Processing helix chain 'W' and resid 19 through 37 removed outlier: 3.955A pdb=" N LYS W 23 " --> pdb=" O GLY W 19 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 61 removed outlier: 4.086A pdb=" N TRP W 60 " --> pdb=" O ILE W 56 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ALA W 61 " --> pdb=" O ARG W 57 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 78 Processing helix chain 'W' and resid 89 through 97 removed outlier: 3.850A pdb=" N SER W 93 " --> pdb=" O LEU W 89 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU W 95 " --> pdb=" O GLN W 91 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER W 97 " --> pdb=" O SER W 93 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 119 Processing helix chain 'W' and resid 150 through 155 removed outlier: 4.946A pdb=" N VAL W 155 " --> pdb=" O ALA W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 167 removed outlier: 3.960A pdb=" N GLU W 162 " --> pdb=" O ILE W 158 " (cutoff:3.500A) Proline residue: W 163 - end of helix Processing helix chain 'W' and resid 196 through 207 Processing helix chain 'X' and resid 4 through 16 removed outlier: 3.568A pdb=" N THR X 8 " --> pdb=" O SER X 4 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 64 removed outlier: 4.859A pdb=" N GLU X 64 " --> pdb=" O TYR X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 78 Processing helix chain 'X' and resid 91 through 103 Processing helix chain 'X' and resid 131 through 140 removed outlier: 3.559A pdb=" N ILE X 135 " --> pdb=" O ASP X 131 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 22 Processing helix chain 'Y' and resid 23 through 32 removed outlier: 3.809A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER Y 32 " --> pdb=" O ARG Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 Processing helix chain 'Y' and resid 100 through 105 removed outlier: 3.675A pdb=" N LEU Y 104 " --> pdb=" O HIS Y 100 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL Y 105 " --> pdb=" O PRO Y 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 100 through 105' Processing helix chain 'Y' and resid 112 through 123 removed outlier: 3.507A pdb=" N GLY Y 123 " --> pdb=" O ILE Y 119 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 67 removed outlier: 3.969A pdb=" N LYS Z 67 " --> pdb=" O ALA Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 81 removed outlier: 3.653A pdb=" N LEU Z 80 " --> pdb=" O ASN Z 76 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU Z 81 " --> pdb=" O TYR Z 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 76 through 81' Processing helix chain 'Z' and resid 92 through 97 removed outlier: 3.937A pdb=" N VAL Z 96 " --> pdb=" O PHE Z 92 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N SER Z 97 " --> pdb=" O LYS Z 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 92 through 97' Processing helix chain 'Z' and resid 98 through 104 removed outlier: 3.557A pdb=" N GLU Z 102 " --> pdb=" O THR Z 98 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLN Z 103 " --> pdb=" O GLU Z 99 " (cutoff:3.500A) Proline residue: Z 104 - end of helix No H-bonds generated for 'chain 'Z' and resid 98 through 104' Processing helix chain 'Z' and resid 105 through 125 removed outlier: 5.152A pdb=" N ALA Z 124 " --> pdb=" O GLU Z 120 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY Z 125 " --> pdb=" O ARG Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 133 removed outlier: 3.694A pdb=" N PHE Z 131 " --> pdb=" O ASN Z 127 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER Z 132 " --> pdb=" O GLN Z 128 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LYS Z 133 " --> pdb=" O TRP Z 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 127 through 133' Processing helix chain 'a' and resid 64 through 69 removed outlier: 4.214A pdb=" N PHE a 68 " --> pdb=" O GLN a 64 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP a 69 " --> pdb=" O GLN a 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 64 through 69' Processing helix chain 'a' and resid 74 through 83 removed outlier: 4.394A pdb=" N TRP a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N THR a 80 " --> pdb=" O ASP a 76 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) Proline residue: a 83 - end of helix Processing helix chain 'a' and resid 84 through 94 removed outlier: 4.458A pdb=" N ASP a 88 " --> pdb=" O GLU a 84 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLN a 89 " --> pdb=" O ASP a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 108 Processing helix chain 'a' and resid 131 through 142 removed outlier: 3.606A pdb=" N GLY a 142 " --> pdb=" O ILE a 138 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 29 Processing helix chain 'b' and resid 38 through 75 Proline residue: b 69 - end of helix removed outlier: 8.957A pdb=" N ASN b 72 " --> pdb=" O PHE b 68 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP b 73 " --> pdb=" O PRO b 69 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N HIS b 75 " --> pdb=" O ILE b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 86 Processing helix chain 'b' and resid 87 through 119 removed outlier: 3.990A pdb=" N PHE b 118 " --> pdb=" O ARG b 114 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY b 119 " --> pdb=" O LEU b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 145 removed outlier: 3.658A pdb=" N LEU b 143 " --> pdb=" O ILE b 139 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG b 144 " --> pdb=" O VAL b 140 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASP b 145 " --> pdb=" O LYS b 141 " (cutoff:3.500A) Processing helix chain 'b' and resid 146 through 161 removed outlier: 3.588A pdb=" N GLN b 152 " --> pdb=" O ALA b 148 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG b 159 " --> pdb=" O GLN b 155 " (cutoff:3.500A) Proline residue: b 161 - end of helix Processing helix chain 'b' and resid 182 through 188 removed outlier: 3.512A pdb=" N THR b 188 " --> pdb=" O LEU b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 233 through 246 removed outlier: 3.694A pdb=" N SER b 239 " --> pdb=" O ILE b 235 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 280 Proline residue: b 276 - end of helix removed outlier: 3.706A pdb=" N ALA b 279 " --> pdb=" O LYS b 275 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ASN b 280 " --> pdb=" O PRO b 276 " (cutoff:3.500A) Processing helix chain 'b' and resid 289 through 294 removed outlier: 5.032A pdb=" N ARG b 294 " --> pdb=" O THR b 290 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 312 removed outlier: 4.057A pdb=" N LYS b 310 " --> pdb=" O LEU b 306 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL b 312 " --> pdb=" O SER b 308 " (cutoff:3.500A) Processing helix chain 'b' and resid 324 through 348 removed outlier: 3.555A pdb=" N VAL b 328 " --> pdb=" O LEU b 324 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 385 removed outlier: 3.540A pdb=" N LEU b 385 " --> pdb=" O SER b 381 " (cutoff:3.500A) Processing helix chain 'b' and resid 398 through 407 removed outlier: 3.756A pdb=" N ILE b 402 " --> pdb=" O LEU b 398 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY b 407 " --> pdb=" O GLU b 403 " (cutoff:3.500A) Processing helix chain 'b' and resid 415 through 420 removed outlier: 4.852A pdb=" N LYS b 419 " --> pdb=" O ASN b 415 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR b 420 " --> pdb=" O LEU b 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 415 through 420' Processing helix chain 'b' and resid 424 through 429 removed outlier: 3.953A pdb=" N LYS b 428 " --> pdb=" O ASP b 424 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASN b 429 " --> pdb=" O ASP b 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 424 through 429' Processing helix chain 'b' and resid 440 through 445 Processing helix chain 'b' and resid 448 through 467 Processing helix chain 'b' and resid 596 through 617 removed outlier: 3.687A pdb=" N ARG b 610 " --> pdb=" O ALA b 606 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG b 611 " --> pdb=" O LYS b 607 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N GLU b 612 " --> pdb=" O MET b 608 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ARG b 613 " --> pdb=" O GLU b 609 " (cutoff:3.500A) Processing helix chain 'b' and resid 631 through 636 removed outlier: 3.758A pdb=" N PHE b 635 " --> pdb=" O SER b 631 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER b 636 " --> pdb=" O LYS b 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 631 through 636' Processing helix chain 'c' and resid 10 through 34 removed outlier: 4.313A pdb=" N SER c 14 " --> pdb=" O PRO c 10 " (cutoff:3.500A) Processing helix chain 'c' and resid 52 through 64 Processing helix chain 'c' and resid 90 through 112 Processing helix chain 'd' and resid 15 through 21 removed outlier: 3.820A pdb=" N ARG d 19 " --> pdb=" O ASN d 15 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N HIS d 21 " --> pdb=" O HIS d 17 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 45 Processing helix chain 'd' and resid 52 through 61 Processing helix chain 'e' and resid 21 through 26 removed outlier: 5.177A pdb=" N HIS e 26 " --> pdb=" O SER e 22 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 45 Processing helix chain 'e' and resid 78 through 87 removed outlier: 3.901A pdb=" N THR e 84 " --> pdb=" O LYS e 80 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU e 85 " --> pdb=" O ASP e 81 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR e 86 " --> pdb=" O LEU e 82 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N MET e 87 " --> pdb=" O GLU e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 116 Processing helix chain 'f' and resid 37 through 45 removed outlier: 4.807A pdb=" N PHE f 43 " --> pdb=" O GLN f 39 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR f 44 " --> pdb=" O ASP f 40 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU f 45 " --> pdb=" O ALA f 41 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 66 removed outlier: 3.711A pdb=" N TYR g 62 " --> pdb=" O ARG g 58 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA g 63 " --> pdb=" O PRO g 59 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR g 64 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL g 65 " --> pdb=" O GLN g 61 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N SER g 66 " --> pdb=" O TYR g 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 58 through 66' Processing helix chain 'g' and resid 81 through 113 Processing helix chain 'h' and resid 5 through 13 removed outlier: 3.716A pdb=" N THR h 11 " --> pdb=" O TYR h 7 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS h 12 " --> pdb=" O GLU h 8 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N SER h 13 " --> pdb=" O LEU h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 14 through 38 removed outlier: 3.581A pdb=" N LEU h 36 " --> pdb=" O LYS h 32 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER h 37 " --> pdb=" O VAL h 33 " (cutoff:3.500A) Processing helix chain 'h' and resid 41 through 71 removed outlier: 4.494A pdb=" N LYS h 45 " --> pdb=" O LEU h 41 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL h 47 " --> pdb=" O LYS h 43 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG h 48 " --> pdb=" O ILE h 44 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU h 69 " --> pdb=" O ALA h 65 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 82 removed outlier: 5.572A pdb=" N ALA h 82 " --> pdb=" O LYS h 78 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 91 Processing helix chain 'h' and resid 93 through 99 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 25 through 31 removed outlier: 4.669A pdb=" N LYS i 29 " --> pdb=" O LYS i 25 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LYS i 30 " --> pdb=" O ILE i 26 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLY i 31 " --> pdb=" O SER i 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 25 through 31' Processing helix chain 'i' and resid 34 through 49 Processing helix chain 'i' and resid 51 through 64 Processing helix chain 'i' and resid 65 through 77 Processing helix chain 'i' and resid 79 through 100 removed outlier: 3.564A pdb=" N ALA i 83 " --> pdb=" O SER i 79 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG i 99 " --> pdb=" O ALA i 95 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N HIS i 100 " --> pdb=" O ALA i 96 " (cutoff:3.500A) Processing helix chain 'j' and resid 4 through 11 removed outlier: 3.784A pdb=" N GLY j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS j 10 " --> pdb=" O PRO j 6 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG j 11 " --> pdb=" O SER j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 Processing helix chain 'j' and resid 65 through 77 removed outlier: 5.484A pdb=" N HIS j 69 " --> pdb=" O ARG j 65 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL j 70 " --> pdb=" O TYR j 66 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ARG j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN j 76 " --> pdb=" O ARG j 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 17 removed outlier: 3.645A pdb=" N PHE k 11 " --> pdb=" O ASP k 7 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG k 17 " --> pdb=" O GLU k 13 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 69 removed outlier: 3.902A pdb=" N GLN k 67 " --> pdb=" O LYS k 63 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 21 removed outlier: 5.089A pdb=" N ARG l 21 " --> pdb=" O LYS l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 4.100A pdb=" N ARG l 28 " --> pdb=" O PRO l 24 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU l 29 " --> pdb=" O GLN l 25 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG l 30 " --> pdb=" O TRP l 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 24 through 30' Processing helix chain 'm' and resid 6 through 15 Processing helix chain 'm' and resid 32 through 44 removed outlier: 3.520A pdb=" N MET m 41 " --> pdb=" O LYS m 37 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR m 42 " --> pdb=" O PHE m 38 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR m 43 " --> pdb=" O LEU m 39 " (cutoff:3.500A) Processing helix chain 'm' and resid 74 through 80 removed outlier: 4.545A pdb=" N PHE m 78 " --> pdb=" O ASP m 74 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY m 79 " --> pdb=" O ARG m 75 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASN m 80 " --> pdb=" O ARG m 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 74 through 80' Processing helix chain 'm' and resid 85 through 99 removed outlier: 4.128A pdb=" N GLY m 97 " --> pdb=" O ARG m 93 " (cutoff:3.500A) Processing helix chain 'm' and resid 114 through 119 Processing helix chain 'm' and resid 130 through 135 removed outlier: 4.481A pdb=" N THR m 134 " --> pdb=" O ARG m 130 " (cutoff:3.500A) Processing helix chain 'm' and resid 136 through 141 Processing helix chain 'm' and resid 156 through 182 removed outlier: 3.669A pdb=" N LEU m 160 " --> pdb=" O ASN m 156 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR m 180 " --> pdb=" O VAL m 176 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU m 181 " --> pdb=" O LEU m 177 " (cutoff:3.500A) Processing helix chain 'm' and resid 185 through 193 removed outlier: 3.653A pdb=" N GLU m 191 " --> pdb=" O GLN m 187 " (cutoff:3.500A) Processing helix chain 'm' and resid 200 through 205 removed outlier: 3.923A pdb=" N SER m 204 " --> pdb=" O GLU m 200 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS m 205 " --> pdb=" O ALA m 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 200 through 205' Processing helix chain 'm' and resid 208 through 222 Processing helix chain 'm' and resid 233 through 238 Processing helix chain 'm' and resid 239 through 249 removed outlier: 3.529A pdb=" N GLU m 243 " --> pdb=" O CYS m 239 " (cutoff:3.500A) Processing helix chain 'm' and resid 266 through 281 removed outlier: 3.773A pdb=" N LYS m 279 " --> pdb=" O LYS m 275 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU m 280 " --> pdb=" O HIS m 276 " (cutoff:3.500A) Processing helix chain 'm' and resid 295 through 311 Processing helix chain 'm' and resid 327 through 337 Processing helix chain 'm' and resid 378 through 386 removed outlier: 4.057A pdb=" N LEU m 383 " --> pdb=" O GLU m 379 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE m 384 " --> pdb=" O GLU m 380 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG m 385 " --> pdb=" O ASP m 381 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLY m 386 " --> pdb=" O ILE m 382 " (cutoff:3.500A) Processing helix chain 'm' and resid 389 through 394 removed outlier: 4.175A pdb=" N VAL m 393 " --> pdb=" O ARG m 389 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N THR m 394 " --> pdb=" O VAL m 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 389 through 394' Processing helix chain 'm' and resid 395 through 407 removed outlier: 4.665A pdb=" N TYR m 399 " --> pdb=" O HIS m 395 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE m 400 " --> pdb=" O PRO m 396 " (cutoff:3.500A) Proline residue: m 401 - end of helix Processing helix chain 'm' and resid 408 through 417 removed outlier: 3.898A pdb=" N ARG m 414 " --> pdb=" O LYS m 410 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR m 416 " --> pdb=" O LEU m 412 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU m 417 " --> pdb=" O GLU m 413 " (cutoff:3.500A) Processing helix chain 'm' and resid 423 through 436 removed outlier: 4.025A pdb=" N GLU m 429 " --> pdb=" O THR m 425 " (cutoff:3.500A) Processing helix chain 'm' and resid 445 through 460 Processing helix chain 'p' and resid 19 through 35 removed outlier: 3.812A pdb=" N LYS p 28 " --> pdb=" O ARG p 24 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU p 29 " --> pdb=" O GLN p 25 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 92 Processing helix chain 'q' and resid 38 through 50 removed outlier: 3.740A pdb=" N VAL q 42 " --> pdb=" O SER q 38 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY q 43 " --> pdb=" O PRO q 39 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU q 44 " --> pdb=" O LYS q 40 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP q 45 " --> pdb=" O LYS q 41 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA q 47 " --> pdb=" O GLY q 43 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LYS q 48 " --> pdb=" O GLU q 44 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALA q 49 " --> pdb=" O ASP q 45 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 85 removed outlier: 3.837A pdb=" N LEU q 85 " --> pdb=" O VAL q 81 " (cutoff:3.500A) Processing helix chain 'q' and resid 105 through 118 removed outlier: 3.724A pdb=" N ILE q 109 " --> pdb=" O GLN q 105 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU q 111 " --> pdb=" O ASP q 107 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET q 116 " --> pdb=" O ILE q 112 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASP q 118 " --> pdb=" O ARG q 114 " (cutoff:3.500A) Processing helix chain 'q' and resid 124 through 140 Processing helix chain 'q' and resid 147 through 158 removed outlier: 4.080A pdb=" N ILE q 151 " --> pdb=" O ASN q 147 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE q 152 " --> pdb=" O PRO q 148 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU q 153 " --> pdb=" O HIS q 149 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 14 Processing helix chain 'r' and resid 20 through 38 removed outlier: 4.146A pdb=" N SER r 32 " --> pdb=" O GLU r 28 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER r 36 " --> pdb=" O SER r 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 74 removed outlier: 4.706A pdb=" N LYS r 74 " --> pdb=" O GLN r 70 " (cutoff:3.500A) Processing helix chain 'r' and resid 129 through 135 removed outlier: 5.280A pdb=" N LYS r 135 " --> pdb=" O GLU r 131 " (cutoff:3.500A) Processing helix chain 'r' and resid 174 through 179 removed outlier: 3.607A pdb=" N ARG r 178 " --> pdb=" O PRO r 174 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN r 179 " --> pdb=" O SER r 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 174 through 179' Processing helix chain 'r' and resid 206 through 213 Processing helix chain 'r' and resid 248 through 253 Processing helix chain 's' and resid 12 through 36 removed outlier: 3.825A pdb=" N LYS s 36 " --> pdb=" O LYS s 32 " (cutoff:3.500A) Processing helix chain 's' and resid 56 through 76 removed outlier: 4.604A pdb=" N MET s 69 " --> pdb=" O GLU s 65 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LYS s 70 " --> pdb=" O ALA s 66 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASP s 71 " --> pdb=" O LYS s 67 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU s 72 " --> pdb=" O LYS s 68 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ARG s 75 " --> pdb=" O ASP s 71 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLU s 76 " --> pdb=" O LEU s 72 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 43 removed outlier: 3.602A pdb=" N ARG u 43 " --> pdb=" O ALA u 39 " (cutoff:3.500A) Processing helix chain 'u' and resid 45 through 50 removed outlier: 5.514A pdb=" N LYS u 50 " --> pdb=" O PRO u 46 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 60 Processing helix chain 'u' and resid 66 through 72 removed outlier: 4.005A pdb=" N THR u 70 " --> pdb=" O ASP u 66 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE u 71 " --> pdb=" O SER u 67 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ALA u 72 " --> pdb=" O THR u 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 66 through 72' Processing helix chain 'u' and resid 82 through 131 removed outlier: 3.633A pdb=" N GLU u 98 " --> pdb=" O ALA u 94 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY u 114 " --> pdb=" O ASN u 110 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASN u 115 " --> pdb=" O ARG u 111 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LYS u 116 " --> pdb=" O MET u 112 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLU u 117 " --> pdb=" O ARG u 113 " (cutoff:3.500A) Proline residue: u 131 - end of helix Processing helix chain 'u' and resid 132 through 149 removed outlier: 3.728A pdb=" N GLN u 149 " --> pdb=" O LEU u 145 " (cutoff:3.500A) Processing helix chain 'v' and resid 10 through 20 removed outlier: 3.670A pdb=" N ARG v 14 " --> pdb=" O ALA v 10 " (cutoff:3.500A) Processing helix chain 'v' and resid 39 through 54 Processing helix chain 'v' and resid 72 through 83 removed outlier: 4.371A pdb=" N ASP v 83 " --> pdb=" O SER v 79 " (cutoff:3.500A) Processing helix chain 'v' and resid 124 through 129 removed outlier: 4.641A pdb=" N PHE v 128 " --> pdb=" O LEU v 124 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LYS v 129 " --> pdb=" O LEU v 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 124 through 129' Processing helix chain 'v' and resid 146 through 151 removed outlier: 3.960A pdb=" N THR v 150 " --> pdb=" O ALA v 146 " (cutoff:3.500A) Processing helix chain 'v' and resid 152 through 166 Processing helix chain 'v' and resid 174 through 179 removed outlier: 3.855A pdb=" N LEU v 178 " --> pdb=" O ASP v 174 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N GLN v 179 " --> pdb=" O VAL v 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 174 through 179' Processing helix chain 'v' and resid 241 through 250 removed outlier: 3.715A pdb=" N HIS v 249 " --> pdb=" O VAL v 245 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LYS v 250 " --> pdb=" O THR v 246 " (cutoff:3.500A) Processing helix chain 'v' and resid 281 through 286 removed outlier: 4.014A pdb=" N LEU v 285 " --> pdb=" O ASP v 281 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLN v 286 " --> pdb=" O LEU v 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 281 through 286' Processing helix chain 'v' and resid 290 through 295 removed outlier: 3.617A pdb=" N LYS v 294 " --> pdb=" O MET v 290 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N SER v 295 " --> pdb=" O LYS v 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 290 through 295' Processing helix chain 'w' and resid 35 through 40 removed outlier: 3.655A pdb=" N LEU w 39 " --> pdb=" O ASP w 35 " (cutoff:3.500A) Processing helix chain 'w' and resid 45 through 68 Processing helix chain 'w' and resid 112 through 122 removed outlier: 4.834A pdb=" N GLY w 122 " --> pdb=" O ALA w 118 " (cutoff:3.500A) Processing helix chain 'w' and resid 152 through 157 removed outlier: 5.052A pdb=" N ASP w 156 " --> pdb=" O LYS w 152 " (cutoff:3.500A) Processing helix chain 'w' and resid 175 through 201 removed outlier: 3.550A pdb=" N ARG w 197 " --> pdb=" O LYS w 193 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET w 199 " --> pdb=" O GLN w 195 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS w 200 " --> pdb=" O ARG w 196 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN w 201 " --> pdb=" O ARG w 197 " (cutoff:3.500A) Processing helix chain 'x' and resid 9 through 19 removed outlier: 3.594A pdb=" N GLN x 17 " --> pdb=" O LYS x 13 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU x 18 " --> pdb=" O LYS x 14 " (cutoff:3.500A) Proline residue: x 19 - end of helix Processing helix chain 'x' and resid 56 through 69 removed outlier: 3.672A pdb=" N LEU x 60 " --> pdb=" O SER x 56 " (cutoff:3.500A) Processing helix chain 'x' and resid 239 through 244 removed outlier: 3.649A pdb=" N VAL x 243 " --> pdb=" O PRO x 239 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LYS x 244 " --> pdb=" O ILE x 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 239 through 244' Processing helix chain 'x' and resid 330 through 337 Processing helix chain 'x' and resid 348 through 367 removed outlier: 3.780A pdb=" N ILE x 363 " --> pdb=" O ASN x 359 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS x 366 " --> pdb=" O LYS x 362 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ASN x 367 " --> pdb=" O ILE x 363 " (cutoff:3.500A) Processing helix chain 'y' and resid 12 through 17 removed outlier: 3.958A pdb=" N PHE y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 32 through 43 removed outlier: 4.240A pdb=" N GLU y 41 " --> pdb=" O ALA y 37 " (cutoff:3.500A) Processing helix chain 'y' and resid 58 through 63 Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 108 Processing helix chain 'y' and resid 122 through 133 Processing helix chain 'y' and resid 147 through 152 Processing helix chain 'y' and resid 166 through 178 Processing helix chain 'y' and resid 192 through 197 Processing helix chain 'y' and resid 211 through 223 Processing helix chain 'z' and resid 7 through 21 removed outlier: 3.823A pdb=" N ARG z 19 " --> pdb=" O SER z 15 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY z 20 " --> pdb=" O VAL z 16 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL z 21 " --> pdb=" O LYS z 17 " (cutoff:3.500A) Processing helix chain 'z' and resid 22 through 51 removed outlier: 3.605A pdb=" N LYS z 50 " --> pdb=" O LEU z 46 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS z 51 " --> pdb=" O GLU z 47 " (cutoff:3.500A) Processing helix chain 'z' and resid 82 through 100 Processing sheet with id= 1, first strand: chain '7' and resid 22 through 25 removed outlier: 6.253A pdb=" N LYS 7 22 " --> pdb=" O LEU 7 93 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU 7 41 " --> pdb=" O ILE 7 92 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS 7 66 " --> pdb=" O LYS 7 40 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.653A pdb=" N GLN A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLN A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 110 through 114 removed outlier: 4.407A pdb=" N THR A 111 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ARG A 147 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 58 through 65 No H-bonds generated for sheet with id= 4 Processing sheet with id= 5, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.635A pdb=" N GLN B 182 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N HIS B 177 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU B 161 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 53 through 58 removed outlier: 6.695A pdb=" N VAL B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG B 334 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N HIS B 273 " --> pdb=" O THR B 221 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 98 through 102 removed outlier: 6.651A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 284 through 288 removed outlier: 3.508A pdb=" N PHE B 321 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY B 288 " --> pdb=" O ASN B 319 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ASN B 319 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 76 through 80 Processing sheet with id= 10, first strand: chain 'B' and resid 88 through 93 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'B' and resid 213 through 216 removed outlier: 4.414A pdb=" N GLU B 213 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 5 through 8 removed outlier: 5.518A pdb=" N ASN C 18 " --> pdb=" O VAL C 8 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 204 through 209 Processing sheet with id= 14, first strand: chain 'D' and resid 60 through 66 Processing sheet with id= 15, first strand: chain 'E' and resid 39 through 43 removed outlier: 4.184A pdb=" N LYS E 50 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'E' and resid 63 through 66 Processing sheet with id= 17, first strand: chain 'F' and resid 113 through 119 removed outlier: 5.037A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LYS F 82 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N TYR F 133 " --> pdb=" O ILE F 89 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 176 through 181 Processing sheet with id= 19, first strand: chain 'H' and resid 5 through 12 removed outlier: 4.991A pdb=" N GLN H 51 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU H 52 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL H 48 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'H' and resid 17 through 20 Processing sheet with id= 21, first strand: chain 'H' and resid 100 through 105 removed outlier: 5.510A pdb=" N LYS H 110 " --> pdb=" O VAL H 128 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 132 through 137 removed outlier: 5.042A pdb=" N GLU H 143 " --> pdb=" O SER H 137 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ASP H 142 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR H 92 " --> pdb=" O ASP H 142 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS H 89 " --> pdb=" O SER H 182 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 86 through 89 Processing sheet with id= 24, first strand: chain 'J' and resid 12 through 15 removed outlier: 4.074A pdb=" N LYS J 13 " --> pdb=" O ASN J 132 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL J 130 " --> pdb=" O GLU J 15 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS J 16 " --> pdb=" O VAL J 130 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA J 66 " --> pdb=" O SER J 48 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 52 through 55 removed outlier: 7.345A pdb=" N TYR J 52 " --> pdb=" O ARG J 61 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ARG J 61 " --> pdb=" O TYR J 52 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 101 through 107 Processing sheet with id= 27, first strand: chain 'L' and resid 56 through 59 Processing sheet with id= 28, first strand: chain 'M' and resid 19 through 24 removed outlier: 4.521A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS M 31 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'N' and resid 113 through 116 removed outlier: 6.823A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN N 117 " --> pdb=" O ILE N 133 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 6 through 10 Processing sheet with id= 31, first strand: chain 'P' and resid 14 through 20 Processing sheet with id= 32, first strand: chain 'P' and resid 124 through 131 removed outlier: 4.044A pdb=" N GLN P 125 " --> pdb=" O SER P 141 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG P 127 " --> pdb=" O TYR P 139 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG P 135 " --> pdb=" O ARG P 131 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Q' and resid 79 through 83 Processing sheet with id= 34, first strand: chain 'S' and resid 24 through 31 removed outlier: 4.184A pdb=" N GLU S 6 " --> pdb=" O ILE S 64 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S' and resid 88 through 96 removed outlier: 3.526A pdb=" N TYR S 81 " --> pdb=" O HIS S 88 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASN S 74 " --> pdb=" O ILE S 129 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'T' and resid 72 through 79 Processing sheet with id= 37, first strand: chain 'U' and resid 54 through 58 removed outlier: 6.176A pdb=" N ASN U 101 " --> pdb=" O THR U 14 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR U 16 " --> pdb=" O ASN U 101 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU U 102 " --> pdb=" O THR U 98 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N TRP U 92 " --> pdb=" O TYR U 108 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'V' and resid 79 through 82 removed outlier: 3.503A pdb=" N ALA V 99 " --> pdb=" O ARG V 80 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA V 82 " --> pdb=" O ASP V 97 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASP V 97 " --> pdb=" O ALA V 82 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN V 98 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA V 21 " --> pdb=" O ILE V 36 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP V 56 " --> pdb=" O VAL V 78 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'V' and resid 84 through 87 Processing sheet with id= 40, first strand: chain 'V' and resid 75 through 78 Processing sheet with id= 41, first strand: chain 'W' and resid 63 through 67 removed outlier: 5.830A pdb=" N VAL W 99 " --> pdb=" O LEU W 45 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ARG W 38 " --> pdb=" O ASN W 223 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N HIS W 44 " --> pdb=" O VAL W 217 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL W 217 " --> pdb=" O HIS W 44 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER W 211 " --> pdb=" O ASP W 123 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'W' and resid 136 through 139 removed outlier: 4.500A pdb=" N GLU W 139 " --> pdb=" O SER W 184 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER W 184 " --> pdb=" O GLU W 139 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'W' and resid 216 through 223 removed outlier: 7.005A pdb=" N VAL W 217 " --> pdb=" O ASN W 232 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN W 232 " --> pdb=" O VAL W 217 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ALA W 219 " --> pdb=" O SER W 230 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER W 230 " --> pdb=" O ALA W 219 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TYR W 221 " --> pdb=" O VAL W 228 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL W 228 " --> pdb=" O TYR W 221 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ASN W 223 " --> pdb=" O SER W 226 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'X' and resid 81 through 86 removed outlier: 3.758A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS X 109 " --> pdb=" O ARG X 125 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Y' and resid 72 through 75 Processing sheet with id= 46, first strand: chain 'Y' and resid 86 through 89 removed outlier: 4.354A pdb=" N ALA Y 93 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'Z' and resid 9 through 14 removed outlier: 4.284A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS Z 21 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'Z' and resid 42 through 45 Processing sheet with id= 49, first strand: chain 'b' and resid 204 through 210 removed outlier: 4.612A pdb=" N ARG b 168 " --> pdb=" O ARG b 215 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR b 221 " --> pdb=" O ILE b 172 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU b 171 " --> pdb=" O CYS b 249 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER b 282 " --> pdb=" O SER b 248 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU b 316 " --> pdb=" O VAL b 283 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'd' and resid 48 through 51 removed outlier: 5.161A pdb=" N ASP d 48 " --> pdb=" O LEU d 89 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR d 9 " --> pdb=" O VAL d 109 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 71 through 77 Processing sheet with id= 52, first strand: chain 'f' and resid 63 through 71 removed outlier: 6.390A pdb=" N LYS f 63 " --> pdb=" O ALA f 55 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS f 47 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) removed outlier: 13.003A pdb=" N ARG f 54 " --> pdb=" O GLY f 95 " (cutoff:3.500A) removed outlier: 15.306A pdb=" N GLY f 95 " --> pdb=" O ARG f 54 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LYS f 10 " --> pdb=" O GLU f 33 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU f 29 " --> pdb=" O LEU f 14 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'g' and resid 19 through 24 removed outlier: 4.807A pdb=" N LYS g 19 " --> pdb=" O VAL g 35 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'k' and resid 2 through 5 removed outlier: 4.408A pdb=" N VAL k 55 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR k 22 " --> pdb=" O ARG k 46 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE k 27 " --> pdb=" O LEU k 78 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'm' and resid 282 through 286 removed outlier: 4.203A pdb=" N CYS m 367 " --> pdb=" O PHE m 320 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY m 322 " --> pdb=" O CYS m 367 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE m 362 " --> pdb=" O LEU m 358 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN m 354 " --> pdb=" O ASP m 366 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'p' and resid 46 through 50 removed outlier: 8.535A pdb=" N THR p 46 " --> pdb=" O SER p 58 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER p 58 " --> pdb=" O THR p 46 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE p 54 " --> pdb=" O GLY p 50 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY p 53 " --> pdb=" O GLY p 66 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS p 62 " --> pdb=" O CYS p 57 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'q' and resid 12 through 16 removed outlier: 5.077A pdb=" N THR q 59 " --> pdb=" O VAL q 74 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER q 72 " --> pdb=" O GLN q 61 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'r' and resid 148 through 151 Processing sheet with id= 59, first strand: chain 'r' and resid 190 through 197 removed outlier: 3.667A pdb=" N VAL r 191 " --> pdb=" O HIS r 186 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LYS r 180 " --> pdb=" O ILE r 197 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N VAL r 255 " --> pdb=" O LYS r 181 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA r 257 " --> pdb=" O ASN r 183 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN r 256 " --> pdb=" O THR r 246 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N TYR r 242 " --> pdb=" O LEU r 260 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR r 219 " --> pdb=" O VAL r 245 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE r 220 " --> pdb=" O LYS r 201 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'u' and resid 3 through 6 removed outlier: 4.356A pdb=" N SER u 11 " --> pdb=" O CYS u 6 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'u' and resid 18 through 23 removed outlier: 3.544A pdb=" N ILE u 19 " --> pdb=" O PHE u 31 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LYS u 27 " --> pdb=" O ARG u 23 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'v' and resid 56 through 60 removed outlier: 7.285A pdb=" N SER v 92 " --> pdb=" O GLY v 35 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER v 85 " --> pdb=" O THR v 105 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR v 105 " --> pdb=" O SER v 85 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN v 98 " --> pdb=" O VAL v 118 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ASP v 231 " --> pdb=" O ALA v 119 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE v 186 " --> pdb=" O GLN v 144 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'v' and resid 262 through 266 removed outlier: 5.985A pdb=" N ASN v 262 " --> pdb=" O ARG v 274 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP v 270 " --> pdb=" O ASP v 266 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'v' and resid 204 through 210 No H-bonds generated for sheet with id= 64 Processing sheet with id= 65, first strand: chain 'w' and resid 17 through 23 removed outlier: 5.134A pdb=" N SER w 31 " --> pdb=" O PRO w 18 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'w' and resid 131 through 136 removed outlier: 9.098A pdb=" N LYS w 131 " --> pdb=" O LYS w 144 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU w 140 " --> pdb=" O ASP w 135 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'x' and resid 48 through 53 removed outlier: 3.927A pdb=" N ALA x 48 " --> pdb=" O PHE x 36 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE x 36 " --> pdb=" O ALA x 48 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL x 32 " --> pdb=" O PRO x 52 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'x' and resid 132 through 135 removed outlier: 5.727A pdb=" N ARG x 500 " --> pdb=" O SER x 495 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'x' and resid 148 through 152 removed outlier: 3.631A pdb=" N ALA x 152 " --> pdb=" O ARG x 158 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG x 158 " --> pdb=" O ALA x 152 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS x 180 " --> pdb=" O ILE x 170 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'x' and resid 190 through 194 Processing sheet with id= 71, first strand: chain 'x' and resid 233 through 238 removed outlier: 3.663A pdb=" N SER x 234 " --> pdb=" O SER x 254 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ARG x 250 " --> pdb=" O GLU x 238 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER x 255 " --> pdb=" O THR x 259 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR x 259 " --> pdb=" O SER x 255 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE x 262 " --> pdb=" O TYR x 272 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'x' and resid 282 through 287 removed outlier: 3.718A pdb=" N CYS x 283 " --> pdb=" O GLY x 295 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU x 291 " --> pdb=" O GLY x 287 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER x 296 " --> pdb=" O THR x 300 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR x 300 " --> pdb=" O SER x 296 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'x' and resid 325 through 328 removed outlier: 3.645A pdb=" N ALA x 396 " --> pdb=" O LEU x 385 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'x' and resid 406 through 411 removed outlier: 5.287A pdb=" N TYR x 416 " --> pdb=" O SER x 411 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'x' and resid 425 through 429 Processing sheet with id= 76, first strand: chain 'x' and resid 448 through 453 removed outlier: 3.509A pdb=" N GLN x 449 " --> pdb=" O CYS x 462 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU x 458 " --> pdb=" O SER x 453 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ARG x 457 " --> pdb=" O VAL x 473 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL x 470 " --> pdb=" O SER x 479 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'x' and resid 467 through 470 removed outlier: 3.692A pdb=" N VAL x 480 " --> pdb=" O VAL x 470 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'y' and resid 1 through 4 Processing sheet with id= 79, first strand: chain 'y' and resid 23 through 27 Processing sheet with id= 80, first strand: chain 'y' and resid 69 through 73 Processing sheet with id= 81, first strand: chain 'y' and resid 158 through 162 2805 hydrogen bonds defined for protein. 8343 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2556 hydrogen bonds 4048 hydrogen bond angles 0 basepair planarities 1042 basepair parallelities 1726 stacking parallelities Total time for adding SS restraints: 189.91 Time building geometry restraints manager: 62.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 16867 1.31 - 1.44: 58978 1.44 - 1.56: 67869 1.56 - 1.69: 6662 1.69 - 1.81: 298 Bond restraints: 150674 Sorted by residual: bond pdb=" C PHE B 16 " pdb=" N LEU B 17 " ideal model delta sigma weight residual 1.331 1.199 0.132 1.59e-02 3.96e+03 6.87e+01 bond pdb=" CA ASN V 47 " pdb=" C ASN V 47 " ideal model delta sigma weight residual 1.523 1.461 0.061 1.48e-02 4.57e+03 1.72e+01 bond pdb=" CB VAL B 114 " pdb=" CG1 VAL B 114 " ideal model delta sigma weight residual 1.521 1.392 0.129 3.30e-02 9.18e+02 1.53e+01 bond pdb=" CG1 ILE G 36 " pdb=" CD1 ILE G 36 " ideal model delta sigma weight residual 1.513 1.402 0.111 3.90e-02 6.57e+02 8.11e+00 bond pdb=" C5 G 12898 " pdb=" C6 G 12898 " ideal model delta sigma weight residual 1.419 1.362 0.057 2.00e-02 2.50e+03 8.02e+00 ... (remaining 150669 not shown) Histogram of bond angle deviations from ideal: 93.88 - 103.01: 7110 103.01 - 112.14: 91269 112.14 - 121.28: 82779 121.28 - 130.41: 36818 130.41 - 139.54: 1668 Bond angle restraints: 219644 Sorted by residual: angle pdb=" C LEU V 46 " pdb=" N ASN V 47 " pdb=" CA ASN V 47 " ideal model delta sigma weight residual 122.65 107.46 15.19 1.60e+00 3.91e-01 9.01e+01 angle pdb=" C2' G 12376 " pdb=" C1' G 12376 " pdb=" N9 G 12376 " ideal model delta sigma weight residual 112.00 123.70 -11.70 1.50e+00 4.44e-01 6.08e+01 angle pdb=" C THR H 188 " pdb=" N GLU H 189 " pdb=" CA GLU H 189 " ideal model delta sigma weight residual 121.70 131.28 -9.58 1.80e+00 3.09e-01 2.83e+01 angle pdb=" O4' G 12376 " pdb=" C1' G 12376 " pdb=" N9 G 12376 " ideal model delta sigma weight residual 108.50 116.44 -7.94 1.50e+00 4.44e-01 2.80e+01 angle pdb=" CB ARG D 23 " pdb=" CG ARG D 23 " pdb=" CD ARG D 23 " ideal model delta sigma weight residual 111.30 123.45 -12.15 2.30e+00 1.89e-01 2.79e+01 ... (remaining 219639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 86366 36.00 - 71.99: 8066 71.99 - 107.99: 849 107.99 - 143.98: 32 143.98 - 179.98: 87 Dihedral angle restraints: 95400 sinusoidal: 70073 harmonic: 25327 Sorted by residual: dihedral pdb=" C4' G 13340 " pdb=" C3' G 13340 " pdb=" C2' G 13340 " pdb=" C1' G 13340 " ideal model delta sinusoidal sigma weight residual -35.00 31.68 -66.68 1 8.00e+00 1.56e-02 9.06e+01 dihedral pdb=" C5' G 13340 " pdb=" C4' G 13340 " pdb=" C3' G 13340 " pdb=" O3' G 13340 " ideal model delta sinusoidal sigma weight residual 147.00 80.82 66.18 1 8.00e+00 1.56e-02 8.94e+01 dihedral pdb=" O4' U 2 156 " pdb=" C1' U 2 156 " pdb=" N1 U 2 156 " pdb=" C2 U 2 156 " ideal model delta sinusoidal sigma weight residual 200.00 20.12 179.88 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 95397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.215: 27148 0.215 - 0.430: 72 0.430 - 0.646: 2 0.646 - 0.861: 0 0.861 - 1.076: 1 Chirality restraints: 27223 Sorted by residual: chirality pdb=" C1' G 12376 " pdb=" O4' G 12376 " pdb=" C2' G 12376 " pdb=" N9 G 12376 " both_signs ideal model delta sigma weight residual False 2.46 1.38 1.08 2.00e-01 2.50e+01 2.89e+01 chirality pdb=" CB ILE G 36 " pdb=" CA ILE G 36 " pdb=" CG1 ILE G 36 " pdb=" CG2 ILE G 36 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.51 2.00e-01 2.50e+01 6.43e+00 chirality pdb=" C3' G 12753 " pdb=" C4' G 12753 " pdb=" O3' G 12753 " pdb=" C2' G 12753 " both_signs ideal model delta sigma weight residual False -2.48 -2.03 -0.45 2.00e-01 2.50e+01 5.00e+00 ... (remaining 27220 not shown) Planarity restraints: 15459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP x 494 " 0.027 2.00e-02 2.50e+03 3.21e-02 2.58e+01 pdb=" CG TRP x 494 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 TRP x 494 " 0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP x 494 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP x 494 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP x 494 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP x 494 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP x 494 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP x 494 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP x 494 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP w 158 " -0.014 2.00e-02 2.50e+03 2.75e-02 1.90e+01 pdb=" CG TRP w 158 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP w 158 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP w 158 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP w 158 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP w 158 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP w 158 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP w 158 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP w 158 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP w 158 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 12969 " 0.052 2.00e-02 2.50e+03 2.58e-02 1.83e+01 pdb=" N9 A 12969 " -0.066 2.00e-02 2.50e+03 pdb=" C8 A 12969 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A 12969 " 0.006 2.00e-02 2.50e+03 pdb=" C5 A 12969 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A 12969 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A 12969 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A 12969 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A 12969 " -0.000 2.00e-02 2.50e+03 pdb=" N3 A 12969 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A 12969 " -0.005 2.00e-02 2.50e+03 ... (remaining 15456 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 3239 2.61 - 3.19: 118742 3.19 - 3.76: 273921 3.76 - 4.33: 375496 4.33 - 4.90: 528655 Nonbonded interactions: 1300053 Sorted by model distance: nonbonded pdb=" OE2 GLU 7 57 " pdb=" OH TYR 7 69 " model vdw 2.043 2.440 nonbonded pdb=" O2' U 12542 " pdb=" O5' U 12543 " model vdw 2.056 2.440 nonbonded pdb=" OP2 G 2 75 " pdb=" OH TYR Y 74 " model vdw 2.061 2.440 nonbonded pdb=" O2' U 1 976 " pdb=" O2 C 1 977 " model vdw 2.070 2.440 nonbonded pdb=" OG1 THR M 113 " pdb=" OE1 GLU M 116 " model vdw 2.073 2.440 ... (remaining 1300048 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=0.00 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: 11.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 31.070 Check model and map are aligned: 1.520 Set scattering table: 0.980 Process input model: 484.070 Find NCS groups from input model: 3.230 Set up NCS constraints: 0.340 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:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 544.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 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 : 0.010 0.132 150674 Z= 0.600 Angle : 0.887 15.189 219644 Z= 0.464 Chirality : 0.052 1.076 27223 Planarity : 0.006 0.076 15459 Dihedral : 22.358 179.978 79016 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.62 % Favored : 95.37 % Rotamer: Outliers : 0.01 % Allowed : 0.59 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.09), residues: 8600 helix: -0.31 (0.09), residues: 3059 sheet: -0.87 (0.14), residues: 1259 loop : -0.79 (0.09), residues: 4282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.004 TRP x 494 HIS 0.035 0.002 HIS v 276 PHE 0.046 0.003 PHE B 199 TYR 0.053 0.003 TYR m 323 ARG 0.036 0.001 ARG S 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1340 residues out of total 7453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1339 time to evaluate : 7.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LYS cc_start: 0.7682 (pttm) cc_final: 0.7147 (pptt) REVERT: D 206 GLN cc_start: 0.7910 (mt0) cc_final: 0.7642 (mt0) REVERT: E 29 LYS cc_start: 0.7742 (mptt) cc_final: 0.7535 (mmtt) REVERT: G 217 THR cc_start: 0.9090 (p) cc_final: 0.8867 (p) REVERT: J 35 LYS cc_start: 0.7875 (tmtt) cc_final: 0.7533 (tptp) REVERT: J 41 SER cc_start: 0.8768 (p) cc_final: 0.8555 (p) REVERT: J 49 LYS cc_start: 0.8106 (mttt) cc_final: 0.7903 (mtmm) REVERT: N 41 ARG cc_start: 0.8512 (ptp-110) cc_final: 0.8188 (ptp-170) REVERT: O 40 GLU cc_start: 0.7407 (tp30) cc_final: 0.7140 (tp30) REVERT: Q 21 SER cc_start: 0.8476 (t) cc_final: 0.8198 (t) REVERT: R 69 SER cc_start: 0.8604 (m) cc_final: 0.8400 (m) REVERT: S 166 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7924 (mtmm) REVERT: T 131 GLN cc_start: 0.8724 (mm110) cc_final: 0.8347 (mm110) REVERT: T 146 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.8088 (p0) REVERT: U 88 GLN cc_start: 0.8241 (mp10) cc_final: 0.7507 (tm-30) REVERT: V 27 ASP cc_start: 0.8493 (p0) cc_final: 0.8158 (p0) REVERT: V 29 SER cc_start: 0.8647 (p) cc_final: 0.8337 (p) REVERT: V 109 MET cc_start: 0.8232 (mmp) cc_final: 0.7942 (mpp) REVERT: W 174 LYS cc_start: 0.7522 (mppt) cc_final: 0.7204 (mptt) REVERT: Y 114 ASP cc_start: 0.7548 (m-30) cc_final: 0.7197 (m-30) REVERT: a 120 ASN cc_start: 0.8430 (t0) cc_final: 0.8100 (t0) REVERT: b 226 ASP cc_start: 0.7793 (p0) cc_final: 0.7566 (p0) REVERT: b 270 LEU cc_start: 0.8340 (tt) cc_final: 0.8068 (tm) REVERT: b 615 ARG cc_start: 0.7246 (ptm-80) cc_final: 0.6951 (ptm160) REVERT: e 123 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7892 (mptm) REVERT: f 63 LYS cc_start: 0.8824 (ttmm) cc_final: 0.8185 (tttm) REVERT: h 19 SER cc_start: 0.8183 (m) cc_final: 0.7386 (m) REVERT: h 107 LYS cc_start: 0.8448 (tptt) cc_final: 0.8127 (ttmm) REVERT: l 21 ARG cc_start: 0.6421 (tpt170) cc_final: 0.6129 (tpm170) REVERT: m 209 LYS cc_start: 0.8003 (mmtt) cc_final: 0.7557 (tppt) REVERT: r 62 ARG cc_start: 0.7620 (ttp80) cc_final: 0.7268 (ttt90) REVERT: r 169 GLU cc_start: 0.7911 (tt0) cc_final: 0.7707 (tt0) REVERT: u 74 ARG cc_start: 0.7480 (ttt90) cc_final: 0.7229 (ttp80) REVERT: u 104 GLU cc_start: 0.6367 (pp20) cc_final: 0.5995 (tm-30) REVERT: w 115 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7616 (mt-10) REVERT: w 140 GLU cc_start: 0.7291 (mm-30) cc_final: 0.7025 (mm-30) REVERT: w 192 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7820 (mt-10) REVERT: z 30 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7492 (tt0) outliers start: 1 outliers final: 1 residues processed: 1340 average time/residue: 2.1736 time to fit residues: 4129.2499 Evaluate side-chains 1065 residues out of total 7453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1063 time to evaluate : 7.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain T residue 146 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1181 random chunks: chunk 997 optimal weight: 2.9990 chunk 895 optimal weight: 0.9980 chunk 496 optimal weight: 0.8980 chunk 305 optimal weight: 8.9990 chunk 603 optimal weight: 6.9990 chunk 478 optimal weight: 0.9990 chunk 925 optimal weight: 7.9990 chunk 358 optimal weight: 0.9990 chunk 562 optimal weight: 5.9990 chunk 688 optimal weight: 8.9990 chunk 1072 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN B 319 ASN D 63 GLN F 157 ASN G 77 GLN G 137 ASN G 192 GLN H 102 ASN ** J 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 HIS L 102 GLN ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 GLN S 122 HIS S 138 GLN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 ASN ** c 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN d 43 HIS d 80 ASN g 11 ASN h 59 ASN h 104 GLN j 48 ASN ** k 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 40 GLN l 4 GLN ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 62 GLN q 65 GLN ** r 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 53 ASN ** v 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 180 HIS ** x 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 150674 Z= 0.158 Angle : 0.600 10.087 219644 Z= 0.311 Chirality : 0.037 0.379 27223 Planarity : 0.005 0.062 15459 Dihedral : 23.574 179.951 61286 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.91 % Allowed : 9.69 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.09), residues: 8600 helix: 0.67 (0.09), residues: 3120 sheet: -0.67 (0.14), residues: 1230 loop : -0.58 (0.09), residues: 4250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP x 494 HIS 0.013 0.001 HIS v 276 PHE 0.025 0.001 PHE F 229 TYR 0.030 0.001 TYR b 420 ARG 0.009 0.000 ARG F 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1361 residues out of total 7453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1219 time to evaluate : 7.613 Fit side-chains revert: symmetry clash REVERT: 7 92 ILE cc_start: 0.9011 (mm) cc_final: 0.8788 (mp) REVERT: A 109 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7550 (tt0) REVERT: A 198 LYS cc_start: 0.7554 (pttm) cc_final: 0.7034 (pptt) REVERT: A 204 MET cc_start: 0.4886 (OUTLIER) cc_final: 0.1814 (mmm) REVERT: B 34 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7820 (tptp) REVERT: B 235 THR cc_start: 0.8561 (m) cc_final: 0.8357 (p) REVERT: D 31 TYR cc_start: 0.6546 (m-80) cc_final: 0.6309 (m-10) REVERT: D 206 GLN cc_start: 0.7928 (mt0) cc_final: 0.7590 (mt0) REVERT: E 62 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8324 (m) REVERT: E 164 SER cc_start: 0.8676 (p) cc_final: 0.8399 (t) REVERT: F 240 VAL cc_start: 0.8755 (t) cc_final: 0.8526 (p) REVERT: G 111 LYS cc_start: 0.8287 (tptt) cc_final: 0.7814 (tmmt) REVERT: H 1 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.7151 (ptm) REVERT: I 103 ASN cc_start: 0.7597 (p0) cc_final: 0.7391 (p0) REVERT: J 35 LYS cc_start: 0.7749 (tmtt) cc_final: 0.7368 (tptp) REVERT: J 39 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7379 (tm130) REVERT: J 41 SER cc_start: 0.8599 (p) cc_final: 0.8382 (p) REVERT: J 60 ARG cc_start: 0.6766 (tpp80) cc_final: 0.6506 (tpp80) REVERT: M 37 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7200 (mt-10) REVERT: N 41 ARG cc_start: 0.8415 (ptp-110) cc_final: 0.8146 (ptp-170) REVERT: O 40 GLU cc_start: 0.7306 (tp30) cc_final: 0.7077 (tp30) REVERT: Q 21 SER cc_start: 0.8430 (t) cc_final: 0.8142 (t) REVERT: R 68 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: S 166 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7858 (mtmm) REVERT: T 131 GLN cc_start: 0.8659 (mm110) cc_final: 0.8254 (mm110) REVERT: U 25 ASN cc_start: 0.7052 (OUTLIER) cc_final: 0.6512 (t0) REVERT: U 88 GLN cc_start: 0.8264 (mp10) cc_final: 0.7503 (tm-30) REVERT: V 27 ASP cc_start: 0.8466 (p0) cc_final: 0.8114 (p0) REVERT: V 29 SER cc_start: 0.8627 (p) cc_final: 0.8292 (p) REVERT: W 60 TRP cc_start: 0.7234 (OUTLIER) cc_final: 0.6545 (p90) REVERT: X 129 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7932 (p0) REVERT: Y 114 ASP cc_start: 0.7321 (m-30) cc_final: 0.7042 (m-30) REVERT: Y 120 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7799 (mp-120) REVERT: Z 31 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7119 (pt0) REVERT: a 120 ASN cc_start: 0.8392 (t0) cc_final: 0.8066 (t0) REVERT: a 135 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8489 (tp30) REVERT: b 226 ASP cc_start: 0.7689 (p0) cc_final: 0.7485 (p0) REVERT: b 270 LEU cc_start: 0.8208 (tt) cc_final: 0.7946 (tm) REVERT: b 394 ASN cc_start: 0.7699 (p0) cc_final: 0.7497 (p0) REVERT: b 647 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7832 (ptm-80) REVERT: e 78 ASN cc_start: 0.8420 (p0) cc_final: 0.7920 (p0) REVERT: e 81 ASP cc_start: 0.7660 (m-30) cc_final: 0.7117 (m-30) REVERT: e 88 HIS cc_start: 0.8003 (m90) cc_final: 0.7790 (m-70) REVERT: e 123 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7736 (mptm) REVERT: f 49 ILE cc_start: 0.9076 (mt) cc_final: 0.8756 (mm) REVERT: f 63 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8196 (tttm) REVERT: h 19 SER cc_start: 0.7883 (m) cc_final: 0.7523 (m) REVERT: h 105 ARG cc_start: 0.8710 (tmm-80) cc_final: 0.8291 (tmm160) REVERT: i 60 LEU cc_start: 0.8519 (mt) cc_final: 0.8172 (mp) REVERT: i 66 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7636 (mm-30) REVERT: j 25 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7698 (tmm-80) REVERT: m 249 GLU cc_start: 0.7268 (tp30) cc_final: 0.7051 (tt0) REVERT: m 389 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7090 (ttm-80) REVERT: m 456 ASP cc_start: 0.8007 (m-30) cc_final: 0.7719 (m-30) REVERT: r 169 GLU cc_start: 0.7676 (tt0) cc_final: 0.7465 (tt0) REVERT: u 74 ARG cc_start: 0.7468 (ttt90) cc_final: 0.7232 (ttp80) REVERT: u 104 GLU cc_start: 0.6307 (pp20) cc_final: 0.5876 (tm-30) REVERT: v 80 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: v 104 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7915 (mtm180) REVERT: w 111 MET cc_start: 0.6621 (tmm) cc_final: 0.6350 (tmm) REVERT: w 115 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7554 (mt-10) REVERT: y 1 MET cc_start: 0.5746 (mtt) cc_final: 0.4756 (mmp) REVERT: z 30 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7321 (tt0) outliers start: 142 outliers final: 35 residues processed: 1273 average time/residue: 2.0680 time to fit residues: 3806.2152 Evaluate side-chains 1135 residues out of total 7453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1085 time to evaluate : 7.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 61 MET Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain S residue 130 GLU Chi-restraints excluded: chain U residue 25 ASN Chi-restraints excluded: chain W residue 18 LYS Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain X residue 129 ASP Chi-restraints excluded: chain Y residue 120 GLN Chi-restraints excluded: chain Z residue 31 GLU Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 322 CYS Chi-restraints excluded: chain b residue 647 ARG Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 104 LEU Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 262 CYS Chi-restraints excluded: chain m residue 389 ARG Chi-restraints excluded: chain q residue 72 SER Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain u residue 68 THR Chi-restraints excluded: chain v residue 80 GLU Chi-restraints excluded: chain v residue 104 ARG Chi-restraints excluded: chain v residue 140 MET Chi-restraints excluded: chain v residue 218 LEU Chi-restraints excluded: chain w residue 20 VAL Chi-restraints excluded: chain w residue 195 GLN Chi-restraints excluded: chain z residue 6 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1181 random chunks: chunk 596 optimal weight: 4.9990 chunk 332 optimal weight: 0.0670 chunk 892 optimal weight: 0.6980 chunk 730 optimal weight: 3.9990 chunk 295 optimal weight: 10.0000 chunk 1074 optimal weight: 7.9990 chunk 1160 optimal weight: 9.9990 chunk 956 optimal weight: 8.9990 chunk 1065 optimal weight: 4.9990 chunk 366 optimal weight: 9.9990 chunk 861 optimal weight: 10.0000 overall best weight: 2.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN C 18 ASN D 63 GLN F 157 ASN G 77 GLN G 79 GLN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 ASN ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 ASN S 138 GLN T 146 ASN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 ASN Z 128 GLN ** c 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN d 80 ASN g 11 ASN h 59 ASN ** k 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 25 GLN q 65 GLN ** r 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 53 ASN ** u 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 280 GLN w 25 ASN x 241 HIS x 321 HIS ** y 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 150674 Z= 0.252 Angle : 0.599 10.674 219644 Z= 0.309 Chirality : 0.038 0.388 27223 Planarity : 0.004 0.056 15459 Dihedral : 23.378 179.988 61284 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.60 % Allowed : 13.39 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.09), residues: 8600 helix: 0.97 (0.09), residues: 3122 sheet: -0.55 (0.14), residues: 1209 loop : -0.53 (0.09), residues: 4269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP b 427 HIS 0.009 0.001 HIS B 163 PHE 0.027 0.002 PHE F 229 TYR 0.031 0.002 TYR b 420 ARG 0.007 0.000 ARG u 113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1328 residues out of total 7453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1134 time to evaluate : 7.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: A 198 LYS cc_start: 0.7577 (pttm) cc_final: 0.7051 (pptt) REVERT: A 204 MET cc_start: 0.4808 (OUTLIER) cc_final: 0.1664 (mmm) REVERT: B 10 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7410 (ttt90) REVERT: B 34 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7781 (tptp) REVERT: C 145 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8554 (tp) REVERT: D 30 TYR cc_start: 0.5386 (p90) cc_final: 0.5118 (p90) REVERT: D 206 GLN cc_start: 0.7919 (mt0) cc_final: 0.7482 (mt0) REVERT: E 164 SER cc_start: 0.8713 (p) cc_final: 0.8402 (t) REVERT: G 111 LYS cc_start: 0.8370 (tptt) cc_final: 0.7881 (tmmt) REVERT: H 1 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7123 (ptm) REVERT: H 143 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: I 96 TYR cc_start: 0.7091 (t80) cc_final: 0.6670 (t80) REVERT: I 103 ASN cc_start: 0.7707 (p0) cc_final: 0.7486 (p0) REVERT: J 35 LYS cc_start: 0.7743 (tmtt) cc_final: 0.7346 (tptp) REVERT: J 41 SER cc_start: 0.8630 (p) cc_final: 0.8419 (p) REVERT: J 89 TYR cc_start: 0.6128 (m-10) cc_final: 0.5836 (m-10) REVERT: J 91 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8214 (pp) REVERT: J 167 TYR cc_start: 0.7620 (m-80) cc_final: 0.7017 (m-80) REVERT: L 169 THR cc_start: 0.9052 (t) cc_final: 0.8804 (t) REVERT: M 37 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7279 (mt-10) REVERT: M 62 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7620 (mp10) REVERT: N 41 ARG cc_start: 0.8446 (ptp-110) cc_final: 0.8171 (ptp-170) REVERT: O 40 GLU cc_start: 0.7434 (tp30) cc_final: 0.7197 (tp30) REVERT: Q 21 SER cc_start: 0.8433 (t) cc_final: 0.8151 (t) REVERT: Q 50 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7604 (mmtt) REVERT: R 68 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8106 (tm-30) REVERT: S 166 LYS cc_start: 0.8114 (mtmm) cc_final: 0.7907 (mtmm) REVERT: T 76 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.6692 (pt) REVERT: T 131 GLN cc_start: 0.8646 (mm110) cc_final: 0.8251 (mm110) REVERT: U 88 GLN cc_start: 0.8235 (mp10) cc_final: 0.7501 (tm-30) REVERT: V 27 ASP cc_start: 0.8403 (p0) cc_final: 0.8044 (p0) REVERT: V 29 SER cc_start: 0.8605 (p) cc_final: 0.8179 (p) REVERT: W 60 TRP cc_start: 0.7401 (OUTLIER) cc_final: 0.6697 (p90) REVERT: W 214 LYS cc_start: 0.6334 (OUTLIER) cc_final: 0.5473 (pptt) REVERT: X 129 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7839 (p0) REVERT: Y 114 ASP cc_start: 0.7403 (m-30) cc_final: 0.7071 (m-30) REVERT: Y 120 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7787 (mp-120) REVERT: a 58 MET cc_start: 0.5451 (OUTLIER) cc_final: 0.5086 (ptt) REVERT: a 120 ASN cc_start: 0.8397 (t0) cc_final: 0.8093 (t0) REVERT: a 135 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8494 (tp30) REVERT: b 270 LEU cc_start: 0.8293 (tt) cc_final: 0.7999 (tm) REVERT: b 394 ASN cc_start: 0.7714 (p0) cc_final: 0.7507 (p0) REVERT: e 78 ASN cc_start: 0.8514 (p0) cc_final: 0.7881 (p0) REVERT: e 81 ASP cc_start: 0.7718 (m-30) cc_final: 0.7155 (m-30) REVERT: e 123 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7781 (mptm) REVERT: f 14 LEU cc_start: 0.9074 (mt) cc_final: 0.8738 (mt) REVERT: f 49 ILE cc_start: 0.9108 (mt) cc_final: 0.8789 (mm) REVERT: f 63 LYS cc_start: 0.8678 (ttmm) cc_final: 0.8216 (tttm) REVERT: h 19 SER cc_start: 0.7866 (m) cc_final: 0.7548 (m) REVERT: h 105 ARG cc_start: 0.8692 (tmm-80) cc_final: 0.8249 (tmm160) REVERT: i 60 LEU cc_start: 0.8643 (mt) cc_final: 0.8282 (mp) REVERT: i 66 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7660 (mm-30) REVERT: j 25 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7722 (tmm-80) REVERT: k 8 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7938 (mm) REVERT: m 151 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6386 (ttp-110) REVERT: m 249 GLU cc_start: 0.7287 (tp30) cc_final: 0.7038 (tt0) REVERT: m 389 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7030 (ttm-80) REVERT: m 456 ASP cc_start: 0.8036 (m-30) cc_final: 0.7707 (m-30) REVERT: p 73 THR cc_start: 0.8743 (m) cc_final: 0.8490 (m) REVERT: r 5 ASP cc_start: 0.6191 (m-30) cc_final: 0.5966 (m-30) REVERT: r 8 GLU cc_start: 0.7445 (mp0) cc_final: 0.6916 (mp0) REVERT: r 69 GLU cc_start: 0.7578 (mp0) cc_final: 0.7369 (mp0) REVERT: u 74 ARG cc_start: 0.7497 (ttt90) cc_final: 0.7247 (ttp80) REVERT: u 104 GLU cc_start: 0.6355 (pp20) cc_final: 0.6029 (tm-30) REVERT: u 117 GLU cc_start: 0.5934 (pm20) cc_final: 0.5557 (tp30) REVERT: v 80 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7842 (tp30) REVERT: w 102 GLU cc_start: 0.6701 (tp30) cc_final: 0.6472 (tp30) REVERT: w 115 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7621 (mt-10) REVERT: w 140 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7039 (mm-30) REVERT: x 272 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.7399 (p90) REVERT: x 470 VAL cc_start: 0.8697 (OUTLIER) cc_final: 0.8335 (t) REVERT: y 1 MET cc_start: 0.5596 (mtt) cc_final: 0.4817 (mmp) REVERT: z 30 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7512 (tt0) outliers start: 194 outliers final: 81 residues processed: 1224 average time/residue: 2.0249 time to fit residues: 3590.5412 Evaluate side-chains 1168 residues out of total 7453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1063 time to evaluate : 7.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 61 MET Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 173 MET Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain Q residue 50 LYS Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 130 GLU Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain T residue 79 MET Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 214 LYS Chi-restraints excluded: chain X residue 129 ASP Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain Y residue 120 GLN Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain b residue 40 THR Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 78 LYS Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain h residue 101 THR Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 14 LEU Chi-restraints excluded: chain m residue 151 ARG Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 262 CYS Chi-restraints excluded: chain m residue 316 ILE Chi-restraints excluded: chain m residue 329 SER Chi-restraints excluded: chain m residue 389 ARG Chi-restraints excluded: chain q residue 72 SER Chi-restraints excluded: chain q residue 106 LEU Chi-restraints excluded: chain r residue 37 GLU Chi-restraints excluded: chain r residue 157 VAL Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain s residue 57 LYS Chi-restraints excluded: chain s residue 69 MET Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain u residue 68 THR Chi-restraints excluded: chain v residue 80 GLU Chi-restraints excluded: chain v residue 140 MET Chi-restraints excluded: chain v residue 218 LEU Chi-restraints excluded: chain w residue 187 LEU Chi-restraints excluded: chain w residue 195 GLN Chi-restraints excluded: chain x residue 207 ASP Chi-restraints excluded: chain x residue 212 LEU Chi-restraints excluded: chain x residue 272 TYR Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 470 VAL Chi-restraints excluded: chain x residue 488 GLU Chi-restraints excluded: chain y residue 24 CYS Chi-restraints excluded: chain y residue 173 LEU Chi-restraints excluded: chain z residue 6 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1181 random chunks: chunk 1061 optimal weight: 5.9990 chunk 807 optimal weight: 4.9990 chunk 557 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 512 optimal weight: 1.9990 chunk 721 optimal weight: 20.0000 chunk 1078 optimal weight: 10.0000 chunk 1141 optimal weight: 2.9990 chunk 563 optimal weight: 1.9990 chunk 1021 optimal weight: 2.9990 chunk 307 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 ASN F 157 ASN G 77 GLN G 79 GLN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 114 HIS S 138 GLN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 ASN b 351 GLN ** c 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN d 80 ASN e 88 HIS g 11 ASN h 59 ASN ** k 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 25 GLN q 65 GLN ** r 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 53 ASN ** u 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 25 ASN w 180 ASN x 407 HIS y 145 ASN y 187 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 150674 Z= 0.221 Angle : 0.576 10.223 219644 Z= 0.298 Chirality : 0.037 0.377 27223 Planarity : 0.004 0.054 15459 Dihedral : 23.318 179.895 61284 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.95 % Allowed : 15.00 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.09), residues: 8600 helix: 1.14 (0.09), residues: 3133 sheet: -0.52 (0.14), residues: 1219 loop : -0.46 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 427 HIS 0.009 0.001 HIS e 88 PHE 0.026 0.001 PHE F 229 TYR 0.029 0.002 TYR b 420 ARG 0.009 0.000 ARG J 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1335 residues out of total 7453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1115 time to evaluate : 7.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7479 (tt0) REVERT: A 198 LYS cc_start: 0.7610 (pttm) cc_final: 0.7091 (pptt) REVERT: A 204 MET cc_start: 0.4934 (OUTLIER) cc_final: 0.1808 (mmm) REVERT: B 34 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7770 (tptp) REVERT: B 308 MET cc_start: 0.8017 (mtm) cc_final: 0.7795 (mtm) REVERT: C 145 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8573 (tp) REVERT: D 183 TRP cc_start: 0.8451 (t60) cc_final: 0.8203 (t60) REVERT: D 206 GLN cc_start: 0.7876 (mt0) cc_final: 0.7544 (mt0) REVERT: E 164 SER cc_start: 0.8693 (p) cc_final: 0.8397 (t) REVERT: G 111 LYS cc_start: 0.8301 (tptt) cc_final: 0.7835 (tmmt) REVERT: H 1 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7214 (ptm) REVERT: H 143 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: H 166 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7771 (ttm170) REVERT: I 14 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.6760 (ttm-80) REVERT: J 35 LYS cc_start: 0.7747 (tmtt) cc_final: 0.7385 (tptp) REVERT: J 89 TYR cc_start: 0.6127 (m-10) cc_final: 0.5913 (m-10) REVERT: J 91 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8233 (pp) REVERT: J 167 TYR cc_start: 0.7633 (m-80) cc_final: 0.7077 (m-80) REVERT: L 169 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8762 (t) REVERT: M 37 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: M 62 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: N 41 ARG cc_start: 0.8453 (ptp-110) cc_final: 0.8170 (ptp-170) REVERT: O 40 GLU cc_start: 0.7446 (tp30) cc_final: 0.7212 (tp30) REVERT: O 87 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8375 (mtt) REVERT: P 75 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8184 (pt0) REVERT: Q 21 SER cc_start: 0.8421 (t) cc_final: 0.8141 (t) REVERT: Q 50 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7605 (mmtt) REVERT: R 68 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: R 86 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7335 (tp30) REVERT: S 53 LYS cc_start: 0.7641 (tptp) cc_final: 0.7245 (tmtm) REVERT: S 166 LYS cc_start: 0.8093 (mtmm) cc_final: 0.7880 (mtmm) REVERT: T 76 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.6661 (pt) REVERT: T 87 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.7110 (tttm) REVERT: T 131 GLN cc_start: 0.8623 (mm110) cc_final: 0.8188 (mm110) REVERT: U 25 ASN cc_start: 0.6936 (OUTLIER) cc_final: 0.6455 (t0) REVERT: U 88 GLN cc_start: 0.8240 (mp10) cc_final: 0.7597 (tm-30) REVERT: V 27 ASP cc_start: 0.8370 (p0) cc_final: 0.8013 (p0) REVERT: V 29 SER cc_start: 0.8596 (p) cc_final: 0.8176 (p) REVERT: W 60 TRP cc_start: 0.7497 (OUTLIER) cc_final: 0.6772 (p90) REVERT: X 129 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7773 (p0) REVERT: X 130 TYR cc_start: 0.8038 (m-80) cc_final: 0.7741 (m-80) REVERT: Y 114 ASP cc_start: 0.7390 (m-30) cc_final: 0.7090 (m-30) REVERT: Y 120 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7715 (mp-120) REVERT: a 58 MET cc_start: 0.5446 (OUTLIER) cc_final: 0.5082 (ptt) REVERT: a 120 ASN cc_start: 0.8388 (t0) cc_final: 0.8073 (t0) REVERT: a 130 VAL cc_start: 0.9061 (m) cc_final: 0.8854 (m) REVERT: a 135 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8449 (tp30) REVERT: b 270 LEU cc_start: 0.8291 (tt) cc_final: 0.7995 (tm) REVERT: b 466 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7299 (tt0) REVERT: e 78 ASN cc_start: 0.8539 (p0) cc_final: 0.7658 (p0) REVERT: e 81 ASP cc_start: 0.7708 (m-30) cc_final: 0.7225 (m-30) REVERT: e 123 LYS cc_start: 0.8076 (mmtt) cc_final: 0.7787 (mptm) REVERT: f 14 LEU cc_start: 0.9060 (mt) cc_final: 0.8710 (mt) REVERT: f 48 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7323 (mmp80) REVERT: f 49 ILE cc_start: 0.9101 (mt) cc_final: 0.8796 (mm) REVERT: f 63 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8227 (tttm) REVERT: g 37 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8286 (mtpm) REVERT: h 105 ARG cc_start: 0.8671 (tmm-80) cc_final: 0.8207 (tmm160) REVERT: i 60 LEU cc_start: 0.8631 (mt) cc_final: 0.8283 (mp) REVERT: i 66 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7686 (mm-30) REVERT: j 25 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7659 (tmm-80) REVERT: k 8 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7922 (mm) REVERT: m 151 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6402 (ttp-110) REVERT: m 249 GLU cc_start: 0.7303 (tp30) cc_final: 0.7046 (tt0) REVERT: m 389 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.7009 (ttm-80) REVERT: m 456 ASP cc_start: 0.8042 (m-30) cc_final: 0.7694 (m-30) REVERT: p 73 THR cc_start: 0.8731 (m) cc_final: 0.8467 (m) REVERT: u 74 ARG cc_start: 0.7510 (ttt90) cc_final: 0.7231 (ttp80) REVERT: u 104 GLU cc_start: 0.6465 (pp20) cc_final: 0.6140 (tm-30) REVERT: u 117 GLU cc_start: 0.5936 (pm20) cc_final: 0.5560 (tp30) REVERT: v 80 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7841 (tp30) REVERT: w 102 GLU cc_start: 0.6640 (tp30) cc_final: 0.6346 (tp30) REVERT: w 111 MET cc_start: 0.6561 (tmm) cc_final: 0.6167 (tmm) REVERT: w 115 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7625 (mt-10) REVERT: w 140 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7055 (mm-30) REVERT: w 177 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6177 (mtm180) REVERT: x 272 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.7257 (p90) REVERT: x 432 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6905 (mmm160) REVERT: x 470 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8386 (t) REVERT: y 1 MET cc_start: 0.5517 (mtt) cc_final: 0.4846 (mmp) outliers start: 220 outliers final: 101 residues processed: 1237 average time/residue: 2.0467 time to fit residues: 3685.3016 Evaluate side-chains 1199 residues out of total 7453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1063 time to evaluate : 7.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 61 MET Chi-restraints excluded: chain 7 residue 98 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 173 MET Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain Q residue 50 LYS Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain U residue 25 ASN Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 98 ASN Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain X residue 129 ASP Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain Y residue 120 GLN Chi-restraints excluded: chain Z residue 30 ASP Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain b residue 40 THR Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain b residue 466 GLU Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 78 LYS Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 48 ARG Chi-restraints excluded: chain g residue 37 LYS Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain h residue 101 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 14 LEU Chi-restraints excluded: chain l residue 46 ARG Chi-restraints excluded: chain m residue 151 ARG Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 262 CYS Chi-restraints excluded: chain m residue 329 SER Chi-restraints excluded: chain m residue 340 VAL Chi-restraints excluded: chain m residue 389 ARG Chi-restraints excluded: chain p residue 89 MET Chi-restraints excluded: chain q residue 72 SER Chi-restraints excluded: chain q residue 106 LEU Chi-restraints excluded: chain r residue 157 VAL Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain s residue 57 LYS Chi-restraints excluded: chain s residue 69 MET Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain u residue 68 THR Chi-restraints excluded: chain v residue 80 GLU Chi-restraints excluded: chain v residue 140 MET Chi-restraints excluded: chain v residue 199 VAL Chi-restraints excluded: chain v residue 218 LEU Chi-restraints excluded: chain w residue 20 VAL Chi-restraints excluded: chain w residue 67 SER Chi-restraints excluded: chain w residue 159 LEU Chi-restraints excluded: chain w residue 177 ARG Chi-restraints excluded: chain w residue 187 LEU Chi-restraints excluded: chain w residue 195 GLN Chi-restraints excluded: chain x residue 207 ASP Chi-restraints excluded: chain x residue 212 LEU Chi-restraints excluded: chain x residue 272 TYR Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 432 ARG Chi-restraints excluded: chain x residue 470 VAL Chi-restraints excluded: chain x residue 491 THR Chi-restraints excluded: chain y residue 24 CYS Chi-restraints excluded: chain y residue 173 LEU Chi-restraints excluded: chain z residue 6 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1181 random chunks: chunk 950 optimal weight: 9.9990 chunk 648 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 849 optimal weight: 0.9980 chunk 471 optimal weight: 9.9990 chunk 974 optimal weight: 0.9980 chunk 789 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 582 optimal weight: 9.9990 chunk 1024 optimal weight: 4.9990 chunk 288 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 36 GLN A 79 ASN C 18 ASN F 157 ASN F 244 ASN G 79 GLN G 221 ASN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 GLN ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN ** S 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 GLN V 7 GLN W 148 GLN X 137 ASN b 367 GLN c 8 ASN ** c 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 80 ASN ** e 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 106 ASN g 11 ASN h 59 ASN ** k 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 25 GLN q 65 GLN r 68 HIS ** r 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 25 ASN ** w 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 82 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 150674 Z= 0.210 Angle : 0.563 10.510 219644 Z= 0.290 Chirality : 0.037 0.372 27223 Planarity : 0.004 0.053 15459 Dihedral : 23.246 179.987 61284 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.39 % Allowed : 16.17 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.09), residues: 8600 helix: 1.29 (0.09), residues: 3127 sheet: -0.49 (0.14), residues: 1221 loop : -0.40 (0.10), residues: 4252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP w 114 HIS 0.008 0.001 HIS e 88 PHE 0.025 0.001 PHE F 229 TYR 0.028 0.002 TYR W 220 ARG 0.009 0.000 ARG F 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1386 residues out of total 7453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1133 time to evaluate : 7.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7499 (tt0) REVERT: A 198 LYS cc_start: 0.7619 (pttm) cc_final: 0.7094 (pptt) REVERT: A 204 MET cc_start: 0.5093 (OUTLIER) cc_final: 0.1840 (mmm) REVERT: B 308 MET cc_start: 0.7991 (mtm) cc_final: 0.7764 (mtm) REVERT: C 73 ARG cc_start: 0.7903 (mtp180) cc_final: 0.7647 (mtt180) REVERT: C 145 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8536 (tp) REVERT: D 183 TRP cc_start: 0.8419 (t60) cc_final: 0.8181 (t60) REVERT: D 206 GLN cc_start: 0.7933 (mt0) cc_final: 0.7521 (mt0) REVERT: E 164 SER cc_start: 0.8682 (p) cc_final: 0.8395 (t) REVERT: G 111 LYS cc_start: 0.8268 (tptt) cc_final: 0.7806 (tmmt) REVERT: H 1 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7149 (ptm) REVERT: H 143 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: H 166 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7646 (ttm170) REVERT: I 14 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.6722 (ttm-80) REVERT: I 43 LYS cc_start: 0.7667 (mmpt) cc_final: 0.7303 (mmtp) REVERT: I 96 TYR cc_start: 0.7094 (t80) cc_final: 0.6653 (t80) REVERT: J 15 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6209 (mp0) REVERT: J 35 LYS cc_start: 0.7728 (tmtt) cc_final: 0.7344 (tptp) REVERT: J 91 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8213 (pp) REVERT: J 167 TYR cc_start: 0.7645 (m-80) cc_final: 0.7135 (m-80) REVERT: L 169 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8773 (t) REVERT: M 62 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7656 (mp10) REVERT: N 41 ARG cc_start: 0.8455 (ptp-110) cc_final: 0.8168 (ptp-170) REVERT: O 40 GLU cc_start: 0.7429 (tp30) cc_final: 0.7208 (tp30) REVERT: O 84 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8380 (tt) REVERT: O 87 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8426 (mtt) REVERT: Q 21 SER cc_start: 0.8422 (t) cc_final: 0.8140 (t) REVERT: Q 50 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7618 (mmtt) REVERT: R 31 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7271 (pm20) REVERT: R 68 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: R 86 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7322 (tp30) REVERT: S 52 LYS cc_start: 0.7431 (mptt) cc_final: 0.6681 (tttt) REVERT: S 166 LYS cc_start: 0.8087 (mtmm) cc_final: 0.7878 (mtmm) REVERT: T 76 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.6659 (pt) REVERT: T 87 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.7162 (tttm) REVERT: T 131 GLN cc_start: 0.8594 (mm110) cc_final: 0.8213 (mm110) REVERT: U 25 ASN cc_start: 0.6783 (OUTLIER) cc_final: 0.6341 (t0) REVERT: U 58 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6574 (pt0) REVERT: U 88 GLN cc_start: 0.8266 (mp10) cc_final: 0.7650 (tm-30) REVERT: V 27 ASP cc_start: 0.8331 (p0) cc_final: 0.7975 (p0) REVERT: V 29 SER cc_start: 0.8575 (p) cc_final: 0.8140 (p) REVERT: W 60 TRP cc_start: 0.7526 (OUTLIER) cc_final: 0.6793 (p90) REVERT: X 129 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7714 (p0) REVERT: X 130 TYR cc_start: 0.8025 (m-80) cc_final: 0.7757 (m-80) REVERT: Y 112 ASP cc_start: 0.7645 (m-30) cc_final: 0.7428 (m-30) REVERT: Y 114 ASP cc_start: 0.7463 (m-30) cc_final: 0.7155 (m-30) REVERT: Y 120 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7739 (mp-120) REVERT: a 58 MET cc_start: 0.5443 (OUTLIER) cc_final: 0.5047 (ptt) REVERT: a 120 ASN cc_start: 0.8362 (t0) cc_final: 0.8071 (t0) REVERT: a 130 VAL cc_start: 0.9067 (m) cc_final: 0.8854 (m) REVERT: a 135 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8493 (tp30) REVERT: b 270 LEU cc_start: 0.8275 (tt) cc_final: 0.7982 (tm) REVERT: b 304 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.7136 (mt0) REVERT: b 466 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7315 (tt0) REVERT: e 78 ASN cc_start: 0.8555 (p0) cc_final: 0.7668 (p0) REVERT: e 81 ASP cc_start: 0.7737 (m-30) cc_final: 0.7238 (m-30) REVERT: e 123 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7740 (mptm) REVERT: f 14 LEU cc_start: 0.9052 (mt) cc_final: 0.8702 (mt) REVERT: f 48 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7283 (mmp80) REVERT: f 49 ILE cc_start: 0.9097 (mt) cc_final: 0.8794 (mm) REVERT: f 63 LYS cc_start: 0.8677 (ttmm) cc_final: 0.8198 (tttm) REVERT: h 105 ARG cc_start: 0.8685 (tmm-80) cc_final: 0.8276 (ttt90) REVERT: i 60 LEU cc_start: 0.8665 (mt) cc_final: 0.8313 (mp) REVERT: i 66 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7751 (mm-30) REVERT: j 25 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7660 (tmm-80) REVERT: k 16 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7576 (mpp-170) REVERT: m 151 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6444 (ttp-110) REVERT: m 249 GLU cc_start: 0.7318 (tp30) cc_final: 0.7075 (tt0) REVERT: m 389 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7013 (ttm-80) REVERT: m 456 ASP cc_start: 0.8059 (m-30) cc_final: 0.7740 (m-30) REVERT: p 73 THR cc_start: 0.8722 (m) cc_final: 0.8397 (p) REVERT: r 66 LYS cc_start: 0.8979 (ttmm) cc_final: 0.8745 (mtpm) REVERT: s 72 LEU cc_start: 0.1932 (OUTLIER) cc_final: 0.1277 (tt) REVERT: u 3 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8703 (mp) REVERT: u 74 ARG cc_start: 0.7527 (ttt90) cc_final: 0.7280 (ttp80) REVERT: u 104 GLU cc_start: 0.6511 (pp20) cc_final: 0.6181 (tm-30) REVERT: u 135 ARG cc_start: 0.5402 (tmt170) cc_final: 0.4991 (tmt170) REVERT: w 15 LYS cc_start: 0.7803 (pttm) cc_final: 0.7581 (mtmm) REVERT: w 102 GLU cc_start: 0.6556 (tp30) cc_final: 0.6254 (tp30) REVERT: w 111 MET cc_start: 0.6638 (tmm) cc_final: 0.6428 (tmm) REVERT: w 115 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7577 (mt-10) REVERT: w 177 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.5940 (mtm180) REVERT: x 272 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7114 (p90) REVERT: y 1 MET cc_start: 0.5457 (mtt) cc_final: 0.4902 (mmp) REVERT: z 30 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7133 (tt0) outliers start: 253 outliers final: 128 residues processed: 1264 average time/residue: 2.0217 time to fit residues: 3725.6707 Evaluate side-chains 1229 residues out of total 7453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1066 time to evaluate : 7.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 61 MET Chi-restraints excluded: chain 7 residue 89 VAL Chi-restraints excluded: chain 7 residue 98 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 221 ASN Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain Q residue 50 LYS Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain S residue 130 GLU Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain T residue 79 MET Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain U residue 25 ASN Chi-restraints excluded: chain U residue 58 GLU Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 98 ASN Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 109 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain X residue 129 ASP Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 134 ASP Chi-restraints excluded: chain Y residue 120 GLN Chi-restraints excluded: chain Z residue 30 ASP Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain b residue 11 VAL Chi-restraints excluded: chain b residue 40 THR Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 236 GLU Chi-restraints excluded: chain b residue 304 GLN Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain b residue 405 GLU Chi-restraints excluded: chain b residue 466 GLU Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 78 LYS Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain e residue 82 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 48 ARG Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 51 LEU Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 101 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain k residue 14 LEU Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain l residue 30 ARG Chi-restraints excluded: chain l residue 46 ARG Chi-restraints excluded: chain m residue 151 ARG Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 262 CYS Chi-restraints excluded: chain m residue 316 ILE Chi-restraints excluded: chain m residue 329 SER Chi-restraints excluded: chain m residue 340 VAL Chi-restraints excluded: chain m residue 389 ARG Chi-restraints excluded: chain p residue 89 MET Chi-restraints excluded: chain q residue 72 SER Chi-restraints excluded: chain r residue 92 LEU Chi-restraints excluded: chain r residue 157 VAL Chi-restraints excluded: chain r residue 237 VAL Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain s residue 57 LYS Chi-restraints excluded: chain s residue 69 MET Chi-restraints excluded: chain s residue 72 LEU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain u residue 68 THR Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain v residue 140 MET Chi-restraints excluded: chain v residue 199 VAL Chi-restraints excluded: chain v residue 218 LEU Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 37 ASN Chi-restraints excluded: chain w residue 67 SER Chi-restraints excluded: chain w residue 80 THR Chi-restraints excluded: chain w residue 91 GLN Chi-restraints excluded: chain w residue 159 LEU Chi-restraints excluded: chain w residue 177 ARG Chi-restraints excluded: chain w residue 187 LEU Chi-restraints excluded: chain w residue 195 GLN Chi-restraints excluded: chain x residue 157 SER Chi-restraints excluded: chain x residue 191 CYS Chi-restraints excluded: chain x residue 207 ASP Chi-restraints excluded: chain x residue 212 LEU Chi-restraints excluded: chain x residue 272 TYR Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 491 THR Chi-restraints excluded: chain y residue 24 CYS Chi-restraints excluded: chain y residue 173 LEU Chi-restraints excluded: chain z residue 6 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1181 random chunks: chunk 384 optimal weight: 5.9990 chunk 1028 optimal weight: 20.0000 chunk 225 optimal weight: 10.0000 chunk 670 optimal weight: 3.9990 chunk 281 optimal weight: 10.0000 chunk 1142 optimal weight: 4.9990 chunk 948 optimal weight: 30.0000 chunk 529 optimal weight: 0.0070 chunk 95 optimal weight: 30.0000 chunk 377 optimal weight: 5.9990 chunk 599 optimal weight: 4.9990 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 36 GLN A 79 ASN C 18 ASN F 157 ASN G 79 GLN ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 72 GLN ** S 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 GLN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 ASN ** c 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 106 ASN g 11 ASN h 59 ASN ** k 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 25 GLN q 65 GLN ** r 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 53 ASN ** u 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 299 GLN w 25 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 150674 Z= 0.313 Angle : 0.608 12.175 219644 Z= 0.312 Chirality : 0.039 0.384 27223 Planarity : 0.004 0.054 15459 Dihedral : 23.219 179.963 61284 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.90 % Allowed : 16.92 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.09), residues: 8600 helix: 1.22 (0.09), residues: 3128 sheet: -0.50 (0.14), residues: 1227 loop : -0.43 (0.10), residues: 4245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP w 114 HIS 0.009 0.001 HIS B 163 PHE 0.029 0.002 PHE F 229 TYR 0.033 0.002 TYR N 94 ARG 0.009 0.000 ARG D 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1382 residues out of total 7453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 1091 time to evaluate : 7.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7541 (tt0) REVERT: A 122 ASP cc_start: 0.8247 (p0) cc_final: 0.8033 (p0) REVERT: A 198 LYS cc_start: 0.7676 (pttm) cc_final: 0.7120 (pptt) REVERT: A 204 MET cc_start: 0.5114 (OUTLIER) cc_final: 0.1824 (mmm) REVERT: B 10 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8391 (ttt90) REVERT: C 145 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8550 (tp) REVERT: D 44 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.7809 (m-80) REVERT: D 183 TRP cc_start: 0.8481 (t60) cc_final: 0.8211 (t60) REVERT: D 206 GLN cc_start: 0.7896 (mt0) cc_final: 0.7495 (mt0) REVERT: E 164 SER cc_start: 0.8691 (p) cc_final: 0.8404 (t) REVERT: G 111 LYS cc_start: 0.8285 (tptt) cc_final: 0.7803 (tmmt) REVERT: H 1 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7112 (ptm) REVERT: H 143 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7452 (tt0) REVERT: H 166 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7601 (ttm170) REVERT: I 14 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.6773 (ttm-80) REVERT: I 43 LYS cc_start: 0.7694 (mmpt) cc_final: 0.7323 (mmtm) REVERT: I 96 TYR cc_start: 0.7178 (t80) cc_final: 0.6674 (t80) REVERT: J 15 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6213 (mp0) REVERT: J 35 LYS cc_start: 0.7768 (tmtt) cc_final: 0.7388 (tptp) REVERT: J 91 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8273 (pp) REVERT: J 167 TYR cc_start: 0.7713 (m-80) cc_final: 0.7210 (m-80) REVERT: L 169 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8802 (t) REVERT: M 62 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7619 (mp10) REVERT: N 41 ARG cc_start: 0.8454 (ptp-110) cc_final: 0.8169 (ptp-170) REVERT: N 109 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.6716 (ttp80) REVERT: O 40 GLU cc_start: 0.7497 (tp30) cc_final: 0.7253 (tp30) REVERT: O 87 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8477 (mtt) REVERT: P 75 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8225 (pt0) REVERT: Q 21 SER cc_start: 0.8448 (t) cc_final: 0.8164 (t) REVERT: Q 50 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7647 (mmtt) REVERT: R 31 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7267 (pm20) REVERT: R 68 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8142 (tm-30) REVERT: S 52 LYS cc_start: 0.7490 (mptt) cc_final: 0.6691 (mttt) REVERT: S 166 LYS cc_start: 0.8093 (mtmm) cc_final: 0.7882 (mtmm) REVERT: T 76 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.6583 (pt) REVERT: T 131 GLN cc_start: 0.8596 (mm110) cc_final: 0.8216 (mm110) REVERT: U 58 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6655 (pt0) REVERT: U 88 GLN cc_start: 0.8280 (mp10) cc_final: 0.7654 (tm-30) REVERT: V 27 ASP cc_start: 0.8297 (p0) cc_final: 0.7948 (p0) REVERT: V 29 SER cc_start: 0.8564 (p) cc_final: 0.8141 (p) REVERT: X 27 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7665 (mmt90) REVERT: X 129 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.7749 (p0) REVERT: X 130 TYR cc_start: 0.8063 (m-80) cc_final: 0.7849 (m-80) REVERT: Y 114 ASP cc_start: 0.7548 (m-30) cc_final: 0.7178 (m-30) REVERT: Y 120 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7813 (mp-120) REVERT: Z 31 GLU cc_start: 0.7423 (pt0) cc_final: 0.6923 (tm-30) REVERT: a 58 MET cc_start: 0.5509 (OUTLIER) cc_final: 0.5119 (ptt) REVERT: a 120 ASN cc_start: 0.8367 (t0) cc_final: 0.8077 (t0) REVERT: a 130 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8880 (m) REVERT: a 135 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8429 (tp30) REVERT: b 270 LEU cc_start: 0.8325 (tt) cc_final: 0.8033 (tm) REVERT: e 78 ASN cc_start: 0.8537 (p0) cc_final: 0.7622 (p0) REVERT: e 81 ASP cc_start: 0.7765 (m-30) cc_final: 0.7264 (m-30) REVERT: e 123 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7869 (mptp) REVERT: e 125 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8584 (mtt180) REVERT: f 48 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7328 (mmp80) REVERT: f 49 ILE cc_start: 0.9123 (mt) cc_final: 0.8818 (mm) REVERT: f 63 LYS cc_start: 0.8689 (ttmm) cc_final: 0.8266 (tttm) REVERT: g 38 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8316 (mm) REVERT: i 60 LEU cc_start: 0.8672 (mt) cc_final: 0.8312 (mp) REVERT: i 66 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7744 (mm-30) REVERT: j 25 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7735 (tmm-80) REVERT: k 16 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7647 (mpp-170) REVERT: m 151 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6523 (ttp-110) REVERT: m 209 LYS cc_start: 0.7807 (mmtt) cc_final: 0.7423 (tppt) REVERT: m 249 GLU cc_start: 0.7335 (tp30) cc_final: 0.7071 (tt0) REVERT: m 389 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7036 (ttm-80) REVERT: p 73 THR cc_start: 0.8748 (m) cc_final: 0.8423 (p) REVERT: r 150 MET cc_start: 0.8348 (ttp) cc_final: 0.8063 (ttp) REVERT: s 72 LEU cc_start: 0.1960 (OUTLIER) cc_final: 0.1290 (tt) REVERT: u 3 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8682 (mp) REVERT: u 74 ARG cc_start: 0.7545 (ttt90) cc_final: 0.7290 (ttp80) REVERT: u 104 GLU cc_start: 0.6569 (pp20) cc_final: 0.6239 (tm-30) REVERT: u 117 GLU cc_start: 0.6021 (OUTLIER) cc_final: 0.5710 (tp30) REVERT: v 90 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.5914 (mpm) REVERT: v 100 MET cc_start: 0.8819 (mtm) cc_final: 0.8534 (mtp) REVERT: w 102 GLU cc_start: 0.6604 (tp30) cc_final: 0.6209 (tp30) REVERT: w 177 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.6262 (mtm180) REVERT: x 40 ASP cc_start: 0.7039 (OUTLIER) cc_final: 0.6686 (p0) REVERT: x 272 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.7004 (p90) REVERT: x 398 MET cc_start: 0.8337 (mtt) cc_final: 0.7514 (mtt) REVERT: x 432 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6847 (mmm160) REVERT: y 1 MET cc_start: 0.5543 (mtt) cc_final: 0.5098 (mmp) REVERT: z 30 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7293 (tt0) outliers start: 291 outliers final: 154 residues processed: 1249 average time/residue: 1.9918 time to fit residues: 3635.3331 Evaluate side-chains 1251 residues out of total 7453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1056 time to evaluate : 7.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 61 MET Chi-restraints excluded: chain 7 residue 89 VAL Chi-restraints excluded: chain 7 residue 98 SER Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 44 TYR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 173 MET Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 221 ASN Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 109 ARG Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 50 LYS Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 130 GLU Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain T residue 79 MET Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain U residue 58 GLU Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 98 ASN Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 109 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 129 ASP Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 120 GLN Chi-restraints excluded: chain Z residue 30 ASP Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 130 VAL Chi-restraints excluded: chain b residue 11 VAL Chi-restraints excluded: chain b residue 40 THR Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain c residue 105 THR Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 78 LYS Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 52 GLN Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 125 ARG Chi-restraints excluded: chain f residue 7 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 48 ARG Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 98 SER Chi-restraints excluded: chain h residue 101 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain k residue 14 LEU Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain l residue 30 ARG Chi-restraints excluded: chain l residue 46 ARG Chi-restraints excluded: chain m residue 151 ARG Chi-restraints excluded: chain m residue 215 LEU Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 262 CYS Chi-restraints excluded: chain m residue 316 ILE Chi-restraints excluded: chain m residue 329 SER Chi-restraints excluded: chain m residue 340 VAL Chi-restraints excluded: chain m residue 389 ARG Chi-restraints excluded: chain p residue 89 MET Chi-restraints excluded: chain q residue 72 SER Chi-restraints excluded: chain r residue 92 LEU Chi-restraints excluded: chain r residue 157 VAL Chi-restraints excluded: chain r residue 237 VAL Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain s residue 57 LYS Chi-restraints excluded: chain s residue 69 MET Chi-restraints excluded: chain s residue 72 LEU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain u residue 68 THR Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 117 GLU Chi-restraints excluded: chain v residue 90 MET Chi-restraints excluded: chain v residue 140 MET Chi-restraints excluded: chain v residue 181 VAL Chi-restraints excluded: chain v residue 199 VAL Chi-restraints excluded: chain v residue 218 LEU Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 20 VAL Chi-restraints excluded: chain w residue 37 ASN Chi-restraints excluded: chain w residue 38 ASP Chi-restraints excluded: chain w residue 67 SER Chi-restraints excluded: chain w residue 80 THR Chi-restraints excluded: chain w residue 91 GLN Chi-restraints excluded: chain w residue 159 LEU Chi-restraints excluded: chain w residue 177 ARG Chi-restraints excluded: chain w residue 187 LEU Chi-restraints excluded: chain w residue 195 GLN Chi-restraints excluded: chain x residue 40 ASP Chi-restraints excluded: chain x residue 157 SER Chi-restraints excluded: chain x residue 191 CYS Chi-restraints excluded: chain x residue 207 ASP Chi-restraints excluded: chain x residue 212 LEU Chi-restraints excluded: chain x residue 272 TYR Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 432 ARG Chi-restraints excluded: chain x residue 470 VAL Chi-restraints excluded: chain x residue 491 THR Chi-restraints excluded: chain y residue 24 CYS Chi-restraints excluded: chain y residue 167 VAL Chi-restraints excluded: chain y residue 173 LEU Chi-restraints excluded: chain z residue 6 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1181 random chunks: chunk 1101 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 651 optimal weight: 0.9980 chunk 834 optimal weight: 10.0000 chunk 646 optimal weight: 0.9990 chunk 961 optimal weight: 10.0000 chunk 638 optimal weight: 5.9990 chunk 1138 optimal weight: 9.9990 chunk 712 optimal weight: 0.4980 chunk 693 optimal weight: 0.8980 chunk 525 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 36 GLN A 79 ASN C 18 ASN D 45 ASN D 175 HIS F 157 ASN G 79 GLN G 221 ASN ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 GLN V 7 GLN X 137 ASN b 616 HIS ** c 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 106 ASN g 11 ASN h 59 ASN ** k 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 301 GLN p 25 GLN q 65 GLN ** r 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 299 GLN w 25 ASN ** w 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 150674 Z= 0.151 Angle : 0.545 12.421 219644 Z= 0.281 Chirality : 0.035 0.359 27223 Planarity : 0.004 0.055 15459 Dihedral : 23.202 179.612 61284 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.80 % Allowed : 18.52 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.09), residues: 8600 helix: 1.51 (0.09), residues: 3109 sheet: -0.43 (0.14), residues: 1221 loop : -0.32 (0.10), residues: 4270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP w 114 HIS 0.007 0.001 HIS S 49 PHE 0.023 0.001 PHE F 229 TYR 0.029 0.001 TYR W 220 ARG 0.009 0.000 ARG J 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1352 residues out of total 7453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1143 time to evaluate : 7.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LYS cc_start: 0.7599 (pttm) cc_final: 0.7088 (pptt) REVERT: B 10 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8324 (ttt90) REVERT: C 145 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8519 (tp) REVERT: D 206 GLN cc_start: 0.7886 (mt0) cc_final: 0.7492 (mt0) REVERT: E 164 SER cc_start: 0.8643 (p) cc_final: 0.8376 (t) REVERT: F 182 ASP cc_start: 0.7763 (m-30) cc_final: 0.7555 (m-30) REVERT: G 111 LYS cc_start: 0.8226 (tptt) cc_final: 0.7756 (tmmt) REVERT: H 1 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7037 (ptm) REVERT: H 166 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7626 (ttm170) REVERT: I 43 LYS cc_start: 0.7708 (mmpt) cc_final: 0.7367 (mmtp) REVERT: I 81 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.6116 (mtp180) REVERT: I 96 TYR cc_start: 0.7063 (t80) cc_final: 0.6581 (t80) REVERT: J 15 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6169 (mp0) REVERT: J 22 SER cc_start: 0.7542 (t) cc_final: 0.6529 (m) REVERT: J 35 LYS cc_start: 0.7690 (tmtt) cc_final: 0.7322 (tptp) REVERT: J 39 GLN cc_start: 0.7587 (tm-30) cc_final: 0.7251 (tm130) REVERT: J 91 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8233 (pp) REVERT: J 167 TYR cc_start: 0.7755 (m-80) cc_final: 0.7389 (m-80) REVERT: J 172 LEU cc_start: 0.5399 (OUTLIER) cc_final: 0.4650 (tt) REVERT: L 169 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8760 (t) REVERT: M 62 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8229 (mt0) REVERT: N 41 ARG cc_start: 0.8423 (ptp-110) cc_final: 0.8152 (ptp-170) REVERT: O 87 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8391 (mtt) REVERT: P 75 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8134 (pt0) REVERT: Q 21 SER cc_start: 0.8449 (t) cc_final: 0.8177 (t) REVERT: Q 50 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7560 (mmtt) REVERT: Q 105 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7890 (mtm-85) REVERT: R 68 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8016 (tm-30) REVERT: R 86 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7335 (tp30) REVERT: S 52 LYS cc_start: 0.7371 (mptt) cc_final: 0.6572 (tttt) REVERT: S 53 LYS cc_start: 0.7570 (tptp) cc_final: 0.7072 (tttt) REVERT: T 76 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.6590 (pt) REVERT: T 90 ASN cc_start: 0.7889 (t0) cc_final: 0.7435 (t0) REVERT: T 131 GLN cc_start: 0.8567 (mm110) cc_final: 0.8199 (mm110) REVERT: U 88 GLN cc_start: 0.8222 (mp10) cc_final: 0.7658 (tm-30) REVERT: V 27 ASP cc_start: 0.8281 (p0) cc_final: 0.7971 (p0) REVERT: V 29 SER cc_start: 0.8552 (p) cc_final: 0.8167 (p) REVERT: W 214 LYS cc_start: 0.6372 (pptt) cc_final: 0.6023 (tmtt) REVERT: X 129 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7636 (p0) REVERT: X 130 TYR cc_start: 0.7963 (m-80) cc_final: 0.7631 (m-80) REVERT: Y 114 ASP cc_start: 0.7409 (m-30) cc_final: 0.7098 (m-30) REVERT: a 89 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7635 (pt0) REVERT: a 120 ASN cc_start: 0.8335 (t0) cc_final: 0.8066 (t0) REVERT: a 130 VAL cc_start: 0.9047 (m) cc_final: 0.8835 (m) REVERT: a 135 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8392 (tp30) REVERT: b 270 LEU cc_start: 0.8246 (tt) cc_final: 0.7963 (tm) REVERT: b 304 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.7159 (mt0) REVERT: c 32 ARG cc_start: 0.7415 (ttm110) cc_final: 0.6577 (tmm-80) REVERT: c 46 LYS cc_start: 0.7340 (mttm) cc_final: 0.6829 (mttp) REVERT: e 78 ASN cc_start: 0.8572 (p0) cc_final: 0.7710 (p0) REVERT: e 81 ASP cc_start: 0.7745 (m-30) cc_final: 0.7246 (m-30) REVERT: e 123 LYS cc_start: 0.7985 (mmtt) cc_final: 0.7623 (mptp) REVERT: f 48 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7295 (mmp80) REVERT: f 49 ILE cc_start: 0.9053 (mt) cc_final: 0.8741 (mm) REVERT: f 63 LYS cc_start: 0.8668 (ttmm) cc_final: 0.8215 (tttm) REVERT: g 38 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8294 (mm) REVERT: h 45 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.7979 (ttmp) REVERT: h 105 ARG cc_start: 0.8662 (tmm-80) cc_final: 0.8271 (ttt90) REVERT: i 60 LEU cc_start: 0.8668 (mt) cc_final: 0.8327 (mp) REVERT: j 25 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7572 (tmm-80) REVERT: k 16 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7576 (mpp-170) REVERT: m 7 GLU cc_start: 0.7269 (tp30) cc_final: 0.6993 (mm-30) REVERT: m 151 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6397 (ttp-110) REVERT: m 249 GLU cc_start: 0.7304 (tp30) cc_final: 0.7060 (tt0) REVERT: m 389 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6973 (ttm-80) REVERT: p 73 THR cc_start: 0.8693 (m) cc_final: 0.8382 (p) REVERT: r 53 LYS cc_start: 0.8289 (tppt) cc_final: 0.8041 (tmtm) REVERT: r 150 MET cc_start: 0.8319 (ttp) cc_final: 0.8043 (ttp) REVERT: s 72 LEU cc_start: 0.1907 (OUTLIER) cc_final: 0.1233 (tt) REVERT: u 3 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8684 (mp) REVERT: u 74 ARG cc_start: 0.7530 (ttt90) cc_final: 0.7262 (ttp80) REVERT: u 104 GLU cc_start: 0.6545 (pp20) cc_final: 0.6214 (tm-30) REVERT: u 117 GLU cc_start: 0.6041 (OUTLIER) cc_final: 0.5675 (tp30) REVERT: v 140 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8286 (mtm) REVERT: v 184 MET cc_start: 0.7595 (mmt) cc_final: 0.7339 (mmt) REVERT: w 115 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7403 (tp30) REVERT: w 177 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6079 (mtm180) REVERT: w 195 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8392 (tt0) REVERT: x 470 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8384 (t) REVERT: y 1 MET cc_start: 0.5372 (mtt) cc_final: 0.4796 (mmp) REVERT: z 30 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7148 (tt0) outliers start: 209 outliers final: 108 residues processed: 1254 average time/residue: 2.0300 time to fit residues: 3719.0505 Evaluate side-chains 1216 residues out of total 7453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1074 time to evaluate : 7.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 89 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain Q residue 50 LYS Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 105 ARG Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain X residue 129 ASP Chi-restraints excluded: chain X residue 134 ASP Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain b residue 11 VAL Chi-restraints excluded: chain b residue 40 THR Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 304 GLN Chi-restraints excluded: chain b residue 405 GLU Chi-restraints excluded: chain c residue 51 LYS Chi-restraints excluded: chain c residue 105 THR Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 78 LYS Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 48 ARG Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 45 LYS Chi-restraints excluded: chain h residue 101 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain k residue 14 LEU Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain l residue 30 ARG Chi-restraints excluded: chain l residue 46 ARG Chi-restraints excluded: chain l residue 51 ILE Chi-restraints excluded: chain m residue 151 ARG Chi-restraints excluded: chain m residue 215 LEU Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 316 ILE Chi-restraints excluded: chain m residue 340 VAL Chi-restraints excluded: chain m residue 389 ARG Chi-restraints excluded: chain p residue 89 MET Chi-restraints excluded: chain q residue 72 SER Chi-restraints excluded: chain r residue 92 LEU Chi-restraints excluded: chain r residue 157 VAL Chi-restraints excluded: chain r residue 237 VAL Chi-restraints excluded: chain s residue 69 MET Chi-restraints excluded: chain s residue 72 LEU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain u residue 68 THR Chi-restraints excluded: chain u residue 117 GLU Chi-restraints excluded: chain v residue 140 MET Chi-restraints excluded: chain v residue 181 VAL Chi-restraints excluded: chain v residue 199 VAL Chi-restraints excluded: chain v residue 218 LEU Chi-restraints excluded: chain v residue 239 THR Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 38 ASP Chi-restraints excluded: chain w residue 67 SER Chi-restraints excluded: chain w residue 159 LEU Chi-restraints excluded: chain w residue 177 ARG Chi-restraints excluded: chain w residue 187 LEU Chi-restraints excluded: chain w residue 195 GLN Chi-restraints excluded: chain x residue 207 ASP Chi-restraints excluded: chain x residue 212 LEU Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 470 VAL Chi-restraints excluded: chain x residue 488 GLU Chi-restraints excluded: chain x residue 491 THR Chi-restraints excluded: chain y residue 24 CYS Chi-restraints excluded: chain y residue 167 VAL Chi-restraints excluded: chain z residue 6 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1181 random chunks: chunk 704 optimal weight: 9.9990 chunk 454 optimal weight: 2.9990 chunk 679 optimal weight: 7.9990 chunk 342 optimal weight: 10.0000 chunk 223 optimal weight: 20.0000 chunk 220 optimal weight: 30.0000 chunk 723 optimal weight: 0.9990 chunk 775 optimal weight: 3.9990 chunk 562 optimal weight: 0.3980 chunk 106 optimal weight: 10.0000 chunk 894 optimal weight: 5.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 36 GLN C 18 ASN F 146 GLN F 157 ASN G 138 HIS G 221 ASN H 102 ASN J 95 ASN ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN R 92 GLN ** S 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 GLN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 ASN ** c 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 80 ASN ** e 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 106 ASN g 11 ASN h 59 ASN ** k 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 65 GLN s 53 ASN ** u 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 299 GLN w 25 ASN ** w 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 145 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 150674 Z= 0.242 Angle : 0.572 12.384 219644 Z= 0.294 Chirality : 0.037 0.368 27223 Planarity : 0.004 0.057 15459 Dihedral : 23.136 179.938 61284 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.10 % Allowed : 18.96 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.09), residues: 8600 helix: 1.45 (0.09), residues: 3120 sheet: -0.41 (0.14), residues: 1218 loop : -0.35 (0.10), residues: 4262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP w 114 HIS 0.008 0.001 HIS B 163 PHE 0.026 0.001 PHE F 229 TYR 0.030 0.002 TYR N 94 ARG 0.009 0.000 ARG F 218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1314 residues out of total 7453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1083 time to evaluate : 7.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8216 (p0) cc_final: 0.8004 (p0) REVERT: A 198 LYS cc_start: 0.7660 (pttm) cc_final: 0.7115 (pptt) REVERT: B 10 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8357 (ttt90) REVERT: B 34 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7793 (tptp) REVERT: C 145 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8528 (tp) REVERT: D 44 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.7852 (m-80) REVERT: D 183 TRP cc_start: 0.8464 (t60) cc_final: 0.8210 (t60) REVERT: D 206 GLN cc_start: 0.7886 (mt0) cc_final: 0.7527 (mt0) REVERT: E 164 SER cc_start: 0.8669 (p) cc_final: 0.8395 (t) REVERT: G 111 LYS cc_start: 0.8273 (tptt) cc_final: 0.7795 (tmmt) REVERT: H 1 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.7053 (ptm) REVERT: H 143 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7283 (tp30) REVERT: H 166 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7589 (ttm170) REVERT: I 14 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.6676 (ttm-80) REVERT: I 43 LYS cc_start: 0.7733 (mmpt) cc_final: 0.7392 (mmtm) REVERT: I 81 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6076 (mtp180) REVERT: I 96 TYR cc_start: 0.7134 (t80) cc_final: 0.6650 (t80) REVERT: J 15 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6239 (mp0) REVERT: J 35 LYS cc_start: 0.7732 (tmtt) cc_final: 0.7362 (tptp) REVERT: J 39 GLN cc_start: 0.7640 (tm-30) cc_final: 0.7300 (tm130) REVERT: J 91 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8265 (pp) REVERT: L 169 THR cc_start: 0.9000 (OUTLIER) cc_final: 0.8782 (t) REVERT: L 186 ARG cc_start: 0.7138 (ptp-110) cc_final: 0.6861 (ptp90) REVERT: M 62 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7668 (mp10) REVERT: N 41 ARG cc_start: 0.8444 (ptp-110) cc_final: 0.8167 (ptp-170) REVERT: O 87 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8444 (mtt) REVERT: P 75 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8166 (pt0) REVERT: Q 21 SER cc_start: 0.8433 (t) cc_final: 0.8151 (t) REVERT: Q 50 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7627 (mmtt) REVERT: R 68 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8120 (tm-30) REVERT: S 134 ASP cc_start: 0.8589 (m-30) cc_final: 0.8299 (m-30) REVERT: T 76 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.6569 (pt) REVERT: T 90 ASN cc_start: 0.7902 (t0) cc_final: 0.7465 (t0) REVERT: T 131 GLN cc_start: 0.8553 (mm110) cc_final: 0.8139 (mm110) REVERT: U 25 ASN cc_start: 0.6523 (OUTLIER) cc_final: 0.6310 (t0) REVERT: U 88 GLN cc_start: 0.8253 (mp10) cc_final: 0.7669 (tm-30) REVERT: V 27 ASP cc_start: 0.8272 (p0) cc_final: 0.7941 (p0) REVERT: V 29 SER cc_start: 0.8565 (p) cc_final: 0.8134 (p) REVERT: X 27 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7718 (mmt90) REVERT: X 129 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7659 (p0) REVERT: X 130 TYR cc_start: 0.8008 (m-80) cc_final: 0.7782 (m-80) REVERT: Y 114 ASP cc_start: 0.7523 (m-30) cc_final: 0.7194 (m-30) REVERT: Y 120 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8056 (mt0) REVERT: Z 31 GLU cc_start: 0.7433 (pt0) cc_final: 0.6941 (tm-30) REVERT: a 89 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7653 (pt0) REVERT: a 120 ASN cc_start: 0.8305 (t0) cc_final: 0.8031 (t0) REVERT: a 130 VAL cc_start: 0.9068 (m) cc_final: 0.8848 (m) REVERT: a 135 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8475 (tp30) REVERT: b 270 LEU cc_start: 0.8306 (tt) cc_final: 0.8011 (tm) REVERT: b 288 ASN cc_start: 0.6662 (m-40) cc_final: 0.6228 (p0) REVERT: b 304 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.7173 (mt0) REVERT: c 32 ARG cc_start: 0.7468 (ttm110) cc_final: 0.6605 (tmm-80) REVERT: c 46 LYS cc_start: 0.7321 (mttm) cc_final: 0.6777 (mttp) REVERT: e 78 ASN cc_start: 0.8576 (p0) cc_final: 0.7664 (p0) REVERT: e 81 ASP cc_start: 0.7750 (m-30) cc_final: 0.7246 (m-30) REVERT: e 123 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7785 (mptp) REVERT: f 48 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7298 (mmp80) REVERT: f 49 ILE cc_start: 0.9098 (mt) cc_final: 0.8789 (mm) REVERT: f 63 LYS cc_start: 0.8679 (ttmm) cc_final: 0.8225 (tttm) REVERT: g 38 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8312 (mm) REVERT: h 45 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.7978 (ttmp) REVERT: h 105 ARG cc_start: 0.8680 (tmm-80) cc_final: 0.8291 (ttt90) REVERT: i 60 LEU cc_start: 0.8718 (mt) cc_final: 0.8358 (mp) REVERT: j 25 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7673 (tmm-80) REVERT: k 16 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7597 (mpp-170) REVERT: l 45 ARG cc_start: 0.8196 (ttt-90) cc_final: 0.7860 (ttt180) REVERT: m 7 GLU cc_start: 0.7285 (tp30) cc_final: 0.7000 (mm-30) REVERT: m 151 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6458 (ttp-110) REVERT: m 249 GLU cc_start: 0.7347 (tp30) cc_final: 0.7089 (tt0) REVERT: m 389 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7021 (ttm-80) REVERT: p 73 THR cc_start: 0.8730 (m) cc_final: 0.8383 (p) REVERT: r 150 MET cc_start: 0.8347 (ttp) cc_final: 0.8067 (ttp) REVERT: s 72 LEU cc_start: 0.1932 (OUTLIER) cc_final: 0.1267 (tt) REVERT: u 3 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8698 (mp) REVERT: u 74 ARG cc_start: 0.7535 (ttt90) cc_final: 0.7277 (ttp80) REVERT: u 104 GLU cc_start: 0.6553 (pp20) cc_final: 0.6077 (tm-30) REVERT: u 117 GLU cc_start: 0.5988 (OUTLIER) cc_final: 0.5688 (tp30) REVERT: v 140 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8237 (mtm) REVERT: w 115 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7438 (tp30) REVERT: w 177 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6376 (mtm180) REVERT: w 183 GLU cc_start: 0.8480 (tp30) cc_final: 0.8056 (tp30) REVERT: w 195 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8431 (tt0) REVERT: x 272 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.6726 (p90) REVERT: y 1 MET cc_start: 0.5413 (mtt) cc_final: 0.5006 (mmp) REVERT: z 30 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7258 (tt0) outliers start: 231 outliers final: 136 residues processed: 1213 average time/residue: 2.0359 time to fit residues: 3609.5461 Evaluate side-chains 1237 residues out of total 7453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1062 time to evaluate : 7.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 89 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 44 TYR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 221 ASN Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain Q residue 50 LYS Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain U residue 25 ASN Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 98 ASN Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 129 ASP Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Y residue 120 GLN Chi-restraints excluded: chain Z residue 30 ASP Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain b residue 11 VAL Chi-restraints excluded: chain b residue 40 THR Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 304 GLN Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain c residue 51 LYS Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 78 LYS Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 48 ARG Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 45 LYS Chi-restraints excluded: chain h residue 101 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain k residue 14 LEU Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain l residue 30 ARG Chi-restraints excluded: chain l residue 46 ARG Chi-restraints excluded: chain m residue 151 ARG Chi-restraints excluded: chain m residue 215 LEU Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 262 CYS Chi-restraints excluded: chain m residue 316 ILE Chi-restraints excluded: chain m residue 389 ARG Chi-restraints excluded: chain p residue 89 MET Chi-restraints excluded: chain q residue 72 SER Chi-restraints excluded: chain r residue 59 VAL Chi-restraints excluded: chain r residue 92 LEU Chi-restraints excluded: chain r residue 157 VAL Chi-restraints excluded: chain r residue 230 MET Chi-restraints excluded: chain r residue 237 VAL Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain s residue 60 ILE Chi-restraints excluded: chain s residue 69 MET Chi-restraints excluded: chain s residue 72 LEU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain u residue 68 THR Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 117 GLU Chi-restraints excluded: chain v residue 140 MET Chi-restraints excluded: chain v residue 181 VAL Chi-restraints excluded: chain v residue 199 VAL Chi-restraints excluded: chain v residue 218 LEU Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 37 ASN Chi-restraints excluded: chain w residue 38 ASP Chi-restraints excluded: chain w residue 67 SER Chi-restraints excluded: chain w residue 80 THR Chi-restraints excluded: chain w residue 112 THR Chi-restraints excluded: chain w residue 159 LEU Chi-restraints excluded: chain w residue 177 ARG Chi-restraints excluded: chain w residue 187 LEU Chi-restraints excluded: chain w residue 195 GLN Chi-restraints excluded: chain x residue 118 THR Chi-restraints excluded: chain x residue 157 SER Chi-restraints excluded: chain x residue 207 ASP Chi-restraints excluded: chain x residue 212 LEU Chi-restraints excluded: chain x residue 272 TYR Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 351 GLU Chi-restraints excluded: chain x residue 470 VAL Chi-restraints excluded: chain x residue 488 GLU Chi-restraints excluded: chain x residue 491 THR Chi-restraints excluded: chain y residue 24 CYS Chi-restraints excluded: chain y residue 167 VAL Chi-restraints excluded: chain z residue 6 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1181 random chunks: chunk 1035 optimal weight: 2.9990 chunk 1090 optimal weight: 8.9990 chunk 994 optimal weight: 3.9990 chunk 1060 optimal weight: 4.9990 chunk 638 optimal weight: 9.9990 chunk 462 optimal weight: 4.9990 chunk 832 optimal weight: 0.6980 chunk 325 optimal weight: 10.0000 chunk 958 optimal weight: 6.9990 chunk 1003 optimal weight: 9.9990 chunk 1057 optimal weight: 0.0570 overall best weight: 2.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 36 GLN C 18 ASN F 157 ASN G 138 HIS ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN Q 73 GLN ** S 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 GLN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 ASN b 616 HIS ** c 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 106 ASN g 11 ASN h 59 ASN ** k 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 65 GLN ** u 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 25 ASN ** w 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 150674 Z= 0.221 Angle : 0.566 12.309 219644 Z= 0.291 Chirality : 0.036 0.364 27223 Planarity : 0.004 0.059 15459 Dihedral : 23.143 179.788 61284 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.92 % Allowed : 19.60 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.09), residues: 8600 helix: 1.46 (0.09), residues: 3113 sheet: -0.41 (0.14), residues: 1213 loop : -0.32 (0.10), residues: 4274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP w 114 HIS 0.009 0.001 HIS e 88 PHE 0.025 0.001 PHE F 229 TYR 0.028 0.002 TYR D 30 ARG 0.009 0.000 ARG F 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1294 residues out of total 7453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1076 time to evaluate : 7.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8216 (p0) cc_final: 0.8002 (p0) REVERT: A 198 LYS cc_start: 0.7643 (pttm) cc_final: 0.7098 (pptt) REVERT: B 10 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8349 (ttt90) REVERT: B 34 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7757 (tptp) REVERT: C 145 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8527 (tp) REVERT: D 183 TRP cc_start: 0.8459 (t60) cc_final: 0.8199 (t60) REVERT: D 206 GLN cc_start: 0.7898 (mt0) cc_final: 0.7491 (mt0) REVERT: E 164 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.8391 (t) REVERT: G 111 LYS cc_start: 0.8270 (tptt) cc_final: 0.7792 (tmmt) REVERT: H 1 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7094 (ptm) REVERT: H 143 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7303 (tp30) REVERT: H 166 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7585 (ttm170) REVERT: I 14 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.6676 (ttm-80) REVERT: I 43 LYS cc_start: 0.7712 (mmpt) cc_final: 0.7376 (mmtm) REVERT: I 81 ARG cc_start: 0.6901 (OUTLIER) cc_final: 0.6070 (mtp180) REVERT: I 96 TYR cc_start: 0.7124 (t80) cc_final: 0.6648 (t80) REVERT: J 15 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6265 (mp0) REVERT: J 35 LYS cc_start: 0.7722 (tmtt) cc_final: 0.7346 (tptp) REVERT: J 39 GLN cc_start: 0.7635 (tm-30) cc_final: 0.7299 (tm130) REVERT: J 91 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8285 (pp) REVERT: L 169 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8780 (t) REVERT: M 62 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7665 (mp10) REVERT: N 41 ARG cc_start: 0.8441 (ptp-110) cc_final: 0.8075 (ptp-170) REVERT: N 109 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.6705 (tpp80) REVERT: O 87 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8438 (mtt) REVERT: P 75 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8167 (pt0) REVERT: Q 21 SER cc_start: 0.8425 (t) cc_final: 0.8140 (t) REVERT: Q 50 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7621 (mmtt) REVERT: R 68 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8068 (tm-30) REVERT: S 134 ASP cc_start: 0.8584 (m-30) cc_final: 0.8294 (m-30) REVERT: T 76 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.6574 (pt) REVERT: T 90 ASN cc_start: 0.7878 (t0) cc_final: 0.7430 (t0) REVERT: T 131 GLN cc_start: 0.8549 (mm110) cc_final: 0.8138 (mm110) REVERT: U 25 ASN cc_start: 0.6517 (OUTLIER) cc_final: 0.6276 (t0) REVERT: U 88 GLN cc_start: 0.8246 (mp10) cc_final: 0.7665 (tm-30) REVERT: V 27 ASP cc_start: 0.8263 (p0) cc_final: 0.7914 (p0) REVERT: V 29 SER cc_start: 0.8562 (p) cc_final: 0.8088 (p) REVERT: X 27 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7707 (mmt90) REVERT: X 129 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7637 (p0) REVERT: X 130 TYR cc_start: 0.8022 (m-80) cc_final: 0.7777 (m-80) REVERT: Y 114 ASP cc_start: 0.7487 (m-30) cc_final: 0.7162 (m-30) REVERT: Y 120 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8040 (mt0) REVERT: Z 52 LYS cc_start: 0.8701 (ttpp) cc_final: 0.8461 (tttp) REVERT: a 89 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7652 (pt0) REVERT: a 120 ASN cc_start: 0.8296 (t0) cc_final: 0.8027 (t0) REVERT: a 130 VAL cc_start: 0.9064 (m) cc_final: 0.8845 (m) REVERT: a 135 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8475 (tp30) REVERT: b 270 LEU cc_start: 0.8287 (tt) cc_final: 0.7999 (tm) REVERT: b 288 ASN cc_start: 0.6678 (m-40) cc_final: 0.6246 (p0) REVERT: b 304 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.7174 (mt0) REVERT: b 318 MET cc_start: 0.7957 (mtt) cc_final: 0.7657 (mtt) REVERT: b 466 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7345 (tt0) REVERT: c 32 ARG cc_start: 0.7418 (ttm110) cc_final: 0.6608 (tmm-80) REVERT: c 46 LYS cc_start: 0.7319 (mttm) cc_final: 0.6773 (mttp) REVERT: e 78 ASN cc_start: 0.8573 (p0) cc_final: 0.7662 (p0) REVERT: e 81 ASP cc_start: 0.7758 (m-30) cc_final: 0.7257 (m-30) REVERT: e 123 LYS cc_start: 0.8133 (mmtt) cc_final: 0.7762 (mptp) REVERT: f 48 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7297 (mmp80) REVERT: f 49 ILE cc_start: 0.9094 (mt) cc_final: 0.8783 (mm) REVERT: f 63 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8218 (tttm) REVERT: g 38 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8300 (mm) REVERT: h 45 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.7999 (ttmp) REVERT: i 60 LEU cc_start: 0.8715 (mt) cc_final: 0.8352 (mp) REVERT: j 25 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7682 (tmm-80) REVERT: k 16 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7593 (mpp-170) REVERT: l 45 ARG cc_start: 0.8199 (ttt-90) cc_final: 0.7867 (ttt180) REVERT: m 7 GLU cc_start: 0.7268 (tp30) cc_final: 0.7006 (mm-30) REVERT: m 151 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6448 (ttp-110) REVERT: m 249 GLU cc_start: 0.7345 (tp30) cc_final: 0.7087 (tt0) REVERT: m 389 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.7006 (ttm-80) REVERT: p 73 THR cc_start: 0.8732 (m) cc_final: 0.8410 (p) REVERT: r 70 GLN cc_start: 0.7464 (pp30) cc_final: 0.7054 (pp30) REVERT: r 150 MET cc_start: 0.8341 (ttp) cc_final: 0.8054 (ttp) REVERT: s 72 LEU cc_start: 0.1932 (OUTLIER) cc_final: 0.1275 (tt) REVERT: u 3 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8691 (mp) REVERT: u 74 ARG cc_start: 0.7542 (ttt90) cc_final: 0.7279 (ttp80) REVERT: u 104 GLU cc_start: 0.6562 (pp20) cc_final: 0.6230 (tm-30) REVERT: u 117 GLU cc_start: 0.5984 (OUTLIER) cc_final: 0.5684 (tp30) REVERT: v 140 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8279 (mtm) REVERT: w 115 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7427 (tp30) REVERT: w 177 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6353 (mtm180) REVERT: w 183 GLU cc_start: 0.8467 (tp30) cc_final: 0.8037 (tp30) REVERT: w 195 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8430 (tt0) REVERT: x 159 MET cc_start: 0.8138 (tmm) cc_final: 0.7616 (ttm) REVERT: x 271 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: x 272 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.6995 (p90) REVERT: y 1 MET cc_start: 0.5407 (mtt) cc_final: 0.5079 (mmp) REVERT: z 30 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7275 (tt0) outliers start: 218 outliers final: 140 residues processed: 1203 average time/residue: 2.0679 time to fit residues: 3637.5526 Evaluate side-chains 1240 residues out of total 7453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1058 time to evaluate : 7.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 89 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 221 ASN Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 109 ARG Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain Q residue 50 LYS Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain U residue 25 ASN Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 98 ASN Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 113 LYS Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 224 ASP Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 129 ASP Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Y residue 120 GLN Chi-restraints excluded: chain Z residue 30 ASP Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain b residue 11 VAL Chi-restraints excluded: chain b residue 40 THR Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 304 GLN Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain b residue 466 GLU Chi-restraints excluded: chain c residue 51 LYS Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 78 LYS Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain f residue 7 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 48 ARG Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 45 LYS Chi-restraints excluded: chain h residue 101 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain k residue 14 LEU Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain l residue 46 ARG Chi-restraints excluded: chain m residue 151 ARG Chi-restraints excluded: chain m residue 215 LEU Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 262 CYS Chi-restraints excluded: chain m residue 316 ILE Chi-restraints excluded: chain m residue 389 ARG Chi-restraints excluded: chain p residue 89 MET Chi-restraints excluded: chain q residue 72 SER Chi-restraints excluded: chain r residue 59 VAL Chi-restraints excluded: chain r residue 92 LEU Chi-restraints excluded: chain r residue 157 VAL Chi-restraints excluded: chain r residue 164 ARG Chi-restraints excluded: chain r residue 230 MET Chi-restraints excluded: chain r residue 237 VAL Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain s residue 69 MET Chi-restraints excluded: chain s residue 72 LEU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain u residue 68 THR Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 117 GLU Chi-restraints excluded: chain v residue 140 MET Chi-restraints excluded: chain v residue 181 VAL Chi-restraints excluded: chain v residue 199 VAL Chi-restraints excluded: chain v residue 218 LEU Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 37 ASN Chi-restraints excluded: chain w residue 38 ASP Chi-restraints excluded: chain w residue 67 SER Chi-restraints excluded: chain w residue 112 THR Chi-restraints excluded: chain w residue 159 LEU Chi-restraints excluded: chain w residue 177 ARG Chi-restraints excluded: chain w residue 187 LEU Chi-restraints excluded: chain w residue 195 GLN Chi-restraints excluded: chain x residue 118 THR Chi-restraints excluded: chain x residue 157 SER Chi-restraints excluded: chain x residue 207 ASP Chi-restraints excluded: chain x residue 212 LEU Chi-restraints excluded: chain x residue 271 GLN Chi-restraints excluded: chain x residue 272 TYR Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 470 VAL Chi-restraints excluded: chain x residue 488 GLU Chi-restraints excluded: chain x residue 491 THR Chi-restraints excluded: chain y residue 24 CYS Chi-restraints excluded: chain y residue 167 VAL Chi-restraints excluded: chain z residue 6 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1181 random chunks: chunk 696 optimal weight: 10.0000 chunk 1121 optimal weight: 5.9990 chunk 684 optimal weight: 0.4980 chunk 532 optimal weight: 1.9990 chunk 779 optimal weight: 7.9990 chunk 1176 optimal weight: 9.9990 chunk 1082 optimal weight: 1.9990 chunk 936 optimal weight: 0.9980 chunk 97 optimal weight: 40.0000 chunk 723 optimal weight: 0.1980 chunk 574 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 36 GLN A 79 ASN C 18 ASN F 157 ASN G 138 HIS G 221 ASN ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 GLN ** S 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 GLN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 ASN b 616 HIS ** c 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 106 ASN g 11 ASN h 59 ASN ** k 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 25 ASN w 91 GLN ** w 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 150674 Z= 0.154 Angle : 0.552 12.374 219644 Z= 0.285 Chirality : 0.035 0.357 27223 Planarity : 0.004 0.059 15459 Dihedral : 23.159 179.648 61284 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.36 % Allowed : 20.25 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.09), residues: 8600 helix: 1.50 (0.09), residues: 3119 sheet: -0.43 (0.14), residues: 1216 loop : -0.29 (0.10), residues: 4265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP w 114 HIS 0.008 0.001 HIS e 88 PHE 0.022 0.001 PHE F 229 TYR 0.029 0.001 TYR N 94 ARG 0.011 0.000 ARG L 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 7453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1072 time to evaluate : 7.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LYS cc_start: 0.7612 (pttm) cc_final: 0.7080 (pptt) REVERT: B 10 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8333 (ttt90) REVERT: B 34 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7743 (tptp) REVERT: C 145 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8505 (tp) REVERT: D 206 GLN cc_start: 0.7866 (mt0) cc_final: 0.7543 (mt0) REVERT: E 164 SER cc_start: 0.8658 (p) cc_final: 0.8405 (t) REVERT: G 111 LYS cc_start: 0.8258 (tptt) cc_final: 0.7784 (tmmt) REVERT: H 1 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.7081 (ptm) REVERT: H 143 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7230 (tp30) REVERT: H 166 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7590 (ttm170) REVERT: I 43 LYS cc_start: 0.7730 (mmpt) cc_final: 0.7398 (mmtm) REVERT: I 96 TYR cc_start: 0.7100 (t80) cc_final: 0.6626 (t80) REVERT: J 15 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6262 (mp0) REVERT: J 22 SER cc_start: 0.7511 (t) cc_final: 0.6526 (m) REVERT: J 35 LYS cc_start: 0.7703 (tmtt) cc_final: 0.7326 (tptp) REVERT: J 39 GLN cc_start: 0.7615 (tm-30) cc_final: 0.7224 (tm130) REVERT: J 91 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8295 (pp) REVERT: L 169 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8756 (t) REVERT: L 182 ILE cc_start: 0.7808 (pp) cc_final: 0.7547 (pt) REVERT: M 62 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8216 (mt0) REVERT: N 41 ARG cc_start: 0.8427 (ptp-110) cc_final: 0.8063 (ptp-170) REVERT: O 87 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8409 (mtt) REVERT: P 75 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8168 (pt0) REVERT: Q 21 SER cc_start: 0.8419 (t) cc_final: 0.8132 (t) REVERT: Q 50 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7574 (mmtt) REVERT: R 68 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8042 (tm-30) REVERT: T 76 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.6576 (pt) REVERT: T 90 ASN cc_start: 0.7775 (t0) cc_final: 0.7344 (t0) REVERT: T 131 GLN cc_start: 0.8555 (mm110) cc_final: 0.8201 (mm110) REVERT: U 88 GLN cc_start: 0.8229 (mp10) cc_final: 0.7722 (tm-30) REVERT: V 27 ASP cc_start: 0.8295 (p0) cc_final: 0.7948 (p0) REVERT: V 29 SER cc_start: 0.8562 (p) cc_final: 0.8100 (p) REVERT: W 60 TRP cc_start: 0.7608 (OUTLIER) cc_final: 0.6876 (p90) REVERT: W 214 LYS cc_start: 0.6373 (pptt) cc_final: 0.6013 (tmtt) REVERT: X 27 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7700 (mmt90) REVERT: X 129 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7613 (p0) REVERT: X 130 TYR cc_start: 0.7970 (m-80) cc_final: 0.7739 (m-80) REVERT: Y 114 ASP cc_start: 0.7463 (m-30) cc_final: 0.7148 (m-30) REVERT: Y 120 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7853 (mp10) REVERT: Z 31 GLU cc_start: 0.7413 (pt0) cc_final: 0.6908 (tm-30) REVERT: Z 106 GLN cc_start: 0.7677 (mt0) cc_final: 0.7476 (mt0) REVERT: a 89 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7641 (pt0) REVERT: a 120 ASN cc_start: 0.8277 (t0) cc_final: 0.8010 (t0) REVERT: a 130 VAL cc_start: 0.9034 (m) cc_final: 0.8814 (m) REVERT: a 135 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8474 (tp30) REVERT: b 270 LEU cc_start: 0.8261 (tt) cc_final: 0.7975 (tm) REVERT: b 288 ASN cc_start: 0.6662 (m-40) cc_final: 0.6211 (p0) REVERT: b 304 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7159 (mt0) REVERT: b 318 MET cc_start: 0.7927 (mtt) cc_final: 0.7632 (mtt) REVERT: c 32 ARG cc_start: 0.7406 (ttm110) cc_final: 0.6599 (tmm-80) REVERT: c 46 LYS cc_start: 0.7324 (mttm) cc_final: 0.6816 (mttp) REVERT: e 78 ASN cc_start: 0.8571 (p0) cc_final: 0.7667 (p0) REVERT: e 81 ASP cc_start: 0.7741 (m-30) cc_final: 0.7241 (m-30) REVERT: e 123 LYS cc_start: 0.8077 (mmtt) cc_final: 0.7703 (mptp) REVERT: f 48 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7279 (mmp80) REVERT: f 49 ILE cc_start: 0.9083 (mt) cc_final: 0.8770 (mm) REVERT: f 63 LYS cc_start: 0.8673 (ttmm) cc_final: 0.8204 (tttm) REVERT: g 38 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8288 (mm) REVERT: h 45 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8010 (ttmp) REVERT: h 105 ARG cc_start: 0.8661 (tmm-80) cc_final: 0.8274 (ttt90) REVERT: i 60 LEU cc_start: 0.8699 (mt) cc_final: 0.8342 (mp) REVERT: j 25 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7524 (tmm-80) REVERT: k 16 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7575 (mpp-170) REVERT: l 45 ARG cc_start: 0.8184 (ttt-90) cc_final: 0.7855 (ttt180) REVERT: m 7 GLU cc_start: 0.7273 (tp30) cc_final: 0.7013 (mm-30) REVERT: m 151 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6437 (ttp-110) REVERT: m 249 GLU cc_start: 0.7329 (tp30) cc_final: 0.7076 (tt0) REVERT: m 389 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6986 (ttm-80) REVERT: p 73 THR cc_start: 0.8727 (m) cc_final: 0.8401 (p) REVERT: r 62 ARG cc_start: 0.7656 (tmm160) cc_final: 0.7255 (ttp80) REVERT: r 150 MET cc_start: 0.8339 (ttp) cc_final: 0.8053 (ttp) REVERT: s 72 LEU cc_start: 0.1907 (OUTLIER) cc_final: 0.1240 (tt) REVERT: u 3 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8683 (mp) REVERT: u 74 ARG cc_start: 0.7524 (ttt90) cc_final: 0.7267 (ttp80) REVERT: u 104 GLU cc_start: 0.6538 (pp20) cc_final: 0.6214 (tm-30) REVERT: u 117 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5670 (tp30) REVERT: v 140 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8273 (mtm) REVERT: w 115 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7415 (tp30) REVERT: w 177 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6236 (mtm180) REVERT: w 183 GLU cc_start: 0.8461 (tp30) cc_final: 0.8028 (tp30) REVERT: w 195 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8408 (tt0) REVERT: x 159 MET cc_start: 0.8128 (tmm) cc_final: 0.7671 (ttm) REVERT: x 271 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: x 272 TYR cc_start: 0.7642 (OUTLIER) cc_final: 0.6972 (p90) REVERT: y 1 MET cc_start: 0.5381 (mtt) cc_final: 0.5059 (mmp) outliers start: 176 outliers final: 119 residues processed: 1180 average time/residue: 2.0517 time to fit residues: 3543.0975 Evaluate side-chains 1214 residues out of total 7453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1058 time to evaluate : 7.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 89 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 221 ASN Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain Q residue 50 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 98 ASN Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 113 LYS Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 224 ASP Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 129 ASP Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Y residue 120 GLN Chi-restraints excluded: chain Z residue 30 ASP Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain b residue 11 VAL Chi-restraints excluded: chain b residue 40 THR Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 304 GLN Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain c residue 51 LYS Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 78 LYS Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 48 ARG Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 45 LYS Chi-restraints excluded: chain h residue 101 THR Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain k residue 14 LEU Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain l residue 46 ARG Chi-restraints excluded: chain m residue 151 ARG Chi-restraints excluded: chain m residue 215 LEU Chi-restraints excluded: chain m residue 262 CYS Chi-restraints excluded: chain m residue 316 ILE Chi-restraints excluded: chain m residue 389 ARG Chi-restraints excluded: chain p residue 89 MET Chi-restraints excluded: chain q residue 72 SER Chi-restraints excluded: chain r residue 59 VAL Chi-restraints excluded: chain r residue 92 LEU Chi-restraints excluded: chain r residue 157 VAL Chi-restraints excluded: chain r residue 164 ARG Chi-restraints excluded: chain r residue 237 VAL Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain s residue 69 MET Chi-restraints excluded: chain s residue 72 LEU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain u residue 68 THR Chi-restraints excluded: chain u residue 117 GLU Chi-restraints excluded: chain v residue 140 MET Chi-restraints excluded: chain v residue 181 VAL Chi-restraints excluded: chain v residue 199 VAL Chi-restraints excluded: chain v residue 218 LEU Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 38 ASP Chi-restraints excluded: chain w residue 67 SER Chi-restraints excluded: chain w residue 112 THR Chi-restraints excluded: chain w residue 159 LEU Chi-restraints excluded: chain w residue 177 ARG Chi-restraints excluded: chain w residue 187 LEU Chi-restraints excluded: chain w residue 195 GLN Chi-restraints excluded: chain x residue 118 THR Chi-restraints excluded: chain x residue 157 SER Chi-restraints excluded: chain x residue 207 ASP Chi-restraints excluded: chain x residue 212 LEU Chi-restraints excluded: chain x residue 271 GLN Chi-restraints excluded: chain x residue 272 TYR Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 470 VAL Chi-restraints excluded: chain x residue 488 GLU Chi-restraints excluded: chain y residue 24 CYS Chi-restraints excluded: chain y residue 167 VAL Chi-restraints excluded: chain z residue 6 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1181 random chunks: chunk 744 optimal weight: 9.9990 chunk 998 optimal weight: 0.9990 chunk 287 optimal weight: 10.0000 chunk 863 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 260 optimal weight: 10.0000 chunk 938 optimal weight: 3.9990 chunk 392 optimal weight: 6.9990 chunk 963 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 36 GLN A 79 ASN B 293 ASN C 18 ASN F 157 ASN G 77 GLN G 138 HIS ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN ** N 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 122 GLN Q 73 GLN ** S 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 GLN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 ASN Y 120 GLN ** c 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 106 ASN g 11 ASN h 59 ASN ** k 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 65 GLN s 53 ASN ** u 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 25 ASN w 91 GLN ** w 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.099400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.076704 restraints weight = 297396.131| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.35 r_work: 0.2986 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 150674 Z= 0.381 Angle : 0.649 11.693 219644 Z= 0.332 Chirality : 0.041 0.385 27223 Planarity : 0.005 0.070 15459 Dihedral : 23.140 179.951 61284 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.86 % Allowed : 20.07 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.09), residues: 8600 helix: 1.25 (0.09), residues: 3115 sheet: -0.45 (0.14), residues: 1216 loop : -0.42 (0.10), residues: 4269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP J 162 HIS 0.011 0.001 HIS B 163 PHE 0.031 0.002 PHE F 229 TYR 0.030 0.002 TYR y 151 ARG 0.010 0.001 ARG F 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 50506.62 seconds wall clock time: 875 minutes 4.65 seconds (52504.65 seconds total)