Starting phenix.real_space_refine on Tue Mar 19 21:56:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvr_12610/03_2024/7nvr_12610_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvr_12610/03_2024/7nvr_12610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvr_12610/03_2024/7nvr_12610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvr_12610/03_2024/7nvr_12610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvr_12610/03_2024/7nvr_12610_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvr_12610/03_2024/7nvr_12610_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 18 6.06 5 P 127 5.49 5 Mg 1 5.21 5 S 554 5.16 5 C 60589 2.51 5 N 16776 2.21 5 O 18057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 673": "OD1" <-> "OD2" Residue "0 PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 264": "OE1" <-> "OE2" Residue "3 ARG 276": "NH1" <-> "NH2" Residue "3 TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 11": "NH1" <-> "NH2" Residue "8 TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 53": "OD1" <-> "OD2" Residue "8 ARG 57": "NH1" <-> "NH2" Residue "8 GLU 68": "OE1" <-> "OE2" Residue "8 ASP 79": "OD1" <-> "OD2" Residue "8 GLU 95": "OE1" <-> "OE2" Residue "8 ASP 97": "OD1" <-> "OD2" Residue "8 TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 137": "OD1" <-> "OD2" Residue "8 GLU 147": "OE1" <-> "OE2" Residue "8 ASP 155": "OD1" <-> "OD2" Residue "8 PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 167": "NH1" <-> "NH2" Residue "8 ASP 195": "OD1" <-> "OD2" Residue "8 ASP 220": "OD1" <-> "OD2" Residue "8 ASP 239": "OD1" <-> "OD2" Residue "8 PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 270": "OD1" <-> "OD2" Residue "8 PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 309": "NH1" <-> "NH2" Residue "9 ASP 44": "OD1" <-> "OD2" Residue "9 GLU 52": "OE1" <-> "OE2" Residue "9 TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 137": "OE1" <-> "OE2" Residue "9 ASP 173": "OD1" <-> "OD2" Residue "9 TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 182": "OE1" <-> "OE2" Residue "9 PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 202": "OD1" <-> "OD2" Residue "9 ARG 242": "NH1" <-> "NH2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 845": "OE1" <-> "OE2" Residue "A TYR 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 132": "OD1" <-> "OD2" Residue "E ASP 46": "OD1" <-> "OD2" Residue "G TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 141": "OD1" <-> "OD2" Residue "H PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 252": "OD1" <-> "OD2" Residue "Q PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 80": "OE1" <-> "OE2" Residue "R TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 23": "NH1" <-> "NH2" Residue "W GLU 29": "OE1" <-> "OE2" Residue "W ASP 35": "OD1" <-> "OD2" Residue "W GLU 45": "OE1" <-> "OE2" Residue "W ASP 69": "OD1" <-> "OD2" Residue "W ASP 83": "OD1" <-> "OD2" Residue "W TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 164": "OD1" <-> "OD2" Residue "W PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 182": "OE1" <-> "OE2" Residue "W GLU 185": "OE1" <-> "OE2" Residue "W ARG 192": "NH1" <-> "NH2" Residue "X PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 101": "OE1" <-> "OE2" Residue "X ASP 104": "OD1" <-> "OD2" Residue "X ASP 110": "OD1" <-> "OD2" Residue "X TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 169": "OE1" <-> "OE2" Residue "X GLU 214": "OE1" <-> "OE2" Residue "X GLU 215": "OE1" <-> "OE2" Residue "X PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 75": "OE1" <-> "OE2" Residue "a ASP 97": "OD1" <-> "OD2" Residue "a TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 110": "NH1" <-> "NH2" Residue "b GLU 121": "OE1" <-> "OE2" Residue "c ARG 10": "NH1" <-> "NH2" Residue "c ARG 47": "NH1" <-> "NH2" Residue "c ARG 68": "NH1" <-> "NH2" Residue "c ARG 87": "NH1" <-> "NH2" Residue "c ARG 96": "NH1" <-> "NH2" Residue "d ARG 99": "NH1" <-> "NH2" Residue "d ARG 181": "NH1" <-> "NH2" Residue "d ARG 313": "NH1" <-> "NH2" Residue "d ASP 366": "OD1" <-> "OD2" Residue "d ARG 404": "NH1" <-> "NH2" Residue "d ARG 406": "NH1" <-> "NH2" Residue "d ARG 441": "NH1" <-> "NH2" Residue "d GLU 472": "OE1" <-> "OE2" Residue "d ARG 507": "NH1" <-> "NH2" Residue "d PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 587": "OE1" <-> "OE2" Residue "d PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 640": "OE1" <-> "OE2" Residue "e GLU 33": "OE1" <-> "OE2" Residue "e ARG 38": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ASP 53": "OD1" <-> "OD2" Residue "e ARG 74": "NH1" <-> "NH2" Residue "e ARG 86": "NH1" <-> "NH2" Residue "e GLU 112": "OE1" <-> "OE2" Residue "e PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 124": "NH1" <-> "NH2" Residue "e PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 137": "NH1" <-> "NH2" Residue "e ARG 150": "NH1" <-> "NH2" Residue "e ASP 180": "OD1" <-> "OD2" Residue "e GLU 191": "OE1" <-> "OE2" Residue "e GLU 200": "OE1" <-> "OE2" Residue "f ARG 26": "NH1" <-> "NH2" Residue "f ASP 42": "OD1" <-> "OD2" Residue "f TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 143": "OE1" <-> "OE2" Residue "f ARG 201": "NH1" <-> "NH2" Residue "g PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 35": "OE1" <-> "OE2" Residue "g ARG 64": "NH1" <-> "NH2" Residue "g GLU 110": "OE1" <-> "OE2" Residue "g ASP 121": "OD1" <-> "OD2" Residue "g GLU 133": "OE1" <-> "OE2" Residue "h ARG 29": "NH1" <-> "NH2" Residue "h ARG 42": "NH1" <-> "NH2" Residue "h ARG 52": "NH1" <-> "NH2" Residue "h GLU 62": "OE1" <-> "OE2" Residue "h GLU 67": "OE1" <-> "OE2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h GLU 75": "OE1" <-> "OE2" Residue "h PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 92": "OE1" <-> "OE2" Residue "h GLU 97": "OE1" <-> "OE2" Residue "h GLU 136": "OE1" <-> "OE2" Residue "h ARG 154": "NH1" <-> "NH2" Residue "i TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 28": "OE1" <-> "OE2" Residue "i ARG 79": "NH1" <-> "NH2" Residue "i PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 125": "OE1" <-> "OE2" Residue "i ARG 127": "NH1" <-> "NH2" Residue "i ARG 132": "NH1" <-> "NH2" Residue "i GLU 133": "OE1" <-> "OE2" Residue "i ARG 136": "NH1" <-> "NH2" Residue "i ARG 144": "NH1" <-> "NH2" Residue "i ARG 146": "NH1" <-> "NH2" Residue "i ARG 152": "NH1" <-> "NH2" Residue "i PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 159": "NH1" <-> "NH2" Residue "j PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 86": "OD1" <-> "OD2" Residue "j PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 98": "NH1" <-> "NH2" Residue "j GLU 112": "OE1" <-> "OE2" Residue "j ARG 122": "NH1" <-> "NH2" Residue "j GLU 123": "OE1" <-> "OE2" Residue "j ARG 126": "NH1" <-> "NH2" Residue "k PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 6": "OD1" <-> "OD2" Residue "k GLU 9": "OE1" <-> "OE2" Residue "k GLU 13": "OE1" <-> "OE2" Residue "k GLU 17": "OE1" <-> "OE2" Residue "k ARG 20": "NH1" <-> "NH2" Residue "k ASP 28": "OD1" <-> "OD2" Residue "k ARG 55": "NH1" <-> "NH2" Residue "k PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 69": "OE1" <-> "OE2" Residue "k ARG 87": "NH1" <-> "NH2" Residue "k PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 125": "NH1" <-> "NH2" Residue "k ARG 128": "NH1" <-> "NH2" Residue "k ASP 131": "OD1" <-> "OD2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 61": "NH1" <-> "NH2" Residue "l TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 75": "NH1" <-> "NH2" Residue "l ARG 81": "NH1" <-> "NH2" Residue "l PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 135": "NH1" <-> "NH2" Residue "l ARG 141": "NH1" <-> "NH2" Residue "l ASP 142": "OD1" <-> "OD2" Residue "l TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 202": "NH1" <-> "NH2" Residue "l ARG 225": "NH1" <-> "NH2" Residue "l GLU 258": "OE1" <-> "OE2" Residue "l ARG 281": "NH1" <-> "NH2" Residue "l ARG 317": "NH1" <-> "NH2" Residue "l ARG 319": "NH1" <-> "NH2" Residue "l GLU 327": "OE1" <-> "OE2" Residue "l ARG 328": "NH1" <-> "NH2" Residue "l ASP 403": "OD1" <-> "OD2" Residue "l ARG 408": "NH1" <-> "NH2" Residue "l ASP 485": "OD1" <-> "OD2" Residue "l TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 553": "OE1" <-> "OE2" Residue "l PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 128": "NH1" <-> "NH2" Residue "m ARG 153": "NH1" <-> "NH2" Residue "m ARG 164": "NH1" <-> "NH2" Residue "n PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 45": "OD1" <-> "OD2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ASP 68": "OD1" <-> "OD2" Residue "n TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 110": "NH1" <-> "NH2" Residue "n ASP 112": "OD1" <-> "OD2" Residue "n ARG 133": "NH1" <-> "NH2" Residue "o ARG 15": "NH1" <-> "NH2" Residue "o GLU 21": "OE1" <-> "OE2" Residue "o ARG 40": "NH1" <-> "NH2" Residue "o TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 77": "OE1" <-> "OE2" Residue "o GLU 82": "OE1" <-> "OE2" Residue "p ASP 163": "OD1" <-> "OD2" Residue "p PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 182": "NH1" <-> "NH2" Residue "p ARG 205": "NH1" <-> "NH2" Residue "p ASP 244": "OD1" <-> "OD2" Residue "p PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 89": "NH1" <-> "NH2" Residue "q ASP 114": "OD1" <-> "OD2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 96126 Number of models: 1 Model: "" Number of chains: 71 Chain: "0" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5751 Classifications: {'peptide': 714} Link IDs: {'PTRANS': 32, 'TRANS': 681} Chain breaks: 1 Chain: "1" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2167 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 5 Chain: "2" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3158 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 369} Chain breaks: 4 Chain: "3" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1737 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain breaks: 1 Chain: "4" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2066 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain breaks: 1 Chain: "5" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "6" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2732 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 328} Chain breaks: 2 Chain: "7" Number of atoms: 4890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4890 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 24, 'TRANS': 580} Chain breaks: 1 Chain: "8" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2376 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 18, 'TRANS': 279} Chain breaks: 1 Chain: "9" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2293 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 15, 'TRANS': 265} Chain breaks: 1 Chain: "A" Number of atoms: 11274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1423, 11274 Classifications: {'peptide': 1423} Link IDs: {'PCIS': 3, 'PTRANS': 67, 'TRANS': 1352} Chain breaks: 4 Chain: "B" Number of atoms: 9076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 9076 Classifications: {'peptide': 1136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1082} Chain breaks: 2 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1050 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 928 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1953 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 13, 'TRANS': 238} Chain breaks: 1 Chain: "N" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1318 Classifications: {'DNA': 64} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 63} Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1422 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "Q" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "R" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Chain: "T" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1303 Classifications: {'DNA': 64} Link IDs: {'rna3p': 63} Chain: "U" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 930 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "V" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 806 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "W" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1659 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain breaks: 1 Chain: "X" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} Chain: "Y" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "Z" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "a" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1167 Classifications: {'peptide': 143} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 135} Chain: "b" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1046 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain breaks: 2 Chain: "c" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 858 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "d" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3510 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 17, 'TRANS': 421} Chain breaks: 8 Chain: "e" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1353 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain breaks: 4 Chain: "f" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1448 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 177} Chain breaks: 2 Chain: "g" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1063 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain: "h" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1114 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 2 Chain: "i" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 960 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain breaks: 2 Chain: "j" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 596 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Chain: "k" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1088 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain: "l" Number of atoms: 4031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 4031 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 23, 'TRANS': 477} Chain breaks: 11 Chain: "m" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 655 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 8, 'TRANS': 75} Chain: "n" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1005 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "o" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 804 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "p" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1262 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "q" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 591 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "r" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 100 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 Chain: "s" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 369 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "v" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "w" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "x" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 55 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "y" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "z" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 115 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1541 SG CYS 0 190 82.466 111.839 74.367 1.00146.88 S ATOM 943 SG CYS 0 116 88.590 114.226 74.486 1.00145.22 S ATOM 1083 SG CYS 0 134 84.896 114.554 79.674 1.00155.07 S ATOM 1252 SG CYS 0 155 83.245 117.819 74.200 1.00153.83 S ATOM 11119 SG CYS 3 6 102.231 139.603 119.036 1.00115.84 S ATOM 11143 SG CYS 3 9 105.172 140.212 121.205 1.00135.52 S ATOM 11315 SG CYS 3 31 103.266 136.987 121.481 1.00134.36 S ATOM 11336 SG CYS 3 34 101.538 140.702 122.874 1.00136.67 S ATOM 11280 SG CYS 3 26 90.059 140.391 119.855 1.00105.47 S ATOM 11423 SG CYS 3 46 93.205 142.284 121.311 1.00109.99 S ATOM 11445 SG CYS 3 49 91.194 143.616 118.477 1.00113.50 S ATOM 14700 SG CYS 4 268 125.479 81.351 29.985 1.00165.16 S ATOM 14719 SG CYS 4 271 124.080 77.896 28.976 1.00170.45 S ATOM 14804 SG CYS 4 282 123.408 81.400 26.680 1.00152.59 S ATOM 14824 SG CYS 4 285 121.650 80.662 30.311 1.00157.37 S ATOM 14592 SG CYS 4 255 131.474 78.015 17.122 1.00175.26 S ATOM 14609 SG CYS 4 257 127.607 78.423 16.684 1.00176.32 S ATOM 14758 SG CYS 4 276 129.923 81.726 15.477 1.00171.99 S ATOM 17812 SG CYS 6 345 133.396 49.912 46.765 1.00180.66 S ATOM 17834 SG CYS 6 348 137.137 50.142 47.521 1.00191.59 S ATOM 17991 SG CYS 6 368 134.631 51.920 49.778 1.00188.16 S ATOM 18012 SG CYS 6 371 135.317 53.189 46.357 1.00192.59 S ATOM 17932 SG CYS 6 360 125.502 56.246 40.972 1.00172.32 S ATOM 17950 SG CYS 6 363 126.207 53.326 38.749 1.00179.04 S ATOM 18099 SG CYS 6 382 128.957 56.154 39.748 1.00177.50 S ATOM 18116 SG CYS 6 385 125.747 56.768 36.713 1.00176.83 S ATOM 17376 SG CYS 6 291 145.073 90.186 24.954 1.00146.81 S ATOM 17398 SG CYS 6 294 145.977 93.354 26.937 1.00148.93 S ATOM 17487 SG CYS 6 305 143.377 91.046 28.217 1.00138.20 S ATOM 17510 SG CYS 6 308 142.941 93.567 25.376 1.00138.44 S ATOM 28157 SG CYS A 71 120.782 161.928 155.348 1.00 64.54 S ATOM 28179 SG CYS A 74 120.859 159.641 158.107 1.00 58.13 S ATOM 28226 SG CYS A 81 124.085 161.328 156.995 1.00 44.36 S ATOM 28461 SG CYS A 111 142.573 128.647 127.544 1.00104.65 S ATOM 28489 SG CYS A 114 139.893 126.359 128.256 1.00110.71 S ATOM 28802 SG CYS A 154 143.334 125.022 127.389 1.00104.06 S ATOM 28825 SG CYS A 184 141.247 126.546 124.696 1.00102.89 S ATOM 47612 SG CYS B1119 122.213 142.788 156.752 1.00 40.86 S ATOM 47634 SG CYS B1122 124.464 143.148 153.742 1.00 45.37 S ATOM 47749 SG CYS B1137 121.928 145.720 154.404 1.00 52.08 S ATOM 47770 SG CYS B1140 120.648 141.847 153.461 1.00 50.29 S ATOM 48737 SG CYS C 88 135.370 202.075 206.070 1.00 11.83 S ATOM 48750 SG CYS C 90 135.080 202.614 202.194 1.00 4.88 S ATOM 48785 SG CYS C 94 136.164 205.243 204.531 1.00 9.39 S ATOM 48807 SG CYS C 97 138.301 202.311 203.804 1.00 12.38 S ATOM 56093 SG CYS I 17 212.668 150.744 124.092 1.00 81.06 S ATOM 56117 SG CYS I 20 209.168 152.147 123.563 1.00 93.22 S ATOM 56278 SG CYS I 39 209.605 148.691 124.784 1.00 81.03 S ATOM 56303 SG CYS I 42 210.823 149.866 121.113 1.00 78.02 S ATOM 56655 SG CYS I 86 226.019 163.742 164.491 1.00 37.77 S ATOM 56679 SG CYS I 89 227.887 167.001 164.474 1.00 31.61 S ATOM 56883 SG CYS I 114 224.171 167.003 164.463 1.00 35.77 S ATOM 56918 SG CYS I 119 226.089 165.934 161.434 1.00 49.55 S ATOM 57029 SG CYS J 7 168.339 193.540 200.543 1.00 14.08 S ATOM 57053 SG CYS J 10 167.435 193.789 204.297 1.00 9.86 S ATOM 57317 SG CYS J 44 170.537 191.829 203.135 1.00 21.55 S ATOM 57323 SG CYS J 45 170.330 195.533 203.180 1.00 25.84 S ATOM 58443 SG CYS L 19 155.174 211.274 162.847 1.00 14.22 S ATOM 58462 SG CYS L 22 155.292 214.837 163.815 1.00 22.51 S ATOM 58579 SG CYS L 36 152.765 213.677 161.092 1.00 16.82 S ATOM 58605 SG CYS L 39 157.242 213.726 160.580 1.00 24.07 S ATOM 58787 SG CYS M 15 116.080 173.937 172.175 1.00 57.43 S ATOM 58934 SG CYS M 34 117.208 177.451 173.301 1.00 53.56 S ATOM 58956 SG CYS M 37 117.079 174.787 175.622 1.00 58.54 S ATOM 70430 SG CYS W 129 104.804 166.257 145.487 1.00130.72 S ATOM 70450 SG CYS W 132 107.896 165.561 147.384 1.00133.59 S ATOM 70622 SG CYS W 154 104.660 163.189 148.228 1.00129.59 S ATOM 70646 SG CYS W 157 104.578 167.083 148.346 1.00136.74 S ATOM 94344 SG CYS p 281 89.109 214.508 220.039 1.00141.75 S ATOM 94370 SG CYS p 284 92.454 213.725 221.370 1.00148.81 S ATOM 94578 SG CYS p 309 89.490 211.928 223.184 1.00150.34 S Time building chain proxies: 36.78, per 1000 atoms: 0.38 Number of scatterers: 96126 At special positions: 0 Unit cell: (255.15, 248.85, 283.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 18 29.99 Fe 4 26.01 S 554 16.00 P 127 15.00 Mg 1 11.99 O 18057 8.00 N 16776 7.00 C 60589 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: 30.06 Conformation dependent library (CDL) restraints added in 12.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 01000 " pdb="FE1 SF4 01000 " - pdb=" SG CYS 0 190 " pdb="FE4 SF4 01000 " - pdb=" SG CYS 0 155 " pdb="FE2 SF4 01000 " - pdb=" SG CYS 0 116 " pdb="FE3 SF4 01000 " - pdb=" SG CYS 0 134 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 3 400 " pdb="ZN ZN 3 400 " - pdb=" SG CYS 3 6 " pdb="ZN ZN 3 400 " - pdb=" SG CYS 3 9 " pdb="ZN ZN 3 400 " - pdb=" SG CYS 3 31 " pdb="ZN ZN 3 400 " - pdb=" SG CYS 3 34 " pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" NE2 HIS 3 28 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 49 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 46 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 26 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 268 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 285 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 271 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 282 " pdb=" ZN 4 402 " pdb="ZN ZN 4 402 " - pdb=" ND1 HIS 4 258 " pdb="ZN ZN 4 402 " - pdb=" SG CYS 4 276 " pdb="ZN ZN 4 402 " - pdb=" SG CYS 4 257 " pdb="ZN ZN 4 402 " - pdb=" SG CYS 4 255 " pdb=" ZN 6 401 " pdb="ZN ZN 6 401 " - pdb=" SG CYS 6 371 " pdb="ZN ZN 6 401 " - pdb=" SG CYS 6 368 " pdb="ZN ZN 6 401 " - pdb=" SG CYS 6 348 " pdb="ZN ZN 6 401 " - pdb=" SG CYS 6 345 " pdb=" ZN 6 402 " pdb="ZN ZN 6 402 " - pdb=" SG CYS 6 360 " pdb="ZN ZN 6 402 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 402 " - pdb=" SG CYS 6 382 " pdb="ZN ZN 6 402 " - pdb=" SG CYS 6 385 " pdb=" ZN 6 403 " pdb="ZN ZN 6 403 " - pdb=" SG CYS 6 294 " pdb="ZN ZN 6 403 " - pdb=" SG CYS 6 305 " pdb="ZN ZN 6 403 " - pdb=" SG CYS 6 308 " pdb="ZN ZN 6 403 " - pdb=" SG CYS 6 291 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 37 " pdb="ZN ZN M 401 " - pdb=" NE2 HIS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 34 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 15 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 157 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 129 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 132 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 154 " pdb=" ZN p 401 " pdb="ZN ZN p 401 " - pdb=" ND1 HIS p 306 " pdb="ZN ZN p 401 " - pdb=" SG CYS p 284 " pdb="ZN ZN p 401 " - pdb=" SG CYS p 281 " pdb="ZN ZN p 401 " - pdb=" SG CYS p 309 " Number of angles added : 93 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22256 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 440 helices and 92 sheets defined 45.9% alpha, 10.4% beta 59 base pairs and 100 stacking pairs defined. Time for finding SS restraints: 31.75 Creating SS restraints... Processing helix chain '0' and resid 19 through 34 Processing helix chain '0' and resid 48 through 62 Processing helix chain '0' and resid 77 through 98 removed outlier: 3.813A pdb=" N LYS 0 82 " --> pdb=" O PRO 0 78 " (cutoff:3.500A) Processing helix chain '0' and resid 119 through 122 No H-bonds generated for 'chain '0' and resid 119 through 122' Processing helix chain '0' and resid 127 through 137 Processing helix chain '0' and resid 140 through 148 Processing helix chain '0' and resid 156 through 164 Processing helix chain '0' and resid 177 through 187 Processing helix chain '0' and resid 191 through 198 removed outlier: 3.666A pdb=" N ALA 0 195 " --> pdb=" O PRO 0 191 " (cutoff:3.500A) Processing helix chain '0' and resid 209 through 211 No H-bonds generated for 'chain '0' and resid 209 through 211' Processing helix chain '0' and resid 215 through 221 removed outlier: 3.872A pdb=" N ASP 0 219 " --> pdb=" O PRO 0 215 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LEU 0 220 " --> pdb=" O LYS 0 216 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL 0 221 " --> pdb=" O ILE 0 217 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 215 through 221' Processing helix chain '0' and resid 236 through 245 removed outlier: 3.595A pdb=" N ILE 0 239 " --> pdb=" O ALA 0 236 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP 0 240 " --> pdb=" O HIS 0 237 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASN 0 241 " --> pdb=" O ASN 0 238 " (cutoff:3.500A) Processing helix chain '0' and resid 253 through 276 Processing helix chain '0' and resid 279 through 290 removed outlier: 4.514A pdb=" N GLU 0 284 " --> pdb=" O ARG 0 280 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N TYR 0 285 " --> pdb=" O LEU 0 281 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG 0 286 " --> pdb=" O ARG 0 282 " (cutoff:3.500A) Processing helix chain '0' and resid 326 through 345 Processing helix chain '0' and resid 354 through 365 removed outlier: 4.161A pdb=" N LEU 0 358 " --> pdb=" O PRO 0 354 " (cutoff:3.500A) Processing helix chain '0' and resid 369 through 373 Processing helix chain '0' and resid 375 through 385 Processing helix chain '0' and resid 395 through 409 Processing helix chain '0' and resid 441 through 450 Proline residue: 0 446 - end of helix Processing helix chain '0' and resid 464 through 470 Proline residue: 0 468 - end of helix No H-bonds generated for 'chain '0' and resid 464 through 470' Processing helix chain '0' and resid 514 through 530 Processing helix chain '0' and resid 542 through 554 Processing helix chain '0' and resid 557 through 564 Processing helix chain '0' and resid 574 through 589 Processing helix chain '0' and resid 603 through 607 Processing helix chain '0' and resid 631 through 642 removed outlier: 3.530A pdb=" N LEU 0 640 " --> pdb=" O ARG 0 636 " (cutoff:3.500A) Processing helix chain '0' and resid 648 through 668 removed outlier: 4.543A pdb=" N ARG 0 666 " --> pdb=" O GLN 0 662 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA 0 667 " --> pdb=" O CYS 0 663 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ILE 0 668 " --> pdb=" O VAL 0 664 " (cutoff:3.500A) Processing helix chain '0' and resid 682 through 685 Processing helix chain '0' and resid 687 through 692 Processing helix chain '0' and resid 695 through 700 removed outlier: 3.582A pdb=" N HIS 0 700 " --> pdb=" O TRP 0 696 " (cutoff:3.500A) Processing helix chain '0' and resid 710 through 725 Processing helix chain '1' and resid 109 through 119 removed outlier: 4.664A pdb=" N GLN 1 119 " --> pdb=" O ASN 1 115 " (cutoff:3.500A) Processing helix chain '1' and resid 122 through 133 removed outlier: 3.765A pdb=" N VAL 1 132 " --> pdb=" O TYR 1 128 " (cutoff:3.500A) Processing helix chain '1' and resid 140 through 145 Processing helix chain '1' and resid 191 through 199 Processing helix chain '1' and resid 201 through 209 Processing helix chain '1' and resid 217 through 225 removed outlier: 4.235A pdb=" N PHE 1 225 " --> pdb=" O TRP 1 221 " (cutoff:3.500A) Processing helix chain '1' and resid 298 through 318 removed outlier: 3.744A pdb=" N ILE 1 304 " --> pdb=" O ASN 1 300 " (cutoff:3.500A) Processing helix chain '1' and resid 380 through 383 No H-bonds generated for 'chain '1' and resid 380 through 383' Processing helix chain '1' and resid 397 through 412 removed outlier: 3.653A pdb=" N ILE 1 401 " --> pdb=" O SER 1 397 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET 1 411 " --> pdb=" O ILE 1 407 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLU 1 412 " --> pdb=" O ARG 1 408 " (cutoff:3.500A) Processing helix chain '1' and resid 424 through 434 Processing helix chain '1' and resid 456 through 475 removed outlier: 3.905A pdb=" N GLU 1 460 " --> pdb=" O ASP 1 456 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS 1 474 " --> pdb=" O GLU 1 470 " (cutoff:3.500A) Processing helix chain '1' and resid 486 through 514 removed outlier: 4.135A pdb=" N VAL 1 491 " --> pdb=" O GLU 1 487 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS 1 492 " --> pdb=" O GLU 1 488 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU 1 505 " --> pdb=" O GLN 1 501 " (cutoff:3.500A) Proline residue: 1 507 - end of helix Processing helix chain '1' and resid 524 through 546 Processing helix chain '2' and resid 19 through 24 Processing helix chain '2' and resid 28 through 34 removed outlier: 3.633A pdb=" N ARG 2 33 " --> pdb=" O GLY 2 29 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 47 removed outlier: 3.575A pdb=" N PHE 2 45 " --> pdb=" O CYS 2 41 " (cutoff:3.500A) Processing helix chain '2' and resid 52 through 60 Processing helix chain '2' and resid 68 through 73 Processing helix chain '2' and resid 80 through 93 Processing helix chain '2' and resid 112 through 121 Processing helix chain '2' and resid 146 through 163 Processing helix chain '2' and resid 173 through 181 Processing helix chain '2' and resid 198 through 205 removed outlier: 3.660A pdb=" N GLN 2 202 " --> pdb=" O SER 2 198 " (cutoff:3.500A) Processing helix chain '2' and resid 208 through 226 Processing helix chain '2' and resid 230 through 241 removed outlier: 3.596A pdb=" N PHE 2 236 " --> pdb=" O GLU 2 232 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU 2 237 " --> pdb=" O ILE 2 233 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER 2 241 " --> pdb=" O LEU 2 237 " (cutoff:3.500A) Processing helix chain '2' and resid 256 through 268 Processing helix chain '2' and resid 285 through 288 No H-bonds generated for 'chain '2' and resid 285 through 288' Processing helix chain '2' and resid 322 through 329 Processing helix chain '2' and resid 348 through 357 Processing helix chain '2' and resid 361 through 370 Processing helix chain '2' and resid 374 through 377 No H-bonds generated for 'chain '2' and resid 374 through 377' Processing helix chain '2' and resid 385 through 398 removed outlier: 3.625A pdb=" N ARG 2 398 " --> pdb=" O TRP 2 394 " (cutoff:3.500A) Processing helix chain '2' and resid 415 through 428 Processing helix chain '2' and resid 445 through 457 removed outlier: 3.720A pdb=" N SER 2 449 " --> pdb=" O PRO 2 445 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP 2 450 " --> pdb=" O ALA 2 446 " (cutoff:3.500A) Processing helix chain '3' and resid 12 through 15 No H-bonds generated for 'chain '3' and resid 12 through 15' Processing helix chain '3' and resid 32 through 40 removed outlier: 3.700A pdb=" N LEU 3 37 " --> pdb=" O SER 3 33 " (cutoff:3.500A) Processing helix chain '3' and resid 66 through 80 removed outlier: 3.932A pdb=" N LYS 3 80 " --> pdb=" O LYS 3 76 " (cutoff:3.500A) Processing helix chain '3' and resid 86 through 88 No H-bonds generated for 'chain '3' and resid 86 through 88' Processing helix chain '3' and resid 92 through 111 removed outlier: 4.521A pdb=" N ASN 3 96 " --> pdb=" O LEU 3 92 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE 3 98 " --> pdb=" O GLU 3 94 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU 3 99 " --> pdb=" O TYR 3 95 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN 3 111 " --> pdb=" O PHE 3 107 " (cutoff:3.500A) Processing helix chain '3' and resid 115 through 148 removed outlier: 3.740A pdb=" N LYS 3 127 " --> pdb=" O GLU 3 123 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LYS 3 130 " --> pdb=" O GLN 3 126 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP 3 131 " --> pdb=" O LYS 3 127 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE 3 133 " --> pdb=" O ASN 3 129 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLN 3 134 " --> pdb=" O LYS 3 130 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR 3 141 " --> pdb=" O LYS 3 137 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG 3 142 " --> pdb=" O LEU 3 138 " (cutoff:3.500A) Processing helix chain '3' and resid 271 through 274 Processing helix chain '3' and resid 280 through 284 Processing helix chain '3' and resid 290 through 300 Processing helix chain '4' and resid 19 through 28 Processing helix chain '4' and resid 34 through 51 Processing helix chain '4' and resid 102 through 120 Processing helix chain '4' and resid 134 through 150 Processing helix chain '4' and resid 171 through 187 removed outlier: 4.665A pdb=" N MET 4 175 " --> pdb=" O LEU 4 172 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN 4 176 " --> pdb=" O GLN 4 173 " (cutoff:3.500A) Processing helix chain '4' and resid 201 through 210 removed outlier: 3.657A pdb=" N THR 4 210 " --> pdb=" O ALA 4 206 " (cutoff:3.500A) Processing helix chain '4' and resid 220 through 229 removed outlier: 4.933A pdb=" N LEU 4 224 " --> pdb=" O PRO 4 221 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN 4 225 " --> pdb=" O SER 4 222 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP 4 229 " --> pdb=" O TYR 4 226 " (cutoff:3.500A) Processing helix chain '4' and resid 235 through 238 No H-bonds generated for 'chain '4' and resid 235 through 238' Processing helix chain '5' and resid 14 through 26 Processing helix chain '5' and resid 47 through 64 removed outlier: 4.555A pdb=" N ASN 5 51 " --> pdb=" O GLU 5 48 " (cutoff:3.500A) Processing helix chain '6' and resid 10 through 13 No H-bonds generated for 'chain '6' and resid 10 through 13' Processing helix chain '6' and resid 18 through 21 removed outlier: 3.801A pdb=" N ILE 6 21 " --> pdb=" O THR 6 18 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 18 through 21' Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 80 through 98 removed outlier: 3.642A pdb=" N TYR 6 90 " --> pdb=" O LYS 6 86 " (cutoff:3.500A) Processing helix chain '6' and resid 124 through 136 removed outlier: 4.367A pdb=" N ASP 6 136 " --> pdb=" O LYS 6 132 " (cutoff:3.500A) Processing helix chain '6' and resid 145 through 157 Processing helix chain '6' and resid 182 through 192 removed outlier: 3.524A pdb=" N LYS 6 187 " --> pdb=" O TYR 6 183 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR 6 188 " --> pdb=" O ASP 6 184 " (cutoff:3.500A) Processing helix chain '6' and resid 206 through 215 Processing helix chain '6' and resid 225 through 236 Processing helix chain '6' and resid 315 through 325 removed outlier: 4.133A pdb=" N SER 6 321 " --> pdb=" O HIS 6 317 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR 6 322 " --> pdb=" O LEU 6 318 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N HIS 6 323 " --> pdb=" O ALA 6 319 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N HIS 6 324 " --> pdb=" O ARG 6 320 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU 6 325 " --> pdb=" O SER 6 321 " (cutoff:3.500A) Processing helix chain '6' and resid 369 through 377 Processing helix chain '6' and resid 383 through 386 No H-bonds generated for 'chain '6' and resid 383 through 386' Processing helix chain '7' and resid 93 through 103 Processing helix chain '7' and resid 120 through 129 Processing helix chain '7' and resid 133 through 143 removed outlier: 4.407A pdb=" N TYR 7 139 " --> pdb=" O ASP 7 135 " (cutoff:3.500A) Processing helix chain '7' and resid 150 through 161 Processing helix chain '7' and resid 182 through 188 Processing helix chain '7' and resid 192 through 197 Processing helix chain '7' and resid 275 through 287 removed outlier: 4.322A pdb=" N GLU 7 278 " --> pdb=" O GLU 7 275 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE 7 285 " --> pdb=" O LYS 7 282 " (cutoff:3.500A) Processing helix chain '7' and resid 318 through 327 Processing helix chain '7' and resid 342 through 344 No H-bonds generated for 'chain '7' and resid 342 through 344' Processing helix chain '7' and resid 346 through 357 Processing helix chain '7' and resid 368 through 381 Processing helix chain '7' and resid 386 through 388 No H-bonds generated for 'chain '7' and resid 386 through 388' Processing helix chain '7' and resid 410 through 413 No H-bonds generated for 'chain '7' and resid 410 through 413' Processing helix chain '7' and resid 421 through 432 Processing helix chain '7' and resid 443 through 445 No H-bonds generated for 'chain '7' and resid 443 through 445' Processing helix chain '7' and resid 449 through 457 removed outlier: 3.540A pdb=" N VAL 7 454 " --> pdb=" O MET 7 450 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU 7 455 " --> pdb=" O PHE 7 451 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR 7 456 " --> pdb=" O ARG 7 452 " (cutoff:3.500A) Processing helix chain '7' and resid 477 through 483 removed outlier: 4.078A pdb=" N ASN 7 481 " --> pdb=" O ILE 7 477 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE 7 482 " --> pdb=" O VAL 7 478 " (cutoff:3.500A) Processing helix chain '7' and resid 493 through 499 Processing helix chain '7' and resid 516 through 524 Processing helix chain '7' and resid 529 through 534 removed outlier: 4.457A pdb=" N TYR 7 534 " --> pdb=" O ILE 7 531 " (cutoff:3.500A) Processing helix chain '7' and resid 538 through 553 Processing helix chain '7' and resid 565 through 574 Processing helix chain '7' and resid 586 through 598 Processing helix chain '7' and resid 609 through 613 Processing helix chain '7' and resid 633 through 642 removed outlier: 3.920A pdb=" N ARG 7 642 " --> pdb=" O GLN 7 638 " (cutoff:3.500A) Processing helix chain '7' and resid 668 through 676 Processing helix chain '7' and resid 678 through 683 Processing helix chain '7' and resid 706 through 719 Processing helix chain '8' and resid 57 through 68 removed outlier: 4.086A pdb=" N GLU 8 68 " --> pdb=" O LYS 8 64 " (cutoff:3.500A) Processing helix chain '8' and resid 98 through 103 Processing helix chain '8' and resid 111 through 130 Processing helix chain '8' and resid 140 through 142 No H-bonds generated for 'chain '8' and resid 140 through 142' Processing helix chain '8' and resid 176 through 178 No H-bonds generated for 'chain '8' and resid 176 through 178' Processing helix chain '8' and resid 181 through 184 No H-bonds generated for 'chain '8' and resid 181 through 184' Processing helix chain '8' and resid 193 through 208 Processing helix chain '8' and resid 218 through 229 Processing helix chain '8' and resid 240 through 242 No H-bonds generated for 'chain '8' and resid 240 through 242' Processing helix chain '8' and resid 257 through 260 No H-bonds generated for 'chain '8' and resid 257 through 260' Processing helix chain '8' and resid 266 through 275 Processing helix chain '8' and resid 286 through 290 Processing helix chain '8' and resid 293 through 296 No H-bonds generated for 'chain '8' and resid 293 through 296' Processing helix chain '9' and resid 2 through 4 No H-bonds generated for 'chain '9' and resid 2 through 4' Processing helix chain '9' and resid 6 through 9 No H-bonds generated for 'chain '9' and resid 6 through 9' Processing helix chain '9' and resid 16 through 36 Processing helix chain '9' and resid 50 through 70 Processing helix chain '9' and resid 77 through 93 Processing helix chain '9' and resid 101 through 115 Processing helix chain '9' and resid 122 through 127 Processing helix chain '9' and resid 133 through 153 removed outlier: 4.525A pdb=" N LEU 9 148 " --> pdb=" O LEU 9 144 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU 9 149 " --> pdb=" O GLU 9 145 " (cutoff:3.500A) Processing helix chain '9' and resid 163 through 177 Processing helix chain '9' and resid 186 through 200 Processing helix chain '9' and resid 202 through 205 Processing helix chain '9' and resid 209 through 224 Processing helix chain '9' and resid 229 through 233 Processing helix chain '9' and resid 242 through 260 Processing helix chain '9' and resid 268 through 282 Processing helix chain 'A' and resid 28 through 34 Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 137 through 149 Processing helix chain 'A' and resid 218 through 227 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.594A pdb=" N PHE A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 248 Processing helix chain 'A' and resid 275 through 296 Processing helix chain 'A' and resid 300 through 318 Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 486 through 492 removed outlier: 3.576A pdb=" N THR A 489 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) Proline residue: A 491 - end of helix No H-bonds generated for 'chain 'A' and resid 486 through 492' Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 539 through 549 Processing helix chain 'A' and resid 557 through 566 removed outlier: 3.979A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 642 through 645 No H-bonds generated for 'chain 'A' and resid 642 through 645' Processing helix chain 'A' and resid 652 through 659 Processing helix chain 'A' and resid 662 through 683 removed outlier: 4.026A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 692 No H-bonds generated for 'chain 'A' and resid 689 through 692' Processing helix chain 'A' and resid 696 through 721 Processing helix chain 'A' and resid 733 through 759 Processing helix chain 'A' and resid 765 through 772 Processing helix chain 'A' and resid 778 through 785 Processing helix chain 'A' and resid 817 through 820 No H-bonds generated for 'chain 'A' and resid 817 through 820' Processing helix chain 'A' and resid 833 through 867 removed outlier: 3.559A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLY A 858 " --> pdb=" O THR A 854 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLN A 861 " --> pdb=" O THR A 857 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 862 " --> pdb=" O GLY A 858 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS A 866 " --> pdb=" O ARG A 862 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 867 " --> pdb=" O ARG A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 907 through 910 No H-bonds generated for 'chain 'A' and resid 907 through 910' Processing helix chain 'A' and resid 913 through 920 Processing helix chain 'A' and resid 927 through 933 Processing helix chain 'A' and resid 936 through 944 Processing helix chain 'A' and resid 946 through 969 Processing helix chain 'A' and resid 983 through 994 Processing helix chain 'A' and resid 1006 through 1019 Processing helix chain 'A' and resid 1028 through 1037 Processing helix chain 'A' and resid 1039 through 1048 Processing helix chain 'A' and resid 1051 through 1056 Processing helix chain 'A' and resid 1062 through 1079 Processing helix chain 'A' and resid 1087 through 1101 Proline residue: A1098 - end of helix removed outlier: 4.105A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1128 Processing helix chain 'A' and resid 1146 through 1149 No H-bonds generated for 'chain 'A' and resid 1146 through 1149' Processing helix chain 'A' and resid 1151 through 1161 Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1187 through 1198 removed outlier: 3.520A pdb=" N GLU A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TRP A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1223 Processing helix chain 'A' and resid 1228 through 1239 removed outlier: 3.877A pdb=" N ALA A1232 " --> pdb=" O MET A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1266 No H-bonds generated for 'chain 'A' and resid 1263 through 1266' Processing helix chain 'A' and resid 1283 through 1294 Processing helix chain 'A' and resid 1343 through 1348 Processing helix chain 'A' and resid 1362 through 1368 Processing helix chain 'A' and resid 1371 through 1388 Processing helix chain 'A' and resid 1395 through 1405 Processing helix chain 'A' and resid 1416 through 1419 No H-bonds generated for 'chain 'A' and resid 1416 through 1419' Processing helix chain 'A' and resid 1426 through 1432 Processing helix chain 'A' and resid 1435 through 1445 Processing helix chain 'A' and resid 1454 through 1460 Processing helix chain 'A' and resid 1467 through 1469 No H-bonds generated for 'chain 'A' and resid 1467 through 1469' Processing helix chain 'A' and resid 1477 through 1481 Processing helix chain 'B' and resid 19 through 36 removed outlier: 4.294A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 61 removed outlier: 4.475A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 116 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 249 through 252 No H-bonds generated for 'chain 'B' and resid 249 through 252' Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 281 through 288 Processing helix chain 'B' and resid 295 through 307 removed outlier: 3.540A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 314 through 324 removed outlier: 3.542A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 345 Processing helix chain 'B' and resid 358 through 377 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 396 through 425 Processing helix chain 'B' and resid 431 through 434 No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 475 through 482 Processing helix chain 'B' and resid 491 through 495 Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 539 through 547 Processing helix chain 'B' and resid 558 through 561 Processing helix chain 'B' and resid 580 through 593 Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 653 through 659 Processing helix chain 'B' and resid 667 through 672 removed outlier: 4.036A pdb=" N THR B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 682 No H-bonds generated for 'chain 'B' and resid 679 through 682' Processing helix chain 'B' and resid 700 through 703 Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing helix chain 'B' and resid 719 through 730 removed outlier: 3.965A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 969 through 975 Proline residue: B 973 - end of helix Processing helix chain 'B' and resid 978 through 993 Processing helix chain 'B' and resid 1008 through 1018 removed outlier: 3.676A pdb=" N TYR B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1058 No H-bonds generated for 'chain 'B' and resid 1055 through 1058' Processing helix chain 'B' and resid 1088 through 1097 Processing helix chain 'B' and resid 1100 through 1107 Processing helix chain 'B' and resid 1109 through 1112 No H-bonds generated for 'chain 'B' and resid 1109 through 1112' Processing helix chain 'B' and resid 1153 through 1164 Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 78 through 81 No H-bonds generated for 'chain 'C' and resid 78 through 81' Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 241 through 270 Processing helix chain 'D' and resid 34 through 49 Processing helix chain 'D' and resid 59 through 71 removed outlier: 3.641A pdb=" N PHE D 71 " --> pdb=" O TYR D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 89 removed outlier: 3.518A pdb=" N ALA D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 103 removed outlier: 3.555A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 124 through 140 removed outlier: 3.836A pdb=" N ILE D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 24 Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 44 Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 112 through 120 removed outlier: 3.730A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 135 No H-bonds generated for 'chain 'E' and resid 132 through 135' Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 153 through 163 Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'F' and resid 59 through 74 Processing helix chain 'F' and resid 89 through 99 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 23 through 34 removed outlier: 3.522A pdb=" N PHE G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 87 Processing helix chain 'I' and resid 64 through 67 No H-bonds generated for 'chain 'I' and resid 64 through 67' Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 31 through 38 Processing helix chain 'J' and resid 43 through 50 removed outlier: 3.718A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.852A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 9 Processing helix chain 'K' and resid 40 through 52 removed outlier: 3.951A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 114 Processing helix chain 'M' and resid 48 through 51 No H-bonds generated for 'chain 'M' and resid 48 through 51' Processing helix chain 'M' and resid 109 through 128 removed outlier: 3.580A pdb=" N ILE M 128 " --> pdb=" O MET M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 148 Processing helix chain 'M' and resid 156 through 171 Processing helix chain 'M' and resid 177 through 183 removed outlier: 3.584A pdb=" N VAL M 183 " --> pdb=" O GLU M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 202 Processing helix chain 'M' and resid 211 through 222 removed outlier: 3.638A pdb=" N MET M 215 " --> pdb=" O THR M 211 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER M 216 " --> pdb=" O GLY M 212 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ARG M 217 " --> pdb=" O ASP M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 242 Processing helix chain 'M' and resid 250 through 264 Processing helix chain 'M' and resid 271 through 278 Processing helix chain 'M' and resid 282 through 299 Proline residue: M 294 - end of helix Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 310 through 312 No H-bonds generated for 'chain 'M' and resid 310 through 312' Processing helix chain 'O' and resid 180 through 186 Processing helix chain 'O' and resid 227 through 243 Processing helix chain 'O' and resid 270 through 276 Processing helix chain 'O' and resid 318 through 335 Proline residue: O 330 - end of helix removed outlier: 3.667A pdb=" N PHE O 335 " --> pdb=" O ILE O 331 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 8 No H-bonds generated for 'chain 'Q' and resid 6 through 8' Processing helix chain 'Q' and resid 33 through 35 No H-bonds generated for 'chain 'Q' and resid 33 through 35' Processing helix chain 'Q' and resid 157 through 166 removed outlier: 3.756A pdb=" N GLU Q 161 " --> pdb=" O ALA Q 157 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU Q 163 " --> pdb=" O GLU Q 159 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG Q 166 " --> pdb=" O GLU Q 162 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 179 Processing helix chain 'R' and resid 10 through 14 Processing helix chain 'R' and resid 25 through 34 removed outlier: 4.178A pdb=" N ALA R 34 " --> pdb=" O GLN R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 63 No H-bonds generated for 'chain 'R' and resid 60 through 63' Processing helix chain 'R' and resid 123 through 137 removed outlier: 3.513A pdb=" N LEU R 127 " --> pdb=" O ASN R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 172 Processing helix chain 'R' and resid 180 through 193 Processing helix chain 'R' and resid 199 through 206 Processing helix chain 'R' and resid 210 through 220 removed outlier: 3.589A pdb=" N ILE R 220 " --> pdb=" O ILE R 216 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 31 removed outlier: 4.441A pdb=" N ASP U 27 " --> pdb=" O ASN U 23 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE U 28 " --> pdb=" O ASP U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 50 Processing helix chain 'U' and resid 325 through 329 Processing helix chain 'V' and resid 6 through 8 No H-bonds generated for 'chain 'V' and resid 6 through 8' Processing helix chain 'V' and resid 10 through 24 Processing helix chain 'V' and resid 30 through 51 Processing helix chain 'W' and resid 12 through 25 Processing helix chain 'W' and resid 28 through 39 removed outlier: 3.712A pdb=" N ALA W 33 " --> pdb=" O GLU W 29 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE W 36 " --> pdb=" O LEU W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 52 Processing helix chain 'W' and resid 56 through 69 Processing helix chain 'W' and resid 96 through 123 removed outlier: 3.734A pdb=" N ASN W 101 " --> pdb=" O ARG W 97 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG W 111 " --> pdb=" O LEU W 107 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG W 112 " --> pdb=" O ASP W 108 " (cutoff:3.500A) Processing helix chain 'W' and resid 138 through 144 Processing helix chain 'W' and resid 164 through 195 removed outlier: 4.100A pdb=" N MET W 168 " --> pdb=" O ASP W 164 " (cutoff:3.500A) Proline residue: W 169 - end of helix removed outlier: 3.598A pdb=" N ALA W 178 " --> pdb=" O ARG W 174 " (cutoff:3.500A) Proline residue: W 186 - end of helix removed outlier: 4.270A pdb=" N ALA W 189 " --> pdb=" O GLU W 185 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU W 190 " --> pdb=" O PRO W 186 " (cutoff:3.500A) Processing helix chain 'W' and resid 279 through 282 No H-bonds generated for 'chain 'W' and resid 279 through 282' Processing helix chain 'X' and resid 76 through 91 Processing helix chain 'X' and resid 99 through 106 Processing helix chain 'X' and resid 113 through 126 removed outlier: 4.430A pdb=" N LEU X 124 " --> pdb=" O MET X 120 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL X 125 " --> pdb=" O THR X 121 " (cutoff:3.500A) Processing helix chain 'X' and resid 148 through 161 Processing helix chain 'X' and resid 168 through 174 Processing helix chain 'X' and resid 178 through 188 removed outlier: 6.095A pdb=" N ASP X 187 " --> pdb=" O LYS X 183 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLN X 188 " --> pdb=" O ALA X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 214 through 222 Processing helix chain 'X' and resid 230 through 239 Processing helix chain 'Y' and resid 8 through 10 No H-bonds generated for 'chain 'Y' and resid 8 through 10' Processing helix chain 'a' and resid 10 through 12 No H-bonds generated for 'chain 'a' and resid 10 through 12' Processing helix chain 'a' and resid 21 through 23 No H-bonds generated for 'chain 'a' and resid 21 through 23' Processing helix chain 'a' and resid 26 through 34 removed outlier: 3.754A pdb=" N LEU a 30 " --> pdb=" O SER a 26 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP a 31 " --> pdb=" O GLY a 27 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 53 removed outlier: 3.518A pdb=" N LYS a 51 " --> pdb=" O ASN a 47 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET a 52 " --> pdb=" O GLU a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 62 removed outlier: 4.239A pdb=" N GLN a 62 " --> pdb=" O GLU a 58 " (cutoff:3.500A) Processing helix chain 'a' and resid 114 through 136 removed outlier: 3.504A pdb=" N SER a 135 " --> pdb=" O ASP a 131 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR a 136 " --> pdb=" O GLU a 132 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 35 removed outlier: 3.596A pdb=" N ALA b 14 " --> pdb=" O ALA b 10 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 63 removed outlier: 4.072A pdb=" N ASP b 47 " --> pdb=" O PRO b 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU b 51 " --> pdb=" O ASP b 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 108 No H-bonds generated for 'chain 'b' and resid 105 through 108' Processing helix chain 'b' and resid 115 through 131 removed outlier: 3.730A pdb=" N GLU b 119 " --> pdb=" O PRO b 115 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN b 120 " --> pdb=" O GLU b 116 " (cutoff:3.500A) Processing helix chain 'b' and resid 134 through 154 removed outlier: 3.683A pdb=" N CYS b 147 " --> pdb=" O ASN b 144 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU b 151 " --> pdb=" O SER b 148 " (cutoff:3.500A) Processing helix chain 'b' and resid 175 through 186 removed outlier: 3.676A pdb=" N ALA b 184 " --> pdb=" O ALA b 180 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA b 186 " --> pdb=" O VAL b 182 " (cutoff:3.500A) Processing helix chain 'c' and resid 11 through 36 removed outlier: 3.976A pdb=" N GLY c 22 " --> pdb=" O GLU c 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER c 36 " --> pdb=" O ILE c 32 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 73 removed outlier: 3.766A pdb=" N SER c 55 " --> pdb=" O ALA c 51 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN c 72 " --> pdb=" O ARG c 68 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL c 73 " --> pdb=" O TYR c 69 " (cutoff:3.500A) Processing helix chain 'c' and resid 87 through 115 removed outlier: 3.670A pdb=" N MET c 114 " --> pdb=" O THR c 110 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU c 115 " --> pdb=" O CYS c 111 " (cutoff:3.500A) Processing helix chain 'd' and resid 95 through 121 removed outlier: 3.613A pdb=" N LEU d 112 " --> pdb=" O GLU d 108 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 142 through 172 removed outlier: 3.553A pdb=" N SER d 148 " --> pdb=" O LEU d 144 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER d 170 " --> pdb=" O ARG d 166 " (cutoff:3.500A) Processing helix chain 'd' and resid 185 through 193 removed outlier: 3.924A pdb=" N ARG d 189 " --> pdb=" O SER d 185 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN d 192 " --> pdb=" O LEU d 188 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS d 193 " --> pdb=" O ARG d 189 " (cutoff:3.500A) Processing helix chain 'd' and resid 290 through 317 removed outlier: 3.854A pdb=" N VAL d 316 " --> pdb=" O SER d 312 " (cutoff:3.500A) Processing helix chain 'd' and resid 371 through 385 removed outlier: 3.734A pdb=" N HIS d 376 " --> pdb=" O GLU d 372 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG d 380 " --> pdb=" O HIS d 376 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU d 381 " --> pdb=" O LEU d 377 " (cutoff:3.500A) Processing helix chain 'd' and resid 403 through 411 Proline residue: d 410 - end of helix Processing helix chain 'd' and resid 415 through 423 removed outlier: 3.657A pdb=" N ASN d 419 " --> pdb=" O LYS d 415 " (cutoff:3.500A) Processing helix chain 'd' and resid 428 through 454 removed outlier: 4.193A pdb=" N GLN d 434 " --> pdb=" O LYS d 430 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE d 439 " --> pdb=" O ALA d 435 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU d 440 " --> pdb=" O LYS d 436 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER d 442 " --> pdb=" O ILE d 438 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR d 447 " --> pdb=" O ARG d 443 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE d 448 " --> pdb=" O ALA d 444 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER d 453 " --> pdb=" O ASP d 449 " (cutoff:3.500A) Processing helix chain 'd' and resid 518 through 543 Processing helix chain 'd' and resid 635 through 646 Processing helix chain 'e' and resid 29 through 42 removed outlier: 3.917A pdb=" N GLU e 33 " --> pdb=" O ASP e 29 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER e 34 " --> pdb=" O HIS e 30 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N HIS e 37 " --> pdb=" O GLU e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 114 through 121 Processing helix chain 'e' and resid 180 through 193 removed outlier: 3.694A pdb=" N MET e 186 " --> pdb=" O VAL e 182 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS e 187 " --> pdb=" O SER e 183 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN e 188 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing helix chain 'f' and resid 17 through 31 removed outlier: 3.695A pdb=" N VAL f 21 " --> pdb=" O VAL f 17 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU f 22 " --> pdb=" O GLN f 18 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU f 31 " --> pdb=" O LYS f 27 " (cutoff:3.500A) Processing helix chain 'f' and resid 89 through 100 removed outlier: 3.645A pdb=" N VAL f 96 " --> pdb=" O VAL f 93 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY f 100 " --> pdb=" O LYS f 97 " (cutoff:3.500A) Processing helix chain 'f' and resid 151 through 164 removed outlier: 5.807A pdb=" N SER f 155 " --> pdb=" O ASP f 152 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU f 158 " --> pdb=" O SER f 155 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN f 162 " --> pdb=" O GLU f 159 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER f 163 " --> pdb=" O PHE f 160 " (cutoff:3.500A) Processing helix chain 'f' and resid 187 through 202 removed outlier: 3.623A pdb=" N VAL f 191 " --> pdb=" O ALA f 187 " (cutoff:3.500A) Processing helix chain 'g' and resid 12 through 39 Processing helix chain 'g' and resid 50 through 89 removed outlier: 3.636A pdb=" N GLU g 55 " --> pdb=" O ALA g 51 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS g 83 " --> pdb=" O VAL g 79 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN g 84 " --> pdb=" O SER g 80 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU g 88 " --> pdb=" O GLN g 84 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 136 removed outlier: 3.506A pdb=" N LEU g 108 " --> pdb=" O GLN g 104 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU g 133 " --> pdb=" O GLU g 129 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR g 135 " --> pdb=" O GLU g 131 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 49 removed outlier: 3.551A pdb=" N LEU h 34 " --> pdb=" O LEU h 30 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU h 37 " --> pdb=" O ALA h 33 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET h 47 " --> pdb=" O GLU h 43 " (cutoff:3.500A) Processing helix chain 'h' and resid 51 through 54 removed outlier: 3.855A pdb=" N GLN h 54 " --> pdb=" O SER h 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 51 through 54' Processing helix chain 'h' and resid 63 through 120 removed outlier: 4.141A pdb=" N MET h 80 " --> pdb=" O PHE h 76 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LYS h 81 " --> pdb=" O GLN h 77 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN h 94 " --> pdb=" O HIS h 90 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL h 95 " --> pdb=" O HIS h 91 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP h 106 " --> pdb=" O LYS h 102 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE h 107 " --> pdb=" O ARG h 103 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN h 108 " --> pdb=" O ASP h 104 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN h 109 " --> pdb=" O SER h 105 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS h 115 " --> pdb=" O GLN h 111 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU h 116 " --> pdb=" O LYS h 112 " (cutoff:3.500A) Processing helix chain 'h' and resid 126 through 136 removed outlier: 3.674A pdb=" N SER h 134 " --> pdb=" O GLU h 130 " (cutoff:3.500A) Processing helix chain 'h' and resid 145 through 152 removed outlier: 3.670A pdb=" N ILE h 149 " --> pdb=" O SER h 145 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS h 150 " --> pdb=" O GLU h 146 " (cutoff:3.500A) Processing helix chain 'h' and resid 180 through 186 removed outlier: 3.948A pdb=" N ARG h 184 " --> pdb=" O ASP h 180 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER h 185 " --> pdb=" O LEU h 181 " (cutoff:3.500A) Processing helix chain 'i' and resid 23 through 28 Processing helix chain 'i' and resid 73 through 94 removed outlier: 3.616A pdb=" N LYS i 80 " --> pdb=" O LYS i 76 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N MET i 83 " --> pdb=" O ARG i 79 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU i 93 " --> pdb=" O PHE i 89 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP i 94 " --> pdb=" O LEU i 90 " (cutoff:3.500A) Processing helix chain 'i' and resid 107 through 165 removed outlier: 4.692A pdb=" N LYS i 113 " --> pdb=" O LEU i 109 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU i 114 " --> pdb=" O GLU i 110 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N HIS i 118 " --> pdb=" O LEU i 114 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL i 119 " --> pdb=" O LEU i 115 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N HIS i 120 " --> pdb=" O PHE i 116 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS i 121 " --> pdb=" O VAL i 117 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU i 122 " --> pdb=" O HIS i 118 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN i 124 " --> pdb=" O HIS i 120 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLU i 125 " --> pdb=" O HIS i 121 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR i 126 " --> pdb=" O LEU i 122 " (cutoff:3.500A) Proline residue: i 128 - end of helix removed outlier: 3.612A pdb=" N VAL i 137 " --> pdb=" O GLU i 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET i 138 " --> pdb=" O THR i 134 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU i 140 " --> pdb=" O ARG i 136 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL i 141 " --> pdb=" O VAL i 137 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS i 143 " --> pdb=" O MET i 139 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG i 144 " --> pdb=" O GLU i 140 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR i 149 " --> pdb=" O GLN i 145 " (cutoff:3.500A) Processing helix chain 'j' and resid 66 through 76 removed outlier: 3.760A pdb=" N HIS j 70 " --> pdb=" O LEU j 66 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN j 71 " --> pdb=" O PRO j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 89 through 103 removed outlier: 3.648A pdb=" N GLN j 95 " --> pdb=" O LYS j 91 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU j 100 " --> pdb=" O GLU j 96 " (cutoff:3.500A) Processing helix chain 'j' and resid 111 through 134 removed outlier: 3.545A pdb=" N GLN j 124 " --> pdb=" O SER j 120 " (cutoff:3.500A) Processing helix chain 'k' and resid 3 through 27 removed outlier: 3.808A pdb=" N HIS k 11 " --> pdb=" O HIS k 7 " (cutoff:3.500A) Processing helix chain 'k' and resid 38 through 57 removed outlier: 3.506A pdb=" N ILE k 51 " --> pdb=" O GLY k 47 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP k 52 " --> pdb=" O LEU k 48 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS k 53 " --> pdb=" O GLN k 49 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN k 56 " --> pdb=" O ASP k 52 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN k 57 " --> pdb=" O LYS k 53 " (cutoff:3.500A) Processing helix chain 'k' and resid 65 through 72 Processing helix chain 'k' and resid 77 through 115 removed outlier: 3.583A pdb=" N PHE k 105 " --> pdb=" O THR k 101 " (cutoff:3.500A) Processing helix chain 'k' and resid 121 through 131 removed outlier: 3.506A pdb=" N ARG k 125 " --> pdb=" O MET k 121 " (cutoff:3.500A) Processing helix chain 'l' and resid 51 through 75 removed outlier: 3.676A pdb=" N LEU l 58 " --> pdb=" O LEU l 54 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP l 71 " --> pdb=" O MET l 67 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU l 72 " --> pdb=" O VAL l 68 " (cutoff:3.500A) Proline residue: l 74 - end of helix Processing helix chain 'l' and resid 78 through 104 removed outlier: 4.280A pdb=" N LYS l 82 " --> pdb=" O ASP l 78 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE l 83 " --> pdb=" O VAL l 79 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU l 84 " --> pdb=" O GLU l 80 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE l 85 " --> pdb=" O ARG l 81 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG l 98 " --> pdb=" O GLN l 94 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU l 99 " --> pdb=" O LEU l 95 " (cutoff:3.500A) Processing helix chain 'l' and resid 106 through 108 No H-bonds generated for 'chain 'l' and resid 106 through 108' Processing helix chain 'l' and resid 113 through 146 removed outlier: 3.765A pdb=" N VAL l 130 " --> pdb=" O ALA l 126 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER l 138 " --> pdb=" O ASP l 134 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG l 141 " --> pdb=" O ALA l 137 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU l 144 " --> pdb=" O ALA l 140 " (cutoff:3.500A) Processing helix chain 'l' and resid 154 through 162 removed outlier: 3.754A pdb=" N LEU l 161 " --> pdb=" O ALA l 157 " (cutoff:3.500A) Processing helix chain 'l' and resid 174 through 178 removed outlier: 3.663A pdb=" N ILE l 178 " --> pdb=" O ARG l 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 174 through 178' Processing helix chain 'l' and resid 185 through 205 removed outlier: 3.520A pdb=" N ILE l 198 " --> pdb=" O GLN l 194 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR l 205 " --> pdb=" O HIS l 201 " (cutoff:3.500A) Processing helix chain 'l' and resid 211 through 213 No H-bonds generated for 'chain 'l' and resid 211 through 213' Processing helix chain 'l' and resid 269 through 281 Processing helix chain 'l' and resid 289 through 318 Processing helix chain 'l' and resid 397 through 423 removed outlier: 3.961A pdb=" N PHE l 423 " --> pdb=" O ILE l 419 " (cutoff:3.500A) Processing helix chain 'l' and resid 472 through 484 removed outlier: 4.125A pdb=" N ASP l 484 " --> pdb=" O LYS l 480 " (cutoff:3.500A) Processing helix chain 'l' and resid 486 through 510 Proline residue: l 491 - end of helix removed outlier: 3.522A pdb=" N LEU l 496 " --> pdb=" O ILE l 493 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS l 497 " --> pdb=" O GLN l 494 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU l 500 " --> pdb=" O LYS l 497 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS l 505 " --> pdb=" O GLN l 502 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE l 509 " --> pdb=" O LYS l 506 " (cutoff:3.500A) Processing helix chain 'l' and resid 585 through 596 Processing helix chain 'l' and resid 637 through 661 removed outlier: 3.681A pdb=" N MET l 647 " --> pdb=" O HIS l 643 " (cutoff:3.500A) Proline residue: l 653 - end of helix Processing helix chain 'm' and resid 83 through 86 No H-bonds generated for 'chain 'm' and resid 83 through 86' Processing helix chain 'm' and resid 90 through 95 Processing helix chain 'm' and resid 106 through 109 No H-bonds generated for 'chain 'm' and resid 106 through 109' Processing helix chain 'm' and resid 122 through 131 removed outlier: 3.948A pdb=" N SER m 126 " --> pdb=" O ASP m 123 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU m 127 " --> pdb=" O ASN m 124 " (cutoff:3.500A) Processing helix chain 'm' and resid 134 through 136 No H-bonds generated for 'chain 'm' and resid 134 through 136' Processing helix chain 'm' and resid 147 through 152 removed outlier: 4.125A pdb=" N GLY m 151 " --> pdb=" O MET m 148 " (cutoff:3.500A) Processing helix chain 'n' and resid 5 through 23 removed outlier: 3.654A pdb=" N CYS n 20 " --> pdb=" O ALA n 16 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 40 No H-bonds generated for 'chain 'n' and resid 38 through 40' Processing helix chain 'n' and resid 48 through 75 Processing helix chain 'n' and resid 83 through 130 removed outlier: 3.873A pdb=" N LEU n 93 " --> pdb=" O SER n 89 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU n 94 " --> pdb=" O LEU n 90 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN n 119 " --> pdb=" O LEU n 115 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA n 121 " --> pdb=" O LYS n 117 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 29 Processing helix chain 'o' and resid 31 through 40 Processing helix chain 'o' and resid 42 through 44 No H-bonds generated for 'chain 'o' and resid 42 through 44' Processing helix chain 'o' and resid 46 through 59 removed outlier: 4.734A pdb=" N TYR o 57 " --> pdb=" O LYS o 53 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TRP o 58 " --> pdb=" O TYR o 54 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS o 59 " --> pdb=" O LEU o 55 " (cutoff:3.500A) Processing helix chain 'o' and resid 61 through 66 removed outlier: 4.784A pdb=" N TYR o 66 " --> pdb=" O GLU o 62 " (cutoff:3.500A) Processing helix chain 'o' and resid 71 through 80 Processing helix chain 'o' and resid 82 through 88 Processing helix chain 'o' and resid 91 through 104 Processing helix chain 'p' and resid 159 through 172 removed outlier: 3.721A pdb=" N ASP p 163 " --> pdb=" O PRO p 159 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG p 171 " --> pdb=" O SER p 167 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET p 172 " --> pdb=" O ARG p 168 " (cutoff:3.500A) Processing helix chain 'p' and resid 237 through 252 removed outlier: 4.123A pdb=" N LEU p 251 " --> pdb=" O THR p 247 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS p 252 " --> pdb=" O THR p 248 " (cutoff:3.500A) Processing helix chain 'p' and resid 259 through 275 removed outlier: 3.917A pdb=" N VAL p 263 " --> pdb=" O PRO p 259 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR p 273 " --> pdb=" O TRP p 269 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE p 274 " --> pdb=" O LEU p 270 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LYS p 275 " --> pdb=" O ARG p 271 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 105 Processing helix chain 'q' and resid 109 through 149 Processing helix chain 'r' and resid 2 through 19 removed outlier: 4.040A pdb=" N UNK r 8 " --> pdb=" O UNK r 4 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N UNK r 9 " --> pdb=" O UNK r 5 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N UNK r 13 " --> pdb=" O UNK r 9 " (cutoff:3.500A) Processing helix chain 's' and resid 135 through 174 removed outlier: 3.575A pdb=" N ILE s 158 " --> pdb=" O GLN s 154 " (cutoff:3.500A) Processing helix chain 'w' and resid 301 through 314 Processing helix chain 'x' and resid 2 through 10 Processing helix chain 'y' and resid 2 through 17 Processing helix chain 'z' and resid 2 through 22 Processing sheet with id= A, first strand: chain '0' and resid 478 through 480 removed outlier: 7.683A pdb=" N VAL 0 39 " --> pdb=" O ALA 0 479 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL 0 231 " --> pdb=" O SER 0 453 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLY 0 173 " --> pdb=" O GLY 0 106 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ALA 0 108 " --> pdb=" O GLY 0 173 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N TYR 0 175 " --> pdb=" O ALA 0 108 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '0' and resid 250 through 252 Processing sheet with id= C, first strand: chain '0' and resid 676 through 680 removed outlier: 3.527A pdb=" N VAL 0 536 " --> pdb=" O ALA 0 617 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU 0 566 " --> pdb=" O ILE 0 595 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU 0 597 " --> pdb=" O LEU 0 566 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE 0 568 " --> pdb=" O LEU 0 597 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N VAL 0 599 " --> pdb=" O PHE 0 568 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 307 through 309 removed outlier: 6.095A pdb=" N GLN 2 345 " --> pdb=" O MET 2 334 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N MET 2 334 " --> pdb=" O GLN 2 345 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '2' and resid 431 through 435 removed outlier: 6.842A pdb=" N VAL 2 442 " --> pdb=" O VAL 2 432 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLU 2 434 " --> pdb=" O LEU 2 440 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU 2 440 " --> pdb=" O GLU 2 434 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 21 through 23 removed outlier: 3.653A pdb=" N ARG 3 59 " --> pdb=" O VAL 3 23 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '4' and resid 190 through 193 removed outlier: 6.635A pdb=" N LYS 4 56 " --> pdb=" O LEU 4 11 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ILE 4 13 " --> pdb=" O LYS 4 56 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA 4 58 " --> pdb=" O ILE 4 13 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL 4 15 " --> pdb=" O ALA 4 58 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE 4 60 " --> pdb=" O VAL 4 15 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL 4 59 " --> pdb=" O TYR 4 71 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR 4 71 " --> pdb=" O VAL 4 59 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA 4 61 " --> pdb=" O PHE 4 69 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N PHE 4 69 " --> pdb=" O ALA 4 61 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '5' and resid 8 through 11 removed outlier: 3.929A pdb=" N GLN 5 36 " --> pdb=" O PHE 5 44 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '6' and resid 164 through 170 removed outlier: 4.044A pdb=" N ASP 6 66 " --> pdb=" O ILE 6 170 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLN 6 103 " --> pdb=" O LEU 6 61 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL 6 63 " --> pdb=" O GLN 6 103 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY 6 105 " --> pdb=" O VAL 6 63 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL 6 65 " --> pdb=" O GLY 6 105 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE 6 107 " --> pdb=" O VAL 6 65 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL 6 108 " --> pdb=" O LYS 6 116 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LYS 6 116 " --> pdb=" O VAL 6 108 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS 6 110 " --> pdb=" O ALA 6 114 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA 6 114 " --> pdb=" O LYS 6 110 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '6' and resid 332 through 334 removed outlier: 3.687A pdb=" N GLN 6 332 " --> pdb=" O VAL 6 359 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL 6 359 " --> pdb=" O GLN 6 332 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '7' and resid 83 through 87 removed outlier: 5.964A pdb=" N LYS 7 117 " --> pdb=" O PRO 7 106 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '7' and resid 174 through 178 removed outlier: 4.479A pdb=" N VAL 7 166 " --> pdb=" O PRO 7 290 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '7' and resid 465 through 467 removed outlier: 3.622A pdb=" N THR 7 467 " --> pdb=" O ILE 7 338 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL 7 339 " --> pdb=" O LEU 7 488 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU 7 490 " --> pdb=" O VAL 7 339 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '7' and resid 437 through 440 removed outlier: 6.481A pdb=" N ALA 7 406 " --> pdb=" O VAL 7 363 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLY 7 365 " --> pdb=" O ALA 7 406 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER 7 408 " --> pdb=" O GLY 7 365 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '7' and resid 688 through 690 removed outlier: 7.757A pdb=" N ALA 7 657 " --> pdb=" O GLN 7 506 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ALA 7 508 " --> pdb=" O ALA 7 657 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE 7 659 " --> pdb=" O ALA 7 508 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL 7 510 " --> pdb=" O PHE 7 659 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER 7 661 " --> pdb=" O VAL 7 510 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '7' and resid 558 through 561 Processing sheet with id= Q, first strand: chain '8' and resid 19 through 21 removed outlier: 4.438A pdb=" N ILE 8 87 " --> pdb=" O ILE 8 43 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASP 8 92 " --> pdb=" O LEU 8 77 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU 8 77 " --> pdb=" O ASP 8 92 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '8' and resid 133 through 135 Processing sheet with id= S, first strand: chain '8' and resid 143 through 145 Processing sheet with id= T, first strand: chain '8' and resid 12 through 16 removed outlier: 6.441A pdb=" N LYS 8 28 " --> pdb=" O LEU 8 15 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 86 through 89 Processing sheet with id= V, first strand: chain 'A' and resid 190 through 193 removed outlier: 4.484A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 264 through 266 Processing sheet with id= X, first strand: chain 'A' and resid 362 through 366 Processing sheet with id= Y, first strand: chain 'A' and resid 367 through 369 removed outlier: 6.418A pdb=" N PHE A 482 " --> pdb=" O THR A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'A' and resid 389 through 393 Processing sheet with id= AA, first strand: chain 'A' and resid 418 through 420 Processing sheet with id= AB, first strand: chain 'A' and resid 602 through 605 removed outlier: 3.821A pdb=" N MET A 637 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLU A 631 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 902 through 905 Processing sheet with id= AD, first strand: chain 'A' and resid 1139 through 1142 removed outlier: 3.531A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.296A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id= AG, first strand: chain 'B' and resid 65 through 68 Processing sheet with id= AH, first strand: chain 'B' and resid 91 through 93 removed outlier: 3.621A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'B' and resid 97 through 99 Processing sheet with id= AJ, first strand: chain 'B' and resid 185 through 187 Processing sheet with id= AK, first strand: chain 'B' and resid 197 through 200 Processing sheet with id= AL, first strand: chain 'B' and resid 205 through 208 removed outlier: 6.593A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR B 218 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL B 237 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU B 220 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE B 235 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ARG B 222 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N SER B 233 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'B' and resid 484 through 486 Processing sheet with id= AN, first strand: chain 'B' and resid 530 through 532 Processing sheet with id= AO, first strand: chain 'B' and resid 550 through 552 removed outlier: 6.747A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'B' and resid 747 through 751 removed outlier: 5.793A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'B' and resid 1042 through 1048 removed outlier: 4.365A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 965 " --> pdb=" O ALA B 781 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL B 794 " --> pdb=" O LYS B 942 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR B 944 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N MET B 796 " --> pdb=" O THR B 944 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N GLY B 946 " --> pdb=" O MET B 796 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'B' and resid 827 through 829 Processing sheet with id= AS, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id= AT, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.623A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'C' and resid 98 through 106 removed outlier: 6.183A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'C' and resid 113 through 116 Processing sheet with id= AW, first strand: chain 'E' and resid 60 through 63 removed outlier: 6.962A pdb=" N ARG E 101 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N PHE E 75 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU E 103 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE E 126 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE E 104 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU E 128 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL E 106 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE E 130 " --> pdb=" O VAL E 106 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'E' and resid 147 through 151 removed outlier: 4.808A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= AZ, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.526A pdb=" N LEU G 13 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'G' and resid 142 through 146 removed outlier: 3.543A pdb=" N LEU G 145 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'G' and resid 127 through 129 Processing sheet with id= BC, first strand: chain 'G' and resid 44 through 48 removed outlier: 6.960A pdb=" N ILE G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'G' and resid 50 through 54 removed outlier: 3.548A pdb=" N THR G 50 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'H' and resid 25 through 31 removed outlier: 5.120A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'I' and resid 24 through 29 removed outlier: 3.548A pdb=" N ILE I 34 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'I' and resid 94 through 97 Processing sheet with id= BH, first strand: chain 'K' and resid 19 through 23 Processing sheet with id= BI, first strand: chain 'L' and resid 25 through 27 Processing sheet with id= BJ, first strand: chain 'M' and resid 23 through 25 Processing sheet with id= BK, first strand: chain 'O' and resid 170 through 173 Processing sheet with id= BL, first strand: chain 'O' and resid 291 through 295 removed outlier: 3.621A pdb=" N ILE O 300 " --> pdb=" O MET O 295 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N SER O 261 " --> pdb=" O LEU O 165 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU O 165 " --> pdb=" O SER O 261 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'Q' and resid 27 through 31 removed outlier: 6.795A pdb=" N ASN Q 142 " --> pdb=" O ILE Q 28 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ALA Q 30 " --> pdb=" O ASN Q 142 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR Q 144 " --> pdb=" O ALA Q 30 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN Q 145 " --> pdb=" O ILE Q 113 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE Q 113 " --> pdb=" O ASN Q 145 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS Q 109 " --> pdb=" O LEU Q 149 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'Q' and resid 125 through 128 removed outlier: 3.579A pdb=" N ILE Q 126 " --> pdb=" O PHE Q 138 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE Q 138 " --> pdb=" O ILE Q 126 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR Q 128 " --> pdb=" O GLU Q 136 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU Q 136 " --> pdb=" O THR Q 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= BN Processing sheet with id= BO, first strand: chain 'R' and resid 41 through 47 removed outlier: 11.251A pdb=" N THR R 52 " --> pdb=" O LEU R 85 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU R 85 " --> pdb=" O THR R 52 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL R 54 " --> pdb=" O PHE R 83 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG R 113 " --> pdb=" O GLN R 86 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU R 20 " --> pdb=" O VAL R 111 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG R 113 " --> pdb=" O LEU R 20 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LYS R 22 " --> pdb=" O ARG R 113 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLU R 115 " --> pdb=" O LYS R 22 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'R' and resid 222 through 224 Processing sheet with id= BQ, first strand: chain 'R' and resid 93 through 98 removed outlier: 4.762A pdb=" N LEU R 93 " --> pdb=" O VAL R 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY R 108 " --> pdb=" O VAL R 95 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR R 97 " --> pdb=" O LEU R 106 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU R 106 " --> pdb=" O THR R 97 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'U' and resid 334 through 337 removed outlier: 3.765A pdb=" N PHE U 367 " --> pdb=" O GLY U 356 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'U' and resid 370 through 375 removed outlier: 3.937A pdb=" N LYS U 348 " --> pdb=" O SER U 345 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS U 341 " --> pdb=" O HIS U 352 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'V' and resid 57 through 59 Processing sheet with id= BU, first strand: chain 'V' and resid 92 through 98 removed outlier: 6.085A pdb=" N ASN V 77 " --> pdb=" O LEU V 62 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU V 62 " --> pdb=" O ASN V 77 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'W' and resid 72 through 77 removed outlier: 3.548A pdb=" N HIS W 89 " --> pdb=" O ARG W 77 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'W' and resid 127 through 129 removed outlier: 3.627A pdb=" N PHE W 127 " --> pdb=" O PHE W 136 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS W 129 " --> pdb=" O SER W 134 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER W 134 " --> pdb=" O CYS W 129 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'X' and resid 130 through 133 Processing sheet with id= BY, first strand: chain 'X' and resid 189 through 192 Processing sheet with id= BZ, first strand: chain 'a' and resid 104 through 107 removed outlier: 6.860A pdb=" N LYS a 83 " --> pdb=" O LEU a 95 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP a 97 " --> pdb=" O ILE a 81 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE a 81 " --> pdb=" O ASP a 97 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR a 99 " --> pdb=" O PHE a 79 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N PHE a 79 " --> pdb=" O TYR a 99 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG a 82 " --> pdb=" O LEU a 70 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LEU a 70 " --> pdb=" O ARG a 82 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLN a 84 " --> pdb=" O TYR a 68 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N TYR a 68 " --> pdb=" O GLN a 84 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG a 86 " --> pdb=" O ILE a 66 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE a 66 " --> pdb=" O ARG a 86 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'd' and resid 223 through 225 Processing sheet with id= CB, first strand: chain 'd' and resid 259 through 261 removed outlier: 3.996A pdb=" N ILE d 343 " --> pdb=" O ILE d 331 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'd' and resid 494 through 496 Processing sheet with id= CD, first strand: chain 'd' and resid 567 through 571 removed outlier: 3.626A pdb=" N SER d 567 " --> pdb=" O ASN d 584 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'd' and resid 592 through 594 removed outlier: 3.527A pdb=" N MET d 593 " --> pdb=" O LYS d 623 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS d 623 " --> pdb=" O MET d 593 " (cutoff:3.500A) No H-bonds generated for sheet with id= CE Processing sheet with id= CF, first strand: chain 'e' and resid 24 through 27 removed outlier: 3.737A pdb=" N GLU e 170 " --> pdb=" O MET e 144 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET e 144 " --> pdb=" O GLU e 170 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY e 133 " --> pdb=" O PHE e 51 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU e 135 " --> pdb=" O GLU e 49 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLU e 49 " --> pdb=" O LEU e 135 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'f' and resid 64 through 67 removed outlier: 3.506A pdb=" N VAL f 65 " --> pdb=" O GLU f 44 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG f 113 " --> pdb=" O THR f 128 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR f 128 " --> pdb=" O ARG f 113 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR f 115 " --> pdb=" O VAL f 126 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL f 126 " --> pdb=" O THR f 115 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR f 117 " --> pdb=" O VAL f 124 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL f 124 " --> pdb=" O TYR f 117 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'f' and resid 34 through 37 removed outlier: 3.686A pdb=" N GLU f 34 " --> pdb=" O GLN f 118 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN f 118 " --> pdb=" O GLU f 34 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN f 36 " --> pdb=" O ARG f 116 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG f 116 " --> pdb=" O GLN f 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= CH Processing sheet with id= CI, first strand: chain 'l' and resid 216 through 218 Processing sheet with id= CJ, first strand: chain 'l' and resid 224 through 226 removed outlier: 4.011A pdb=" N THR l 235 " --> pdb=" O GLU l 258 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'l' and resid 325 through 329 Processing sheet with id= CL, first strand: chain 'l' and resid 453 through 456 Processing sheet with id= CM, first strand: chain 'l' and resid 514 through 517 removed outlier: 3.645A pdb=" N PHE l 539 " --> pdb=" O SER l 517 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'p' and resid 176 through 179 removed outlier: 4.038A pdb=" N LEU p 198 " --> pdb=" O LEU p 194 " (cutoff:3.500A) 3939 hydrogen bonds defined for protein. 11184 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 155 hydrogen bonds 310 hydrogen bond angles 0 basepair planarities 59 basepair parallelities 100 stacking parallelities Total time for adding SS restraints: 46.77 Time building geometry restraints manager: 33.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 40612 1.43 - 1.64: 56694 1.64 - 1.86: 864 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 98182 Sorted by residual: bond pdb=" CB GLN 3 307 " pdb=" CG GLN 3 307 " ideal model delta sigma weight residual 1.520 1.412 0.108 3.00e-02 1.11e+03 1.30e+01 bond pdb=" CG1 ILE X 233 " pdb=" CD1 ILE X 233 " ideal model delta sigma weight residual 1.513 1.389 0.124 3.90e-02 6.57e+02 1.00e+01 bond pdb=" CD2 TYR W 105 " pdb=" CE2 TYR W 105 " ideal model delta sigma weight residual 1.382 1.287 0.095 3.00e-02 1.11e+03 9.99e+00 bond pdb=" N ASP f 121 " pdb=" CA ASP f 121 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.58e-02 4.01e+03 6.58e+00 bond pdb=" CB TYR W 105 " pdb=" CG TYR W 105 " ideal model delta sigma weight residual 1.512 1.457 0.055 2.20e-02 2.07e+03 6.29e+00 ... (remaining 98177 not shown) Histogram of bond angle deviations from ideal: 73.42 - 85.68: 12 85.68 - 97.93: 1 97.93 - 110.19: 19393 110.19 - 122.45: 101435 122.45 - 134.71: 12287 Bond angle restraints: 133128 Sorted by residual: angle pdb=" N HIS b 102 " pdb=" CA HIS b 102 " pdb=" C HIS b 102 " ideal model delta sigma weight residual 111.28 122.80 -11.52 1.09e+00 8.42e-01 1.12e+02 angle pdb=" C SER 8 164 " pdb=" N PRO 8 165 " pdb=" CA PRO 8 165 " ideal model delta sigma weight residual 119.84 129.09 -9.25 1.25e+00 6.40e-01 5.48e+01 angle pdb=" C CYS f 120 " pdb=" N ASP f 121 " pdb=" CA ASP f 121 " ideal model delta sigma weight residual 123.93 134.16 -10.23 1.54e+00 4.22e-01 4.42e+01 angle pdb=" CG1 VAL f 148 " pdb=" CB VAL f 148 " pdb=" CG2 VAL f 148 " ideal model delta sigma weight residual 110.80 121.88 -11.08 2.20e+00 2.07e-01 2.54e+01 angle pdb=" C THR d 513 " pdb=" N LEU d 514 " pdb=" CA LEU d 514 " ideal model delta sigma weight residual 121.54 130.37 -8.83 1.91e+00 2.74e-01 2.14e+01 ... (remaining 133123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.95: 58205 34.95 - 69.90: 1410 69.90 - 104.86: 122 104.86 - 139.81: 1 139.81 - 174.76: 3 Dihedral angle restraints: 59741 sinusoidal: 25532 harmonic: 34209 Sorted by residual: dihedral pdb=" CA THR d 513 " pdb=" C THR d 513 " pdb=" N LEU d 514 " pdb=" CA LEU d 514 " ideal model delta harmonic sigma weight residual 180.00 145.68 34.32 0 5.00e+00 4.00e-02 4.71e+01 dihedral pdb=" CA LEU l 443 " pdb=" C LEU l 443 " pdb=" N GLU l 444 " pdb=" CA GLU l 444 " ideal model delta harmonic sigma weight residual -180.00 -149.05 -30.95 0 5.00e+00 4.00e-02 3.83e+01 dihedral pdb=" CA CYS 4 257 " pdb=" C CYS 4 257 " pdb=" N HIS 4 258 " pdb=" CA HIS 4 258 " ideal model delta harmonic sigma weight residual -180.00 -151.21 -28.79 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 59738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.341: 14962 0.341 - 0.681: 2 0.681 - 1.022: 0 1.022 - 1.362: 0 1.362 - 1.703: 2 Chirality restraints: 14966 Sorted by residual: chirality pdb=" CG LEU d 92 " pdb=" CB LEU d 92 " pdb=" CD1 LEU d 92 " pdb=" CD2 LEU d 92 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.25e+01 chirality pdb=" CB VAL f 148 " pdb=" CA VAL f 148 " pdb=" CG1 VAL f 148 " pdb=" CG2 VAL f 148 " both_signs ideal model delta sigma weight residual False -2.63 -1.07 -1.56 2.00e-01 2.50e+01 6.06e+01 chirality pdb=" CB ILE X 233 " pdb=" CA ILE X 233 " pdb=" CG1 ILE X 233 " pdb=" CG2 ILE X 233 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.53e+00 ... (remaining 14963 not shown) Planarity restraints: 16677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS 4 258 " -0.039 2.00e-02 2.50e+03 4.08e-02 2.50e+01 pdb=" CG HIS 4 258 " 0.083 2.00e-02 2.50e+03 pdb=" ND1 HIS 4 258 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 HIS 4 258 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS 4 258 " 0.013 2.00e-02 2.50e+03 pdb=" NE2 HIS 4 258 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP 4 229 " 0.030 2.00e-02 2.50e+03 2.74e-02 1.87e+01 pdb=" CG TRP 4 229 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP 4 229 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP 4 229 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP 4 229 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP 4 229 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP 4 229 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP 4 229 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP 4 229 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP 4 229 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP 2 55 " 0.028 2.00e-02 2.50e+03 2.43e-02 1.48e+01 pdb=" CG TRP 2 55 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP 2 55 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP 2 55 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP 2 55 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP 2 55 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP 2 55 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP 2 55 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP 2 55 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP 2 55 " 0.000 2.00e-02 2.50e+03 ... (remaining 16674 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 338 2.43 - 3.04: 63388 3.04 - 3.66: 148563 3.66 - 4.28: 220806 4.28 - 4.90: 360556 Nonbonded interactions: 793651 Sorted by model distance: nonbonded pdb=" CD2 PHE G 158 " pdb=" ND2 ASN W 142 " model vdw 1.807 3.420 nonbonded pdb=" CE2 PHE G 158 " pdb=" ND2 ASN W 142 " model vdw 1.809 3.420 nonbonded pdb=" OG SER h 158 " pdb=" O LYS o 68 " model vdw 1.832 2.440 nonbonded pdb=" NH1 ARG W 113 " pdb=" OG SER X 222 " model vdw 1.921 2.520 nonbonded pdb=" O ARG 3 8 " pdb=" ND2 ASN W 181 " model vdw 1.934 2.520 ... (remaining 793646 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'Y' and resid 2 through 19) selection = (chain 'r' and resid 3 through 20) selection = (chain 'v' and resid 805 through 822) selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 18.700 Check model and map are aligned: 1.040 Set scattering table: 0.700 Process input model: 252.010 Find NCS groups from input model: 2.710 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 282.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5699 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 : 0.003 0.124 98182 Z= 0.202 Angle : 0.546 13.627 133128 Z= 0.309 Chirality : 0.044 1.703 14966 Planarity : 0.003 0.093 16677 Dihedral : 15.038 174.759 37485 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.93 % Favored : 96.05 % Rotamer: Outliers : 0.01 % Allowed : 0.14 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.08), residues: 11332 helix: 1.65 (0.07), residues: 5235 sheet: -0.29 (0.14), residues: 1473 loop : -0.57 (0.09), residues: 4624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.001 TRP 4 229 HIS 0.044 0.001 HIS 4 258 PHE 0.064 0.001 PHE W 25 TYR 0.023 0.001 TYR e 167 ARG 0.024 0.000 ARG 2 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1257 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1256 time to evaluate : 8.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 42 MET cc_start: 0.4227 (ttt) cc_final: 0.3956 (ttm) REVERT: 1 528 MET cc_start: -0.7708 (mpp) cc_final: -0.8072 (ttt) REVERT: 2 185 MET cc_start: 0.1335 (mtp) cc_final: -0.0142 (mmt) REVERT: 2 207 ASP cc_start: 0.7465 (m-30) cc_final: 0.7261 (m-30) REVERT: 4 29 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7187 (mm-30) REVERT: 4 119 MET cc_start: -0.4411 (mmm) cc_final: -0.4984 (mtt) REVERT: 4 157 MET cc_start: -0.3642 (ttp) cc_final: -0.3925 (ttt) REVERT: 9 75 MET cc_start: -0.1966 (ttm) cc_final: -0.3001 (ttt) REVERT: A 21 VAL cc_start: 0.8686 (t) cc_final: 0.8466 (t) REVERT: A 26 LEU cc_start: 0.7688 (mt) cc_final: 0.7445 (tp) REVERT: A 77 ASN cc_start: 0.7671 (p0) cc_final: 0.7256 (p0) REVERT: A 452 ASP cc_start: 0.7278 (m-30) cc_final: 0.6596 (t0) REVERT: A 466 LYS cc_start: 0.7556 (mtmt) cc_final: 0.7192 (ptmt) REVERT: A 467 MET cc_start: 0.7764 (mmt) cc_final: 0.7086 (mmt) REVERT: A 470 MET cc_start: 0.8001 (mtm) cc_final: 0.7679 (mtt) REVERT: A 514 GLU cc_start: 0.7861 (tt0) cc_final: 0.7089 (tt0) REVERT: A 561 MET cc_start: 0.8214 (mtt) cc_final: 0.7862 (mtt) REVERT: A 660 MET cc_start: 0.8400 (mmm) cc_final: 0.7904 (mmm) REVERT: A 689 ILE cc_start: 0.9264 (mm) cc_final: 0.8912 (mt) REVERT: A 691 ASP cc_start: 0.8745 (m-30) cc_final: 0.8355 (m-30) REVERT: A 841 MET cc_start: 0.8467 (mtp) cc_final: 0.7913 (ttm) REVERT: A 865 ILE cc_start: 0.8592 (tp) cc_final: 0.7728 (mt) REVERT: A 894 ASP cc_start: 0.8908 (p0) cc_final: 0.8466 (p0) REVERT: A 1049 LEU cc_start: 0.8938 (mt) cc_final: 0.8455 (mt) REVERT: A 1072 ILE cc_start: 0.8906 (mt) cc_final: 0.8542 (mm) REVERT: A 1094 SER cc_start: 0.8399 (m) cc_final: 0.8070 (t) REVERT: A 1365 ILE cc_start: 0.8665 (mm) cc_final: 0.8358 (tp) REVERT: A 1479 LYS cc_start: 0.7375 (tptt) cc_final: 0.6407 (tttt) REVERT: B 197 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8247 (tp40) REVERT: B 235 ILE cc_start: 0.8274 (tt) cc_final: 0.8057 (tp) REVERT: B 290 TYR cc_start: 0.6216 (m-80) cc_final: 0.5937 (m-80) REVERT: B 407 MET cc_start: 0.8271 (mtm) cc_final: 0.8060 (mmp) REVERT: B 508 MET cc_start: 0.7943 (mmt) cc_final: 0.7343 (mmt) REVERT: B 541 ILE cc_start: 0.8714 (mm) cc_final: 0.8396 (tp) REVERT: B 550 MET cc_start: 0.7983 (ttp) cc_final: 0.7506 (tmm) REVERT: B 600 GLU cc_start: 0.7256 (pt0) cc_final: 0.6773 (mp0) REVERT: B 640 ILE cc_start: 0.9196 (mm) cc_final: 0.8955 (tp) REVERT: B 711 ILE cc_start: 0.9191 (mt) cc_final: 0.8609 (mt) REVERT: B 726 SER cc_start: 0.9291 (m) cc_final: 0.8778 (p) REVERT: B 744 MET cc_start: 0.6323 (mtp) cc_final: 0.6074 (mtt) REVERT: B 766 TYR cc_start: 0.7647 (m-80) cc_final: 0.6874 (m-10) REVERT: B 780 VAL cc_start: 0.8795 (t) cc_final: 0.8471 (m) REVERT: B 790 GLN cc_start: 0.7713 (mt0) cc_final: 0.7140 (mt0) REVERT: B 928 ILE cc_start: 0.8451 (mt) cc_final: 0.8189 (mt) REVERT: B 964 ASP cc_start: 0.8999 (m-30) cc_final: 0.8776 (m-30) REVERT: B 983 GLU cc_start: 0.8019 (tt0) cc_final: 0.7581 (tm-30) REVERT: B 1051 LEU cc_start: 0.8410 (mt) cc_final: 0.8087 (mm) REVERT: C 21 PHE cc_start: 0.7942 (p90) cc_final: 0.7044 (p90) REVERT: C 59 LEU cc_start: 0.8011 (mt) cc_final: 0.7807 (mt) REVERT: C 127 VAL cc_start: 0.8049 (t) cc_final: 0.7746 (m) REVERT: C 161 LEU cc_start: 0.8664 (pp) cc_final: 0.8373 (pp) REVERT: E 74 VAL cc_start: 0.7764 (t) cc_final: 0.6333 (t) REVERT: E 156 VAL cc_start: 0.8343 (t) cc_final: 0.7925 (t) REVERT: E 159 LEU cc_start: 0.8675 (tp) cc_final: 0.8426 (tp) REVERT: F 75 MET cc_start: 0.7330 (mtm) cc_final: 0.7025 (mtt) REVERT: F 97 LEU cc_start: 0.9155 (tp) cc_final: 0.8936 (tp) REVERT: G 72 TYR cc_start: 0.7174 (p90) cc_final: 0.6600 (p90) REVERT: G 145 LEU cc_start: 0.6656 (pt) cc_final: 0.6407 (pt) REVERT: H 58 LEU cc_start: 0.8022 (tp) cc_final: 0.7754 (tp) REVERT: H 143 LEU cc_start: 0.7892 (tt) cc_final: 0.7508 (tt) REVERT: K 91 ILE cc_start: 0.8934 (mt) cc_final: 0.8665 (tt) REVERT: K 109 ILE cc_start: 0.8791 (mt) cc_final: 0.7893 (mm) REVERT: L 53 VAL cc_start: 0.7804 (p) cc_final: 0.7440 (m) REVERT: M 124 MET cc_start: 0.6551 (mtm) cc_final: 0.5918 (mtm) REVERT: M 175 ARG cc_start: 0.7547 (mmt-90) cc_final: 0.7107 (mmt90) REVERT: U 51 MET cc_start: 0.5619 (mmp) cc_final: 0.4402 (mpp) REVERT: V 1 MET cc_start: -0.3365 (ptm) cc_final: -0.4563 (mtt) REVERT: X 228 MET cc_start: -0.3309 (mtp) cc_final: -0.3976 (ttt) REVERT: h 47 MET cc_start: -0.0625 (mtp) cc_final: -0.1457 (mtp) outliers start: 1 outliers final: 0 residues processed: 1257 average time/residue: 0.8897 time to fit residues: 1914.6049 Evaluate side-chains 700 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 700 time to evaluate : 8.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1154 random chunks: chunk 974 optimal weight: 2.9990 chunk 874 optimal weight: 30.0000 chunk 485 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 chunk 590 optimal weight: 3.9990 chunk 467 optimal weight: 10.0000 chunk 904 optimal weight: 6.9990 chunk 350 optimal weight: 0.0870 chunk 549 optimal weight: 3.9990 chunk 673 optimal weight: 7.9990 chunk 1047 optimal weight: 50.0000 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 114 ASN ** 0 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 83 GLN 2 181 GLN 2 211 GLN 2 366 HIS 3 24 ASN 4 46 ASN 4 108 ASN 6 387 HIS 8 33 ASN 9 7 GLN A 222 HIS A 267 GLN A 377 GLN A 387 ASN A 472 HIS A 662 HIS A 671 ASN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 GLN A1077 ASN ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 197 GLN B 265 GLN B 370 HIS B 741 HIS B 825 GLN ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1053 HIS B1068 GLN B1071 ASN B1101 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN I 91 HIS O 189 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 159 HIS W 90 ASN d 184 ASN d 324 HIS ** d 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 437 HIS l 275 HIS l 502 GLN ** l 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 39 GLN ** p 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 90 GLN s 164 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5972 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 98182 Z= 0.279 Angle : 0.635 16.182 133128 Z= 0.327 Chirality : 0.042 0.269 14966 Planarity : 0.005 0.101 16677 Dihedral : 10.719 172.804 14024 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 0.17 % Allowed : 4.09 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % 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: 0.56 (0.08), residues: 11332 helix: 1.46 (0.07), residues: 5297 sheet: -0.35 (0.13), residues: 1551 loop : -0.62 (0.09), residues: 4484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP 2 55 HIS 0.010 0.001 HIS B1117 PHE 0.046 0.002 PHE A 225 TYR 0.044 0.002 TYR W 105 ARG 0.026 0.001 ARG l 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 784 time to evaluate : 8.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 478 MET cc_start: 0.3647 (mmt) cc_final: 0.3096 (mmp) REVERT: 1 528 MET cc_start: -0.7568 (mpp) cc_final: -0.8109 (ttt) REVERT: 2 185 MET cc_start: 0.0723 (mtp) cc_final: -0.0044 (mmt) REVERT: 4 51 MET cc_start: -0.1371 (mtt) cc_final: -0.1952 (mtt) REVERT: 4 119 MET cc_start: -0.4183 (mmm) cc_final: -0.5010 (mtt) REVERT: 6 273 MET cc_start: -0.5462 (mtt) cc_final: -0.5728 (mtt) REVERT: 7 650 MET cc_start: -0.2512 (ptt) cc_final: -0.2815 (ptt) REVERT: 9 1 MET cc_start: -0.2241 (mmp) cc_final: -0.2954 (mmp) REVERT: 9 75 MET cc_start: -0.2110 (ttm) cc_final: -0.3011 (ttt) REVERT: A 18 ILE cc_start: 0.8686 (mm) cc_final: 0.8036 (mm) REVERT: A 21 VAL cc_start: 0.8762 (t) cc_final: 0.8539 (t) REVERT: A 355 MET cc_start: 0.8099 (ttp) cc_final: 0.7593 (tpp) REVERT: A 447 GLU cc_start: 0.7768 (mp0) cc_final: 0.7468 (mp0) REVERT: A 452 ASP cc_start: 0.7797 (m-30) cc_final: 0.7092 (t0) REVERT: A 470 MET cc_start: 0.8129 (mtm) cc_final: 0.7786 (mtt) REVERT: A 486 LEU cc_start: 0.8850 (mm) cc_final: 0.8644 (mm) REVERT: A 514 GLU cc_start: 0.8017 (tt0) cc_final: 0.7577 (tt0) REVERT: A 565 MET cc_start: 0.8437 (tpt) cc_final: 0.7597 (tpt) REVERT: A 592 PHE cc_start: 0.8143 (t80) cc_final: 0.7880 (t80) REVERT: A 637 MET cc_start: 0.8710 (ptm) cc_final: 0.8385 (ptm) REVERT: A 660 MET cc_start: 0.8264 (mmm) cc_final: 0.7751 (mmm) REVERT: A 683 GLU cc_start: 0.8702 (tp30) cc_final: 0.7751 (tp30) REVERT: A 691 ASP cc_start: 0.8776 (m-30) cc_final: 0.8505 (m-30) REVERT: A 841 MET cc_start: 0.8536 (mtp) cc_final: 0.8111 (ttm) REVERT: A 865 ILE cc_start: 0.8595 (tp) cc_final: 0.7958 (mp) REVERT: A 1343 LEU cc_start: 0.7696 (tp) cc_final: 0.7373 (tp) REVERT: A 1347 LEU cc_start: 0.7896 (mm) cc_final: 0.7575 (mm) REVERT: B 256 ILE cc_start: 0.8374 (tt) cc_final: 0.8103 (tt) REVERT: B 270 ILE cc_start: 0.8509 (mm) cc_final: 0.7647 (mt) REVERT: B 347 MET cc_start: 0.7055 (mmm) cc_final: 0.6276 (mmm) REVERT: B 407 MET cc_start: 0.8300 (mtm) cc_final: 0.8011 (mmp) REVERT: B 508 MET cc_start: 0.8400 (mmt) cc_final: 0.7628 (mmt) REVERT: B 550 MET cc_start: 0.7999 (ttp) cc_final: 0.7400 (tmm) REVERT: B 600 GLU cc_start: 0.7446 (pt0) cc_final: 0.7131 (mp0) REVERT: B 726 SER cc_start: 0.9071 (m) cc_final: 0.8620 (p) REVERT: B 728 MET cc_start: 0.6651 (mmm) cc_final: 0.5480 (mmt) REVERT: B 790 GLN cc_start: 0.7381 (mt0) cc_final: 0.6998 (mt0) REVERT: B 807 ARG cc_start: 0.7471 (ttm170) cc_final: 0.7218 (mtt180) REVERT: B 866 ILE cc_start: 0.8128 (pt) cc_final: 0.7804 (pt) REVERT: B 867 ILE cc_start: 0.8265 (mp) cc_final: 0.7875 (mp) REVERT: C 127 VAL cc_start: 0.7907 (t) cc_final: 0.7675 (m) REVERT: C 148 ILE cc_start: 0.8629 (mm) cc_final: 0.8301 (mp) REVERT: F 57 MET cc_start: 0.8320 (ttp) cc_final: 0.7571 (ttm) REVERT: F 123 LEU cc_start: 0.8831 (mt) cc_final: 0.8600 (mm) REVERT: H 143 LEU cc_start: 0.7991 (tt) cc_final: 0.7692 (tt) REVERT: I 103 ARG cc_start: 0.6055 (mmp80) cc_final: 0.5720 (mmp80) REVERT: K 91 ILE cc_start: 0.8899 (mt) cc_final: 0.8696 (tt) REVERT: K 109 ILE cc_start: 0.8808 (mt) cc_final: 0.7892 (mm) REVERT: M 118 PHE cc_start: 0.7541 (m-80) cc_final: 0.6370 (m-80) REVERT: U 51 MET cc_start: 0.5648 (mmp) cc_final: 0.4446 (mpp) REVERT: V 1 MET cc_start: -0.3488 (ptm) cc_final: -0.4724 (mtt) REVERT: X 232 LYS cc_start: 0.5920 (mptt) cc_final: 0.5437 (mttt) REVERT: a 52 MET cc_start: 0.0195 (ptp) cc_final: -0.0060 (ptt) REVERT: h 47 MET cc_start: -0.1072 (mtp) cc_final: -0.1403 (mtp) REVERT: l 292 MET cc_start: 0.8196 (mmp) cc_final: 0.7980 (mmm) REVERT: l 571 MET cc_start: 0.5259 (mpp) cc_final: 0.5033 (mpp) REVERT: n 45 ASP cc_start: 0.7293 (t0) cc_final: 0.6993 (t0) outliers start: 17 outliers final: 4 residues processed: 800 average time/residue: 0.8632 time to fit residues: 1213.7088 Evaluate side-chains 576 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 572 time to evaluate : 8.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1154 random chunks: chunk 582 optimal weight: 1.9990 chunk 325 optimal weight: 10.0000 chunk 872 optimal weight: 40.0000 chunk 713 optimal weight: 0.9980 chunk 289 optimal weight: 50.0000 chunk 1049 optimal weight: 20.0000 chunk 1134 optimal weight: 7.9990 chunk 934 optimal weight: 40.0000 chunk 1041 optimal weight: 30.0000 chunk 357 optimal weight: 3.9990 chunk 842 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 114 ASN ** 0 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 366 HIS 2 410 ASN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 45 ASN 6 265 GLN 8 33 ASN 9 7 GLN ** 9 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 142 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN B 265 GLN B 461 GLN B 755 GLN ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 HIS B1053 HIS D 48 ASN G 53 ASN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN O 277 HIS ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 27 GLN a 124 HIS d 184 ASN ** d 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 30 ASN ** s 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 98182 Z= 0.322 Angle : 0.626 14.329 133128 Z= 0.321 Chirality : 0.042 0.255 14966 Planarity : 0.004 0.070 16677 Dihedral : 10.795 172.920 14024 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.80 % Favored : 96.18 % Rotamer: Outliers : 0.16 % Allowed : 4.04 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % 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 (0.08), residues: 11332 helix: 1.39 (0.07), residues: 5297 sheet: -0.39 (0.13), residues: 1520 loop : -0.78 (0.09), residues: 4515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 27 HIS 0.012 0.001 HIS C 66 PHE 0.034 0.002 PHE A 458 TYR 0.038 0.002 TYR g 18 ARG 0.019 0.001 ARG b 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 689 time to evaluate : 9.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 247 MET cc_start: 0.1661 (ptt) cc_final: 0.1165 (ptt) REVERT: 1 528 MET cc_start: -0.7562 (mpp) cc_final: -0.7933 (ttt) REVERT: 2 185 MET cc_start: 0.0739 (mtp) cc_final: -0.0407 (mtt) REVERT: 2 207 ASP cc_start: 0.7313 (m-30) cc_final: 0.6970 (m-30) REVERT: 4 51 MET cc_start: -0.0947 (mtt) cc_final: -0.1899 (mtt) REVERT: 4 119 MET cc_start: -0.4041 (mmm) cc_final: -0.4923 (mtt) REVERT: 6 57 MET cc_start: -0.4193 (mmt) cc_final: -0.4734 (mtp) REVERT: 6 273 MET cc_start: -0.5931 (mtt) cc_final: -0.6154 (mtt) REVERT: 7 650 MET cc_start: -0.2687 (ptt) cc_final: -0.3041 (ptt) REVERT: 8 94 MET cc_start: -0.1211 (ttm) cc_final: -0.1470 (ttt) REVERT: 9 1 MET cc_start: -0.2053 (mmp) cc_final: -0.2466 (mmp) REVERT: 9 75 MET cc_start: -0.2092 (ttm) cc_final: -0.2969 (ttt) REVERT: A 225 PHE cc_start: 0.8298 (m-10) cc_final: 0.7967 (m-80) REVERT: A 355 MET cc_start: 0.7858 (ttp) cc_final: 0.7656 (ttp) REVERT: A 452 ASP cc_start: 0.7704 (m-30) cc_final: 0.7010 (t0) REVERT: A 467 MET cc_start: 0.8426 (mpp) cc_final: 0.8186 (mpp) REVERT: A 470 MET cc_start: 0.7861 (mtm) cc_final: 0.7506 (mtt) REVERT: A 514 GLU cc_start: 0.8067 (tt0) cc_final: 0.7553 (tt0) REVERT: A 565 MET cc_start: 0.8649 (tpt) cc_final: 0.8020 (tpt) REVERT: A 637 MET cc_start: 0.8665 (ptm) cc_final: 0.8426 (ptm) REVERT: A 691 ASP cc_start: 0.8633 (m-30) cc_final: 0.8111 (m-30) REVERT: A 841 MET cc_start: 0.8696 (mtp) cc_final: 0.8228 (ttm) REVERT: A 865 ILE cc_start: 0.8544 (tp) cc_final: 0.7801 (mt) REVERT: A 1375 ARG cc_start: 0.8248 (tmm160) cc_final: 0.7869 (ttp80) REVERT: B 407 MET cc_start: 0.8321 (mtm) cc_final: 0.8085 (mmp) REVERT: B 508 MET cc_start: 0.8449 (mmt) cc_final: 0.7800 (mmt) REVERT: B 550 MET cc_start: 0.7914 (tmm) cc_final: 0.6887 (tmm) REVERT: B 584 MET cc_start: 0.7662 (tpt) cc_final: 0.6812 (tpp) REVERT: B 726 SER cc_start: 0.9108 (m) cc_final: 0.8686 (p) REVERT: B 728 MET cc_start: 0.7022 (mmm) cc_final: 0.5590 (mmt) REVERT: B 758 LEU cc_start: 0.9309 (mt) cc_final: 0.9084 (mt) REVERT: C 148 ILE cc_start: 0.8733 (mm) cc_final: 0.8528 (mp) REVERT: E 13 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8854 (tt) REVERT: H 143 LEU cc_start: 0.8193 (tt) cc_final: 0.7891 (tt) REVERT: I 103 ARG cc_start: 0.6143 (mmp80) cc_final: 0.4912 (mmp80) REVERT: K 16 GLU cc_start: 0.5805 (pt0) cc_final: 0.5604 (pt0) REVERT: K 91 ILE cc_start: 0.8860 (mt) cc_final: 0.8585 (tt) REVERT: K 94 LEU cc_start: 0.8438 (mt) cc_final: 0.8052 (tp) REVERT: K 109 ILE cc_start: 0.8758 (mt) cc_final: 0.7954 (mm) REVERT: Q 177 MET cc_start: 0.3752 (ptm) cc_final: 0.3500 (ptm) REVERT: U 51 MET cc_start: 0.5668 (mmp) cc_final: 0.4363 (mpp) REVERT: V 1 MET cc_start: -0.3425 (ptm) cc_final: -0.4968 (mtt) REVERT: X 228 MET cc_start: -0.1775 (mtm) cc_final: -0.1988 (mpp) REVERT: a 52 MET cc_start: 0.0124 (ptp) cc_final: -0.0365 (ptt) REVERT: b 29 PHE cc_start: 0.6206 (t80) cc_final: 0.5673 (t80) REVERT: e 186 MET cc_start: 0.8392 (ppp) cc_final: 0.8038 (ppp) REVERT: h 47 MET cc_start: -0.0976 (mtp) cc_final: -0.1419 (mtp) REVERT: j 101 ILE cc_start: -0.4311 (OUTLIER) cc_final: -0.5547 (mp) REVERT: l 292 MET cc_start: 0.8260 (mmp) cc_final: 0.7872 (mmm) REVERT: l 571 MET cc_start: 0.5354 (mpp) cc_final: 0.5149 (mpp) REVERT: n 45 ASP cc_start: 0.7287 (t0) cc_final: 0.7015 (t0) REVERT: p 270 LEU cc_start: 0.9260 (mt) cc_final: 0.8949 (pp) REVERT: s 159 MET cc_start: 0.6599 (mmm) cc_final: 0.6381 (mmm) outliers start: 16 outliers final: 5 residues processed: 703 average time/residue: 0.8537 time to fit residues: 1052.9675 Evaluate side-chains 516 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 509 time to evaluate : 8.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1154 random chunks: chunk 1037 optimal weight: 50.0000 chunk 789 optimal weight: 50.0000 chunk 544 optimal weight: 0.9990 chunk 116 optimal weight: 50.0000 chunk 501 optimal weight: 10.0000 chunk 704 optimal weight: 10.0000 chunk 1053 optimal weight: 0.2980 chunk 1115 optimal weight: 50.0000 chunk 550 optimal weight: 0.0270 chunk 998 optimal weight: 9.9990 chunk 300 optimal weight: 50.0000 overall best weight: 4.2646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 114 ASN 0 145 GLN ** 0 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 384 HIS 1 534 ASN 2 83 GLN 2 366 HIS ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 265 GLN 8 33 ASN ** 9 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN A 685 HIS ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 HIS A 905 ASN ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 265 GLN B 390 ASN ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN H 29 HIS ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 143 GLN V 27 GLN d 184 ASN ** d 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 539 GLN ** g 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6125 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 98182 Z= 0.293 Angle : 0.597 13.814 133128 Z= 0.307 Chirality : 0.041 0.210 14966 Planarity : 0.004 0.073 16677 Dihedral : 10.821 173.119 14024 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.90 % Rotamer: Outliers : 0.04 % Allowed : 3.53 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % 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: 0.40 (0.08), residues: 11332 helix: 1.40 (0.07), residues: 5289 sheet: -0.42 (0.13), residues: 1509 loop : -0.81 (0.09), residues: 4534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 27 HIS 0.014 0.001 HIS 7 187 PHE 0.042 0.002 PHE d 635 TYR 0.028 0.001 TYR B 752 ARG 0.010 0.000 ARG X 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 649 time to evaluate : 8.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 247 MET cc_start: 0.2001 (ptt) cc_final: 0.1372 (ptt) REVERT: 0 478 MET cc_start: 0.2881 (mmt) cc_final: 0.2484 (mmp) REVERT: 1 528 MET cc_start: -0.7721 (mpp) cc_final: -0.8125 (ttt) REVERT: 2 185 MET cc_start: 0.0713 (mtp) cc_final: -0.0269 (mmt) REVERT: 4 51 MET cc_start: -0.1052 (mtt) cc_final: -0.1515 (mtp) REVERT: 4 119 MET cc_start: -0.3987 (mmm) cc_final: -0.4930 (mtt) REVERT: 7 650 MET cc_start: -0.2673 (ptt) cc_final: -0.3022 (ptt) REVERT: 8 240 MET cc_start: -0.2274 (tpt) cc_final: -0.2588 (tpt) REVERT: 9 1 MET cc_start: -0.2610 (mmp) cc_final: -0.2952 (mmp) REVERT: 9 75 MET cc_start: -0.2403 (ttm) cc_final: -0.3199 (ttt) REVERT: A 18 ILE cc_start: 0.9292 (mp) cc_final: 0.8641 (mp) REVERT: A 238 MET cc_start: 0.7149 (ppp) cc_final: 0.6943 (ppp) REVERT: A 450 MET cc_start: 0.8546 (ptm) cc_final: 0.8241 (ptm) REVERT: A 452 ASP cc_start: 0.7671 (m-30) cc_final: 0.6989 (t0) REVERT: A 467 MET cc_start: 0.8576 (mpp) cc_final: 0.8280 (mpp) REVERT: A 469 MET cc_start: 0.8148 (mtm) cc_final: 0.7893 (mtm) REVERT: A 470 MET cc_start: 0.7795 (mtm) cc_final: 0.7500 (mtt) REVERT: A 501 MET cc_start: 0.8664 (ttm) cc_final: 0.8430 (ttt) REVERT: A 514 GLU cc_start: 0.8210 (tt0) cc_final: 0.7666 (tt0) REVERT: A 565 MET cc_start: 0.8618 (tpt) cc_final: 0.8021 (tpt) REVERT: A 637 MET cc_start: 0.8638 (ptm) cc_final: 0.8397 (ptm) REVERT: A 691 ASP cc_start: 0.8575 (m-30) cc_final: 0.8103 (m-30) REVERT: A 841 MET cc_start: 0.8662 (mtp) cc_final: 0.8217 (ttm) REVERT: A 865 ILE cc_start: 0.8560 (tp) cc_final: 0.7846 (mp) REVERT: A 1228 MET cc_start: 0.7750 (ptp) cc_final: 0.7542 (mtp) REVERT: A 1375 ARG cc_start: 0.8316 (tmm160) cc_final: 0.7843 (ttp80) REVERT: B 149 ILE cc_start: 0.9245 (pt) cc_final: 0.8547 (mm) REVERT: B 155 MET cc_start: 0.7285 (ttp) cc_final: 0.6841 (ttp) REVERT: B 256 ILE cc_start: 0.8566 (tt) cc_final: 0.8354 (tt) REVERT: B 297 MET cc_start: 0.6607 (ttt) cc_final: 0.6377 (mtp) REVERT: B 508 MET cc_start: 0.8394 (mmt) cc_final: 0.7669 (mmt) REVERT: B 550 MET cc_start: 0.8170 (tmm) cc_final: 0.7616 (tmm) REVERT: B 726 SER cc_start: 0.9006 (m) cc_final: 0.8543 (p) REVERT: B 728 MET cc_start: 0.7144 (mmm) cc_final: 0.5559 (mmt) REVERT: B 758 LEU cc_start: 0.9322 (mt) cc_final: 0.9102 (mt) REVERT: B 764 MET cc_start: 0.8614 (ttm) cc_final: 0.8381 (ttm) REVERT: B 840 MET cc_start: 0.3962 (ppp) cc_final: 0.2498 (ppp) REVERT: B 964 ASP cc_start: 0.8832 (m-30) cc_final: 0.8586 (m-30) REVERT: B 1053 HIS cc_start: 0.7799 (m90) cc_final: 0.7499 (m170) REVERT: F 56 TYR cc_start: 0.7157 (m-80) cc_final: 0.6916 (m-80) REVERT: H 143 LEU cc_start: 0.8221 (tt) cc_final: 0.7933 (tt) REVERT: I 103 ARG cc_start: 0.6103 (mmp80) cc_final: 0.5360 (mmp80) REVERT: K 91 ILE cc_start: 0.8794 (mt) cc_final: 0.8574 (tt) REVERT: K 94 LEU cc_start: 0.8391 (mt) cc_final: 0.8026 (tp) REVERT: K 109 ILE cc_start: 0.8798 (mt) cc_final: 0.8071 (mm) REVERT: M 114 MET cc_start: 0.8404 (mmm) cc_final: 0.7953 (mmm) REVERT: U 51 MET cc_start: 0.5354 (mmp) cc_final: 0.3998 (mpp) REVERT: U 358 MET cc_start: 0.7769 (pmm) cc_final: 0.7439 (pmm) REVERT: V 1 MET cc_start: -0.3429 (ptm) cc_final: -0.4907 (mtt) REVERT: X 228 MET cc_start: -0.1679 (mtm) cc_final: -0.1889 (mpp) REVERT: a 52 MET cc_start: 0.0028 (ptp) cc_final: -0.0509 (ptt) REVERT: h 47 MET cc_start: -0.0901 (mtp) cc_final: -0.1366 (mtp) REVERT: p 270 LEU cc_start: 0.9199 (mt) cc_final: 0.8839 (pp) REVERT: s 159 MET cc_start: 0.6964 (mmm) cc_final: 0.6686 (mmm) outliers start: 4 outliers final: 0 residues processed: 652 average time/residue: 0.8512 time to fit residues: 971.5325 Evaluate side-chains 500 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 500 time to evaluate : 8.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1154 random chunks: chunk 929 optimal weight: 9.9990 chunk 633 optimal weight: 9.9990 chunk 16 optimal weight: 40.0000 chunk 830 optimal weight: 7.9990 chunk 460 optimal weight: 30.0000 chunk 951 optimal weight: 20.0000 chunk 771 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 569 optimal weight: 0.8980 chunk 1001 optimal weight: 6.9990 chunk 281 optimal weight: 20.0000 overall best weight: 7.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 114 ASN ** 0 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 83 GLN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 83 ASN 4 173 GLN 4 179 ASN 6 103 GLN 6 265 GLN 8 33 ASN 9 3 HIS ** 9 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 162 ASN A 465 HIS ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN B 265 GLN ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 GLN B1117 HIS C 6 GLN ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 GLN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN K 69 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 139 GLN ** c 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 91 GLN d 100 ASN ** d 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 89 ASN g 109 GLN i 82 ASN ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 483 ASN ** l 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 109 GLN s 145 ASN s 150 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.151 98182 Z= 0.441 Angle : 0.705 18.863 133128 Z= 0.362 Chirality : 0.043 0.257 14966 Planarity : 0.005 0.102 16677 Dihedral : 11.046 173.190 14024 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.75 % Favored : 95.23 % Rotamer: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % 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: 0.10 (0.08), residues: 11332 helix: 1.21 (0.07), residues: 5236 sheet: -0.59 (0.13), residues: 1520 loop : -1.00 (0.09), residues: 4576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 506 HIS 0.018 0.001 HIS C 66 PHE 0.038 0.002 PHE A 458 TYR 0.038 0.002 TYR A 875 ARG 0.018 0.001 ARG e 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 591 time to evaluate : 8.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 247 MET cc_start: 0.2568 (ptt) cc_final: 0.1921 (ptt) REVERT: 0 478 MET cc_start: 0.3108 (mmt) cc_final: 0.2715 (mmp) REVERT: 1 528 MET cc_start: -0.7791 (mpp) cc_final: -0.8011 (ttt) REVERT: 2 185 MET cc_start: 0.0528 (mtp) cc_final: -0.0614 (mtt) REVERT: 4 42 MET cc_start: 0.7575 (ptt) cc_final: 0.7368 (mmt) REVERT: 4 51 MET cc_start: -0.0992 (mtt) cc_final: -0.1282 (mtp) REVERT: 4 119 MET cc_start: -0.3875 (mmm) cc_final: -0.4866 (mtt) REVERT: 4 157 MET cc_start: -0.3751 (ttp) cc_final: -0.4220 (ttt) REVERT: 6 153 MET cc_start: -0.4946 (mmp) cc_final: -0.5318 (mmt) REVERT: 7 380 MET cc_start: 0.8437 (ptt) cc_final: 0.7905 (mmm) REVERT: 7 650 MET cc_start: -0.2286 (ptt) cc_final: -0.2620 (ptt) REVERT: 8 240 MET cc_start: -0.2202 (tpt) cc_final: -0.2715 (tpt) REVERT: 9 1 MET cc_start: -0.2854 (mmp) cc_final: -0.3085 (mmp) REVERT: 9 75 MET cc_start: -0.3025 (ttm) cc_final: -0.3474 (ttt) REVERT: 9 252 MET cc_start: -0.5834 (mmt) cc_final: -0.6046 (mmt) REVERT: A 238 MET cc_start: 0.7404 (ppp) cc_final: 0.7025 (ppp) REVERT: A 501 MET cc_start: 0.8855 (ttm) cc_final: 0.8597 (ttt) REVERT: A 514 GLU cc_start: 0.8076 (tt0) cc_final: 0.7516 (tt0) REVERT: A 520 MET cc_start: 0.9204 (tpp) cc_final: 0.8954 (mmm) REVERT: A 565 MET cc_start: 0.8534 (tpt) cc_final: 0.8087 (tpt) REVERT: A 691 ASP cc_start: 0.8547 (m-30) cc_final: 0.8139 (m-30) REVERT: A 832 THR cc_start: 0.8473 (p) cc_final: 0.8243 (p) REVERT: A 841 MET cc_start: 0.8679 (mtp) cc_final: 0.8206 (ttm) REVERT: A 865 ILE cc_start: 0.8510 (tp) cc_final: 0.7908 (mp) REVERT: A 1054 MET cc_start: 0.7294 (mmm) cc_final: 0.6885 (mmm) REVERT: A 1257 LEU cc_start: 0.8720 (tp) cc_final: 0.8476 (tp) REVERT: A 1375 ARG cc_start: 0.8646 (tmm160) cc_final: 0.8133 (tmm160) REVERT: A 1414 ILE cc_start: 0.8120 (mm) cc_final: 0.7826 (mm) REVERT: B 66 ASP cc_start: 0.6043 (t0) cc_final: 0.5838 (t0) REVERT: B 149 ILE cc_start: 0.9385 (pt) cc_final: 0.8981 (tp) REVERT: B 508 MET cc_start: 0.8331 (mmt) cc_final: 0.7582 (mmm) REVERT: B 677 MET cc_start: 0.7718 (mmm) cc_final: 0.7474 (mmm) REVERT: B 726 SER cc_start: 0.8837 (m) cc_final: 0.8461 (p) REVERT: B 728 MET cc_start: 0.7336 (mmm) cc_final: 0.7061 (mmt) REVERT: B 764 MET cc_start: 0.8681 (ttm) cc_final: 0.8332 (ttm) REVERT: B 840 MET cc_start: 0.4298 (ppp) cc_final: 0.2751 (ppp) REVERT: H 143 LEU cc_start: 0.8144 (tt) cc_final: 0.7930 (tt) REVERT: I 103 ARG cc_start: 0.6118 (mmp80) cc_final: 0.5526 (mmp80) REVERT: K 16 GLU cc_start: 0.6418 (pt0) cc_final: 0.6190 (pt0) REVERT: K 94 LEU cc_start: 0.8411 (mt) cc_final: 0.8153 (tp) REVERT: K 109 ILE cc_start: 0.8712 (mt) cc_final: 0.8294 (mt) REVERT: M 114 MET cc_start: 0.8226 (mmm) cc_final: 0.8005 (mmm) REVERT: M 292 ILE cc_start: 0.7473 (pt) cc_final: 0.6374 (pt) REVERT: Q 121 ASN cc_start: 0.6031 (t0) cc_final: 0.5762 (p0) REVERT: U 51 MET cc_start: 0.5447 (mmp) cc_final: 0.4099 (mpp) REVERT: U 358 MET cc_start: 0.7727 (pmm) cc_final: 0.7389 (pmm) REVERT: V 1 MET cc_start: -0.3424 (ptm) cc_final: -0.4859 (mtt) REVERT: h 47 MET cc_start: -0.0873 (mtp) cc_final: -0.1368 (mtp) REVERT: l 478 MET cc_start: 0.5691 (ptt) cc_final: 0.5457 (ptt) REVERT: p 270 LEU cc_start: 0.9203 (mt) cc_final: 0.8844 (pp) outliers start: 6 outliers final: 3 residues processed: 596 average time/residue: 0.8882 time to fit residues: 925.7822 Evaluate side-chains 477 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 474 time to evaluate : 8.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1154 random chunks: chunk 375 optimal weight: 1.9990 chunk 1004 optimal weight: 50.0000 chunk 220 optimal weight: 8.9990 chunk 654 optimal weight: 1.9990 chunk 275 optimal weight: 50.0000 chunk 1116 optimal weight: 1.9990 chunk 926 optimal weight: 6.9990 chunk 516 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 369 optimal weight: 0.5980 chunk 586 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 114 ASN ** 0 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 83 GLN 2 366 HIS ** 3 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 179 ASN ** 4 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 265 GLN 7 576 ASN 8 33 ASN ** 9 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 ASN A1457 ASN ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 HIS O 327 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 103 ASN W 101 ASN ** W 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 GLN d 142 GLN ** d 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 373 HIS ** d 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 483 ASN l 507 GLN p 218 ASN q 109 GLN ** s 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 98182 Z= 0.187 Angle : 0.557 14.241 133128 Z= 0.285 Chirality : 0.040 0.287 14966 Planarity : 0.004 0.068 16677 Dihedral : 10.887 173.311 14024 Min Nonbonded Distance : 1.591 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.01 % Favored : 95.98 % Rotamer: Outliers : 0.05 % Allowed : 1.77 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.08), residues: 11332 helix: 1.46 (0.07), residues: 5249 sheet: -0.46 (0.13), residues: 1493 loop : -0.86 (0.09), residues: 4590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 453 HIS 0.016 0.001 HIS M 18 PHE 0.033 0.001 PHE 0 720 TYR 0.025 0.001 TYR B 388 ARG 0.014 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 630 time to evaluate : 8.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 247 MET cc_start: 0.2674 (ptt) cc_final: 0.2038 (ptt) REVERT: 0 478 MET cc_start: 0.3214 (mmt) cc_final: 0.2637 (mmp) REVERT: 0 493 MET cc_start: 0.1579 (tpt) cc_final: 0.0833 (mmm) REVERT: 0 724 MET cc_start: 0.2092 (mtt) cc_final: 0.1315 (mpp) REVERT: 1 528 MET cc_start: -0.7582 (mpp) cc_final: -0.8005 (ttt) REVERT: 2 185 MET cc_start: -0.0221 (mtp) cc_final: -0.0651 (mtt) REVERT: 2 207 ASP cc_start: 0.7392 (m-30) cc_final: 0.7051 (m-30) REVERT: 4 42 MET cc_start: 0.7586 (ptt) cc_final: 0.7382 (mmt) REVERT: 4 51 MET cc_start: -0.1037 (mtt) cc_final: -0.1269 (mtp) REVERT: 4 119 MET cc_start: -0.4027 (mmm) cc_final: -0.5003 (mtt) REVERT: 4 157 MET cc_start: -0.3731 (ttp) cc_final: -0.4233 (ttt) REVERT: 7 380 MET cc_start: 0.8590 (ptt) cc_final: 0.8057 (mmm) REVERT: 7 450 MET cc_start: -0.6457 (ttt) cc_final: -0.6726 (mtp) REVERT: 7 650 MET cc_start: -0.2246 (ptt) cc_final: -0.2587 (ptt) REVERT: 8 94 MET cc_start: 0.0064 (ttm) cc_final: -0.1045 (ttt) REVERT: 8 240 MET cc_start: -0.2545 (tpt) cc_final: -0.2949 (tpt) REVERT: 9 1 MET cc_start: -0.2772 (mmp) cc_final: -0.2990 (mmp) REVERT: 9 75 MET cc_start: -0.2725 (ttm) cc_final: -0.3185 (ttt) REVERT: 9 252 MET cc_start: -0.5950 (mmt) cc_final: -0.6292 (mmt) REVERT: A 253 LEU cc_start: 0.8129 (tp) cc_final: 0.7912 (tp) REVERT: A 266 MET cc_start: -0.1240 (ppp) cc_final: -0.2354 (ttt) REVERT: A 486 LEU cc_start: 0.8918 (mm) cc_final: 0.8665 (mm) REVERT: A 501 MET cc_start: 0.8648 (ttm) cc_final: 0.8398 (ttt) REVERT: A 514 GLU cc_start: 0.8047 (tt0) cc_final: 0.7627 (tt0) REVERT: A 565 MET cc_start: 0.8492 (tpt) cc_final: 0.8148 (tpp) REVERT: A 637 MET cc_start: 0.8576 (ptm) cc_final: 0.8242 (ptm) REVERT: A 691 ASP cc_start: 0.8568 (m-30) cc_final: 0.7988 (m-30) REVERT: A 832 THR cc_start: 0.8616 (p) cc_final: 0.8316 (p) REVERT: A 841 MET cc_start: 0.8527 (mtp) cc_final: 0.7989 (ttm) REVERT: A 865 ILE cc_start: 0.8580 (tp) cc_final: 0.7824 (mt) REVERT: A 1054 MET cc_start: 0.7064 (mmm) cc_final: 0.6629 (mmm) REVERT: A 1379 GLU cc_start: 0.8620 (pp20) cc_final: 0.8411 (tm-30) REVERT: A 1427 LEU cc_start: 0.8219 (mm) cc_final: 0.7979 (mm) REVERT: B 155 MET cc_start: 0.7229 (ttp) cc_final: 0.6702 (mtp) REVERT: B 297 MET cc_start: 0.6482 (mtp) cc_final: 0.5849 (mtp) REVERT: B 508 MET cc_start: 0.8316 (mmt) cc_final: 0.7763 (mmt) REVERT: B 550 MET cc_start: 0.8115 (tmm) cc_final: 0.7660 (tmm) REVERT: B 726 SER cc_start: 0.8933 (m) cc_final: 0.8591 (p) REVERT: B 728 MET cc_start: 0.7038 (mmm) cc_final: 0.6831 (mmt) REVERT: B 764 MET cc_start: 0.8608 (ttm) cc_final: 0.8304 (ttm) REVERT: B 919 CYS cc_start: 0.7427 (p) cc_final: 0.7226 (p) REVERT: B 964 ASP cc_start: 0.8521 (m-30) cc_final: 0.8165 (m-30) REVERT: C 148 ILE cc_start: 0.8723 (mm) cc_final: 0.8427 (mp) REVERT: F 56 TYR cc_start: 0.7052 (m-80) cc_final: 0.6830 (m-80) REVERT: H 143 LEU cc_start: 0.7913 (tt) cc_final: 0.7677 (tt) REVERT: I 103 ARG cc_start: 0.5882 (mmp80) cc_final: 0.5147 (mmp80) REVERT: K 94 LEU cc_start: 0.8328 (mt) cc_final: 0.8122 (tp) REVERT: U 51 MET cc_start: 0.5390 (mmp) cc_final: 0.4195 (mpp) REVERT: V 1 MET cc_start: -0.3406 (ptm) cc_final: -0.4900 (mtt) REVERT: W 168 MET cc_start: 0.7541 (tpt) cc_final: 0.7337 (tpp) REVERT: a 52 MET cc_start: -0.1063 (ptp) cc_final: -0.1678 (ptt) REVERT: h 47 MET cc_start: -0.0844 (mtp) cc_final: -0.1392 (mtp) REVERT: l 478 MET cc_start: 0.5680 (ptt) cc_final: 0.5417 (ptt) REVERT: p 172 MET cc_start: 0.4548 (pmm) cc_final: 0.4279 (pmm) outliers start: 5 outliers final: 0 residues processed: 635 average time/residue: 0.8450 time to fit residues: 946.0069 Evaluate side-chains 488 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 488 time to evaluate : 8.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1154 random chunks: chunk 1076 optimal weight: 10.0000 chunk 125 optimal weight: 50.0000 chunk 636 optimal weight: 1.9990 chunk 815 optimal weight: 50.0000 chunk 631 optimal weight: 6.9990 chunk 939 optimal weight: 40.0000 chunk 623 optimal weight: 9.9990 chunk 1112 optimal weight: 50.0000 chunk 696 optimal weight: 0.1980 chunk 678 optimal weight: 9.9990 chunk 513 optimal weight: 3.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 114 ASN 2 54 ASN 2 83 GLN 2 366 HIS ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 265 GLN 7 683 GLN 8 33 ASN ** 9 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1077 ASN B 56 GLN ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 152 ASN ** W 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 310 GLN ** d 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 483 ASN l 507 GLN q 109 GLN s 150 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 98182 Z= 0.317 Angle : 0.614 14.259 133128 Z= 0.314 Chirality : 0.041 0.259 14966 Planarity : 0.004 0.057 16677 Dihedral : 10.911 173.601 14024 Min Nonbonded Distance : 1.616 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.48 % Favored : 95.51 % Rotamer: Outliers : 0.02 % Allowed : 1.77 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.08), residues: 11332 helix: 1.43 (0.07), residues: 5248 sheet: -0.53 (0.13), residues: 1515 loop : -0.90 (0.09), residues: 4569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 27 HIS 0.011 0.001 HIS C 66 PHE 0.033 0.002 PHE A 458 TYR 0.035 0.002 TYR B 752 ARG 0.013 0.000 ARG A1375 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 578 time to evaluate : 8.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 247 MET cc_start: 0.2880 (ptt) cc_final: 0.2087 (ptt) REVERT: 0 478 MET cc_start: 0.3195 (mmt) cc_final: 0.2663 (mmp) REVERT: 0 493 MET cc_start: 0.1715 (tpt) cc_final: 0.0985 (mmm) REVERT: 1 528 MET cc_start: -0.7704 (mpp) cc_final: -0.8017 (ttm) REVERT: 2 185 MET cc_start: 0.0406 (mtp) cc_final: -0.0933 (mtt) REVERT: 4 119 MET cc_start: -0.3990 (mmm) cc_final: -0.4957 (mtt) REVERT: 6 57 MET cc_start: -0.2479 (mtm) cc_final: -0.3221 (mtm) REVERT: 7 380 MET cc_start: 0.8635 (ptt) cc_final: 0.8053 (mmm) REVERT: 7 450 MET cc_start: -0.6515 (ttt) cc_final: -0.6789 (mtp) REVERT: 7 650 MET cc_start: -0.1949 (ptt) cc_final: -0.2379 (ptt) REVERT: 8 240 MET cc_start: -0.2703 (tpt) cc_final: -0.3067 (tpt) REVERT: 9 1 MET cc_start: -0.2825 (mmp) cc_final: -0.3044 (mmp) REVERT: 9 75 MET cc_start: -0.2927 (ttm) cc_final: -0.3342 (ttt) REVERT: A 238 MET cc_start: 0.7300 (ppp) cc_final: 0.7097 (ppp) REVERT: A 266 MET cc_start: -0.1214 (ppp) cc_final: -0.1484 (ppp) REVERT: A 467 MET cc_start: 0.7993 (mpp) cc_final: 0.7464 (mpp) REVERT: A 469 MET cc_start: 0.8207 (mtm) cc_final: 0.7880 (mtm) REVERT: A 470 MET cc_start: 0.7572 (mtp) cc_final: 0.7057 (mtp) REVERT: A 501 MET cc_start: 0.8704 (ttm) cc_final: 0.8465 (ttt) REVERT: A 514 GLU cc_start: 0.8188 (tt0) cc_final: 0.7768 (tt0) REVERT: A 520 MET cc_start: 0.9416 (mmm) cc_final: 0.9153 (tpp) REVERT: A 565 MET cc_start: 0.8721 (tpt) cc_final: 0.8277 (tpp) REVERT: A 637 MET cc_start: 0.8569 (ptm) cc_final: 0.8318 (ptm) REVERT: A 832 THR cc_start: 0.8501 (p) cc_final: 0.8277 (p) REVERT: A 841 MET cc_start: 0.8546 (mtp) cc_final: 0.8131 (ttm) REVERT: A 865 ILE cc_start: 0.8547 (tp) cc_final: 0.7864 (mp) REVERT: A 1054 MET cc_start: 0.7100 (mmm) cc_final: 0.6844 (mmm) REVERT: A 1379 GLU cc_start: 0.8893 (pp20) cc_final: 0.8638 (tm-30) REVERT: A 1414 ILE cc_start: 0.7850 (mm) cc_final: 0.7486 (mm) REVERT: A 1427 LEU cc_start: 0.8164 (mm) cc_final: 0.7904 (mm) REVERT: B 155 MET cc_start: 0.7357 (ttp) cc_final: 0.6902 (mtp) REVERT: B 508 MET cc_start: 0.8365 (mmt) cc_final: 0.7609 (mmt) REVERT: B 726 SER cc_start: 0.8906 (m) cc_final: 0.8482 (p) REVERT: B 728 MET cc_start: 0.7213 (mmm) cc_final: 0.6958 (mmt) REVERT: B 758 LEU cc_start: 0.9355 (mt) cc_final: 0.9137 (mt) REVERT: B 764 MET cc_start: 0.8666 (ttm) cc_final: 0.8371 (ttm) REVERT: B 840 MET cc_start: 0.4096 (ppp) cc_final: 0.2215 (ppp) REVERT: B 964 ASP cc_start: 0.8437 (m-30) cc_final: 0.7983 (m-30) REVERT: B 1053 HIS cc_start: 0.7841 (m-70) cc_final: 0.7633 (m170) REVERT: F 56 TYR cc_start: 0.7176 (m-80) cc_final: 0.6927 (m-80) REVERT: G 12 LEU cc_start: 0.8318 (mm) cc_final: 0.7951 (mt) REVERT: H 143 LEU cc_start: 0.7981 (tt) cc_final: 0.7740 (tt) REVERT: I 103 ARG cc_start: 0.5920 (mmp80) cc_final: 0.5173 (mmp80) REVERT: K 94 LEU cc_start: 0.8433 (mt) cc_final: 0.8209 (tp) REVERT: M 124 MET cc_start: 0.7326 (mmp) cc_final: 0.7041 (tpp) REVERT: U 51 MET cc_start: 0.5396 (mmp) cc_final: 0.4106 (pmm) REVERT: U 358 MET cc_start: 0.7616 (pmm) cc_final: 0.7282 (pmm) REVERT: V 1 MET cc_start: -0.3298 (ptm) cc_final: -0.4804 (mtt) REVERT: W 168 MET cc_start: 0.7561 (tpt) cc_final: 0.7333 (tpp) REVERT: a 52 MET cc_start: -0.1268 (ptp) cc_final: -0.1653 (ptt) REVERT: h 47 MET cc_start: -0.0615 (mtp) cc_final: -0.1235 (mtp) REVERT: p 172 MET cc_start: 0.4705 (pmm) cc_final: 0.4413 (pmm) outliers start: 2 outliers final: 0 residues processed: 580 average time/residue: 0.8236 time to fit residues: 847.4550 Evaluate side-chains 464 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 464 time to evaluate : 8.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1154 random chunks: chunk 688 optimal weight: 7.9990 chunk 444 optimal weight: 0.0050 chunk 664 optimal weight: 10.0000 chunk 335 optimal weight: 40.0000 chunk 218 optimal weight: 0.0980 chunk 215 optimal weight: 40.0000 chunk 707 optimal weight: 5.9990 chunk 757 optimal weight: 8.9990 chunk 549 optimal weight: 1.9990 chunk 103 optimal weight: 50.0000 chunk 874 optimal weight: 50.0000 overall best weight: 3.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 114 ASN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 265 GLN 7 181 HIS 7 709 GLN 8 33 ASN ** 9 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 350 HIS ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 GLN B1071 ASN D 48 ASN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 422 GLN ** d 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 483 ASN l 507 GLN ** s 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 98182 Z= 0.240 Angle : 0.572 15.067 133128 Z= 0.292 Chirality : 0.040 0.243 14966 Planarity : 0.004 0.060 16677 Dihedral : 10.872 173.703 14024 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.26 % Favored : 95.73 % Rotamer: Outliers : 0.02 % Allowed : 1.14 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.08), residues: 11332 helix: 1.48 (0.07), residues: 5253 sheet: -0.49 (0.13), residues: 1485 loop : -0.87 (0.09), residues: 4594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 453 HIS 0.010 0.001 HIS M 18 PHE 0.045 0.002 PHE b 49 TYR 0.032 0.001 TYR B1048 ARG 0.011 0.000 ARG b 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 584 time to evaluate : 9.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 478 MET cc_start: 0.2992 (mmt) cc_final: 0.2520 (mmp) REVERT: 0 493 MET cc_start: 0.1484 (tpt) cc_final: -0.0496 (mmt) REVERT: 0 677 MET cc_start: -0.1197 (pmm) cc_final: -0.1618 (pmm) REVERT: 0 724 MET cc_start: 0.1550 (mtt) cc_final: 0.0673 (mpp) REVERT: 1 528 MET cc_start: -0.7726 (mpp) cc_final: -0.8056 (ttm) REVERT: 2 185 MET cc_start: -0.0289 (mtp) cc_final: -0.0922 (mtt) REVERT: 3 1 MET cc_start: 0.0996 (tpt) cc_final: 0.0340 (tpt) REVERT: 4 51 MET cc_start: -0.1908 (mtt) cc_final: -0.2423 (mtt) REVERT: 4 119 MET cc_start: -0.3960 (mmm) cc_final: -0.4966 (mtp) REVERT: 4 157 MET cc_start: -0.3666 (ttp) cc_final: -0.4136 (ttt) REVERT: 6 57 MET cc_start: -0.2832 (mtm) cc_final: -0.3331 (mtm) REVERT: 7 380 MET cc_start: 0.8620 (ptt) cc_final: 0.8061 (mmm) REVERT: 7 450 MET cc_start: -0.6534 (ttt) cc_final: -0.6823 (mtp) REVERT: 7 650 MET cc_start: -0.2088 (ptt) cc_final: -0.2483 (ptt) REVERT: 8 240 MET cc_start: -0.2784 (tpt) cc_final: -0.3127 (tpt) REVERT: 9 75 MET cc_start: -0.2781 (ttm) cc_final: -0.3184 (ttt) REVERT: A 253 LEU cc_start: 0.8108 (tp) cc_final: 0.7904 (tp) REVERT: A 266 MET cc_start: -0.1424 (ppp) cc_final: -0.2030 (ttt) REVERT: A 469 MET cc_start: 0.8117 (mtm) cc_final: 0.7786 (mtm) REVERT: A 514 GLU cc_start: 0.8187 (tt0) cc_final: 0.7784 (tt0) REVERT: A 520 MET cc_start: 0.9427 (mmm) cc_final: 0.9221 (tpp) REVERT: A 565 MET cc_start: 0.8667 (tpt) cc_final: 0.8299 (tpp) REVERT: A 637 MET cc_start: 0.8584 (ptm) cc_final: 0.8263 (ptm) REVERT: A 832 THR cc_start: 0.8540 (p) cc_final: 0.8252 (p) REVERT: A 841 MET cc_start: 0.8559 (mtp) cc_final: 0.8080 (ttm) REVERT: A 865 ILE cc_start: 0.8518 (tp) cc_final: 0.7695 (mt) REVERT: A 1257 LEU cc_start: 0.8607 (tp) cc_final: 0.8334 (tp) REVERT: A 1379 GLU cc_start: 0.8892 (pp20) cc_final: 0.8636 (tm-30) REVERT: A 1427 LEU cc_start: 0.8137 (mm) cc_final: 0.7904 (mm) REVERT: A 1428 MET cc_start: 0.7911 (tpp) cc_final: 0.7551 (tpp) REVERT: B 343 LEU cc_start: 0.8963 (pp) cc_final: 0.8741 (mm) REVERT: B 508 MET cc_start: 0.8348 (mmt) cc_final: 0.7533 (mmt) REVERT: B 726 SER cc_start: 0.8925 (m) cc_final: 0.8476 (p) REVERT: B 764 MET cc_start: 0.8613 (ttm) cc_final: 0.8298 (ttm) REVERT: B 785 TYR cc_start: 0.8088 (t80) cc_final: 0.7615 (t80) REVERT: B 919 CYS cc_start: 0.7682 (p) cc_final: 0.7090 (p) REVERT: B 964 ASP cc_start: 0.8373 (m-30) cc_final: 0.7606 (m-30) REVERT: C 148 ILE cc_start: 0.8682 (mm) cc_final: 0.8440 (mp) REVERT: G 12 LEU cc_start: 0.8224 (mm) cc_final: 0.7828 (mt) REVERT: H 143 LEU cc_start: 0.7945 (tt) cc_final: 0.7728 (tt) REVERT: I 103 ARG cc_start: 0.5728 (mmp80) cc_final: 0.4966 (mmp80) REVERT: U 51 MET cc_start: 0.5368 (mmp) cc_final: 0.4073 (pmm) REVERT: U 358 MET cc_start: 0.7650 (pmm) cc_final: 0.7417 (pmm) REVERT: V 1 MET cc_start: -0.3294 (ptm) cc_final: -0.4797 (mtt) REVERT: W 168 MET cc_start: 0.7458 (tpt) cc_final: 0.7189 (tpp) REVERT: a 52 MET cc_start: -0.1064 (ptp) cc_final: -0.1353 (ptt) REVERT: e 186 MET cc_start: 0.8175 (ppp) cc_final: 0.7786 (ppp) REVERT: h 47 MET cc_start: -0.0621 (mtp) cc_final: -0.1275 (mtp) REVERT: l 486 MET cc_start: 0.5135 (ttt) cc_final: 0.4910 (ttt) REVERT: p 172 MET cc_start: 0.4859 (pmm) cc_final: 0.4590 (pmm) REVERT: s 159 MET cc_start: 0.7253 (mmm) cc_final: 0.6676 (mmm) outliers start: 2 outliers final: 0 residues processed: 586 average time/residue: 0.8328 time to fit residues: 865.0505 Evaluate side-chains 472 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 472 time to evaluate : 8.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1154 random chunks: chunk 1011 optimal weight: 10.0000 chunk 1065 optimal weight: 9.9990 chunk 972 optimal weight: 10.0000 chunk 1036 optimal weight: 8.9990 chunk 623 optimal weight: 10.0000 chunk 451 optimal weight: 4.9990 chunk 813 optimal weight: 0.0970 chunk 318 optimal weight: 30.0000 chunk 936 optimal weight: 30.0000 chunk 980 optimal weight: 50.0000 chunk 1032 optimal weight: 40.0000 overall best weight: 6.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 114 ASN 3 24 ASN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 179 ASN ** 4 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 103 GLN 6 265 GLN 8 33 ASN ** 9 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 HIS ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 ASN ** B1117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 101 ASN W 181 ASN ** X 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 85 GLN ** c 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 321 GLN ** d 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 483 ASN l 507 GLN p 179 HIS ** s 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.145 98182 Z= 0.421 Angle : 0.688 15.194 133128 Z= 0.352 Chirality : 0.043 0.225 14966 Planarity : 0.005 0.082 16677 Dihedral : 11.052 173.866 14024 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.15 % Favored : 94.84 % Rotamer: Outliers : 0.03 % Allowed : 0.63 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.08), residues: 11332 helix: 1.31 (0.07), residues: 5245 sheet: -0.58 (0.13), residues: 1468 loop : -1.04 (0.09), residues: 4619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 27 HIS 0.014 0.001 HIS C 66 PHE 0.062 0.002 PHE W 180 TYR 0.043 0.002 TYR e 167 ARG 0.021 0.001 ARG b 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 551 time to evaluate : 8.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 478 MET cc_start: 0.3164 (mmt) cc_final: 0.2519 (mmp) REVERT: 0 493 MET cc_start: 0.1530 (tpt) cc_final: -0.0589 (mmt) REVERT: 0 724 MET cc_start: 0.1608 (mtt) cc_final: 0.0781 (mtt) REVERT: 2 185 MET cc_start: 0.0619 (mtp) cc_final: -0.0449 (mtt) REVERT: 3 1 MET cc_start: 0.1134 (tpt) cc_final: 0.0490 (tpt) REVERT: 4 51 MET cc_start: -0.1718 (mtt) cc_final: -0.2298 (mtt) REVERT: 4 119 MET cc_start: -0.3956 (mmm) cc_final: -0.4623 (mmt) REVERT: 4 157 MET cc_start: -0.3646 (ttp) cc_final: -0.4132 (ttt) REVERT: 4 175 MET cc_start: -0.5198 (mmt) cc_final: -0.5533 (mmt) REVERT: 6 57 MET cc_start: -0.2968 (mtm) cc_final: -0.3243 (mtm) REVERT: 7 380 MET cc_start: 0.8607 (ptt) cc_final: 0.8050 (mmm) REVERT: 7 450 MET cc_start: -0.6527 (ttt) cc_final: -0.6867 (mtp) REVERT: 7 650 MET cc_start: -0.1922 (ptt) cc_final: -0.2271 (ptt) REVERT: 8 240 MET cc_start: -0.2691 (tpt) cc_final: -0.3049 (tpt) REVERT: 9 1 MET cc_start: -0.2449 (mmp) cc_final: -0.3055 (mmt) REVERT: 9 75 MET cc_start: -0.2868 (ttm) cc_final: -0.3282 (ttt) REVERT: A 238 MET cc_start: 0.7393 (ppp) cc_final: 0.7135 (ppp) REVERT: A 266 MET cc_start: -0.1711 (ppp) cc_final: -0.1944 (ttt) REVERT: A 467 MET cc_start: 0.8347 (mpp) cc_final: 0.8077 (mpp) REVERT: A 469 MET cc_start: 0.8224 (mtm) cc_final: 0.7879 (mtm) REVERT: A 501 MET cc_start: 0.8892 (ttm) cc_final: 0.8669 (ttt) REVERT: A 514 GLU cc_start: 0.8189 (tt0) cc_final: 0.7733 (tt0) REVERT: A 565 MET cc_start: 0.8670 (tpt) cc_final: 0.8309 (tpp) REVERT: A 637 MET cc_start: 0.8504 (ptm) cc_final: 0.8216 (ptm) REVERT: A 832 THR cc_start: 0.8526 (p) cc_final: 0.8284 (p) REVERT: A 841 MET cc_start: 0.8579 (mtp) cc_final: 0.8125 (ttm) REVERT: A 865 ILE cc_start: 0.8569 (tp) cc_final: 0.8028 (mp) REVERT: A 1379 GLU cc_start: 0.8975 (pp20) cc_final: 0.8231 (pp20) REVERT: A 1383 TYR cc_start: 0.7636 (t80) cc_final: 0.7192 (t80) REVERT: B 269 ILE cc_start: 0.8269 (tp) cc_final: 0.7738 (tp) REVERT: B 273 PHE cc_start: 0.8328 (m-80) cc_final: 0.8064 (m-80) REVERT: B 343 LEU cc_start: 0.9063 (pp) cc_final: 0.8840 (mm) REVERT: B 508 MET cc_start: 0.8200 (mmt) cc_final: 0.7543 (mmt) REVERT: B 677 MET cc_start: 0.7711 (mmm) cc_final: 0.7491 (mmm) REVERT: B 726 SER cc_start: 0.8820 (m) cc_final: 0.8441 (p) REVERT: B 758 LEU cc_start: 0.9352 (mt) cc_final: 0.9122 (mt) REVERT: B 764 MET cc_start: 0.8731 (ttm) cc_final: 0.8363 (ttm) REVERT: B 919 CYS cc_start: 0.7551 (p) cc_final: 0.6906 (p) REVERT: G 12 LEU cc_start: 0.8475 (mm) cc_final: 0.7989 (mt) REVERT: H 143 LEU cc_start: 0.8104 (tt) cc_final: 0.7902 (tt) REVERT: I 71 ASP cc_start: 0.7234 (m-30) cc_final: 0.6982 (m-30) REVERT: I 103 ARG cc_start: 0.5900 (mmp80) cc_final: 0.5235 (mmp80) REVERT: M 114 MET cc_start: 0.8481 (mmp) cc_final: 0.8091 (mmm) REVERT: M 124 MET cc_start: 0.7079 (mmp) cc_final: 0.6727 (tpp) REVERT: U 51 MET cc_start: 0.5501 (mmp) cc_final: 0.3760 (pmm) REVERT: U 358 MET cc_start: 0.7744 (pmm) cc_final: 0.7487 (pmm) REVERT: V 1 MET cc_start: -0.3189 (ptm) cc_final: -0.4882 (mtt) REVERT: W 168 MET cc_start: 0.7232 (tpt) cc_final: 0.7017 (tpp) REVERT: a 52 MET cc_start: -0.0827 (ptp) cc_final: -0.1227 (ptt) REVERT: h 47 MET cc_start: -0.0640 (mtp) cc_final: -0.1253 (mtp) REVERT: l 486 MET cc_start: 0.5118 (ttt) cc_final: 0.4884 (ttt) REVERT: l 571 MET cc_start: 0.5453 (mpp) cc_final: 0.5235 (mpp) REVERT: p 172 MET cc_start: 0.5079 (pmm) cc_final: 0.4778 (pmm) REVERT: s 159 MET cc_start: 0.7034 (mmm) cc_final: 0.6834 (mmm) outliers start: 3 outliers final: 0 residues processed: 554 average time/residue: 0.8388 time to fit residues: 823.1065 Evaluate side-chains 449 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 449 time to evaluate : 8.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1154 random chunks: chunk 680 optimal weight: 1.9990 chunk 1096 optimal weight: 10.0000 chunk 668 optimal weight: 30.0000 chunk 519 optimal weight: 1.9990 chunk 761 optimal weight: 6.9990 chunk 1149 optimal weight: 50.0000 chunk 1058 optimal weight: 0.5980 chunk 915 optimal weight: 40.0000 chunk 95 optimal weight: 50.0000 chunk 707 optimal weight: 3.9990 chunk 561 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 114 ASN 2 366 HIS 3 24 ASN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 265 GLN 8 33 ASN ** 9 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 ASN ** B1117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 38 ASN ** a 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 26 GLN ** d 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 113 ASN ** f 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 507 GLN ** s 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 98182 Z= 0.207 Angle : 0.581 14.812 133128 Z= 0.295 Chirality : 0.041 0.228 14966 Planarity : 0.004 0.075 16677 Dihedral : 10.969 173.950 14024 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.25 % Favored : 95.74 % Rotamer: Outliers : 0.03 % Allowed : 0.31 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.08), residues: 11332 helix: 1.47 (0.07), residues: 5232 sheet: -0.52 (0.13), residues: 1473 loop : -0.94 (0.09), residues: 4627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 453 HIS 0.009 0.001 HIS M 18 PHE 0.048 0.002 PHE W 180 TYR 0.038 0.001 TYR e 167 ARG 0.013 0.000 ARG b 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22664 Ramachandran restraints generated. 11332 Oldfield, 0 Emsley, 11332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 578 time to evaluate : 8.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 247 MET cc_start: 0.1334 (ptt) cc_final: 0.0426 (ptt) REVERT: 0 478 MET cc_start: 0.3256 (mmt) cc_final: 0.2669 (mmp) REVERT: 0 493 MET cc_start: 0.1263 (tpt) cc_final: -0.0801 (mmt) REVERT: 0 677 MET cc_start: -0.1566 (pmm) cc_final: -0.1976 (pmm) REVERT: 0 724 MET cc_start: 0.1745 (mtt) cc_final: 0.1050 (mtt) REVERT: 2 185 MET cc_start: 0.0886 (mtp) cc_final: -0.0179 (mtt) REVERT: 3 1 MET cc_start: 0.0737 (tpt) cc_final: 0.0080 (tpt) REVERT: 4 51 MET cc_start: -0.1881 (mtt) cc_final: -0.2431 (mtt) REVERT: 4 119 MET cc_start: -0.3875 (mmm) cc_final: -0.4599 (mmt) REVERT: 4 157 MET cc_start: -0.3871 (ttp) cc_final: -0.4307 (ttt) REVERT: 4 175 MET cc_start: -0.5273 (mmt) cc_final: -0.5602 (mmt) REVERT: 6 57 MET cc_start: -0.2999 (mtm) cc_final: -0.3305 (mtm) REVERT: 7 380 MET cc_start: 0.8612 (ptt) cc_final: 0.8050 (mmm) REVERT: 7 450 MET cc_start: -0.6576 (ttt) cc_final: -0.6883 (mtp) REVERT: 7 650 MET cc_start: -0.1955 (ptt) cc_final: -0.2304 (ptt) REVERT: 8 240 MET cc_start: -0.2899 (tpt) cc_final: -0.3206 (tpt) REVERT: 9 1 MET cc_start: -0.2163 (mmp) cc_final: -0.2863 (mmt) REVERT: 9 75 MET cc_start: -0.2861 (ttm) cc_final: -0.3278 (ttt) REVERT: A 469 MET cc_start: 0.8138 (mtm) cc_final: 0.7852 (mtm) REVERT: A 514 GLU cc_start: 0.8205 (tt0) cc_final: 0.7795 (tt0) REVERT: A 520 MET cc_start: 0.9440 (mmm) cc_final: 0.8383 (mpp) REVERT: A 565 MET cc_start: 0.8647 (tpt) cc_final: 0.8289 (tpp) REVERT: A 637 MET cc_start: 0.8484 (ptm) cc_final: 0.8183 (ptm) REVERT: A 832 THR cc_start: 0.8553 (p) cc_final: 0.8278 (p) REVERT: A 841 MET cc_start: 0.8438 (mtp) cc_final: 0.7959 (ttm) REVERT: A 865 ILE cc_start: 0.8444 (tp) cc_final: 0.7812 (mp) REVERT: A 868 MET cc_start: 0.8929 (mmm) cc_final: 0.8362 (mmp) REVERT: A 1379 GLU cc_start: 0.8955 (pp20) cc_final: 0.8202 (pp20) REVERT: A 1383 TYR cc_start: 0.7552 (t80) cc_final: 0.7185 (t80) REVERT: B 149 ILE cc_start: 0.9357 (pt) cc_final: 0.9001 (tt) REVERT: B 155 MET cc_start: 0.7532 (ttp) cc_final: 0.7318 (ttp) REVERT: B 343 LEU cc_start: 0.9003 (pp) cc_final: 0.8787 (mm) REVERT: B 508 MET cc_start: 0.8337 (mmt) cc_final: 0.7798 (mmt) REVERT: B 726 SER cc_start: 0.8970 (m) cc_final: 0.8648 (p) REVERT: B 764 MET cc_start: 0.8578 (ttm) cc_final: 0.8244 (ttm) REVERT: B 840 MET cc_start: 0.4764 (ppp) cc_final: 0.2621 (ppp) REVERT: B 919 CYS cc_start: 0.7453 (p) cc_final: 0.6873 (p) REVERT: B 964 ASP cc_start: 0.8259 (m-30) cc_final: 0.7820 (m-30) REVERT: B 1090 GLU cc_start: 0.6578 (mp0) cc_final: 0.6378 (mp0) REVERT: C 148 ILE cc_start: 0.8708 (mm) cc_final: 0.8444 (mp) REVERT: G 12 LEU cc_start: 0.8328 (mm) cc_final: 0.8012 (mt) REVERT: H 37 MET cc_start: 0.7619 (mmm) cc_final: 0.7274 (mmm) REVERT: H 143 LEU cc_start: 0.8032 (tt) cc_final: 0.7772 (tt) REVERT: I 103 ARG cc_start: 0.5572 (mmp80) cc_final: 0.4945 (mmp80) REVERT: M 114 MET cc_start: 0.8393 (mmp) cc_final: 0.7997 (mmm) REVERT: U 51 MET cc_start: 0.5552 (mmp) cc_final: 0.3809 (pmm) REVERT: U 358 MET cc_start: 0.7852 (pmm) cc_final: 0.7636 (pmm) REVERT: V 1 MET cc_start: -0.3289 (ptm) cc_final: -0.5040 (mtt) REVERT: W 168 MET cc_start: 0.7188 (tpt) cc_final: 0.6952 (tpp) REVERT: a 52 MET cc_start: -0.0954 (ptp) cc_final: -0.1357 (ptt) REVERT: h 47 MET cc_start: -0.0974 (mtp) cc_final: -0.1569 (mtp) REVERT: i 138 MET cc_start: 0.7717 (ppp) cc_final: 0.7302 (ppp) REVERT: l 571 MET cc_start: 0.5478 (mpp) cc_final: 0.5262 (mpp) REVERT: p 172 MET cc_start: 0.5018 (pmm) cc_final: 0.4743 (pmm) outliers start: 3 outliers final: 0 residues processed: 581 average time/residue: 0.8664 time to fit residues: 892.0604 Evaluate side-chains 461 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 461 time to evaluate : 8.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1154 random chunks: chunk 727 optimal weight: 0.0770 chunk 975 optimal weight: 5.9990 chunk 280 optimal weight: 9.9990 chunk 844 optimal weight: 8.9990 chunk 135 optimal weight: 30.0000 chunk 254 optimal weight: 7.9990 chunk 916 optimal weight: 20.0000 chunk 383 optimal weight: 0.0030 chunk 941 optimal weight: 0.0970 chunk 116 optimal weight: 7.9990 chunk 168 optimal weight: 50.0000 overall best weight: 2.8350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 114 ASN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 265 GLN 8 33 ASN ** 9 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 ASN ** B1117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 101 ASN ** X 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 26 GLN ** d 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 482 GLN ** f 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 507 GLN ** s 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.093561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.084982 restraints weight = 716089.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.084728 restraints weight = 1612980.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.083846 restraints weight = 1066794.301| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5580 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 98182 Z= 0.227 Angle : 0.579 14.599 133128 Z= 0.294 Chirality : 0.041 0.247 14966 Planarity : 0.004 0.070 16677 Dihedral : 10.910 174.198 14024 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.02 % Allowed : 0.30 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.08), residues: 11332 helix: 1.48 (0.07), residues: 5255 sheet: -0.43 (0.14), residues: 1449 loop : -0.91 (0.09), residues: 4628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 453 HIS 0.009 0.001 HIS M 18 PHE 0.042 0.002 PHE W 180 TYR 0.035 0.001 TYR e 167 ARG 0.013 0.000 ARG B 605 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17524.56 seconds wall clock time: 313 minutes 31.32 seconds (18811.32 seconds total)