Starting phenix.real_space_refine on Sun Feb 18 04:51:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm4_21849/02_2024/6wm4_21849_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm4_21849/02_2024/6wm4_21849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm4_21849/02_2024/6wm4_21849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm4_21849/02_2024/6wm4_21849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm4_21849/02_2024/6wm4_21849_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm4_21849/02_2024/6wm4_21849_updated.pdb" } resolution = 3.6 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= 0.017 sd= 1.157 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 412 5.16 5 C 46255 2.51 5 N 12166 2.21 5 O 13473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 38": "NH1" <-> "NH2" Residue "R ARG 49": "NH1" <-> "NH2" Residue "R ARG 56": "NH1" <-> "NH2" Residue "R ARG 57": "NH1" <-> "NH2" Residue "R GLU 59": "OE1" <-> "OE2" Residue "R GLU 60": "OE1" <-> "OE2" Residue "R ARG 63": "NH1" <-> "NH2" Residue "R ARG 66": "NH1" <-> "NH2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "R GLU 87": "OE1" <-> "OE2" Residue "R ARG 92": "NH1" <-> "NH2" Residue "R ASP 96": "OD1" <-> "OD2" Residue "R ARG 120": "NH1" <-> "NH2" Residue "R PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 133": "NH1" <-> "NH2" Residue "R ARG 177": "NH1" <-> "NH2" Residue "R GLU 178": "OE1" <-> "OE2" Residue "R ARG 179": "NH1" <-> "NH2" Residue "R ARG 185": "NH1" <-> "NH2" Residue "R ARG 189": "NH1" <-> "NH2" Residue "R ARG 192": "NH1" <-> "NH2" Residue "R ARG 198": "NH1" <-> "NH2" Residue "R GLU 201": "OE1" <-> "OE2" Residue "R GLU 207": "OE1" <-> "OE2" Residue "R ASP 208": "OD1" <-> "OD2" Residue "R PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 232": "NH1" <-> "NH2" Residue "R ARG 241": "NH1" <-> "NH2" Residue "R ARG 254": "NH1" <-> "NH2" Residue "R ARG 264": "NH1" <-> "NH2" Residue "R GLU 276": "OE1" <-> "OE2" Residue "R ARG 279": "NH1" <-> "NH2" Residue "R ARG 281": "NH1" <-> "NH2" Residue "R ARG 291": "NH1" <-> "NH2" Residue "R ARG 298": "NH1" <-> "NH2" Residue "R GLU 322": "OE1" <-> "OE2" Residue "R ASP 329": "OD1" <-> "OD2" Residue "R ARG 338": "NH1" <-> "NH2" Residue "R ARG 339": "NH1" <-> "NH2" Residue "R ARG 354": "NH1" <-> "NH2" Residue "R GLU 388": "OE1" <-> "OE2" Residue "R PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 495": "NH1" <-> "NH2" Residue "R PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 660": "NH1" <-> "NH2" Residue "R ARG 665": "NH1" <-> "NH2" Residue "R GLU 794": "OE1" <-> "OE2" Residue "R PHE 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 56": "OD1" <-> "OD2" Residue "O ASP 62": "OD1" <-> "OD2" Residue "O ASP 78": "OD1" <-> "OD2" Residue "O GLU 81": "OE1" <-> "OE2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O GLU 123": "OE1" <-> "OE2" Residue "O ASP 133": "OD1" <-> "OD2" Residue "O ARG 139": "NH1" <-> "NH2" Residue "O ARG 155": "NH1" <-> "NH2" Residue "O ARG 164": "NH1" <-> "NH2" Residue "O GLU 180": "OE1" <-> "OE2" Residue "O ASP 196": "OD1" <-> "OD2" Residue "O ARG 211": "NH1" <-> "NH2" Residue "O ARG 231": "NH1" <-> "NH2" Residue "O ARG 238": "NH1" <-> "NH2" Residue "O ARG 242": "NH1" <-> "NH2" Residue "O ARG 249": "NH1" <-> "NH2" Residue "O GLU 257": "OE1" <-> "OE2" Residue "O ASP 261": "OD1" <-> "OD2" Residue "O GLU 263": "OE1" <-> "OE2" Residue "O GLU 264": "OE1" <-> "OE2" Residue "O ARG 267": "NH1" <-> "NH2" Residue "O ASP 271": "OD1" <-> "OD2" Residue "O ARG 281": "NH1" <-> "NH2" Residue "O ARG 301": "NH1" <-> "NH2" Residue "O PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 309": "NH1" <-> "NH2" Residue "O ARG 332": "NH1" <-> "NH2" Residue "O GLU 333": "OE1" <-> "OE2" Residue "O TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 7": "OD1" <-> "OD2" Residue "J GLU 20": "OE1" <-> "OE2" Residue "J ASP 31": "OD1" <-> "OD2" Residue "J GLU 37": "OE1" <-> "OE2" Residue "J PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 41": "OE1" <-> "OE2" Residue "J ARG 44": "NH1" <-> "NH2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "J ASP 88": "OD1" <-> "OD2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J ASP 201": "OD1" <-> "OD2" Residue "M GLU 15": "OE1" <-> "OE2" Residue "M ARG 17": "NH1" <-> "NH2" Residue "M ARG 26": "NH1" <-> "NH2" Residue "M ARG 28": "NH1" <-> "NH2" Residue "M ARG 31": "NH1" <-> "NH2" Residue "M ARG 32": "NH1" <-> "NH2" Residue "M GLU 38": "OE1" <-> "OE2" Residue "M GLU 39": "OE1" <-> "OE2" Residue "M GLU 45": "OE1" <-> "OE2" Residue "M ARG 48": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M ARG 66": "NH1" <-> "NH2" Residue "M ARG 89": "NH1" <-> "NH2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "I ASP 7": "OD1" <-> "OD2" Residue "I ARG 44": "NH1" <-> "NH2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "I ASP 88": "OD1" <-> "OD2" Residue "I PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 17": "NH1" <-> "NH2" Residue "L ARG 26": "NH1" <-> "NH2" Residue "L ARG 28": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 32": "NH1" <-> "NH2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "L ARG 48": "NH1" <-> "NH2" Residue "L ARG 51": "NH1" <-> "NH2" Residue "L ARG 66": "NH1" <-> "NH2" Residue "L ARG 89": "NH1" <-> "NH2" Residue "L GLU 109": "OE1" <-> "OE2" Residue "H ASP 7": "OD1" <-> "OD2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 25": "OE1" <-> "OE2" Residue "H ARG 44": "NH1" <-> "NH2" Residue "H ARG 50": "NH1" <-> "NH2" Residue "H TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 65": "OE1" <-> "OE2" Residue "H TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "K ARG 26": "NH1" <-> "NH2" Residue "K ARG 28": "NH1" <-> "NH2" Residue "K ARG 31": "NH1" <-> "NH2" Residue "K ARG 32": "NH1" <-> "NH2" Residue "K GLU 38": "OE1" <-> "OE2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K ARG 48": "NH1" <-> "NH2" Residue "K ARG 51": "NH1" <-> "NH2" Residue "K ARG 66": "NH1" <-> "NH2" Residue "K GLU 76": "OE1" <-> "OE2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "K PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 89": "NH1" <-> "NH2" Residue "K GLU 109": "OE1" <-> "OE2" Residue "S GLU 71": "OE1" <-> "OE2" Residue "T GLU 91": "OE1" <-> "OE2" Residue "T PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 127": "NH1" <-> "NH2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B ASP 488": "OD1" <-> "OD2" Residue "B GLU 491": "OE1" <-> "OE2" Residue "B TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C GLU 293": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 388": "NH1" <-> "NH2" Residue "C ASP 416": "OD1" <-> "OD2" Residue "C GLU 481": "OE1" <-> "OE2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A ASP 562": "OD1" <-> "OD2" Residue "A ASP 576": "OD1" <-> "OD2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 249": "OE1" <-> "OE2" Residue "E GLU 315": "OE1" <-> "OE2" Residue "E TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 460": "NH1" <-> "NH2" Residue "F TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "F GLU 201": "OE1" <-> "OE2" Residue "F ASP 221": "OD1" <-> "OD2" Residue "F ASP 247": "OD1" <-> "OD2" Residue "F GLU 315": "OE1" <-> "OE2" Residue "F TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 342": "OE1" <-> "OE2" Residue "F GLU 374": "OE1" <-> "OE2" Residue "F TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 417": "OD1" <-> "OD2" Residue "F ASP 448": "OD1" <-> "OD2" Residue "F ARG 460": "NH1" <-> "NH2" Residue "F GLU 475": "OE1" <-> "OE2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 441": "OE1" <-> "OE2" Residue "D PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "D TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y GLU 67": "OE1" <-> "OE2" Residue "Y ASP 79": "OD1" <-> "OD2" Residue "Y PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 171": "OD1" <-> "OD2" Residue "Y GLU 209": "OE1" <-> "OE2" Residue "Y TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 244": "OD1" <-> "OD2" Residue "Z ASP 37": "OD1" <-> "OD2" Residue "Z PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 170": "OE1" <-> "OE2" Residue "Z ASP 231": "OD1" <-> "OD2" Residue "Z ASP 261": "OD1" <-> "OD2" Residue "Z GLU 269": "OE1" <-> "OE2" Residue "Z GLU 271": "OE1" <-> "OE2" Residue "X ASP 51": "OD1" <-> "OD2" Residue "X GLU 57": "OE1" <-> "OE2" Residue "X GLU 63": "OE1" <-> "OE2" Residue "X GLU 67": "OE1" <-> "OE2" Residue "X ASP 79": "OD1" <-> "OD2" Residue "X GLU 109": "OE1" <-> "OE2" Residue "X GLU 170": "OE1" <-> "OE2" Residue "X GLU 210": "OE1" <-> "OE2" Residue "X PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 220": "OE1" <-> "OE2" Residue "X ASP 244": "OD1" <-> "OD2" Residue "X ASP 261": "OD1" <-> "OD2" Residue "G PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 214": "OE1" <-> "OE2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N ASP 79": "OD1" <-> "OD2" Residue "N GLU 95": "OE1" <-> "OE2" Residue "N ARG 107": "NH1" <-> "NH2" Residue "N ARG 110": "NH1" <-> "NH2" Residue "U ARG 266": "NH1" <-> "NH2" Residue "U GLU 314": "OE1" <-> "OE2" Residue "U PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 455": "NH1" <-> "NH2" Residue "V TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 116": "OE1" <-> "OE2" Residue "0 PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 9": "OE1" <-> "OE2" Residue "3 TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 50": "OE1" <-> "OE2" Residue "4 GLU 9": "OE1" <-> "OE2" Residue "4 PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 53": "OD1" <-> "OD2" Residue "Q ARG 73": "NH1" <-> "NH2" Residue "Q GLU 149": "OE1" <-> "OE2" Residue "Q GLU 170": "OE1" <-> "OE2" Residue "Q GLU 179": "OE1" <-> "OE2" Residue "Q TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 215": "OE1" <-> "OE2" Residue "Q GLU 273": "OE1" <-> "OE2" Residue "Q GLU 334": "OE1" <-> "OE2" Residue "P GLU 45": "OE1" <-> "OE2" Residue "P GLU 48": "OE1" <-> "OE2" Residue "P PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 64": "OE1" <-> "OE2" Residue "P GLU 69": "OE1" <-> "OE2" Residue "P PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 113": "OD1" <-> "OD2" Residue "P TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 143": "NH1" <-> "NH2" Residue "P PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 220": "OE1" <-> "OE2" Residue "P PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 271": "OD1" <-> "OD2" Residue "P GLU 300": "OE1" <-> "OE2" Residue "P ASP 330": "OD1" <-> "OD2" Residue "P GLU 344": "OE1" <-> "OE2" Residue "P PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 354": "OE1" <-> "OE2" Residue "P GLU 365": "OE1" <-> "OE2" Residue "P GLU 373": "OE1" <-> "OE2" Residue "P ASP 403": "OD1" <-> "OD2" Residue "P GLU 429": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 72308 Number of models: 1 Model: "" Number of chains: 38 Chain: "R" Number of atoms: 6147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 6147 Classifications: {'peptide': 753} Link IDs: {'PTRANS': 32, 'TRANS': 720} Chain breaks: 2 Chain: "O" Number of atoms: 3035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3035 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 11, 'TRANS': 363} Chain: "J" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1822 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "M" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 938 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "I" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1822 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "L" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 938 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "H" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1817 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 938 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "S" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 631 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain: "T" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 658 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "B" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "C" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "A" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "E" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3666 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "F" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3666 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "D" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3666 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "Y" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2110 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 252} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "Z" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2136 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 257} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2111 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 252} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "G" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1717 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 3, 'TRANS': 209} Chain: "N" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "U" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1662 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "V" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 411 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "0" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1498 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 5, 'TRANS': 198} Chain: "1" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "2" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "3" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "4" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "5" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "6" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "7" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "8" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "9" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "Q" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2844 Classifications: {'peptide': 351} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 337} Chain: "P" Number of atoms: 3508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3508 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 9, 'TRANS': 417} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 27.20, per 1000 atoms: 0.38 Number of scatterers: 72308 At special positions: 0 Unit cell: (206.28, 278.64, 218.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 412 16.00 P 2 15.00 O 13473 8.00 N 12166 7.00 C 46255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS U 371 " - pdb=" SG CYS U 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R 901 " - " ASN R 488 " " NAG U 501 " - " ASN U 350 " " NAG U 502 " - " ASN U 296 " " NAG U 503 " - " ASN U 261 " " NAG U 504 " - " ASN U 303 " " NAG U 505 " - " ASN U 357 " " NAG U 506 " - " ASN U 273 " Time building additional restraints: 21.51 Conformation dependent library (CDL) restraints added in 9.4 seconds 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17132 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 312 helices and 43 sheets defined 55.2% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.43 Creating SS restraints... Processing helix chain 'R' and resid 19 through 32 removed outlier: 4.200A pdb=" N CYS R 24 " --> pdb=" O GLU R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 75 removed outlier: 3.513A pdb=" N ALA R 75 " --> pdb=" O GLU R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 124 removed outlier: 4.139A pdb=" N GLU R 116 " --> pdb=" O THR R 113 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU R 124 " --> pdb=" O ASN R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 131 Processing helix chain 'R' and resid 180 through 189 removed outlier: 3.683A pdb=" N ARG R 185 " --> pdb=" O PRO R 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 240 removed outlier: 3.715A pdb=" N ASN R 231 " --> pdb=" O ASP R 227 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS R 234 " --> pdb=" O LYS R 230 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS R 235 " --> pdb=" O ASN R 231 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU R 238 " --> pdb=" O LYS R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 308 removed outlier: 3.577A pdb=" N ALA R 258 " --> pdb=" O ARG R 254 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER R 259 " --> pdb=" O LYS R 255 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY R 260 " --> pdb=" O GLU R 256 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP R 266 " --> pdb=" O ASN R 262 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP R 267 " --> pdb=" O THR R 263 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS R 288 " --> pdb=" O GLN R 284 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASN R 289 " --> pdb=" O ALA R 285 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG R 291 " --> pdb=" O ALA R 287 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N VAL R 292 " --> pdb=" O LYS R 288 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE R 295 " --> pdb=" O ARG R 291 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS R 296 " --> pdb=" O VAL R 292 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL R 297 " --> pdb=" O TRP R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 327 through 329 No H-bonds generated for 'chain 'R' and resid 327 through 329' Processing helix chain 'R' and resid 334 through 343 Processing helix chain 'R' and resid 373 through 379 removed outlier: 3.918A pdb=" N ILE R 377 " --> pdb=" O GLY R 373 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL R 378 " --> pdb=" O PHE R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 406 removed outlier: 4.377A pdb=" N ILE R 397 " --> pdb=" O PRO R 393 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE R 399 " --> pdb=" O THR R 395 " (cutoff:3.500A) Proline residue: R 400 - end of helix removed outlier: 3.598A pdb=" N ALA R 404 " --> pdb=" O PRO R 400 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL R 405 " --> pdb=" O PHE R 401 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET R 406 " --> pdb=" O LEU R 402 " (cutoff:3.500A) Processing helix chain 'R' and resid 410 through 422 removed outlier: 3.937A pdb=" N LEU R 415 " --> pdb=" O GLY R 411 " (cutoff:3.500A) Processing helix chain 'R' and resid 427 through 431 Processing helix chain 'R' and resid 438 through 463 removed outlier: 3.726A pdb=" N SER R 445 " --> pdb=" O SER R 441 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY R 446 " --> pdb=" O THR R 442 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG R 447 " --> pdb=" O VAL R 443 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR R 448 " --> pdb=" O PHE R 444 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE R 449 " --> pdb=" O SER R 445 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU R 452 " --> pdb=" O TYR R 448 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY R 454 " --> pdb=" O ILE R 450 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER R 457 " --> pdb=" O MET R 453 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU R 462 " --> pdb=" O MET R 458 " (cutoff:3.500A) Processing helix chain 'R' and resid 491 through 493 No H-bonds generated for 'chain 'R' and resid 491 through 493' Processing helix chain 'R' and resid 522 through 524 No H-bonds generated for 'chain 'R' and resid 522 through 524' Processing helix chain 'R' and resid 528 through 561 removed outlier: 4.082A pdb=" N ASN R 533 " --> pdb=" O LEU R 529 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE R 535 " --> pdb=" O PHE R 531 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS R 538 " --> pdb=" O SER R 534 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE R 546 " --> pdb=" O ILE R 542 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N HIS R 547 " --> pdb=" O LEU R 543 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY R 551 " --> pdb=" O HIS R 547 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU R 554 " --> pdb=" O PHE R 550 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER R 555 " --> pdb=" O GLY R 551 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU R 556 " --> pdb=" O VAL R 552 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE R 557 " --> pdb=" O SER R 553 " (cutoff:3.500A) Processing helix chain 'R' and resid 572 through 596 removed outlier: 3.621A pdb=" N PHE R 578 " --> pdb=" O PRO R 574 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET R 579 " --> pdb=" O GLU R 575 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU R 582 " --> pdb=" O PHE R 578 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR R 585 " --> pdb=" O SER R 581 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU R 586 " --> pdb=" O LEU R 582 " (cutoff:3.500A) Processing helix chain 'R' and resid 599 through 601 No H-bonds generated for 'chain 'R' and resid 599 through 601' Processing helix chain 'R' and resid 608 through 617 removed outlier: 4.084A pdb=" N PHE R 612 " --> pdb=" O LEU R 608 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE R 616 " --> pdb=" O PHE R 612 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU R 617 " --> pdb=" O ILE R 613 " (cutoff:3.500A) Processing helix chain 'R' and resid 632 through 636 Processing helix chain 'R' and resid 638 through 645 removed outlier: 3.907A pdb=" N ALA R 643 " --> pdb=" O LEU R 639 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU R 645 " --> pdb=" O VAL R 641 " (cutoff:3.500A) Processing helix chain 'R' and resid 653 through 665 Processing helix chain 'R' and resid 713 through 758 removed outlier: 3.629A pdb=" N HIS R 719 " --> pdb=" O ASP R 715 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR R 727 " --> pdb=" O HIS R 723 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU R 729 " --> pdb=" O ILE R 725 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU R 739 " --> pdb=" O THR R 735 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ARG R 740 " --> pdb=" O ALA R 736 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEU R 741 " --> pdb=" O SER R 737 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TRP R 742 " --> pdb=" O TYR R 738 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA R 747 " --> pdb=" O ALA R 743 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN R 750 " --> pdb=" O LEU R 746 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU R 755 " --> pdb=" O LEU R 751 " (cutoff:3.500A) Processing helix chain 'R' and resid 760 through 763 No H-bonds generated for 'chain 'R' and resid 760 through 763' Processing helix chain 'R' and resid 774 through 788 removed outlier: 3.658A pdb=" N LEU R 785 " --> pdb=" O ALA R 781 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR R 786 " --> pdb=" O PHE R 782 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL R 787 " --> pdb=" O ALA R 783 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA R 788 " --> pdb=" O THR R 784 " (cutoff:3.500A) Processing helix chain 'R' and resid 793 through 808 removed outlier: 3.569A pdb=" N HIS R 806 " --> pdb=" O ALA R 802 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 21 removed outlier: 4.182A pdb=" N GLU O 20 " --> pdb=" O GLN O 17 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS O 21 " --> pdb=" O THR O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 78 removed outlier: 3.825A pdb=" N ASP O 56 " --> pdb=" O VAL O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 103 Processing helix chain 'O' and resid 118 through 156 removed outlier: 4.072A pdb=" N SER O 141 " --> pdb=" O LYS O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 166 through 168 No H-bonds generated for 'chain 'O' and resid 166 through 168' Processing helix chain 'O' and resid 194 through 204 removed outlier: 3.879A pdb=" N LYS O 199 " --> pdb=" O ASN O 195 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU O 202 " --> pdb=" O ILE O 198 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR O 203 " --> pdb=" O LYS O 199 " (cutoff:3.500A) Processing helix chain 'O' and resid 231 through 241 removed outlier: 4.394A pdb=" N ASP O 235 " --> pdb=" O ARG O 231 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP O 236 " --> pdb=" O LYS O 232 " (cutoff:3.500A) Processing helix chain 'O' and resid 255 through 310 removed outlier: 4.159A pdb=" N ASP O 261 " --> pdb=" O GLU O 257 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LYS O 262 " --> pdb=" O MET O 258 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU O 263 " --> pdb=" O LYS O 259 " (cutoff:3.500A) Proline residue: O 278 - end of helix removed outlier: 4.687A pdb=" N ARG O 281 " --> pdb=" O GLY O 277 " (cutoff:3.500A) Processing helix chain 'O' and resid 328 through 339 Processing helix chain 'J' and resid 5 through 107 removed outlier: 4.341A pdb=" N LYS J 107 " --> pdb=" O SER J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 127 Processing helix chain 'J' and resid 138 through 158 Proline residue: J 142 - end of helix removed outlier: 4.164A pdb=" N VAL J 148 " --> pdb=" O LYS J 145 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE J 152 " --> pdb=" O GLN J 149 " (cutoff:3.500A) Proline residue: J 153 - end of helix Processing helix chain 'J' and resid 196 through 214 removed outlier: 3.621A pdb=" N GLN J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Proline residue: J 209 - end of helix Processing helix chain 'M' and resid 5 through 102 removed outlier: 3.679A pdb=" N ALA M 19 " --> pdb=" O GLU M 15 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU M 20 " --> pdb=" O LYS M 16 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS M 21 " --> pdb=" O ARG M 17 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN M 35 " --> pdb=" O ARG M 31 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY M 64 " --> pdb=" O ALA M 60 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP M 93 " --> pdb=" O ARG M 89 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N GLU M 94 " --> pdb=" O GLN M 90 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE M 102 " --> pdb=" O ASN M 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 107 removed outlier: 4.314A pdb=" N LYS I 107 " --> pdb=" O SER I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 127 removed outlier: 3.730A pdb=" N GLY I 118 " --> pdb=" O VAL I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 158 Proline residue: I 142 - end of helix removed outlier: 4.451A pdb=" N ILE I 152 " --> pdb=" O GLN I 149 " (cutoff:3.500A) Proline residue: I 153 - end of helix Processing helix chain 'I' and resid 196 through 206 removed outlier: 3.557A pdb=" N GLN I 206 " --> pdb=" O LEU I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 216 Processing helix chain 'L' and resid 4 through 90 Processing helix chain 'L' and resid 92 through 102 Processing helix chain 'H' and resid 4 through 107 removed outlier: 3.523A pdb=" N VAL H 8 " --> pdb=" O SER H 4 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYS H 107 " --> pdb=" O SER H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 127 removed outlier: 4.216A pdb=" N GLN H 126 " --> pdb=" O GLN H 122 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU H 127 " --> pdb=" O GLY H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 158 removed outlier: 3.593A pdb=" N PHE H 141 " --> pdb=" O LYS H 138 " (cutoff:3.500A) Proline residue: H 142 - end of helix removed outlier: 4.332A pdb=" N VAL H 148 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE H 152 " --> pdb=" O GLN H 149 " (cutoff:3.500A) Proline residue: H 153 - end of helix Processing helix chain 'H' and resid 196 through 204 Processing helix chain 'H' and resid 208 through 215 Processing helix chain 'K' and resid 4 through 102 removed outlier: 4.531A pdb=" N LYS K 21 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU K 33 " --> pdb=" O LYS K 29 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS K 34 " --> pdb=" O ASN K 30 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN K 35 " --> pdb=" O ARG K 31 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG K 66 " --> pdb=" O ALA K 62 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLY K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER K 68 " --> pdb=" O GLY K 64 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N CYS K 69 " --> pdb=" O SER K 65 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER K 70 " --> pdb=" O ARG K 66 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR K 71 " --> pdb=" O GLY K 67 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU K 72 " --> pdb=" O SER K 68 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR K 82 " --> pdb=" O GLN K 78 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN K 85 " --> pdb=" O MET K 81 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN K 90 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG K 92 " --> pdb=" O PHE K 88 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASP K 93 " --> pdb=" O ARG K 89 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLU K 94 " --> pdb=" O GLN K 90 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP K 97 " --> pdb=" O ASP K 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 8 through 21 Processing helix chain 'S' and resid 24 through 27 No H-bonds generated for 'chain 'S' and resid 24 through 27' Processing helix chain 'S' and resid 34 through 58 removed outlier: 3.530A pdb=" N ILE S 38 " --> pdb=" O ARG S 34 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR S 39 " --> pdb=" O GLY S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 79 removed outlier: 3.896A pdb=" N TYR S 75 " --> pdb=" O GLU S 71 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR S 78 " --> pdb=" O TRP S 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 73 removed outlier: 3.663A pdb=" N ALA T 52 " --> pdb=" O LYS T 49 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N CYS T 53 " --> pdb=" O LEU T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 126 Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.882A pdb=" N SER B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 266 removed outlier: 3.540A pdb=" N SER B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 removed outlier: 3.848A pdb=" N LEU B 288 " --> pdb=" O MET B 284 " (cutoff:3.500A) Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 320 through 338 removed outlier: 4.948A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TYR B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 364 Processing helix chain 'B' and resid 378 through 388 removed outlier: 5.026A pdb=" N ARG B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 427 removed outlier: 4.185A pdb=" N GLY B 427 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 442 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 473 through 496 removed outlier: 3.941A pdb=" N GLU B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 518 Processing helix chain 'B' and resid 534 through 557 Processing helix chain 'B' and resid 567 through 573 Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 594 through 615 Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 256 through 265 removed outlier: 3.596A pdb=" N GLN C 261 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 262 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 263 " --> pdb=" O SER C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 290 removed outlier: 4.725A pdb=" N LEU C 288 " --> pdb=" O MET C 284 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 323 No H-bonds generated for 'chain 'C' and resid 320 through 323' Processing helix chain 'C' and resid 327 through 338 Processing helix chain 'C' and resid 351 through 365 removed outlier: 3.803A pdb=" N LEU C 365 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 388 removed outlier: 3.603A pdb=" N PHE C 385 " --> pdb=" O ARG C 381 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ARG C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 428 Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 472 through 495 removed outlier: 4.259A pdb=" N GLU C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 518 Processing helix chain 'C' and resid 534 through 557 removed outlier: 4.152A pdb=" N LEU C 541 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET C 544 " --> pdb=" O MET C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 573 Processing helix chain 'C' and resid 576 through 583 Processing helix chain 'C' and resid 594 through 614 Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 321 through 336 removed outlier: 3.508A pdb=" N GLU A 324 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 365 removed outlier: 3.503A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 420 through 425 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 473 through 495 removed outlier: 4.339A pdb=" N GLU A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 removed outlier: 3.506A pdb=" N LEU A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 559 removed outlier: 4.118A pdb=" N THR A 558 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 573 Processing helix chain 'A' and resid 575 through 582 Processing helix chain 'A' and resid 594 through 615 Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 175 through 180 Processing helix chain 'E' and resid 199 through 208 Processing helix chain 'E' and resid 219 through 224 Processing helix chain 'E' and resid 238 through 249 Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 269 through 272 removed outlier: 3.878A pdb=" N ILE E 272 " --> pdb=" O ILE E 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 269 through 272' Processing helix chain 'E' and resid 274 through 287 removed outlier: 3.520A pdb=" N THR E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 313 removed outlier: 3.653A pdb=" N ALA E 306 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL E 310 " --> pdb=" O ALA E 306 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA E 313 " --> pdb=" O GLU E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 322 No H-bonds generated for 'chain 'E' and resid 320 through 322' Processing helix chain 'E' and resid 325 through 335 removed outlier: 4.615A pdb=" N TYR E 328 " --> pdb=" O GLY E 325 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR E 329 " --> pdb=" O TYR E 326 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR E 333 " --> pdb=" O ASP E 330 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR E 335 " --> pdb=" O ALA E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 359 No H-bonds generated for 'chain 'E' and resid 357 through 359' Processing helix chain 'E' and resid 364 through 372 Processing helix chain 'E' and resid 382 through 385 No H-bonds generated for 'chain 'E' and resid 382 through 385' Processing helix chain 'E' and resid 415 through 439 Processing helix chain 'E' and resid 446 through 461 Processing helix chain 'E' and resid 473 through 486 removed outlier: 5.167A pdb=" N ILE E 486 " --> pdb=" O GLN E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 503 Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 199 through 209 Processing helix chain 'F' and resid 219 through 223 Processing helix chain 'F' and resid 238 through 250 removed outlier: 3.585A pdb=" N PHE F 248 " --> pdb=" O PHE F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 270 through 272 No H-bonds generated for 'chain 'F' and resid 270 through 272' Processing helix chain 'F' and resid 274 through 289 Processing helix chain 'F' and resid 300 through 313 removed outlier: 3.709A pdb=" N ALA F 313 " --> pdb=" O GLU F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 322 No H-bonds generated for 'chain 'F' and resid 320 through 322' Processing helix chain 'F' and resid 327 through 335 Processing helix chain 'F' and resid 357 through 359 No H-bonds generated for 'chain 'F' and resid 357 through 359' Processing helix chain 'F' and resid 364 through 372 Processing helix chain 'F' and resid 382 through 385 No H-bonds generated for 'chain 'F' and resid 382 through 385' Processing helix chain 'F' and resid 415 through 438 removed outlier: 3.848A pdb=" N ALA F 437 " --> pdb=" O GLN F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 461 Processing helix chain 'F' and resid 473 through 486 removed outlier: 4.502A pdb=" N ILE F 486 " --> pdb=" O GLN F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 491 No H-bonds generated for 'chain 'F' and resid 489 through 491' Processing helix chain 'F' and resid 497 through 503 Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 238 through 251 removed outlier: 3.684A pdb=" N PHE D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN D 251 " --> pdb=" O ASP D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'D' and resid 274 through 287 Processing helix chain 'D' and resid 300 through 313 removed outlier: 3.912A pdb=" N ALA D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 327 through 335 removed outlier: 3.850A pdb=" N ILE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 359 No H-bonds generated for 'chain 'D' and resid 357 through 359' Processing helix chain 'D' and resid 364 through 372 Processing helix chain 'D' and resid 381 through 384 No H-bonds generated for 'chain 'D' and resid 381 through 384' Processing helix chain 'D' and resid 415 through 439 removed outlier: 3.788A pdb=" N VAL D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 443 No H-bonds generated for 'chain 'D' and resid 441 through 443' Processing helix chain 'D' and resid 446 through 461 removed outlier: 3.821A pdb=" N ARG D 460 " --> pdb=" O GLN D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 486 removed outlier: 4.890A pdb=" N ILE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 503 Processing helix chain 'Y' and resid 15 through 36 Processing helix chain 'Y' and resid 43 through 48 Processing helix chain 'Y' and resid 50 through 53 No H-bonds generated for 'chain 'Y' and resid 50 through 53' Processing helix chain 'Y' and resid 62 through 71 Processing helix chain 'Y' and resid 78 through 96 Processing helix chain 'Y' and resid 105 through 116 Processing helix chain 'Y' and resid 125 through 140 Processing helix chain 'Y' and resid 147 through 166 Processing helix chain 'Y' and resid 173 through 186 Processing helix chain 'Y' and resid 193 through 205 Processing helix chain 'Y' and resid 219 through 234 Processing helix chain 'Y' and resid 240 through 251 removed outlier: 5.027A pdb=" N SER Y 251 " --> pdb=" O SER Y 247 " (cutoff:3.500A) Processing helix chain 'Y' and resid 257 through 273 Processing helix chain 'Z' and resid 15 through 36 Processing helix chain 'Z' and resid 43 through 51 removed outlier: 5.309A pdb=" N ASP Z 51 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 64 through 70 Processing helix chain 'Z' and resid 78 through 96 removed outlier: 3.783A pdb=" N LEU Z 88 " --> pdb=" O ARG Z 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 105 through 116 Processing helix chain 'Z' and resid 125 through 141 removed outlier: 3.566A pdb=" N LEU Z 136 " --> pdb=" O GLN Z 132 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 166 removed outlier: 3.862A pdb=" N VAL Z 158 " --> pdb=" O ALA Z 154 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU Z 159 " --> pdb=" O MET Z 155 " (cutoff:3.500A) Processing helix chain 'Z' and resid 173 through 186 Processing helix chain 'Z' and resid 194 through 206 Processing helix chain 'Z' and resid 219 through 236 Proline residue: Z 235 - end of helix Processing helix chain 'Z' and resid 240 through 251 removed outlier: 4.544A pdb=" N SER Z 251 " --> pdb=" O SER Z 247 " (cutoff:3.500A) Processing helix chain 'Z' and resid 257 through 273 removed outlier: 3.569A pdb=" N LEU Z 273 " --> pdb=" O GLU Z 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 16 through 36 Processing helix chain 'X' and resid 43 through 48 Processing helix chain 'X' and resid 50 through 53 No H-bonds generated for 'chain 'X' and resid 50 through 53' Processing helix chain 'X' and resid 62 through 70 Processing helix chain 'X' and resid 78 through 96 removed outlier: 3.633A pdb=" N LEU X 88 " --> pdb=" O ARG X 84 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU X 91 " --> pdb=" O ILE X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 117 removed outlier: 3.893A pdb=" N GLN X 117 " --> pdb=" O GLU X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 121 through 123 No H-bonds generated for 'chain 'X' and resid 121 through 123' Processing helix chain 'X' and resid 125 through 141 Processing helix chain 'X' and resid 147 through 165 Processing helix chain 'X' and resid 173 through 187 Processing helix chain 'X' and resid 193 through 206 Processing helix chain 'X' and resid 219 through 232 Processing helix chain 'X' and resid 240 through 249 removed outlier: 4.462A pdb=" N LEU X 249 " --> pdb=" O LYS X 245 " (cutoff:3.500A) Processing helix chain 'X' and resid 257 through 273 removed outlier: 4.196A pdb=" N LYS X 272 " --> pdb=" O LYS X 268 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU X 273 " --> pdb=" O GLU X 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 75 removed outlier: 4.055A pdb=" N GLU G 60 " --> pdb=" O MET G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 85 Processing helix chain 'G' and resid 130 through 174 Processing helix chain 'G' and resid 176 through 215 Processing helix chain 'N' and resid 14 through 23 Processing helix chain 'N' and resid 45 through 57 Processing helix chain 'N' and resid 68 through 73 Processing helix chain 'N' and resid 75 through 79 Processing helix chain 'N' and resid 100 through 102 No H-bonds generated for 'chain 'N' and resid 100 through 102' Processing helix chain 'N' and resid 104 through 108 removed outlier: 3.802A pdb=" N ARG N 108 " --> pdb=" O ILE N 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 424 through 449 removed outlier: 3.623A pdb=" N SER U 449 " --> pdb=" O HIS U 445 " (cutoff:3.500A) Processing helix chain 'V' and resid 303 through 328 Processing helix chain '0' and resid 3 through 28 Processing helix chain '0' and resid 32 through 34 No H-bonds generated for 'chain '0' and resid 32 through 34' Processing helix chain '0' and resid 38 through 42 Processing helix chain '0' and resid 46 through 79 removed outlier: 4.706A pdb=" N ILE 0 58 " --> pdb=" O ILE 0 54 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP 0 67 " --> pdb=" O VAL 0 63 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER 0 75 " --> pdb=" O ILE 0 71 " (cutoff:3.500A) Processing helix chain '0' and resid 84 through 86 No H-bonds generated for 'chain '0' and resid 84 through 86' Processing helix chain '0' and resid 92 through 114 removed outlier: 3.975A pdb=" N VAL 0 100 " --> pdb=" O PHE 0 96 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ALA 0 101 " --> pdb=" O CYS 0 97 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE 0 102 " --> pdb=" O GLU 0 98 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN 0 113 " --> pdb=" O ILE 0 109 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N MET 0 114 " --> pdb=" O VAL 0 110 " (cutoff:3.500A) Processing helix chain '0' and resid 130 through 168 removed outlier: 3.578A pdb=" N VAL 0 153 " --> pdb=" O LEU 0 149 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN 0 168 " --> pdb=" O LEU 0 164 " (cutoff:3.500A) Processing helix chain '0' and resid 173 through 176 No H-bonds generated for 'chain '0' and resid 173 through 176' Processing helix chain '0' and resid 178 through 198 removed outlier: 4.211A pdb=" N ILE 0 186 " --> pdb=" O PHE 0 182 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLY 0 187 " --> pdb=" O GLY 0 183 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU 0 188 " --> pdb=" O SER 0 184 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU 0 196 " --> pdb=" O ILE 0 192 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR 0 198 " --> pdb=" O ALA 0 194 " (cutoff:3.500A) Processing helix chain '1' and resid 13 through 44 removed outlier: 4.064A pdb=" N SER 1 26 " --> pdb=" O ALA 1 22 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER 1 37 " --> pdb=" O GLY 1 33 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY 1 40 " --> pdb=" O LYS 1 36 " (cutoff:3.500A) Processing helix chain '1' and resid 49 through 51 No H-bonds generated for 'chain '1' and resid 49 through 51' Processing helix chain '1' and resid 53 through 79 removed outlier: 3.670A pdb=" N ILE 1 56 " --> pdb=" O MET 1 53 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE 1 57 " --> pdb=" O LYS 1 54 " (cutoff:3.500A) Proline residue: 1 58 - end of helix removed outlier: 4.000A pdb=" N ILE 1 64 " --> pdb=" O MET 1 61 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN 1 78 " --> pdb=" O LEU 1 75 " (cutoff:3.500A) Processing helix chain '1' and resid 89 through 121 removed outlier: 3.572A pdb=" N PHE 1 108 " --> pdb=" O LEU 1 104 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG 1 119 " --> pdb=" O ASP 1 115 " (cutoff:3.500A) Processing helix chain '1' and resid 125 through 153 removed outlier: 3.917A pdb=" N PHE 1 128 " --> pdb=" O PRO 1 125 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL 1 129 " --> pdb=" O ARG 1 126 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL 1 140 " --> pdb=" O PHE 1 137 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER 1 153 " --> pdb=" O LEU 1 150 " (cutoff:3.500A) Processing helix chain '2' and resid 12 through 44 removed outlier: 3.730A pdb=" N SER 2 26 " --> pdb=" O ALA 2 22 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY 2 40 " --> pdb=" O LYS 2 36 " (cutoff:3.500A) Processing helix chain '2' and resid 49 through 51 No H-bonds generated for 'chain '2' and resid 49 through 51' Processing helix chain '2' and resid 57 through 79 removed outlier: 3.925A pdb=" N ILE 2 65 " --> pdb=" O MET 2 61 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA 2 66 " --> pdb=" O ALA 2 62 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY 2 69 " --> pdb=" O ILE 2 65 " (cutoff:3.500A) Processing helix chain '2' and resid 88 through 123 removed outlier: 3.914A pdb=" N GLN 2 123 " --> pdb=" O ARG 2 119 " (cutoff:3.500A) Processing helix chain '2' and resid 127 through 154 removed outlier: 3.976A pdb=" N THR 2 154 " --> pdb=" O ILE 2 151 " (cutoff:3.500A) Processing helix chain '3' and resid 12 through 44 Processing helix chain '3' and resid 57 through 79 removed outlier: 4.087A pdb=" N ILE 3 65 " --> pdb=" O MET 3 61 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA 3 66 " --> pdb=" O ALA 3 62 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE 3 67 " --> pdb=" O GLY 3 63 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER 3 79 " --> pdb=" O LEU 3 75 " (cutoff:3.500A) Processing helix chain '3' and resid 88 through 120 Processing helix chain '3' and resid 128 through 154 removed outlier: 3.550A pdb=" N GLY 3 142 " --> pdb=" O ALA 3 138 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY 3 145 " --> pdb=" O LEU 3 141 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU 3 146 " --> pdb=" O GLY 3 142 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR 3 154 " --> pdb=" O LEU 3 150 " (cutoff:3.500A) Processing helix chain '4' and resid 12 through 44 removed outlier: 3.585A pdb=" N ALA 4 21 " --> pdb=" O MET 4 17 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER 4 26 " --> pdb=" O ALA 4 22 " (cutoff:3.500A) Processing helix chain '4' and resid 49 through 51 No H-bonds generated for 'chain '4' and resid 49 through 51' Processing helix chain '4' and resid 57 through 78 removed outlier: 4.113A pdb=" N ALA 4 66 " --> pdb=" O ALA 4 62 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE 4 67 " --> pdb=" O GLY 4 63 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL 4 72 " --> pdb=" O TYR 4 68 " (cutoff:3.500A) Processing helix chain '4' and resid 88 through 121 Processing helix chain '4' and resid 125 through 153 removed outlier: 3.661A pdb=" N PHE 4 128 " --> pdb=" O PRO 4 125 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL 4 129 " --> pdb=" O ARG 4 126 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU 4 141 " --> pdb=" O ALA 4 138 " (cutoff:3.500A) Processing helix chain '5' and resid 12 through 43 removed outlier: 4.097A pdb=" N SER 5 26 " --> pdb=" O ALA 5 22 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER 5 37 " --> pdb=" O GLY 5 33 " (cutoff:3.500A) Processing helix chain '5' and resid 49 through 51 No H-bonds generated for 'chain '5' and resid 49 through 51' Processing helix chain '5' and resid 57 through 78 removed outlier: 4.180A pdb=" N ILE 5 65 " --> pdb=" O MET 5 61 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA 5 66 " --> pdb=" O ALA 5 62 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE 5 67 " --> pdb=" O GLY 5 63 " (cutoff:3.500A) Processing helix chain '5' and resid 87 through 121 removed outlier: 3.589A pdb=" N LEU 5 91 " --> pdb=" O TYR 5 87 " (cutoff:3.500A) Processing helix chain '5' and resid 128 through 153 removed outlier: 4.385A pdb=" N LEU 5 141 " --> pdb=" O PHE 5 137 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLY 5 142 " --> pdb=" O ALA 5 138 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU 5 143 " --> pdb=" O GLU 5 139 " (cutoff:3.500A) Processing helix chain '6' and resid 12 through 44 removed outlier: 3.784A pdb=" N SER 6 26 " --> pdb=" O ALA 6 22 " (cutoff:3.500A) Processing helix chain '6' and resid 49 through 51 No H-bonds generated for 'chain '6' and resid 49 through 51' Processing helix chain '6' and resid 57 through 78 removed outlier: 3.509A pdb=" N MET 6 61 " --> pdb=" O ILE 6 57 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA 6 66 " --> pdb=" O ALA 6 62 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY 6 69 " --> pdb=" O ILE 6 65 " (cutoff:3.500A) Processing helix chain '6' and resid 88 through 120 Processing helix chain '6' and resid 128 through 153 removed outlier: 3.866A pdb=" N GLY 6 142 " --> pdb=" O ALA 6 138 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY 6 145 " --> pdb=" O LEU 6 141 " (cutoff:3.500A) Processing helix chain '7' and resid 11 through 46 removed outlier: 3.763A pdb=" N ALA 7 15 " --> pdb=" O ALA 7 11 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA 7 43 " --> pdb=" O THR 7 39 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET 7 44 " --> pdb=" O GLY 7 40 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL 7 46 " --> pdb=" O ALA 7 42 " (cutoff:3.500A) Processing helix chain '7' and resid 49 through 51 No H-bonds generated for 'chain '7' and resid 49 through 51' Processing helix chain '7' and resid 53 through 55 No H-bonds generated for 'chain '7' and resid 53 through 55' Processing helix chain '7' and resid 57 through 79 removed outlier: 3.994A pdb=" N ILE 7 65 " --> pdb=" O MET 7 61 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA 7 66 " --> pdb=" O ALA 7 62 " (cutoff:3.500A) Processing helix chain '7' and resid 88 through 120 Processing helix chain '7' and resid 127 through 154 removed outlier: 3.815A pdb=" N LEU 7 141 " --> pdb=" O ALA 7 138 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER 7 153 " --> pdb=" O LEU 7 150 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR 7 154 " --> pdb=" O ILE 7 151 " (cutoff:3.500A) Processing helix chain '8' and resid 11 through 44 removed outlier: 5.020A pdb=" N PHE 8 25 " --> pdb=" O ALA 8 22 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS 8 36 " --> pdb=" O GLY 8 33 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER 8 37 " --> pdb=" O THR 8 34 " (cutoff:3.500A) Processing helix chain '8' and resid 49 through 51 No H-bonds generated for 'chain '8' and resid 49 through 51' Processing helix chain '8' and resid 57 through 79 Processing helix chain '8' and resid 88 through 122 Processing helix chain '8' and resid 125 through 153 removed outlier: 4.478A pdb=" N VAL 8 129 " --> pdb=" O ARG 8 126 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE 8 132 " --> pdb=" O VAL 8 129 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU 8 141 " --> pdb=" O ALA 8 138 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR 8 144 " --> pdb=" O LEU 8 141 " (cutoff:3.500A) Processing helix chain '9' and resid 11 through 47 removed outlier: 3.890A pdb=" N ALA 9 15 " --> pdb=" O ALA 9 11 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET 9 23 " --> pdb=" O ALA 9 19 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER 9 26 " --> pdb=" O ALA 9 22 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER 9 37 " --> pdb=" O GLY 9 33 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL 9 46 " --> pdb=" O ALA 9 42 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N MET 9 47 " --> pdb=" O ALA 9 43 " (cutoff:3.500A) Processing helix chain '9' and resid 54 through 79 removed outlier: 3.936A pdb=" N ILE 9 57 " --> pdb=" O LYS 9 54 " (cutoff:3.500A) Proline residue: 9 58 - end of helix removed outlier: 3.599A pdb=" N ILE 9 64 " --> pdb=" O MET 9 61 " (cutoff:3.500A) Processing helix chain '9' and resid 88 through 123 removed outlier: 3.724A pdb=" N GLN 9 123 " --> pdb=" O ARG 9 119 " (cutoff:3.500A) Processing helix chain '9' and resid 125 through 153 removed outlier: 4.476A pdb=" N VAL 9 129 " --> pdb=" O ARG 9 126 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE 9 136 " --> pdb=" O LEU 9 133 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU 9 141 " --> pdb=" O ALA 9 138 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR 9 144 " --> pdb=" O LEU 9 141 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 26 removed outlier: 6.765A pdb=" N TYR Q 15 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEU Q 16 " --> pdb=" O ASP Q 12 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY Q 26 " --> pdb=" O GLY Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 36 Processing helix chain 'Q' and resid 43 through 50 Processing helix chain 'Q' and resid 67 through 87 removed outlier: 3.925A pdb=" N MET Q 78 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 112 removed outlier: 4.783A pdb=" N PHE Q 96 " --> pdb=" O PRO Q 92 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER Q 103 " --> pdb=" O PHE Q 99 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR Q 104 " --> pdb=" O ILE Q 100 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP Q 107 " --> pdb=" O SER Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 122 through 128 Proline residue: Q 127 - end of helix Processing helix chain 'Q' and resid 147 through 156 Processing helix chain 'Q' and resid 164 through 167 No H-bonds generated for 'chain 'Q' and resid 164 through 167' Processing helix chain 'Q' and resid 172 through 175 No H-bonds generated for 'chain 'Q' and resid 172 through 175' Processing helix chain 'Q' and resid 179 through 199 removed outlier: 3.885A pdb=" N ALA Q 188 " --> pdb=" O THR Q 184 " (cutoff:3.500A) Processing helix chain 'Q' and resid 204 through 226 Proline residue: Q 210 - end of helix removed outlier: 4.207A pdb=" N PHE Q 214 " --> pdb=" O PRO Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 234 through 240 removed outlier: 4.657A pdb=" N LEU Q 240 " --> pdb=" O ASP Q 236 " (cutoff:3.500A) Processing helix chain 'Q' and resid 252 through 255 No H-bonds generated for 'chain 'Q' and resid 252 through 255' Processing helix chain 'Q' and resid 261 through 268 Processing helix chain 'Q' and resid 273 through 279 removed outlier: 3.690A pdb=" N LEU Q 277 " --> pdb=" O GLU Q 273 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE Q 278 " --> pdb=" O TYR Q 274 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU Q 279 " --> pdb=" O LYS Q 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 273 through 279' Processing helix chain 'Q' and resid 290 through 305 removed outlier: 4.247A pdb=" N ALA Q 305 " --> pdb=" O LEU Q 301 " (cutoff:3.500A) Processing helix chain 'Q' and resid 312 through 337 removed outlier: 4.477A pdb=" N GLU Q 323 " --> pdb=" O LYS Q 320 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 27 removed outlier: 3.600A pdb=" N ALA P 23 " --> pdb=" O ILE P 19 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA P 24 " --> pdb=" O ALA P 20 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU P 25 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL P 26 " --> pdb=" O LYS P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 48 Processing helix chain 'P' and resid 59 through 68 removed outlier: 4.320A pdb=" N MET P 65 " --> pdb=" O GLU P 61 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU P 66 " --> pdb=" O LYS P 62 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN P 67 " --> pdb=" O GLN P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 83 removed outlier: 6.354A pdb=" N THR P 82 " --> pdb=" O ILE P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 103 Processing helix chain 'P' and resid 116 through 118 No H-bonds generated for 'chain 'P' and resid 116 through 118' Processing helix chain 'P' and resid 124 through 126 No H-bonds generated for 'chain 'P' and resid 124 through 126' Processing helix chain 'P' and resid 137 through 144 removed outlier: 3.693A pdb=" N ARG P 143 " --> pdb=" O HIS P 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 158 through 162 Processing helix chain 'P' and resid 168 through 171 No H-bonds generated for 'chain 'P' and resid 168 through 171' Processing helix chain 'P' and resid 195 through 210 removed outlier: 4.053A pdb=" N ARG P 210 " --> pdb=" O GLN P 206 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 220 removed outlier: 3.864A pdb=" N ALA P 217 " --> pdb=" O GLU P 213 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 232 Processing helix chain 'P' and resid 237 through 252 removed outlier: 3.802A pdb=" N PHE P 252 " --> pdb=" O TRP P 248 " (cutoff:3.500A) Processing helix chain 'P' and resid 254 through 260 removed outlier: 4.098A pdb=" N GLU P 258 " --> pdb=" O PRO P 254 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 274 Processing helix chain 'P' and resid 281 through 295 Processing helix chain 'P' and resid 301 through 310 removed outlier: 3.764A pdb=" N GLU P 304 " --> pdb=" O THR P 301 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR P 305 " --> pdb=" O ARG P 302 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU P 307 " --> pdb=" O GLU P 304 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 323 Processing helix chain 'P' and resid 329 through 349 removed outlier: 3.579A pdb=" N GLN P 347 " --> pdb=" O GLY P 343 " (cutoff:3.500A) Processing helix chain 'P' and resid 352 through 360 Processing helix chain 'P' and resid 368 through 371 No H-bonds generated for 'chain 'P' and resid 368 through 371' Processing helix chain 'P' and resid 373 through 377 Processing helix chain 'P' and resid 380 through 383 No H-bonds generated for 'chain 'P' and resid 380 through 383' Processing helix chain 'P' and resid 386 through 400 removed outlier: 5.807A pdb=" N LEU P 390 " --> pdb=" O ASN P 387 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE P 393 " --> pdb=" O LEU P 390 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU P 398 " --> pdb=" O THR P 395 " (cutoff:3.500A) Processing helix chain 'P' and resid 404 through 420 Processing helix chain 'P' and resid 422 through 431 removed outlier: 4.175A pdb=" N ARG P 426 " --> pdb=" O PRO P 422 " (cutoff:3.500A) Processing helix chain 'P' and resid 433 through 442 removed outlier: 4.943A pdb=" N HIS P 442 " --> pdb=" O MET P 438 " (cutoff:3.500A) Processing helix chain 'P' and resid 446 through 459 removed outlier: 3.989A pdb=" N ASN P 451 " --> pdb=" O GLN P 447 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'R' and resid 352 through 355 removed outlier: 3.520A pdb=" N CYS R 325 " --> pdb=" O THR R 11 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA R 13 " --> pdb=" O VAL R 323 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL R 323 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA R 321 " --> pdb=" O LEU R 15 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'O' and resid 370 through 374 removed outlier: 3.754A pdb=" N LEU O 321 " --> pdb=" O TRP O 5 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA O 9 " --> pdb=" O GLN O 317 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN O 317 " --> pdb=" O ALA O 9 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'O' and resid 183 through 189 removed outlier: 3.531A pdb=" N LEU O 229 " --> pdb=" O VAL O 183 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N CYS O 225 " --> pdb=" O VAL O 187 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL O 189 " --> pdb=" O TYR O 223 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASN O 226 " --> pdb=" O VAL O 215 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL O 215 " --> pdb=" O ASN O 226 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'J' and resid 131 through 134 removed outlier: 6.096A pdb=" N ASP J 164 " --> pdb=" O MET J 132 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL J 134 " --> pdb=" O ASP J 164 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN J 166 " --> pdb=" O VAL J 134 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'J' and resid 180 through 184 Processing sheet with id= F, first strand: chain 'I' and resid 164 through 167 Processing sheet with id= G, first strand: chain 'H' and resid 164 through 167 Processing sheet with id= H, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.466A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N VAL B 21 " --> pdb=" O CYS B 32 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 87 through 90 Processing sheet with id= J, first strand: chain 'B' and resid 183 through 185 removed outlier: 5.386A pdb=" N ASP B 134 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER B 157 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE B 166 " --> pdb=" O TYR B 153 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE B 155 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N HIS B 164 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 146 through 148 removed outlier: 6.712A pdb=" N GLU B 193 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 309 through 314 removed outlier: 6.875A pdb=" N ILE B 272 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N VAL B 312 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N TYR B 274 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ASN B 314 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLY B 276 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 271 " --> pdb=" O HIS B 343 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N SER B 403 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N MET B 346 " --> pdb=" O SER B 403 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N SER B 405 " --> pdb=" O MET B 346 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ALA B 348 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL B 407 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 295 through 297 Processing sheet with id= N, first strand: chain 'C' and resid 42 through 45 Processing sheet with id= O, first strand: chain 'C' and resid 87 through 90 Processing sheet with id= P, first strand: chain 'C' and resid 183 through 185 removed outlier: 5.314A pdb=" N ASP C 134 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER C 157 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE C 166 " --> pdb=" O TYR C 153 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ILE C 155 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS C 164 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 199 through 203 removed outlier: 3.529A pdb=" N VAL C 199 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 178 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU C 195 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL C 176 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 246 through 249 removed outlier: 6.616A pdb=" N VAL C 271 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N MET C 347 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE C 273 " --> pdb=" O MET C 347 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASP C 349 " --> pdb=" O ILE C 273 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL C 275 " --> pdb=" O ASP C 349 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 390 through 392 removed outlier: 3.544A pdb=" N VAL C 392 " --> pdb=" O GLY C 402 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 18 through 20 Processing sheet with id= U, first strand: chain 'A' and resid 87 through 90 Processing sheet with id= V, first strand: chain 'A' and resid 183 through 185 removed outlier: 5.440A pdb=" N ASP A 134 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER A 157 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE A 166 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE A 155 " --> pdb=" O HIS A 164 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N HIS A 164 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 247 through 249 removed outlier: 8.524A pdb=" N ILE A 248 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N GLY A 408 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 405 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE A 273 " --> pdb=" O MET A 347 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ASP A 349 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL A 275 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 295 through 297 Processing sheet with id= Y, first strand: chain 'A' and resid 175 through 179 removed outlier: 6.896A pdb=" N GLU A 193 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE A 179 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N VAL A 191 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N PHE A 203 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU A 193 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU A 201 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 57 through 61 removed outlier: 3.718A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU E 88 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER E 111 " --> pdb=" O THR E 75 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 120 through 123 Processing sheet with id= AB, first strand: chain 'E' and resid 131 through 133 removed outlier: 8.133A pdb=" N PHE E 132 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU E 259 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE E 229 " --> pdb=" O CYS E 258 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N PHE E 260 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE E 231 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN E 262 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ALA E 233 " --> pdb=" O ASN E 262 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL E 230 " --> pdb=" O HIS E 292 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU E 294 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA E 232 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE E 296 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N MET E 234 " --> pdb=" O ILE E 296 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR E 298 " --> pdb=" O MET E 234 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N SER E 347 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL E 295 " --> pdb=" O SER E 347 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR E 349 " --> pdb=" O VAL E 295 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LEU E 297 " --> pdb=" O THR E 349 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'E' and resid 191 through 193 Processing sheet with id= AD, first strand: chain 'F' and resid 50 through 54 removed outlier: 6.449A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER F 90 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU F 88 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 120 through 123 Processing sheet with id= AF, first strand: chain 'F' and resid 376 through 378 Processing sheet with id= AG, first strand: chain 'F' and resid 347 through 350 removed outlier: 4.273A pdb=" N ALA F 228 " --> pdb=" O HIS F 292 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET F 234 " --> pdb=" O THR F 298 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 50 through 54 removed outlier: 6.821A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU D 88 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'D' and resid 120 through 123 Processing sheet with id= AJ, first strand: chain 'D' and resid 131 through 133 removed outlier: 8.339A pdb=" N PHE D 132 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU D 259 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE D 229 " --> pdb=" O CYS D 258 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N PHE D 260 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE D 231 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N SER D 347 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL D 295 " --> pdb=" O SER D 347 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR D 349 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU D 297 " --> pdb=" O THR D 349 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'D' and resid 191 through 193 Processing sheet with id= AL, first strand: chain 'G' and resid 92 through 97 Processing sheet with id= AM, first strand: chain 'N' and resid 36 through 38 removed outlier: 7.215A pdb=" N VAL N 10 " --> pdb=" O LEU N 37 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN N 67 " --> pdb=" O ILE N 11 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'U' and resid 258 through 260 removed outlier: 3.637A pdb=" N ILE U 267 " --> pdb=" O TYR U 260 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'U' and resid 282 through 284 removed outlier: 3.597A pdb=" N ASN U 273 " --> pdb=" O GLN U 398 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'U' and resid 306 through 313 removed outlier: 3.589A pdb=" N ILE U 326 " --> pdb=" O ARG U 344 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG U 344 " --> pdb=" O ILE U 326 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'U' and resid 328 through 332 removed outlier: 3.743A pdb=" N TYR U 332 " --> pdb=" O ARG U 337 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG U 337 " --> pdb=" O TYR U 332 " (cutoff:3.500A) 3824 hydrogen bonds defined for protein. 10320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 24.84 Time building geometry restraints manager: 23.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 23566 1.34 - 1.46: 16484 1.46 - 1.59: 32877 1.59 - 1.71: 3 1.71 - 1.83: 721 Bond restraints: 73651 Sorted by residual: bond pdb=" CB TRP P 151 " pdb=" CG TRP P 151 " ideal model delta sigma weight residual 1.498 1.781 -0.283 3.10e-02 1.04e+03 8.34e+01 bond pdb=" CA ALA 5 22 " pdb=" C ALA 5 22 " ideal model delta sigma weight residual 1.522 1.448 0.074 1.41e-02 5.03e+03 2.76e+01 bond pdb=" C LEU G 212 " pdb=" N LYS G 213 " ideal model delta sigma weight residual 1.333 1.386 -0.053 1.45e-02 4.76e+03 1.35e+01 bond pdb=" CA ARG D 271 " pdb=" C ARG D 271 " ideal model delta sigma weight residual 1.522 1.460 0.062 1.72e-02 3.38e+03 1.31e+01 bond pdb=" C ALA P 149 " pdb=" N ALA P 150 " ideal model delta sigma weight residual 1.334 1.378 -0.045 1.30e-02 5.92e+03 1.18e+01 ... (remaining 73646 not shown) Histogram of bond angle deviations from ideal: 98.70 - 106.16: 1679 106.16 - 113.62: 41698 113.62 - 121.07: 38154 121.07 - 128.53: 17637 128.53 - 135.99: 379 Bond angle restraints: 99547 Sorted by residual: angle pdb=" CA TRP P 151 " pdb=" CB TRP P 151 " pdb=" CG TRP P 151 " ideal model delta sigma weight residual 113.60 135.99 -22.39 1.90e+00 2.77e-01 1.39e+02 angle pdb=" N ALA P 150 " pdb=" CA ALA P 150 " pdb=" C ALA P 150 " ideal model delta sigma weight residual 111.24 103.00 8.24 1.29e+00 6.01e-01 4.08e+01 angle pdb=" N VAL F 439 " pdb=" CA VAL F 439 " pdb=" C VAL F 439 " ideal model delta sigma weight residual 112.83 106.60 6.23 9.90e-01 1.02e+00 3.96e+01 angle pdb=" N ALA P 149 " pdb=" CA ALA P 149 " pdb=" C ALA P 149 " ideal model delta sigma weight residual 111.04 120.18 -9.14 1.55e+00 4.16e-01 3.48e+01 angle pdb=" N CYS C 32 " pdb=" CA CYS C 32 " pdb=" C CYS C 32 " ideal model delta sigma weight residual 107.73 115.33 -7.60 1.34e+00 5.57e-01 3.22e+01 ... (remaining 99542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.19: 41862 23.19 - 46.37: 2557 46.37 - 69.56: 231 69.56 - 92.75: 74 92.75 - 115.93: 1 Dihedral angle restraints: 44725 sinusoidal: 18074 harmonic: 26651 Sorted by residual: dihedral pdb=" CA ALA P 150 " pdb=" C ALA P 150 " pdb=" N TRP P 151 " pdb=" CA TRP P 151 " ideal model delta harmonic sigma weight residual 180.00 110.24 69.76 0 5.00e+00 4.00e-02 1.95e+02 dihedral pdb=" CA TYR C 20 " pdb=" C TYR C 20 " pdb=" N VAL C 21 " pdb=" CA VAL C 21 " ideal model delta harmonic sigma weight residual -180.00 -138.96 -41.04 0 5.00e+00 4.00e-02 6.74e+01 dihedral pdb=" CA GLU 1 9 " pdb=" C GLU 1 9 " pdb=" N TYR 1 10 " pdb=" CA TYR 1 10 " ideal model delta harmonic sigma weight residual -180.00 -144.20 -35.80 0 5.00e+00 4.00e-02 5.13e+01 ... (remaining 44722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 10124 0.073 - 0.146: 1163 0.146 - 0.219: 22 0.219 - 0.292: 2 0.292 - 0.365: 1 Chirality restraints: 11312 Sorted by residual: chirality pdb=" CA ASP C 33 " pdb=" N ASP C 33 " pdb=" C ASP C 33 " pdb=" CB ASP C 33 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA PRO S 29 " pdb=" N PRO S 29 " pdb=" C PRO S 29 " pdb=" CB PRO S 29 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA GLU Q 91 " pdb=" N GLU Q 91 " pdb=" C GLU Q 91 " pdb=" CB GLU Q 91 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 11309 not shown) Planarity restraints: 12753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU G 212 " 0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C LEU G 212 " -0.061 2.00e-02 2.50e+03 pdb=" O LEU G 212 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS G 213 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA P 146 " -0.015 2.00e-02 2.50e+03 3.15e-02 9.94e+00 pdb=" C ALA P 146 " 0.055 2.00e-02 2.50e+03 pdb=" O ALA P 146 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS P 147 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP P 134 " 0.050 5.00e-02 4.00e+02 7.61e-02 9.27e+00 pdb=" N PRO P 135 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO P 135 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO P 135 " 0.042 5.00e-02 4.00e+02 ... (remaining 12750 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 1365 2.66 - 3.22: 74349 3.22 - 3.78: 111103 3.78 - 4.34: 151582 4.34 - 4.90: 245906 Nonbonded interactions: 584305 Sorted by model distance: nonbonded pdb=" NH1 ARG B 391 " pdb=" OE2 GLU B 401 " model vdw 2.099 2.520 nonbonded pdb=" O THR U 298 " pdb=" OG SER U 310 " model vdw 2.114 2.440 nonbonded pdb=" OD2 ASP Q 217 " pdb=" OH TYR Q 274 " model vdw 2.122 2.440 nonbonded pdb=" OE1 GLU H 97 " pdb=" NH2 ARG K 92 " model vdw 2.130 2.520 nonbonded pdb=" O ALA Y 144 " pdb=" ND2 ASN Y 149 " model vdw 2.132 2.520 ... (remaining 584300 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 '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' } ncs_group { reference = (chain 'A' and resid 17 through 616) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = (chain 'I' and resid 3 through 226) selection = (chain 'J' and resid 3 through 226) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = (chain 'X' and (resid 14 through 219 or (resid 220 and (name N or name CA or nam \ e C or name O or name CB )) or resid 221 through 222 or (resid 223 and (name N o \ r name CA or name C or name O or name CB )) or resid 224 through 235 or (resid 2 \ 36 and (name CA or name C or name O or name CB or name CG or name CD or name CE \ or name NZ )) or resid 237 through 275)) selection = (chain 'Y' and (resid 14 through 219 or (resid 220 and (name N or name CA or nam \ e C or name O or name CB )) or resid 221 through 222 or (resid 223 and (name N o \ r name CA or name C or name O or name CB )) or resid 224 through 275)) selection = (chain 'Z' and (resid 14 through 235 or (resid 236 and (name CA or name C or nam \ e O or name CB or name CG or name CD or name CE or name NZ )) or resid 237 throu \ gh 275)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 12.820 Check model and map are aligned: 0.790 Set scattering table: 0.510 Process input model: 141.650 Find NCS groups from input model: 3.050 Set up NCS constraints: 0.560 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.007 0.283 73651 Z= 0.431 Angle : 0.779 22.387 99547 Z= 0.467 Chirality : 0.046 0.365 11312 Planarity : 0.004 0.076 12746 Dihedral : 14.402 115.932 27590 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.28 % Favored : 92.65 % Rotamer: Outliers : 0.06 % Allowed : 7.40 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.08), residues: 9131 helix: -1.12 (0.06), residues: 5182 sheet: -2.99 (0.17), residues: 710 loop : -3.51 (0.09), residues: 3239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 450 HIS 0.013 0.001 HIS P 440 PHE 0.025 0.002 PHE Q 193 TYR 0.021 0.002 TYR C 20 ARG 0.006 0.001 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1295 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1290 time to evaluate : 6.248 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 TARDY: cannot create tardy model for: "LYS Y 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 80 MET cc_start: 0.6475 (pmm) cc_final: 0.6219 (pmm) REVERT: R 355 MET cc_start: 0.3357 (mmm) cc_final: 0.3083 (tpp) REVERT: R 370 PHE cc_start: 0.8946 (t80) cc_final: 0.8712 (t80) REVERT: R 423 MET cc_start: 0.8714 (mtm) cc_final: 0.8027 (ptm) REVERT: R 453 MET cc_start: 0.7806 (mtm) cc_final: 0.7546 (mtp) REVERT: R 627 MET cc_start: 0.8525 (mmm) cc_final: 0.8038 (mmm) REVERT: O 319 MET cc_start: 0.5030 (mmm) cc_final: 0.4589 (mmm) REVERT: O 369 TYR cc_start: 0.7931 (p90) cc_final: 0.7731 (p90) REVERT: J 50 ARG cc_start: 0.8467 (ttt180) cc_final: 0.8159 (tpp-160) REVERT: J 54 MET cc_start: 0.8149 (ttp) cc_final: 0.7929 (ptm) REVERT: L 93 ASP cc_start: 0.8065 (p0) cc_final: 0.7864 (p0) REVERT: H 39 ASN cc_start: 0.9157 (m-40) cc_final: 0.8750 (p0) REVERT: K 27 LYS cc_start: 0.9302 (ttmt) cc_final: 0.8955 (mtpp) REVERT: K 93 ASP cc_start: 0.8036 (t0) cc_final: 0.7608 (t0) REVERT: K 97 ASP cc_start: 0.8236 (m-30) cc_final: 0.7764 (m-30) REVERT: S 11 ILE cc_start: 0.8244 (mm) cc_final: 0.8029 (tt) REVERT: S 52 TRP cc_start: 0.7497 (t60) cc_final: 0.7297 (t60) REVERT: S 75 TYR cc_start: 0.7190 (t80) cc_final: 0.6431 (t80) REVERT: B 60 ASP cc_start: 0.8099 (p0) cc_final: 0.7720 (t0) REVERT: B 261 GLN cc_start: 0.8534 (mt0) cc_final: 0.8182 (pt0) REVERT: B 393 LYS cc_start: 0.9129 (ttmt) cc_final: 0.8850 (ttmm) REVERT: C 56 ARG cc_start: 0.8317 (ttp-110) cc_final: 0.8029 (mtp-110) REVERT: C 248 ILE cc_start: 0.9039 (mt) cc_final: 0.8817 (pt) REVERT: C 360 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7481 (mt-10) REVERT: C 487 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7879 (tm-30) REVERT: C 608 MET cc_start: 0.7940 (ttp) cc_final: 0.7706 (ptm) REVERT: A 266 TYR cc_start: 0.9140 (m-80) cc_final: 0.8930 (m-80) REVERT: A 340 MET cc_start: 0.9272 (mtt) cc_final: 0.9001 (mtt) REVERT: E 168 GLU cc_start: 0.8343 (pm20) cc_final: 0.8004 (pt0) REVERT: E 382 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8303 (tp40) REVERT: E 436 LYS cc_start: 0.8247 (tmmt) cc_final: 0.7989 (tmmt) REVERT: F 215 LYS cc_start: 0.2779 (pptt) cc_final: 0.2157 (pptt) REVERT: F 242 ARG cc_start: 0.7891 (tpp80) cc_final: 0.7458 (ttm-80) REVERT: F 359 ASP cc_start: 0.7727 (t0) cc_final: 0.7424 (t0) REVERT: F 456 GLN cc_start: 0.8248 (tp-100) cc_final: 0.8004 (tt0) REVERT: D 234 MET cc_start: 0.9249 (mtm) cc_final: 0.9025 (mtm) REVERT: D 360 ASP cc_start: 0.8277 (t0) cc_final: 0.7836 (p0) REVERT: Y 74 CYS cc_start: 0.7542 (m) cc_final: 0.7214 (m) REVERT: Y 169 THR cc_start: 0.7592 (p) cc_final: 0.6842 (p) REVERT: Y 198 HIS cc_start: 0.7703 (t70) cc_final: 0.7491 (t-90) REVERT: Y 229 MET cc_start: 0.7774 (ptp) cc_final: 0.7419 (tpt) REVERT: Z 155 MET cc_start: 0.8582 (mtp) cc_final: 0.8351 (mtp) REVERT: X 151 PHE cc_start: 0.7380 (m-10) cc_final: 0.6695 (m-80) REVERT: X 197 TYR cc_start: 0.8272 (m-80) cc_final: 0.7872 (t80) REVERT: G 62 MET cc_start: 0.8700 (mmm) cc_final: 0.8454 (mmp) REVERT: G 99 ASP cc_start: 0.7692 (t0) cc_final: 0.7466 (t0) REVERT: G 186 TYR cc_start: 0.8832 (t80) cc_final: 0.8616 (t80) REVERT: N 29 ASN cc_start: 0.8482 (t0) cc_final: 0.7889 (t0) REVERT: N 30 LYS cc_start: 0.9353 (ptpp) cc_final: 0.8719 (mmtm) REVERT: N 31 ASN cc_start: 0.8555 (p0) cc_final: 0.7540 (p0) REVERT: N 32 ARG cc_start: 0.9050 (mmm160) cc_final: 0.8623 (tpp-160) REVERT: N 33 HIS cc_start: 0.8679 (m170) cc_final: 0.8323 (m90) REVERT: N 46 ASN cc_start: 0.8937 (t0) cc_final: 0.8464 (t0) REVERT: N 49 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8628 (mm-30) REVERT: N 82 GLN cc_start: 0.7283 (mm-40) cc_final: 0.7015 (mm-40) REVERT: N 99 ASP cc_start: 0.8725 (t0) cc_final: 0.8210 (t0) REVERT: N 107 ARG cc_start: 0.8266 (ttp-110) cc_final: 0.8054 (ttp-110) REVERT: N 112 MET cc_start: 0.8909 (mtt) cc_final: 0.8705 (mtp) REVERT: U 293 GLN cc_start: 0.9045 (mp10) cc_final: 0.8661 (mp10) REVERT: U 373 TYR cc_start: 0.8661 (m-10) cc_final: 0.8410 (m-80) REVERT: V 302 GLU cc_start: 0.7618 (pm20) cc_final: 0.7401 (pm20) REVERT: 0 103 TYR cc_start: 0.8521 (m-10) cc_final: 0.8087 (m-80) REVERT: 1 44 MET cc_start: 0.8518 (ppp) cc_final: 0.8209 (ppp) REVERT: 1 123 GLN cc_start: 0.8781 (mp10) cc_final: 0.8532 (mp10) REVERT: 1 143 LEU cc_start: 0.8974 (mt) cc_final: 0.8757 (tp) REVERT: 3 139 GLU cc_start: 0.8050 (tp30) cc_final: 0.7806 (tp30) REVERT: 4 54 LYS cc_start: 0.8886 (mttt) cc_final: 0.8193 (mmtm) REVERT: 8 23 MET cc_start: 0.8869 (tpt) cc_final: 0.8649 (tpp) REVERT: 9 54 LYS cc_start: 0.8608 (mtmt) cc_final: 0.7943 (mmtt) REVERT: Q 208 MET cc_start: 0.8557 (mmm) cc_final: 0.8203 (tpp) REVERT: Q 236 ASP cc_start: 0.8048 (t0) cc_final: 0.7808 (t0) REVERT: P 30 LYS cc_start: 0.8983 (mmmt) cc_final: 0.8729 (mmmm) REVERT: P 81 MET cc_start: 0.8302 (ptp) cc_final: 0.7985 (ptp) REVERT: P 139 HIS cc_start: 0.8373 (m90) cc_final: 0.8131 (m90) REVERT: P 140 MET cc_start: 0.8846 (tmm) cc_final: 0.8527 (tmm) REVERT: P 259 HIS cc_start: 0.8096 (OUTLIER) cc_final: 0.7335 (p90) outliers start: 5 outliers final: 1 residues processed: 1295 average time/residue: 0.6995 time to fit residues: 1509.4176 Evaluate side-chains 953 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 951 time to evaluate : 6.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 133 LEU Chi-restraints excluded: chain P residue 259 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 768 optimal weight: 1.9990 chunk 689 optimal weight: 5.9990 chunk 382 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 chunk 465 optimal weight: 2.9990 chunk 368 optimal weight: 5.9990 chunk 713 optimal weight: 9.9990 chunk 276 optimal weight: 7.9990 chunk 433 optimal weight: 0.8980 chunk 530 optimal weight: 0.9990 chunk 826 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 48 GLN ** R 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 273 ASN R 289 ASN R 343 HIS R 435 ASN R 473 ASN R 523 ASN R 547 HIS R 600 HIS ** R 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 750 GLN ** R 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 806 HIS O 31 ASN O 200 GLN ** O 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 HIS ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 113 GLN I 206 GLN L 10 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 ASN S 61 ASN T 129 ASN B 146 HIS B 207 GLN B 314 ASN B 397 ASN B 430 GLN B 444 HIS C 397 ASN C 449 ASN C 468 HIS C 484 GLN C 573 HIS A 397 ASN A 444 HIS A 468 HIS ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN F 171 GLN F 363 HIS ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 421 GLN D 470 ASN Y 17 GLN Y 59 ASN Y 76 ASN Y 198 HIS Y 274 ASN Z 19 HIS Z 190 ASN Z 270 ASN ** X 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 120 ASN X 131 ASN X 134 ASN X 150 ASN X 160 GLN X 198 HIS ** X 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN G 113 HIS G 130 GLN G 174 HIS N 29 ASN N 57 ASN U 329 ASN U 445 HIS ** 1 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 123 GLN 9 78 ASN ** Q 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 84 HIS Q 297 HIS Q 340 HIS P 72 GLN P 206 GLN ** P 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 274 GLN P 291 ASN P 311 GLN P 384 ASN P 430 GLN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 73651 Z= 0.210 Angle : 0.618 16.462 99547 Z= 0.323 Chirality : 0.042 0.222 11312 Planarity : 0.005 0.078 12746 Dihedral : 5.510 87.652 10155 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.51 % Favored : 94.45 % Rotamer: Outliers : 1.73 % Allowed : 13.00 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.08), residues: 9131 helix: 0.11 (0.07), residues: 5223 sheet: -2.51 (0.18), residues: 740 loop : -2.95 (0.10), residues: 3168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP P 151 HIS 0.019 0.001 HIS O 336 PHE 0.030 0.001 PHE R 591 TYR 0.040 0.001 TYR O 75 ARG 0.009 0.000 ARG P 419 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1247 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1112 time to evaluate : 6.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS Y 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 20 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6887 (tp30) REVERT: R 80 MET cc_start: 0.6695 (pmm) cc_final: 0.6433 (pmm) REVERT: R 370 PHE cc_start: 0.8973 (t80) cc_final: 0.8744 (t80) REVERT: R 627 MET cc_start: 0.8449 (mmm) cc_final: 0.7968 (mmm) REVERT: R 650 MET cc_start: 0.6722 (ptp) cc_final: 0.6429 (ptp) REVERT: O 36 SER cc_start: 0.7918 (m) cc_final: 0.7252 (m) REVERT: O 123 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8884 (mt-10) REVERT: O 294 TRP cc_start: 0.7960 (t60) cc_final: 0.7305 (t60) REVERT: O 298 LYS cc_start: 0.8964 (mmtp) cc_final: 0.8284 (mptt) REVERT: O 319 MET cc_start: 0.4752 (mmm) cc_final: 0.4284 (mmm) REVERT: O 339 TYR cc_start: 0.8630 (m-80) cc_final: 0.8381 (m-80) REVERT: O 369 TYR cc_start: 0.7976 (p90) cc_final: 0.7599 (p90) REVERT: J 50 ARG cc_start: 0.8464 (ttt180) cc_final: 0.8156 (tpp-160) REVERT: J 57 TYR cc_start: 0.6680 (t80) cc_final: 0.6241 (t80) REVERT: L 74 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8082 (tp30) REVERT: L 84 LEU cc_start: 0.8678 (mp) cc_final: 0.8393 (mp) REVERT: H 28 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8034 (mm-30) REVERT: H 58 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7712 (mm-30) REVERT: K 27 LYS cc_start: 0.9309 (ttmt) cc_final: 0.8952 (mtpp) REVERT: K 33 LEU cc_start: 0.8896 (tt) cc_final: 0.8419 (pp) REVERT: K 93 ASP cc_start: 0.8005 (t0) cc_final: 0.7515 (t0) REVERT: K 97 ASP cc_start: 0.8169 (m-30) cc_final: 0.7716 (m-30) REVERT: T 102 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8141 (mm-30) REVERT: B 60 ASP cc_start: 0.8045 (p0) cc_final: 0.7696 (t0) REVERT: B 261 GLN cc_start: 0.8422 (mt0) cc_final: 0.8100 (pt0) REVERT: B 393 LYS cc_start: 0.9068 (ttmt) cc_final: 0.8802 (ttmt) REVERT: B 540 MET cc_start: 0.7176 (mtp) cc_final: 0.6951 (mtp) REVERT: C 360 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7394 (mt-10) REVERT: C 487 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7891 (tm-30) REVERT: A 263 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8526 (mp) REVERT: A 283 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8103 (mm-30) REVERT: E 168 GLU cc_start: 0.8074 (pm20) cc_final: 0.7635 (pt0) REVERT: E 382 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8331 (tp40) REVERT: E 456 GLN cc_start: 0.7738 (tm-30) cc_final: 0.7485 (tm-30) REVERT: F 215 LYS cc_start: 0.2570 (pptt) cc_final: 0.1936 (pptt) REVERT: F 242 ARG cc_start: 0.7834 (tpp80) cc_final: 0.7538 (ttm-80) REVERT: F 359 ASP cc_start: 0.7618 (t0) cc_final: 0.7310 (t0) REVERT: F 456 GLN cc_start: 0.8167 (tp-100) cc_final: 0.7958 (tt0) REVERT: F 474 PHE cc_start: 0.5636 (t80) cc_final: 0.5433 (t80) REVERT: D 234 MET cc_start: 0.9230 (mtm) cc_final: 0.9024 (mtm) REVERT: D 360 ASP cc_start: 0.8062 (t0) cc_final: 0.7628 (p0) REVERT: D 457 LYS cc_start: 0.9052 (mttm) cc_final: 0.8784 (mttp) REVERT: Y 61 ARG cc_start: 0.8302 (mmm-85) cc_final: 0.7816 (tpp80) REVERT: Y 74 CYS cc_start: 0.7525 (m) cc_final: 0.7234 (m) REVERT: Z 155 MET cc_start: 0.8505 (mtp) cc_final: 0.8065 (mtp) REVERT: Z 165 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8219 (mm-40) REVERT: X 151 PHE cc_start: 0.7234 (m-10) cc_final: 0.6714 (m-80) REVERT: X 197 TYR cc_start: 0.8328 (m-80) cc_final: 0.7879 (t80) REVERT: N 29 ASN cc_start: 0.8420 (t0) cc_final: 0.7704 (t0) REVERT: N 30 LYS cc_start: 0.9346 (ptpp) cc_final: 0.8693 (mmtm) REVERT: N 31 ASN cc_start: 0.8470 (p0) cc_final: 0.7524 (p0) REVERT: N 32 ARG cc_start: 0.9026 (mmm160) cc_final: 0.8535 (tpp-160) REVERT: N 33 HIS cc_start: 0.8600 (m170) cc_final: 0.8258 (m90) REVERT: N 46 ASN cc_start: 0.8860 (t0) cc_final: 0.8517 (t0) REVERT: N 47 GLU cc_start: 0.9326 (tp30) cc_final: 0.9108 (tp30) REVERT: N 49 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8617 (mm-30) REVERT: N 73 MET cc_start: 0.9201 (mtm) cc_final: 0.8979 (ptp) REVERT: N 94 LYS cc_start: 0.8723 (tttm) cc_final: 0.8186 (tttm) REVERT: U 293 GLN cc_start: 0.9083 (mp10) cc_final: 0.8526 (mp10) REVERT: U 373 TYR cc_start: 0.8480 (m-10) cc_final: 0.8220 (m-80) REVERT: V 302 GLU cc_start: 0.7527 (pm20) cc_final: 0.7275 (pm20) REVERT: 0 103 TYR cc_start: 0.8503 (m-10) cc_final: 0.8093 (m-80) REVERT: 0 164 LEU cc_start: 0.8980 (mt) cc_final: 0.8726 (mt) REVERT: 1 123 GLN cc_start: 0.8655 (mp10) cc_final: 0.8454 (mp10) REVERT: 3 50 GLU cc_start: 0.8136 (tp30) cc_final: 0.7912 (tp30) REVERT: 3 139 GLU cc_start: 0.7971 (tp30) cc_final: 0.7412 (tm-30) REVERT: 4 44 MET cc_start: 0.8380 (ppp) cc_final: 0.7960 (ppp) REVERT: 4 51 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7737 (mp10) REVERT: 4 54 LYS cc_start: 0.8604 (mttt) cc_final: 0.8199 (mmtm) REVERT: 5 44 MET cc_start: 0.5100 (tpp) cc_final: 0.4825 (mmt) REVERT: 5 54 LYS cc_start: 0.8233 (tttt) cc_final: 0.7965 (tttm) REVERT: 9 54 LYS cc_start: 0.8518 (mtmt) cc_final: 0.7830 (mmtt) REVERT: Q 6 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8258 (pt0) REVERT: Q 150 LEU cc_start: 0.8514 (tp) cc_final: 0.8267 (tt) REVERT: Q 236 ASP cc_start: 0.8010 (t0) cc_final: 0.7766 (t0) REVERT: P 55 MET cc_start: 0.9210 (mmp) cc_final: 0.9001 (tpp) REVERT: P 64 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8043 (pt0) REVERT: P 81 MET cc_start: 0.8429 (ptp) cc_final: 0.8174 (ptp) REVERT: P 140 MET cc_start: 0.8826 (tmm) cc_final: 0.8341 (tmm) REVERT: P 151 TRP cc_start: 0.6206 (OUTLIER) cc_final: 0.5608 (m-90) REVERT: P 256 MET cc_start: 0.8228 (mmm) cc_final: 0.7822 (mmm) REVERT: P 259 HIS cc_start: 0.7784 (OUTLIER) cc_final: 0.6993 (p90) REVERT: P 307 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8849 (tt) REVERT: P 438 MET cc_start: 0.8366 (mtp) cc_final: 0.7959 (mpp) outliers start: 135 outliers final: 61 residues processed: 1184 average time/residue: 0.6613 time to fit residues: 1334.1017 Evaluate side-chains 1040 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 973 time to evaluate : 6.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 333 ILE Chi-restraints excluded: chain R residue 406 MET Chi-restraints excluded: chain R residue 488 ASN Chi-restraints excluded: chain R residue 518 ILE Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain L residue 69 CYS Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 88 PHE Chi-restraints excluded: chain H residue 18 PHE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain K residue 55 PHE Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 109 LYS Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain Y residue 35 THR Chi-restraints excluded: chain Y residue 155 MET Chi-restraints excluded: chain Z residue 99 SER Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain U residue 447 ILE Chi-restraints excluded: chain U residue 454 ASP Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 42 THR Chi-restraints excluded: chain 0 residue 151 CYS Chi-restraints excluded: chain 2 residue 112 ILE Chi-restraints excluded: chain 2 residue 141 LEU Chi-restraints excluded: chain 3 residue 110 ILE Chi-restraints excluded: chain 3 residue 140 VAL Chi-restraints excluded: chain 4 residue 36 LYS Chi-restraints excluded: chain 4 residue 51 GLN Chi-restraints excluded: chain 4 residue 127 LEU Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 115 ASP Chi-restraints excluded: chain 9 residue 135 LEU Chi-restraints excluded: chain Q residue 6 GLU Chi-restraints excluded: chain P residue 151 TRP Chi-restraints excluded: chain P residue 259 HIS Chi-restraints excluded: chain P residue 307 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 459 optimal weight: 3.9990 chunk 256 optimal weight: 9.9990 chunk 687 optimal weight: 8.9990 chunk 562 optimal weight: 20.0000 chunk 227 optimal weight: 7.9990 chunk 827 optimal weight: 10.0000 chunk 894 optimal weight: 0.9980 chunk 737 optimal weight: 10.0000 chunk 820 optimal weight: 9.9990 chunk 282 optimal weight: 8.9990 chunk 664 optimal weight: 0.4980 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN ** R 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 811 GLN ** O 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN ** O 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 461 ASN ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 GLN D 470 ASN D 497 GLN ** Y 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 59 ASN Z 160 GLN ** X 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS N 57 ASN U 360 GLN ** V 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 132 HIS ** 1 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 84 HIS Q 338 GLN ** P 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 435 GLN P 440 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 73651 Z= 0.361 Angle : 0.660 13.208 99547 Z= 0.341 Chirality : 0.043 0.211 11312 Planarity : 0.005 0.077 12746 Dihedral : 5.415 76.202 10153 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.44 % Favored : 93.52 % Rotamer: Outliers : 2.71 % Allowed : 15.65 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.09), residues: 9131 helix: 0.44 (0.07), residues: 5195 sheet: -2.28 (0.18), residues: 704 loop : -2.77 (0.10), residues: 3232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP P 151 HIS 0.005 0.001 HIS U 370 PHE 0.047 0.002 PHE P 292 TYR 0.026 0.002 TYR T 101 ARG 0.007 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1199 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 988 time to evaluate : 6.310 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: R 20 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6675 (tp30) REVERT: R 61 MET cc_start: 0.8722 (tpp) cc_final: 0.8273 (mmt) REVERT: R 80 MET cc_start: 0.6651 (pmm) cc_final: 0.6447 (pmm) REVERT: R 370 PHE cc_start: 0.8992 (t80) cc_final: 0.8773 (t80) REVERT: R 423 MET cc_start: 0.8636 (mtm) cc_final: 0.8020 (ptm) REVERT: R 627 MET cc_start: 0.8533 (mmm) cc_final: 0.8042 (mmt) REVERT: R 650 MET cc_start: 0.6934 (ptp) cc_final: 0.6637 (ptp) REVERT: O 75 TYR cc_start: 0.8326 (m-80) cc_final: 0.7984 (m-80) REVERT: O 294 TRP cc_start: 0.8028 (t60) cc_final: 0.7395 (t60) REVERT: O 298 LYS cc_start: 0.8998 (mmtp) cc_final: 0.8367 (mptt) REVERT: O 319 MET cc_start: 0.4739 (mmm) cc_final: 0.4305 (mmm) REVERT: O 339 TYR cc_start: 0.8628 (m-80) cc_final: 0.8421 (m-10) REVERT: O 354 MET cc_start: 0.0715 (mmt) cc_final: -0.0849 (mmt) REVERT: O 369 TYR cc_start: 0.8146 (p90) cc_final: 0.7698 (p90) REVERT: J 57 TYR cc_start: 0.6641 (t80) cc_final: 0.4354 (t80) REVERT: I 56 TYR cc_start: 0.7095 (OUTLIER) cc_final: 0.6891 (t80) REVERT: L 74 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8153 (tp30) REVERT: H 13 LYS cc_start: 0.8994 (mtpt) cc_final: 0.8346 (tmtt) REVERT: H 28 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7976 (mm-30) REVERT: K 27 LYS cc_start: 0.9332 (ttmt) cc_final: 0.8976 (mtpp) REVERT: K 37 LYS cc_start: 0.7538 (mmtp) cc_final: 0.6684 (mmtt) REVERT: K 93 ASP cc_start: 0.8044 (t0) cc_final: 0.7516 (t0) REVERT: K 97 ASP cc_start: 0.8146 (m-30) cc_final: 0.7668 (m-30) REVERT: T 102 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8111 (mm-30) REVERT: B 60 ASP cc_start: 0.8190 (p0) cc_final: 0.7880 (t0) REVERT: B 261 GLN cc_start: 0.8451 (mt0) cc_final: 0.8153 (pt0) REVERT: B 393 LYS cc_start: 0.9078 (ttmt) cc_final: 0.8839 (ttmt) REVERT: B 540 MET cc_start: 0.7123 (mtp) cc_final: 0.6858 (mtp) REVERT: C 360 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7424 (mt-10) REVERT: C 487 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7857 (tm-30) REVERT: A 283 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8221 (mm-30) REVERT: E 168 GLU cc_start: 0.8171 (pm20) cc_final: 0.7936 (pt0) REVERT: E 382 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8354 (tp40) REVERT: E 436 LYS cc_start: 0.8106 (tmmt) cc_final: 0.7854 (tmmt) REVERT: E 456 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7436 (tm-30) REVERT: F 215 LYS cc_start: 0.2709 (pptt) cc_final: 0.2061 (pptt) REVERT: F 242 ARG cc_start: 0.7924 (tpp80) cc_final: 0.7441 (ttm-80) REVERT: F 359 ASP cc_start: 0.7672 (t0) cc_final: 0.7399 (t0) REVERT: F 456 GLN cc_start: 0.8201 (tp-100) cc_final: 0.7923 (tt0) REVERT: F 474 PHE cc_start: 0.5798 (t80) cc_final: 0.5557 (t80) REVERT: D 234 MET cc_start: 0.9269 (mtm) cc_final: 0.9007 (mtm) REVERT: D 360 ASP cc_start: 0.8156 (t0) cc_final: 0.7704 (p0) REVERT: Y 61 ARG cc_start: 0.8317 (mmm-85) cc_final: 0.7977 (tpp80) REVERT: Y 74 CYS cc_start: 0.7452 (m) cc_final: 0.7141 (m) REVERT: Z 155 MET cc_start: 0.8458 (mtp) cc_final: 0.8235 (mtp) REVERT: X 49 TYR cc_start: 0.6288 (m-80) cc_final: 0.6056 (m-80) REVERT: X 151 PHE cc_start: 0.7346 (m-10) cc_final: 0.6727 (m-80) REVERT: X 153 ARG cc_start: 0.7454 (tpp80) cc_final: 0.7229 (tpp80) REVERT: X 197 TYR cc_start: 0.8314 (m-80) cc_final: 0.7846 (t80) REVERT: G 206 GLN cc_start: 0.8859 (tp40) cc_final: 0.8523 (tp40) REVERT: N 29 ASN cc_start: 0.8486 (t0) cc_final: 0.8119 (t0) REVERT: N 30 LYS cc_start: 0.9365 (ptpp) cc_final: 0.8881 (mmtm) REVERT: N 31 ASN cc_start: 0.8515 (p0) cc_final: 0.7716 (p0) REVERT: N 32 ARG cc_start: 0.9029 (mmm160) cc_final: 0.8632 (tpp-160) REVERT: N 33 HIS cc_start: 0.8648 (m170) cc_final: 0.8340 (m90) REVERT: N 41 LYS cc_start: 0.9177 (mtmm) cc_final: 0.8957 (mtmm) REVERT: N 46 ASN cc_start: 0.8973 (t0) cc_final: 0.8679 (t0) REVERT: N 50 ASP cc_start: 0.8692 (m-30) cc_final: 0.8097 (m-30) REVERT: N 73 MET cc_start: 0.9195 (mtm) cc_final: 0.8904 (ptp) REVERT: N 94 LYS cc_start: 0.8836 (tttm) cc_final: 0.8198 (tttm) REVERT: N 99 ASP cc_start: 0.8512 (t0) cc_final: 0.8094 (t70) REVERT: N 102 LYS cc_start: 0.8845 (mttm) cc_final: 0.8513 (mttp) REVERT: U 293 GLN cc_start: 0.9055 (mp10) cc_final: 0.8736 (mp10) REVERT: U 373 TYR cc_start: 0.8526 (m-10) cc_final: 0.8297 (m-80) REVERT: U 426 ILE cc_start: 0.9091 (mm) cc_final: 0.8812 (mm) REVERT: U 430 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8625 (mt) REVERT: 0 103 TYR cc_start: 0.8552 (m-10) cc_final: 0.8153 (m-80) REVERT: 1 78 ASN cc_start: 0.8574 (m-40) cc_final: 0.8369 (m-40) REVERT: 1 123 GLN cc_start: 0.8718 (mp10) cc_final: 0.8518 (mp10) REVERT: 3 139 GLU cc_start: 0.8046 (tp30) cc_final: 0.7466 (tm-30) REVERT: 4 54 LYS cc_start: 0.8758 (mttt) cc_final: 0.8168 (mmtm) REVERT: 4 115 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8144 (t0) REVERT: 5 44 MET cc_start: 0.5251 (tpp) cc_final: 0.4800 (mmt) REVERT: 9 54 LYS cc_start: 0.8589 (mtmt) cc_final: 0.7845 (mmtt) REVERT: Q 6 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8326 (pt0) REVERT: Q 150 LEU cc_start: 0.8629 (tp) cc_final: 0.8274 (tt) REVERT: Q 208 MET cc_start: 0.8592 (mmm) cc_final: 0.8331 (mmm) REVERT: Q 236 ASP cc_start: 0.8059 (t0) cc_final: 0.7797 (t0) REVERT: P 30 LYS cc_start: 0.9012 (mmmm) cc_final: 0.8769 (mmtt) REVERT: P 64 GLU cc_start: 0.8232 (mt-10) cc_final: 0.8011 (pt0) REVERT: P 101 LEU cc_start: 0.8923 (mt) cc_final: 0.8592 (tp) REVERT: P 140 MET cc_start: 0.8787 (tmm) cc_final: 0.8339 (tmm) REVERT: P 151 TRP cc_start: 0.6131 (OUTLIER) cc_final: 0.5629 (m-90) REVERT: P 256 MET cc_start: 0.8273 (mmm) cc_final: 0.7875 (mmm) REVERT: P 307 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.8782 (tt) outliers start: 211 outliers final: 136 residues processed: 1121 average time/residue: 0.6573 time to fit residues: 1271.0104 Evaluate side-chains 1072 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 930 time to evaluate : 6.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain R residue 333 ILE Chi-restraints excluded: chain R residue 360 THR Chi-restraints excluded: chain R residue 363 THR Chi-restraints excluded: chain R residue 488 ASN Chi-restraints excluded: chain R residue 518 ILE Chi-restraints excluded: chain R residue 594 TRP Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 324 ASN Chi-restraints excluded: chain O residue 363 GLN Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 226 ASP Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain I residue 56 TYR Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain L residue 69 CYS Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 88 PHE Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 18 PHE Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain K residue 55 PHE Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 67 GLN Chi-restraints excluded: chain T residue 80 ILE Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 109 LYS Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain Y residue 35 THR Chi-restraints excluded: chain Y residue 188 MET Chi-restraints excluded: chain Y residue 204 VAL Chi-restraints excluded: chain Y residue 246 LEU Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain Z residue 99 SER Chi-restraints excluded: chain Z residue 179 PHE Chi-restraints excluded: chain Z residue 263 ILE Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 112 MET Chi-restraints excluded: chain U residue 289 THR Chi-restraints excluded: chain U residue 324 LYS Chi-restraints excluded: chain U residue 385 VAL Chi-restraints excluded: chain U residue 408 MET Chi-restraints excluded: chain U residue 430 LEU Chi-restraints excluded: chain U residue 441 THR Chi-restraints excluded: chain U residue 454 ASP Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 42 THR Chi-restraints excluded: chain 0 residue 69 ILE Chi-restraints excluded: chain 0 residue 98 GLU Chi-restraints excluded: chain 0 residue 151 CYS Chi-restraints excluded: chain 0 residue 181 ILE Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 2 residue 10 TYR Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 2 residue 83 ASP Chi-restraints excluded: chain 2 residue 112 ILE Chi-restraints excluded: chain 2 residue 141 LEU Chi-restraints excluded: chain 2 residue 154 THR Chi-restraints excluded: chain 3 residue 74 VAL Chi-restraints excluded: chain 3 residue 78 ASN Chi-restraints excluded: chain 3 residue 110 ILE Chi-restraints excluded: chain 3 residue 140 VAL Chi-restraints excluded: chain 4 residue 60 VAL Chi-restraints excluded: chain 4 residue 115 ASP Chi-restraints excluded: chain 4 residue 127 LEU Chi-restraints excluded: chain 6 residue 16 VAL Chi-restraints excluded: chain 6 residue 102 SER Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 115 ASP Chi-restraints excluded: chain 9 residue 135 LEU Chi-restraints excluded: chain Q residue 6 GLU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain Q residue 321 LEU Chi-restraints excluded: chain P residue 151 TRP Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain P residue 442 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 817 optimal weight: 6.9990 chunk 622 optimal weight: 5.9990 chunk 429 optimal weight: 0.9990 chunk 91 optimal weight: 0.0670 chunk 395 optimal weight: 4.9990 chunk 555 optimal weight: 3.9990 chunk 830 optimal weight: 0.9990 chunk 879 optimal weight: 0.0040 chunk 434 optimal weight: 0.9990 chunk 787 optimal weight: 6.9990 chunk 237 optimal weight: 5.9990 overall best weight: 0.6136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN O 145 ASN ** O 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 HIS I 66 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 HIS ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 GLN ** K 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN F 97 GLN ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 ASN Y 59 ASN ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN G 113 HIS N 81 HIS 1 92 GLN 4 51 GLN ** Q 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 440 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.099 73651 Z= 0.160 Angle : 0.573 12.105 99547 Z= 0.295 Chirality : 0.040 0.227 11312 Planarity : 0.004 0.078 12746 Dihedral : 4.968 76.596 10151 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.81 % Favored : 95.16 % Rotamer: Outliers : 2.26 % Allowed : 17.23 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: -0.80 (0.09), residues: 9131 helix: 0.87 (0.07), residues: 5157 sheet: -2.09 (0.18), residues: 742 loop : -2.48 (0.10), residues: 3232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP O 282 HIS 0.005 0.001 HIS O 336 PHE 0.039 0.001 PHE P 292 TYR 0.031 0.001 TYR T 101 ARG 0.010 0.000 ARG O 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1101 time to evaluate : 6.289 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: R 20 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6682 (tp30) REVERT: R 61 MET cc_start: 0.8636 (tpp) cc_final: 0.8382 (mmt) REVERT: R 423 MET cc_start: 0.8599 (mtm) cc_final: 0.7979 (ptm) REVERT: R 627 MET cc_start: 0.8473 (mmm) cc_final: 0.8002 (mmm) REVERT: O 75 TYR cc_start: 0.8162 (m-80) cc_final: 0.7889 (m-80) REVERT: O 107 TRP cc_start: 0.7176 (t-100) cc_final: 0.6914 (t-100) REVERT: O 298 LYS cc_start: 0.8972 (mmtp) cc_final: 0.8018 (mmtm) REVERT: O 354 MET cc_start: 0.0131 (mmt) cc_final: -0.0513 (mmt) REVERT: O 369 TYR cc_start: 0.8077 (p90) cc_final: 0.7761 (p90) REVERT: L 84 LEU cc_start: 0.8672 (mp) cc_final: 0.8410 (mp) REVERT: H 13 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8264 (tmtt) REVERT: H 24 ASN cc_start: 0.9024 (m-40) cc_final: 0.8141 (m-40) REVERT: H 28 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7926 (mm-30) REVERT: H 39 ASN cc_start: 0.9167 (m-40) cc_final: 0.8698 (m110) REVERT: H 58 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8124 (mm-30) REVERT: K 27 LYS cc_start: 0.9313 (ttmt) cc_final: 0.9015 (mtpp) REVERT: K 75 LYS cc_start: 0.8787 (ttpt) cc_final: 0.8569 (pttm) REVERT: K 93 ASP cc_start: 0.8041 (t0) cc_final: 0.7431 (t0) REVERT: K 97 ASP cc_start: 0.8067 (m-30) cc_final: 0.7556 (m-30) REVERT: S 19 PHE cc_start: 0.8081 (t80) cc_final: 0.7728 (t80) REVERT: B 60 ASP cc_start: 0.8104 (p0) cc_final: 0.7736 (t0) REVERT: B 261 GLN cc_start: 0.8373 (mt0) cc_final: 0.8109 (pt0) REVERT: B 305 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8637 (mt) REVERT: B 393 LYS cc_start: 0.9083 (ttmt) cc_final: 0.8809 (ttmt) REVERT: C 55 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8876 (pt) REVERT: C 360 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7365 (mt-10) REVERT: C 487 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7953 (tm-30) REVERT: C 518 ASP cc_start: 0.8405 (t70) cc_final: 0.7952 (t0) REVERT: E 456 GLN cc_start: 0.7769 (tm-30) cc_final: 0.7435 (tm-30) REVERT: F 215 LYS cc_start: 0.2387 (pptt) cc_final: 0.1803 (pptt) REVERT: F 242 ARG cc_start: 0.7852 (tpp80) cc_final: 0.7609 (ttm-80) REVERT: F 359 ASP cc_start: 0.7594 (t0) cc_final: 0.7329 (t0) REVERT: F 382 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8238 (mm-40) REVERT: F 456 GLN cc_start: 0.8154 (tp-100) cc_final: 0.7883 (tt0) REVERT: F 474 PHE cc_start: 0.5639 (t80) cc_final: 0.5420 (t80) REVERT: D 360 ASP cc_start: 0.7979 (t0) cc_final: 0.7556 (p0) REVERT: D 457 LYS cc_start: 0.9054 (mttm) cc_final: 0.8784 (mttp) REVERT: D 506 ARG cc_start: 0.7292 (mmm160) cc_final: 0.7046 (mmm160) REVERT: Y 33 MET cc_start: 0.8175 (tpp) cc_final: 0.7950 (tpt) REVERT: Y 61 ARG cc_start: 0.8333 (mmm-85) cc_final: 0.7944 (tpp80) REVERT: Y 74 CYS cc_start: 0.7413 (m) cc_final: 0.7098 (m) REVERT: Z 74 CYS cc_start: 0.7561 (m) cc_final: 0.6993 (m) REVERT: X 49 TYR cc_start: 0.6214 (m-80) cc_final: 0.5915 (m-80) REVERT: X 151 PHE cc_start: 0.7253 (m-10) cc_final: 0.6781 (m-80) REVERT: X 197 TYR cc_start: 0.8183 (m-80) cc_final: 0.7929 (t80) REVERT: G 206 GLN cc_start: 0.8842 (tp40) cc_final: 0.8421 (tp40) REVERT: N 29 ASN cc_start: 0.8321 (t0) cc_final: 0.7665 (t0) REVERT: N 30 LYS cc_start: 0.9330 (ptpp) cc_final: 0.8656 (mmtm) REVERT: N 31 ASN cc_start: 0.8452 (p0) cc_final: 0.7652 (p0) REVERT: N 32 ARG cc_start: 0.8929 (mmm160) cc_final: 0.8484 (tpp-160) REVERT: N 33 HIS cc_start: 0.8613 (m170) cc_final: 0.8291 (m90) REVERT: N 46 ASN cc_start: 0.9010 (t0) cc_final: 0.8700 (t0) REVERT: N 47 GLU cc_start: 0.9292 (tp30) cc_final: 0.8808 (pt0) REVERT: N 73 MET cc_start: 0.9165 (mtm) cc_final: 0.8923 (ptp) REVERT: N 94 LYS cc_start: 0.8763 (tttm) cc_final: 0.8188 (tttm) REVERT: U 293 GLN cc_start: 0.9054 (mp10) cc_final: 0.8471 (mp-120) REVERT: U 373 TYR cc_start: 0.8387 (m-10) cc_final: 0.8176 (m-80) REVERT: U 430 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8577 (mt) REVERT: 0 89 LYS cc_start: 0.8504 (ttmm) cc_final: 0.8197 (ttmm) REVERT: 0 103 TYR cc_start: 0.8469 (m-10) cc_final: 0.8021 (m-80) REVERT: 0 107 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.7995 (mpp) REVERT: 1 78 ASN cc_start: 0.8469 (m-40) cc_final: 0.8211 (m-40) REVERT: 1 97 LEU cc_start: 0.8791 (tt) cc_final: 0.8565 (tp) REVERT: 1 123 GLN cc_start: 0.8601 (mp10) cc_final: 0.8397 (mp10) REVERT: 3 139 GLU cc_start: 0.7925 (tp30) cc_final: 0.7399 (tm-30) REVERT: 4 44 MET cc_start: 0.8373 (ppp) cc_final: 0.7894 (ppp) REVERT: 4 54 LYS cc_start: 0.8512 (mttt) cc_final: 0.8069 (mmtm) REVERT: 5 54 LYS cc_start: 0.8269 (tttt) cc_final: 0.7945 (tttm) REVERT: 7 10 TYR cc_start: 0.4524 (m-80) cc_final: 0.3398 (m-80) REVERT: 9 53 MET cc_start: 0.8073 (mmt) cc_final: 0.7354 (ptt) REVERT: Q 150 LEU cc_start: 0.8521 (tp) cc_final: 0.8299 (tt) REVERT: Q 236 ASP cc_start: 0.7960 (t0) cc_final: 0.7315 (t0) REVERT: P 30 LYS cc_start: 0.8927 (mmmm) cc_final: 0.8678 (mmmt) REVERT: P 64 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8072 (pt0) REVERT: P 92 TYR cc_start: 0.8149 (m-80) cc_final: 0.7473 (m-80) REVERT: P 101 LEU cc_start: 0.8853 (mt) cc_final: 0.8542 (tp) REVERT: P 140 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8538 (tmm) REVERT: P 151 TRP cc_start: 0.6073 (OUTLIER) cc_final: 0.5657 (m-90) REVERT: P 277 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8576 (m) REVERT: P 307 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8707 (tt) outliers start: 176 outliers final: 107 residues processed: 1215 average time/residue: 0.6735 time to fit residues: 1413.8135 Evaluate side-chains 1100 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 985 time to evaluate : 6.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 GLU Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain R residue 328 THR Chi-restraints excluded: chain R residue 360 THR Chi-restraints excluded: chain R residue 363 THR Chi-restraints excluded: chain R residue 395 THR Chi-restraints excluded: chain R residue 488 ASN Chi-restraints excluded: chain R residue 497 ASN Chi-restraints excluded: chain R residue 518 ILE Chi-restraints excluded: chain R residue 579 MET Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 123 GLU Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 324 ASN Chi-restraints excluded: chain O residue 363 GLN Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain L residue 69 CYS Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 88 PHE Chi-restraints excluded: chain H residue 18 PHE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain K residue 55 PHE Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain T residue 80 ILE Chi-restraints excluded: chain T residue 105 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 112 CYS Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain Y residue 98 ILE Chi-restraints excluded: chain Y residue 155 MET Chi-restraints excluded: chain Y residue 188 MET Chi-restraints excluded: chain Y residue 246 LEU Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain Z residue 99 SER Chi-restraints excluded: chain Z residue 179 PHE Chi-restraints excluded: chain Z residue 263 ILE Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain U residue 289 THR Chi-restraints excluded: chain U residue 324 LYS Chi-restraints excluded: chain U residue 385 VAL Chi-restraints excluded: chain U residue 430 LEU Chi-restraints excluded: chain U residue 447 ILE Chi-restraints excluded: chain U residue 454 ASP Chi-restraints excluded: chain U residue 455 ARG Chi-restraints excluded: chain 0 residue 69 ILE Chi-restraints excluded: chain 0 residue 98 GLU Chi-restraints excluded: chain 0 residue 106 ILE Chi-restraints excluded: chain 0 residue 107 MET Chi-restraints excluded: chain 0 residue 151 CYS Chi-restraints excluded: chain 1 residue 146 LEU Chi-restraints excluded: chain 2 residue 10 TYR Chi-restraints excluded: chain 2 residue 83 ASP Chi-restraints excluded: chain 2 residue 141 LEU Chi-restraints excluded: chain 3 residue 110 ILE Chi-restraints excluded: chain 3 residue 140 VAL Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 4 residue 60 VAL Chi-restraints excluded: chain 4 residue 110 ILE Chi-restraints excluded: chain 6 residue 16 VAL Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain 8 residue 92 GLN Chi-restraints excluded: chain 8 residue 115 ASP Chi-restraints excluded: chain 9 residue 135 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 174 ASP Chi-restraints excluded: chain Q residue 321 LEU Chi-restraints excluded: chain Q residue 336 ILE Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 151 TRP Chi-restraints excluded: chain P residue 277 VAL Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain P residue 442 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 732 optimal weight: 0.6980 chunk 499 optimal weight: 6.9990 chunk 12 optimal weight: 30.0000 chunk 654 optimal weight: 10.0000 chunk 362 optimal weight: 0.4980 chunk 750 optimal weight: 6.9990 chunk 608 optimal weight: 10.0000 chunk 1 optimal weight: 30.0000 chunk 449 optimal weight: 7.9990 chunk 789 optimal weight: 8.9990 chunk 221 optimal weight: 0.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 523 ASN ** R 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 HIS ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 59 ASN ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN ** N 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 ASN Q 84 HIS ** P 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 440 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 73651 Z= 0.277 Angle : 0.608 12.559 99547 Z= 0.312 Chirality : 0.042 0.213 11312 Planarity : 0.004 0.078 12746 Dihedral : 4.942 76.579 10151 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.95 % Favored : 94.01 % Rotamer: Outliers : 3.00 % Allowed : 18.27 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: -0.68 (0.09), residues: 9131 helix: 0.93 (0.07), residues: 5174 sheet: -1.83 (0.18), residues: 763 loop : -2.44 (0.10), residues: 3194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP S 52 HIS 0.005 0.001 HIS O 336 PHE 0.031 0.001 PHE 1 128 TYR 0.040 0.001 TYR Y 60 ARG 0.006 0.000 ARG F 185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1229 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 995 time to evaluate : 6.404 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: R 61 MET cc_start: 0.8734 (tpp) cc_final: 0.8478 (mmt) REVERT: R 416 MET cc_start: 0.8581 (ppp) cc_final: 0.8295 (ppp) REVERT: R 423 MET cc_start: 0.8640 (mtm) cc_final: 0.8029 (ptm) REVERT: R 627 MET cc_start: 0.8505 (mmm) cc_final: 0.7981 (mmm) REVERT: O 75 TYR cc_start: 0.8105 (m-80) cc_final: 0.7890 (m-80) REVERT: O 298 LYS cc_start: 0.8905 (mmtp) cc_final: 0.8582 (mmtm) REVERT: O 319 MET cc_start: 0.5972 (mmm) cc_final: 0.5306 (mmm) REVERT: O 369 TYR cc_start: 0.8155 (p90) cc_final: 0.7729 (p90) REVERT: J 50 ARG cc_start: 0.8574 (ttt180) cc_final: 0.8317 (tpp-160) REVERT: M 66 ARG cc_start: 0.6954 (tmm160) cc_final: 0.6710 (tmt170) REVERT: L 84 LEU cc_start: 0.8756 (mp) cc_final: 0.8476 (mp) REVERT: H 24 ASN cc_start: 0.9046 (m-40) cc_final: 0.8168 (m-40) REVERT: H 28 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7975 (mm-30) REVERT: H 39 ASN cc_start: 0.9202 (m-40) cc_final: 0.8719 (m110) REVERT: H 58 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8238 (mm-30) REVERT: K 27 LYS cc_start: 0.9303 (ttmt) cc_final: 0.9003 (mtpp) REVERT: K 75 LYS cc_start: 0.8776 (ttpt) cc_final: 0.8562 (pttm) REVERT: K 93 ASP cc_start: 0.8087 (t0) cc_final: 0.7459 (t0) REVERT: K 97 ASP cc_start: 0.8086 (m-30) cc_final: 0.7595 (m-30) REVERT: S 19 PHE cc_start: 0.8049 (t80) cc_final: 0.7718 (t80) REVERT: T 71 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.5970 (m-80) REVERT: B 60 ASP cc_start: 0.8160 (p0) cc_final: 0.7922 (t0) REVERT: B 261 GLN cc_start: 0.8424 (mt0) cc_final: 0.8220 (pt0) REVERT: B 347 MET cc_start: 0.8701 (tpp) cc_final: 0.8121 (tpp) REVERT: B 393 LYS cc_start: 0.9035 (ttmt) cc_final: 0.8824 (ttmt) REVERT: B 540 MET cc_start: 0.7095 (mtp) cc_final: 0.6836 (mtp) REVERT: B 574 MET cc_start: 0.8540 (tpp) cc_final: 0.8337 (tpp) REVERT: C 283 GLU cc_start: 0.6862 (mp0) cc_final: 0.6591 (mp0) REVERT: C 360 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7403 (mt-10) REVERT: C 487 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7978 (tm-30) REVERT: E 180 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8514 (mtm) REVERT: E 456 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7572 (tm-30) REVERT: F 215 LYS cc_start: 0.2524 (pptt) cc_final: 0.1944 (pptt) REVERT: F 242 ARG cc_start: 0.7939 (tpp80) cc_final: 0.7603 (ttm-80) REVERT: F 359 ASP cc_start: 0.7635 (t0) cc_final: 0.7373 (t0) REVERT: F 382 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8343 (mm-40) REVERT: F 456 GLN cc_start: 0.8168 (tp-100) cc_final: 0.7857 (tt0) REVERT: F 474 PHE cc_start: 0.5769 (t80) cc_final: 0.5531 (t80) REVERT: D 212 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8887 (mp) REVERT: D 360 ASP cc_start: 0.8067 (t0) cc_final: 0.7606 (p0) REVERT: D 457 LYS cc_start: 0.9057 (mttm) cc_final: 0.8771 (mttp) REVERT: D 506 ARG cc_start: 0.7302 (mmm160) cc_final: 0.7056 (mmm160) REVERT: Y 61 ARG cc_start: 0.8390 (mmm-85) cc_final: 0.8185 (tpp-160) REVERT: Y 74 CYS cc_start: 0.7471 (m) cc_final: 0.7130 (m) REVERT: Z 74 CYS cc_start: 0.7631 (m) cc_final: 0.7079 (m) REVERT: X 151 PHE cc_start: 0.7262 (m-10) cc_final: 0.6783 (m-80) REVERT: X 197 TYR cc_start: 0.8206 (m-80) cc_final: 0.7923 (t80) REVERT: G 206 GLN cc_start: 0.8868 (tp40) cc_final: 0.8404 (tp40) REVERT: N 29 ASN cc_start: 0.8464 (t0) cc_final: 0.7905 (t0) REVERT: N 30 LYS cc_start: 0.9378 (ptpp) cc_final: 0.8712 (mmtm) REVERT: N 31 ASN cc_start: 0.8563 (p0) cc_final: 0.7734 (p0) REVERT: N 32 ARG cc_start: 0.9038 (mmm160) cc_final: 0.8600 (tpp-160) REVERT: N 33 HIS cc_start: 0.8658 (m170) cc_final: 0.8305 (m90) REVERT: N 46 ASN cc_start: 0.8953 (t0) cc_final: 0.8667 (t0) REVERT: N 50 ASP cc_start: 0.8842 (m-30) cc_final: 0.8420 (m-30) REVERT: N 73 MET cc_start: 0.9138 (mtm) cc_final: 0.8901 (ttm) REVERT: N 107 ARG cc_start: 0.8209 (ttp-110) cc_final: 0.7914 (ttp80) REVERT: U 293 GLN cc_start: 0.9050 (mp10) cc_final: 0.8730 (mp10) REVERT: U 373 TYR cc_start: 0.8420 (m-10) cc_final: 0.8201 (m-80) REVERT: U 430 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8617 (mt) REVERT: V 302 GLU cc_start: 0.7610 (pm20) cc_final: 0.7256 (pm20) REVERT: V 314 MET cc_start: 0.8596 (tpp) cc_final: 0.8387 (mmm) REVERT: 0 103 TYR cc_start: 0.8530 (m-10) cc_final: 0.8119 (m-80) REVERT: 1 97 LEU cc_start: 0.8913 (tt) cc_final: 0.8659 (tp) REVERT: 1 123 GLN cc_start: 0.8699 (mp10) cc_final: 0.8487 (mp10) REVERT: 3 139 GLU cc_start: 0.8008 (tp30) cc_final: 0.7425 (tm-30) REVERT: 4 54 LYS cc_start: 0.8563 (mttt) cc_final: 0.8190 (mptt) REVERT: 5 44 MET cc_start: 0.5250 (tpp) cc_final: 0.5009 (mmp) REVERT: 7 10 TYR cc_start: 0.4589 (m-80) cc_final: 0.3371 (m-80) REVERT: 7 139 GLU cc_start: 0.8360 (tp30) cc_final: 0.8127 (tp30) REVERT: 9 53 MET cc_start: 0.8159 (mmt) cc_final: 0.7336 (ptt) REVERT: 9 119 ARG cc_start: 0.8482 (mtp-110) cc_final: 0.8241 (mtp-110) REVERT: Q 6 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7894 (pt0) REVERT: Q 150 LEU cc_start: 0.8588 (tp) cc_final: 0.8260 (tt) REVERT: Q 208 MET cc_start: 0.8582 (mmm) cc_final: 0.8307 (mmm) REVERT: Q 236 ASP cc_start: 0.8008 (t0) cc_final: 0.7451 (t0) REVERT: P 30 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8664 (mmmt) REVERT: P 81 MET cc_start: 0.8033 (ptp) cc_final: 0.7697 (ptp) REVERT: P 92 TYR cc_start: 0.8183 (m-80) cc_final: 0.7511 (m-80) REVERT: P 101 LEU cc_start: 0.8865 (mt) cc_final: 0.8553 (tt) REVERT: P 140 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8426 (tmm) REVERT: P 151 TRP cc_start: 0.5940 (OUTLIER) cc_final: 0.5658 (m-90) REVERT: P 440 HIS cc_start: 0.8686 (OUTLIER) cc_final: 0.8006 (m90) outliers start: 234 outliers final: 159 residues processed: 1152 average time/residue: 0.6451 time to fit residues: 1288.1553 Evaluate side-chains 1121 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 954 time to evaluate : 6.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 GLU Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain R residue 333 ILE Chi-restraints excluded: chain R residue 360 THR Chi-restraints excluded: chain R residue 363 THR Chi-restraints excluded: chain R residue 497 ASN Chi-restraints excluded: chain R residue 518 ILE Chi-restraints excluded: chain R residue 529 LEU Chi-restraints excluded: chain R residue 530 THR Chi-restraints excluded: chain R residue 579 MET Chi-restraints excluded: chain R residue 594 TRP Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 123 GLU Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 324 ASN Chi-restraints excluded: chain O residue 341 HIS Chi-restraints excluded: chain O residue 363 GLN Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain L residue 69 CYS Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 88 PHE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain T residue 71 PHE Chi-restraints excluded: chain T residue 80 ILE Chi-restraints excluded: chain T residue 105 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 112 CYS Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain Y residue 35 THR Chi-restraints excluded: chain Y residue 98 ILE Chi-restraints excluded: chain Y residue 155 MET Chi-restraints excluded: chain Y residue 188 MET Chi-restraints excluded: chain Y residue 246 LEU Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain Z residue 99 SER Chi-restraints excluded: chain Z residue 179 PHE Chi-restraints excluded: chain Z residue 263 ILE Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain U residue 289 THR Chi-restraints excluded: chain U residue 304 ASP Chi-restraints excluded: chain U residue 324 LYS Chi-restraints excluded: chain U residue 385 VAL Chi-restraints excluded: chain U residue 430 LEU Chi-restraints excluded: chain U residue 441 THR Chi-restraints excluded: chain U residue 447 ILE Chi-restraints excluded: chain U residue 454 ASP Chi-restraints excluded: chain U residue 455 ARG Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 36 ASP Chi-restraints excluded: chain 0 residue 98 GLU Chi-restraints excluded: chain 0 residue 151 CYS Chi-restraints excluded: chain 0 residue 181 ILE Chi-restraints excluded: chain 1 residue 146 LEU Chi-restraints excluded: chain 2 residue 10 TYR Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 2 residue 44 MET Chi-restraints excluded: chain 2 residue 53 MET Chi-restraints excluded: chain 2 residue 83 ASP Chi-restraints excluded: chain 2 residue 112 ILE Chi-restraints excluded: chain 2 residue 141 LEU Chi-restraints excluded: chain 3 residue 78 ASN Chi-restraints excluded: chain 3 residue 81 ASN Chi-restraints excluded: chain 3 residue 140 VAL Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 4 residue 34 THR Chi-restraints excluded: chain 4 residue 60 VAL Chi-restraints excluded: chain 4 residue 127 LEU Chi-restraints excluded: chain 5 residue 47 MET Chi-restraints excluded: chain 5 residue 110 ILE Chi-restraints excluded: chain 6 residue 102 SER Chi-restraints excluded: chain 6 residue 110 ILE Chi-restraints excluded: chain 6 residue 150 LEU Chi-restraints excluded: chain 7 residue 115 ASP Chi-restraints excluded: chain 7 residue 118 VAL Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 92 GLN Chi-restraints excluded: chain 8 residue 115 ASP Chi-restraints excluded: chain 9 residue 133 LEU Chi-restraints excluded: chain 9 residue 135 LEU Chi-restraints excluded: chain Q residue 6 GLU Chi-restraints excluded: chain Q residue 10 ASN Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain Q residue 174 ASP Chi-restraints excluded: chain Q residue 321 LEU Chi-restraints excluded: chain Q residue 336 ILE Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 151 TRP Chi-restraints excluded: chain P residue 440 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 295 optimal weight: 7.9990 chunk 792 optimal weight: 9.9990 chunk 173 optimal weight: 30.0000 chunk 516 optimal weight: 7.9990 chunk 217 optimal weight: 9.9990 chunk 880 optimal weight: 3.9990 chunk 730 optimal weight: 7.9990 chunk 407 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 291 optimal weight: 7.9990 chunk 462 optimal weight: 9.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 ASN K 9 GLN B 172 ASN F 421 GLN Y 59 ASN ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN ** N 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 84 HIS ** P 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 311 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 73651 Z= 0.422 Angle : 0.681 13.245 99547 Z= 0.350 Chirality : 0.044 0.207 11312 Planarity : 0.005 0.076 12746 Dihedral : 5.174 75.635 10151 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.70 % Favored : 93.25 % Rotamer: Outliers : 3.48 % Allowed : 18.95 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.09), residues: 9131 helix: 0.81 (0.07), residues: 5188 sheet: -1.76 (0.18), residues: 786 loop : -2.48 (0.10), residues: 3157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP S 52 HIS 0.043 0.001 HIS P 440 PHE 0.033 0.002 PHE U 440 TYR 0.034 0.002 TYR C 20 ARG 0.008 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 949 time to evaluate : 6.362 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: R 10 MET cc_start: 0.6855 (mmm) cc_final: 0.6490 (tpp) REVERT: R 61 MET cc_start: 0.8819 (tpp) cc_final: 0.8472 (mmt) REVERT: R 423 MET cc_start: 0.8721 (mtm) cc_final: 0.7995 (ptm) REVERT: R 717 MET cc_start: 0.8112 (tmm) cc_final: 0.7852 (tmm) REVERT: O 319 MET cc_start: 0.6435 (mmm) cc_final: 0.6012 (mmm) REVERT: O 369 TYR cc_start: 0.8228 (p90) cc_final: 0.7926 (p90) REVERT: J 184 TYR cc_start: 0.8965 (m-80) cc_final: 0.8764 (m-80) REVERT: M 66 ARG cc_start: 0.7109 (tmm160) cc_final: 0.6883 (tmt170) REVERT: H 24 ASN cc_start: 0.9072 (m-40) cc_final: 0.8215 (m-40) REVERT: H 28 GLU cc_start: 0.8444 (mm-30) cc_final: 0.7989 (mm-30) REVERT: K 27 LYS cc_start: 0.9277 (ttmt) cc_final: 0.8975 (mtpp) REVERT: K 59 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7385 (tp30) REVERT: K 75 LYS cc_start: 0.8782 (ttpt) cc_final: 0.8555 (pttm) REVERT: K 93 ASP cc_start: 0.8133 (t0) cc_final: 0.7537 (t0) REVERT: K 97 ASP cc_start: 0.8177 (m-30) cc_final: 0.7665 (m-30) REVERT: S 19 PHE cc_start: 0.8216 (t80) cc_final: 0.7848 (t80) REVERT: T 88 LYS cc_start: 0.8855 (mmmt) cc_final: 0.7942 (mttt) REVERT: B 347 MET cc_start: 0.8707 (tpp) cc_final: 0.8183 (tpp) REVERT: B 393 LYS cc_start: 0.9117 (ttmt) cc_final: 0.8897 (ttmt) REVERT: B 540 MET cc_start: 0.7158 (mtp) cc_final: 0.6881 (mtp) REVERT: C 283 GLU cc_start: 0.7000 (mp0) cc_final: 0.6766 (mp0) REVERT: C 306 MET cc_start: 0.8932 (tpt) cc_final: 0.8608 (tpt) REVERT: C 360 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7548 (mt-10) REVERT: C 487 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8006 (tm-30) REVERT: E 180 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8545 (mtm) REVERT: E 456 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7501 (tm-30) REVERT: F 97 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8542 (tt0) REVERT: F 215 LYS cc_start: 0.2632 (pptt) cc_final: 0.2020 (pptt) REVERT: F 242 ARG cc_start: 0.7941 (tpp80) cc_final: 0.7589 (ttm-80) REVERT: F 359 ASP cc_start: 0.7701 (t0) cc_final: 0.7416 (t0) REVERT: F 456 GLN cc_start: 0.8209 (tp-100) cc_final: 0.7891 (tt0) REVERT: F 474 PHE cc_start: 0.5858 (t80) cc_final: 0.5616 (t80) REVERT: D 212 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8894 (mp) REVERT: D 360 ASP cc_start: 0.8195 (t0) cc_final: 0.7742 (p0) REVERT: Y 61 ARG cc_start: 0.8417 (mmm-85) cc_final: 0.8135 (tpp-160) REVERT: Y 74 CYS cc_start: 0.7446 (m) cc_final: 0.7104 (m) REVERT: Z 83 ARG cc_start: 0.7907 (ttm-80) cc_final: 0.7630 (mtm-85) REVERT: X 153 ARG cc_start: 0.7432 (tpp80) cc_final: 0.7177 (tpp80) REVERT: X 197 TYR cc_start: 0.8242 (m-80) cc_final: 0.7920 (t80) REVERT: G 186 TYR cc_start: 0.8729 (t80) cc_final: 0.8375 (t80) REVERT: G 206 GLN cc_start: 0.8834 (tp40) cc_final: 0.8416 (tp40) REVERT: N 29 ASN cc_start: 0.8533 (t0) cc_final: 0.8247 (t0) REVERT: N 30 LYS cc_start: 0.9378 (ptpp) cc_final: 0.8909 (mmtm) REVERT: N 31 ASN cc_start: 0.8586 (p0) cc_final: 0.7789 (p0) REVERT: N 32 ARG cc_start: 0.9086 (mmm160) cc_final: 0.8684 (tpp-160) REVERT: N 33 HIS cc_start: 0.8677 (m170) cc_final: 0.8350 (m90) REVERT: N 46 ASN cc_start: 0.8936 (t0) cc_final: 0.8632 (t0) REVERT: N 50 ASP cc_start: 0.8861 (m-30) cc_final: 0.8436 (m-30) REVERT: N 107 ARG cc_start: 0.8275 (ttp-110) cc_final: 0.7942 (ttp80) REVERT: U 293 GLN cc_start: 0.9023 (mp10) cc_final: 0.8451 (mp-120) REVERT: U 373 TYR cc_start: 0.8472 (m-10) cc_final: 0.8228 (m-80) REVERT: V 302 GLU cc_start: 0.7666 (pm20) cc_final: 0.7431 (pm20) REVERT: 0 103 TYR cc_start: 0.8580 (m-10) cc_final: 0.8186 (m-80) REVERT: 3 47 MET cc_start: 0.8275 (pmm) cc_final: 0.8073 (pmm) REVERT: 3 139 GLU cc_start: 0.8085 (tp30) cc_final: 0.7521 (tp30) REVERT: 4 54 LYS cc_start: 0.8663 (mttt) cc_final: 0.8242 (mptt) REVERT: 5 44 MET cc_start: 0.5351 (tpp) cc_final: 0.5136 (mmt) REVERT: 7 139 GLU cc_start: 0.8365 (tp30) cc_final: 0.8142 (tp30) REVERT: 9 53 MET cc_start: 0.8193 (mmt) cc_final: 0.7380 (ptt) REVERT: 9 115 ASP cc_start: 0.8157 (t0) cc_final: 0.7886 (t0) REVERT: Q 6 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7986 (pt0) REVERT: Q 150 LEU cc_start: 0.8566 (tp) cc_final: 0.8155 (tt) REVERT: Q 208 MET cc_start: 0.8598 (mmm) cc_final: 0.8211 (tpp) REVERT: Q 236 ASP cc_start: 0.8079 (t0) cc_final: 0.7520 (t0) REVERT: P 30 LYS cc_start: 0.9033 (mmmm) cc_final: 0.8756 (mmmt) REVERT: P 81 MET cc_start: 0.8140 (ptp) cc_final: 0.7742 (ptp) REVERT: P 92 TYR cc_start: 0.8223 (m-80) cc_final: 0.7507 (m-80) REVERT: P 101 LEU cc_start: 0.8891 (mt) cc_final: 0.8603 (tt) REVERT: P 140 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8548 (tmm) REVERT: P 151 TRP cc_start: 0.6033 (OUTLIER) cc_final: 0.5663 (m-90) outliers start: 271 outliers final: 204 residues processed: 1141 average time/residue: 0.6526 time to fit residues: 1297.2810 Evaluate side-chains 1134 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 924 time to evaluate : 6.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 GLU Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 120 ARG Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain R residue 333 ILE Chi-restraints excluded: chain R residue 363 THR Chi-restraints excluded: chain R residue 488 ASN Chi-restraints excluded: chain R residue 497 ASN Chi-restraints excluded: chain R residue 518 ILE Chi-restraints excluded: chain R residue 530 THR Chi-restraints excluded: chain R residue 532 LEU Chi-restraints excluded: chain R residue 594 TRP Chi-restraints excluded: chain R residue 757 THR Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 118 LEU Chi-restraints excluded: chain O residue 123 GLU Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 324 ASN Chi-restraints excluded: chain O residue 363 GLN Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain L residue 69 CYS Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 88 PHE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain T residue 80 ILE Chi-restraints excluded: chain T residue 105 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 112 CYS Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain Y residue 35 THR Chi-restraints excluded: chain Y residue 98 ILE Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 188 MET Chi-restraints excluded: chain Y residue 204 VAL Chi-restraints excluded: chain Y residue 246 LEU Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain Y residue 260 LEU Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain Z residue 99 SER Chi-restraints excluded: chain Z residue 179 PHE Chi-restraints excluded: chain Z residue 229 MET Chi-restraints excluded: chain Z residue 263 ILE Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain U residue 289 THR Chi-restraints excluded: chain U residue 304 ASP Chi-restraints excluded: chain U residue 324 LYS Chi-restraints excluded: chain U residue 370 HIS Chi-restraints excluded: chain U residue 385 VAL Chi-restraints excluded: chain U residue 408 MET Chi-restraints excluded: chain U residue 430 LEU Chi-restraints excluded: chain U residue 441 THR Chi-restraints excluded: chain U residue 447 ILE Chi-restraints excluded: chain U residue 454 ASP Chi-restraints excluded: chain U residue 455 ARG Chi-restraints excluded: chain V residue 305 VAL Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 69 ILE Chi-restraints excluded: chain 0 residue 98 GLU Chi-restraints excluded: chain 0 residue 151 CYS Chi-restraints excluded: chain 0 residue 181 ILE Chi-restraints excluded: chain 0 residue 192 ILE Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 102 SER Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 2 residue 10 TYR Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 2 residue 44 MET Chi-restraints excluded: chain 2 residue 53 MET Chi-restraints excluded: chain 2 residue 83 ASP Chi-restraints excluded: chain 2 residue 112 ILE Chi-restraints excluded: chain 2 residue 141 LEU Chi-restraints excluded: chain 2 residue 154 THR Chi-restraints excluded: chain 3 residue 74 VAL Chi-restraints excluded: chain 3 residue 78 ASN Chi-restraints excluded: chain 3 residue 81 ASN Chi-restraints excluded: chain 3 residue 110 ILE Chi-restraints excluded: chain 3 residue 140 VAL Chi-restraints excluded: chain 4 residue 34 THR Chi-restraints excluded: chain 4 residue 60 VAL Chi-restraints excluded: chain 4 residue 121 THR Chi-restraints excluded: chain 4 residue 127 LEU Chi-restraints excluded: chain 5 residue 47 MET Chi-restraints excluded: chain 5 residue 110 ILE Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 98 SER Chi-restraints excluded: chain 6 residue 102 SER Chi-restraints excluded: chain 6 residue 110 ILE Chi-restraints excluded: chain 6 residue 121 THR Chi-restraints excluded: chain 6 residue 129 VAL Chi-restraints excluded: chain 6 residue 150 LEU Chi-restraints excluded: chain 7 residue 115 ASP Chi-restraints excluded: chain 7 residue 118 VAL Chi-restraints excluded: chain 8 residue 9 GLU Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain 8 residue 92 GLN Chi-restraints excluded: chain 8 residue 115 ASP Chi-restraints excluded: chain 9 residue 104 LEU Chi-restraints excluded: chain 9 residue 121 THR Chi-restraints excluded: chain 9 residue 135 LEU Chi-restraints excluded: chain Q residue 6 GLU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain Q residue 174 ASP Chi-restraints excluded: chain Q residue 321 LEU Chi-restraints excluded: chain Q residue 336 ILE Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 151 TRP Chi-restraints excluded: chain P residue 233 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 848 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 501 optimal weight: 3.9990 chunk 642 optimal weight: 8.9990 chunk 498 optimal weight: 6.9990 chunk 741 optimal weight: 3.9990 chunk 491 optimal weight: 10.0000 chunk 877 optimal weight: 0.0270 chunk 548 optimal weight: 6.9990 chunk 534 optimal weight: 4.9990 chunk 404 optimal weight: 5.9990 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 HIS ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN F 421 GLN Y 59 ASN ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 338 HIS ** Q 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 84 HIS ** P 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 73651 Z= 0.283 Angle : 0.626 13.258 99547 Z= 0.320 Chirality : 0.042 0.218 11312 Planarity : 0.004 0.078 12746 Dihedral : 5.066 74.814 10151 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.95 % Favored : 94.01 % Rotamer: Outliers : 3.31 % Allowed : 20.12 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.62 (0.09), residues: 9131 helix: 0.95 (0.07), residues: 5184 sheet: -1.78 (0.19), residues: 724 loop : -2.38 (0.10), residues: 3223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP S 52 HIS 0.006 0.001 HIS P 139 PHE 0.028 0.001 PHE B 203 TYR 0.034 0.001 TYR O 75 ARG 0.007 0.000 ARG Y 153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 973 time to evaluate : 6.259 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: R 10 MET cc_start: 0.6890 (mmm) cc_final: 0.6628 (tpp) REVERT: R 61 MET cc_start: 0.8821 (tpp) cc_final: 0.8479 (mmt) REVERT: R 423 MET cc_start: 0.8694 (mtm) cc_final: 0.7972 (ptm) REVERT: R 627 MET cc_start: 0.8564 (mmm) cc_final: 0.8028 (mmt) REVERT: R 717 MET cc_start: 0.8126 (tmm) cc_final: 0.7830 (tmm) REVERT: O 258 MET cc_start: 0.4514 (mtp) cc_final: 0.4031 (mtm) REVERT: O 319 MET cc_start: 0.6049 (mmm) cc_final: 0.5691 (mmm) REVERT: O 369 TYR cc_start: 0.8210 (p90) cc_final: 0.7931 (p90) REVERT: M 66 ARG cc_start: 0.7085 (tmm160) cc_final: 0.6849 (tmt170) REVERT: H 24 ASN cc_start: 0.9049 (m-40) cc_final: 0.8200 (m-40) REVERT: H 28 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7974 (mm-30) REVERT: K 59 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7231 (tp30) REVERT: K 75 LYS cc_start: 0.8775 (ttpt) cc_final: 0.8544 (pttm) REVERT: K 93 ASP cc_start: 0.8092 (t0) cc_final: 0.7494 (t0) REVERT: K 97 ASP cc_start: 0.8122 (m-30) cc_final: 0.7617 (m-30) REVERT: S 19 PHE cc_start: 0.8196 (t80) cc_final: 0.7807 (t80) REVERT: T 71 PHE cc_start: 0.6876 (OUTLIER) cc_final: 0.5896 (m-80) REVERT: B 347 MET cc_start: 0.8717 (tpp) cc_final: 0.8143 (tpp) REVERT: B 393 LYS cc_start: 0.9100 (ttmt) cc_final: 0.8849 (ttmt) REVERT: B 540 MET cc_start: 0.7125 (mtp) cc_final: 0.6859 (mtp) REVERT: C 283 GLU cc_start: 0.6971 (mp0) cc_final: 0.6730 (mp0) REVERT: C 306 MET cc_start: 0.8870 (tpt) cc_final: 0.8618 (tpt) REVERT: C 360 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7555 (mt-10) REVERT: C 487 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7971 (tm-30) REVERT: A 18 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7903 (t80) REVERT: A 283 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8027 (mm-30) REVERT: E 180 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8519 (mtm) REVERT: E 456 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7490 (tm-30) REVERT: F 170 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8376 (tt) REVERT: F 215 LYS cc_start: 0.2560 (pptt) cc_final: 0.1945 (pptt) REVERT: F 242 ARG cc_start: 0.7934 (tpp80) cc_final: 0.7597 (ttm-80) REVERT: F 359 ASP cc_start: 0.7680 (t0) cc_final: 0.7384 (t0) REVERT: F 456 GLN cc_start: 0.8162 (tp-100) cc_final: 0.7887 (tt0) REVERT: F 474 PHE cc_start: 0.5792 (t80) cc_final: 0.5560 (t80) REVERT: D 212 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8883 (mp) REVERT: D 360 ASP cc_start: 0.8230 (t0) cc_final: 0.7809 (p0) REVERT: D 457 LYS cc_start: 0.9065 (mttm) cc_final: 0.8779 (mttp) REVERT: Y 33 MET cc_start: 0.8091 (tpp) cc_final: 0.7814 (tpt) REVERT: Y 61 ARG cc_start: 0.8391 (mmm-85) cc_final: 0.8141 (tpp-160) REVERT: Y 74 CYS cc_start: 0.7353 (m) cc_final: 0.7003 (m) REVERT: Z 83 ARG cc_start: 0.7847 (ttm-80) cc_final: 0.7560 (mtm-85) REVERT: X 151 PHE cc_start: 0.7246 (m-10) cc_final: 0.6909 (m-80) REVERT: X 153 ARG cc_start: 0.7544 (tpp80) cc_final: 0.7296 (tpp80) REVERT: X 197 TYR cc_start: 0.8211 (m-80) cc_final: 0.7973 (t80) REVERT: G 186 TYR cc_start: 0.8660 (t80) cc_final: 0.8301 (t80) REVERT: G 206 GLN cc_start: 0.8815 (tp40) cc_final: 0.8327 (tp40) REVERT: N 29 ASN cc_start: 0.8500 (t0) cc_final: 0.8215 (t0) REVERT: N 30 LYS cc_start: 0.9379 (ptpp) cc_final: 0.8924 (mmtm) REVERT: N 31 ASN cc_start: 0.8548 (p0) cc_final: 0.7773 (p0) REVERT: N 32 ARG cc_start: 0.9015 (mmm160) cc_final: 0.8610 (tpp-160) REVERT: N 33 HIS cc_start: 0.8661 (m170) cc_final: 0.8355 (m90) REVERT: N 46 ASN cc_start: 0.8986 (t0) cc_final: 0.8743 (t0) REVERT: N 47 GLU cc_start: 0.9239 (tp30) cc_final: 0.8776 (pt0) REVERT: N 50 ASP cc_start: 0.8843 (m-30) cc_final: 0.8513 (m-30) REVERT: N 73 MET cc_start: 0.9204 (mtm) cc_final: 0.8830 (ptp) REVERT: N 107 ARG cc_start: 0.8271 (ttp-110) cc_final: 0.7956 (ttp80) REVERT: U 293 GLN cc_start: 0.9047 (mp10) cc_final: 0.8743 (mp10) REVERT: U 373 TYR cc_start: 0.8435 (m-10) cc_final: 0.8200 (m-80) REVERT: V 302 GLU cc_start: 0.7593 (pm20) cc_final: 0.7369 (pm20) REVERT: 0 103 TYR cc_start: 0.8538 (m-10) cc_final: 0.8149 (m-80) REVERT: 1 97 LEU cc_start: 0.8941 (tt) cc_final: 0.8668 (tp) REVERT: 3 139 GLU cc_start: 0.8031 (tp30) cc_final: 0.7434 (tm-30) REVERT: 4 54 LYS cc_start: 0.8408 (mttt) cc_final: 0.8174 (mptt) REVERT: 5 44 MET cc_start: 0.5372 (tpp) cc_final: 0.5172 (mmt) REVERT: 6 155 LYS cc_start: 0.7280 (tttm) cc_final: 0.7039 (ttmm) REVERT: 7 10 TYR cc_start: 0.4567 (m-80) cc_final: 0.3305 (m-80) REVERT: 7 139 GLU cc_start: 0.8337 (tp30) cc_final: 0.8113 (tp30) REVERT: 9 53 MET cc_start: 0.8134 (mmt) cc_final: 0.7418 (ptt) REVERT: Q 6 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7865 (pt0) REVERT: Q 150 LEU cc_start: 0.8565 (tp) cc_final: 0.8227 (tt) REVERT: Q 208 MET cc_start: 0.8508 (mmm) cc_final: 0.8010 (tpp) REVERT: Q 236 ASP cc_start: 0.8036 (t0) cc_final: 0.7498 (t0) REVERT: P 30 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8756 (mmmt) REVERT: P 92 TYR cc_start: 0.8213 (m-80) cc_final: 0.7494 (m-80) REVERT: P 101 LEU cc_start: 0.8864 (mt) cc_final: 0.8554 (tt) REVERT: P 140 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8577 (tmm) REVERT: P 151 TRP cc_start: 0.5772 (OUTLIER) cc_final: 0.5433 (m-90) REVERT: P 331 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8882 (mm) outliers start: 258 outliers final: 195 residues processed: 1148 average time/residue: 0.6390 time to fit residues: 1274.0638 Evaluate side-chains 1140 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 936 time to evaluate : 6.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 GLU Chi-restraints excluded: chain R residue 120 ARG Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain R residue 333 ILE Chi-restraints excluded: chain R residue 363 THR Chi-restraints excluded: chain R residue 488 ASN Chi-restraints excluded: chain R residue 497 ASN Chi-restraints excluded: chain R residue 518 ILE Chi-restraints excluded: chain R residue 529 LEU Chi-restraints excluded: chain R residue 530 THR Chi-restraints excluded: chain R residue 594 TRP Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 118 LEU Chi-restraints excluded: chain O residue 123 GLU Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 324 ASN Chi-restraints excluded: chain O residue 341 HIS Chi-restraints excluded: chain O residue 363 GLN Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain L residue 69 CYS Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 88 PHE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain T residue 55 ILE Chi-restraints excluded: chain T residue 71 PHE Chi-restraints excluded: chain T residue 80 ILE Chi-restraints excluded: chain T residue 105 SER Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 112 CYS Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain Y residue 35 THR Chi-restraints excluded: chain Y residue 59 ASN Chi-restraints excluded: chain Y residue 98 ILE Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 204 VAL Chi-restraints excluded: chain Y residue 246 LEU Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain Z residue 99 SER Chi-restraints excluded: chain Z residue 179 PHE Chi-restraints excluded: chain Z residue 194 ASP Chi-restraints excluded: chain Z residue 229 MET Chi-restraints excluded: chain Z residue 263 ILE Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain U residue 289 THR Chi-restraints excluded: chain U residue 304 ASP Chi-restraints excluded: chain U residue 324 LYS Chi-restraints excluded: chain U residue 370 HIS Chi-restraints excluded: chain U residue 385 VAL Chi-restraints excluded: chain U residue 426 ILE Chi-restraints excluded: chain U residue 430 LEU Chi-restraints excluded: chain U residue 441 THR Chi-restraints excluded: chain U residue 447 ILE Chi-restraints excluded: chain U residue 454 ASP Chi-restraints excluded: chain U residue 455 ARG Chi-restraints excluded: chain V residue 305 VAL Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 69 ILE Chi-restraints excluded: chain 0 residue 98 GLU Chi-restraints excluded: chain 0 residue 147 SER Chi-restraints excluded: chain 0 residue 151 CYS Chi-restraints excluded: chain 0 residue 181 ILE Chi-restraints excluded: chain 1 residue 102 SER Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 1 residue 146 LEU Chi-restraints excluded: chain 2 residue 10 TYR Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 2 residue 44 MET Chi-restraints excluded: chain 2 residue 83 ASP Chi-restraints excluded: chain 2 residue 112 ILE Chi-restraints excluded: chain 2 residue 141 LEU Chi-restraints excluded: chain 3 residue 78 ASN Chi-restraints excluded: chain 3 residue 81 ASN Chi-restraints excluded: chain 3 residue 110 ILE Chi-restraints excluded: chain 3 residue 140 VAL Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 4 residue 34 THR Chi-restraints excluded: chain 4 residue 36 LYS Chi-restraints excluded: chain 4 residue 110 ILE Chi-restraints excluded: chain 4 residue 121 THR Chi-restraints excluded: chain 4 residue 127 LEU Chi-restraints excluded: chain 5 residue 47 MET Chi-restraints excluded: chain 5 residue 110 ILE Chi-restraints excluded: chain 5 residue 134 ILE Chi-restraints excluded: chain 6 residue 28 LEU Chi-restraints excluded: chain 6 residue 102 SER Chi-restraints excluded: chain 6 residue 110 ILE Chi-restraints excluded: chain 6 residue 118 VAL Chi-restraints excluded: chain 6 residue 129 VAL Chi-restraints excluded: chain 6 residue 150 LEU Chi-restraints excluded: chain 7 residue 115 ASP Chi-restraints excluded: chain 7 residue 118 VAL Chi-restraints excluded: chain 8 residue 9 GLU Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain 8 residue 92 GLN Chi-restraints excluded: chain 8 residue 115 ASP Chi-restraints excluded: chain 9 residue 26 SER Chi-restraints excluded: chain 9 residue 104 LEU Chi-restraints excluded: chain 9 residue 135 LEU Chi-restraints excluded: chain Q residue 6 GLU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain Q residue 174 ASP Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 321 LEU Chi-restraints excluded: chain Q residue 336 ILE Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 126 PHE Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 151 TRP Chi-restraints excluded: chain P residue 293 LEU Chi-restraints excluded: chain P residue 331 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 542 optimal weight: 0.0970 chunk 350 optimal weight: 8.9990 chunk 523 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 557 optimal weight: 8.9990 chunk 597 optimal weight: 10.0000 chunk 433 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 689 optimal weight: 0.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 ASN ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 GLN F 97 GLN F 421 GLN D 421 GLN Y 59 ASN ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN ** N 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 84 HIS ** P 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 73651 Z= 0.251 Angle : 0.617 13.241 99547 Z= 0.314 Chirality : 0.042 0.231 11312 Planarity : 0.004 0.078 12746 Dihedral : 4.945 74.803 10151 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.92 % Favored : 94.03 % Rotamer: Outliers : 3.03 % Allowed : 20.83 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: -0.49 (0.09), residues: 9131 helix: 1.04 (0.07), residues: 5196 sheet: -1.74 (0.19), residues: 726 loop : -2.30 (0.10), residues: 3209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP S 52 HIS 0.011 0.001 HIS I 14 PHE 0.022 0.001 PHE P 111 TYR 0.034 0.001 TYR Y 60 ARG 0.017 0.000 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1214 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 978 time to evaluate : 6.367 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: R 10 MET cc_start: 0.7000 (mmm) cc_final: 0.6694 (tpp) REVERT: R 61 MET cc_start: 0.8832 (tpp) cc_final: 0.8505 (mmt) REVERT: R 423 MET cc_start: 0.8654 (mtm) cc_final: 0.8230 (mtp) REVERT: R 627 MET cc_start: 0.8579 (mmm) cc_final: 0.8084 (mmt) REVERT: R 717 MET cc_start: 0.8132 (tmm) cc_final: 0.7801 (tmm) REVERT: O 107 TRP cc_start: 0.7446 (t-100) cc_final: 0.6986 (t-100) REVERT: O 258 MET cc_start: 0.4535 (mtp) cc_final: 0.3944 (mtm) REVERT: O 319 MET cc_start: 0.5951 (mmm) cc_final: 0.5489 (mmm) REVERT: O 369 TYR cc_start: 0.8296 (p90) cc_final: 0.7936 (p90) REVERT: J 50 ARG cc_start: 0.8638 (ttt180) cc_final: 0.8361 (tpp-160) REVERT: M 66 ARG cc_start: 0.7156 (tmm160) cc_final: 0.6916 (tmt170) REVERT: H 24 ASN cc_start: 0.9050 (m-40) cc_final: 0.8202 (m-40) REVERT: H 28 GLU cc_start: 0.8486 (mm-30) cc_final: 0.7984 (mm-30) REVERT: H 39 ASN cc_start: 0.9192 (m110) cc_final: 0.8689 (m110) REVERT: K 34 LYS cc_start: 0.9141 (mmtp) cc_final: 0.8444 (mttt) REVERT: K 75 LYS cc_start: 0.8771 (ttpt) cc_final: 0.8538 (pttm) REVERT: K 93 ASP cc_start: 0.8123 (t0) cc_final: 0.7529 (t0) REVERT: K 97 ASP cc_start: 0.8127 (m-30) cc_final: 0.7600 (m-30) REVERT: S 19 PHE cc_start: 0.8237 (t80) cc_final: 0.7823 (t80) REVERT: S 30 LYS cc_start: 0.6051 (OUTLIER) cc_final: 0.5709 (ttpt) REVERT: T 71 PHE cc_start: 0.6988 (OUTLIER) cc_final: 0.5731 (m-80) REVERT: B 347 MET cc_start: 0.8722 (tpp) cc_final: 0.8154 (tpp) REVERT: B 393 LYS cc_start: 0.9087 (ttmt) cc_final: 0.8868 (ttmt) REVERT: B 540 MET cc_start: 0.7115 (mtp) cc_final: 0.6845 (mtp) REVERT: C 306 MET cc_start: 0.8803 (tpt) cc_final: 0.8488 (tpt) REVERT: C 360 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7439 (mt-10) REVERT: C 487 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7968 (tm-30) REVERT: A 18 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7911 (t80) REVERT: E 161 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8542 (tp40) REVERT: E 456 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7496 (tm-30) REVERT: F 170 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8367 (tt) REVERT: F 215 LYS cc_start: 0.2636 (pptt) cc_final: 0.2094 (pptt) REVERT: F 242 ARG cc_start: 0.7974 (tpp80) cc_final: 0.7714 (ttm-80) REVERT: F 359 ASP cc_start: 0.7661 (t0) cc_final: 0.7370 (t0) REVERT: F 456 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7882 (tt0) REVERT: F 474 PHE cc_start: 0.5741 (t80) cc_final: 0.5515 (t80) REVERT: D 212 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8878 (mp) REVERT: D 360 ASP cc_start: 0.8193 (t0) cc_final: 0.7776 (p0) REVERT: D 457 LYS cc_start: 0.9058 (mttm) cc_final: 0.8768 (mttp) REVERT: Y 33 MET cc_start: 0.8148 (tpp) cc_final: 0.7892 (tpt) REVERT: Y 61 ARG cc_start: 0.8461 (mmm-85) cc_final: 0.7998 (tpp80) REVERT: Y 74 CYS cc_start: 0.7505 (m) cc_final: 0.7142 (m) REVERT: X 151 PHE cc_start: 0.7195 (m-10) cc_final: 0.6875 (m-80) REVERT: X 153 ARG cc_start: 0.7532 (tpp80) cc_final: 0.7304 (tpp80) REVERT: X 197 TYR cc_start: 0.8211 (m-80) cc_final: 0.7977 (t80) REVERT: G 186 TYR cc_start: 0.8632 (t80) cc_final: 0.8276 (t80) REVERT: N 29 ASN cc_start: 0.8494 (t0) cc_final: 0.8212 (t0) REVERT: N 30 LYS cc_start: 0.9368 (ptpp) cc_final: 0.8909 (mmtm) REVERT: N 31 ASN cc_start: 0.8538 (p0) cc_final: 0.7765 (p0) REVERT: N 32 ARG cc_start: 0.8987 (mmm160) cc_final: 0.8581 (tpp-160) REVERT: N 33 HIS cc_start: 0.8642 (m170) cc_final: 0.8328 (m90) REVERT: N 46 ASN cc_start: 0.9014 (t0) cc_final: 0.8769 (t0) REVERT: N 47 GLU cc_start: 0.9270 (tp30) cc_final: 0.8812 (pt0) REVERT: N 73 MET cc_start: 0.9188 (mtm) cc_final: 0.8827 (ttm) REVERT: U 293 GLN cc_start: 0.9046 (mp10) cc_final: 0.8754 (mp10) REVERT: U 373 TYR cc_start: 0.8399 (m-10) cc_final: 0.8161 (m-80) REVERT: V 302 GLU cc_start: 0.7559 (pm20) cc_final: 0.7337 (pm20) REVERT: V 314 MET cc_start: 0.8613 (tpp) cc_final: 0.8335 (mmm) REVERT: 0 103 TYR cc_start: 0.8514 (m-10) cc_final: 0.8120 (m-80) REVERT: 1 97 LEU cc_start: 0.8907 (tt) cc_final: 0.8646 (tp) REVERT: 3 139 GLU cc_start: 0.8002 (tp30) cc_final: 0.7414 (tm-30) REVERT: 5 44 MET cc_start: 0.5430 (tpp) cc_final: 0.5162 (mmt) REVERT: 6 135 LEU cc_start: 0.8877 (mp) cc_final: 0.8243 (mp) REVERT: 7 10 TYR cc_start: 0.4575 (m-80) cc_final: 0.3423 (m-80) REVERT: 7 139 GLU cc_start: 0.8385 (tp30) cc_final: 0.8140 (tp30) REVERT: 9 53 MET cc_start: 0.8121 (mmt) cc_final: 0.7425 (ptt) REVERT: Q 6 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7794 (pt0) REVERT: Q 150 LEU cc_start: 0.8600 (tp) cc_final: 0.8278 (tt) REVERT: Q 208 MET cc_start: 0.8494 (mmm) cc_final: 0.8047 (tpp) REVERT: Q 236 ASP cc_start: 0.8059 (t0) cc_final: 0.7517 (t0) REVERT: P 30 LYS cc_start: 0.9044 (mmmm) cc_final: 0.8769 (mmmt) REVERT: P 92 TYR cc_start: 0.8220 (m-80) cc_final: 0.7479 (m-80) REVERT: P 101 LEU cc_start: 0.8854 (mt) cc_final: 0.8546 (tt) REVERT: P 140 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8563 (tmm) REVERT: P 151 TRP cc_start: 0.5874 (OUTLIER) cc_final: 0.5495 (m-90) REVERT: P 205 LEU cc_start: 0.9572 (tt) cc_final: 0.9324 (mm) REVERT: P 331 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8888 (mm) REVERT: P 398 LEU cc_start: 0.8736 (tp) cc_final: 0.8490 (tp) outliers start: 236 outliers final: 200 residues processed: 1144 average time/residue: 0.6518 time to fit residues: 1303.1328 Evaluate side-chains 1151 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 941 time to evaluate : 6.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 GLU Chi-restraints excluded: chain R residue 120 ARG Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain R residue 363 THR Chi-restraints excluded: chain R residue 488 ASN Chi-restraints excluded: chain R residue 497 ASN Chi-restraints excluded: chain R residue 518 ILE Chi-restraints excluded: chain R residue 529 LEU Chi-restraints excluded: chain R residue 530 THR Chi-restraints excluded: chain R residue 532 LEU Chi-restraints excluded: chain R residue 594 TRP Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 118 LEU Chi-restraints excluded: chain O residue 123 GLU Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 324 ASN Chi-restraints excluded: chain O residue 341 HIS Chi-restraints excluded: chain O residue 363 GLN Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 226 ASP Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain L residue 69 CYS Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 88 PHE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain K residue 32 ARG Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain T residue 55 ILE Chi-restraints excluded: chain T residue 71 PHE Chi-restraints excluded: chain T residue 80 ILE Chi-restraints excluded: chain T residue 105 SER Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 112 CYS Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain Y residue 35 THR Chi-restraints excluded: chain Y residue 59 ASN Chi-restraints excluded: chain Y residue 98 ILE Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 155 MET Chi-restraints excluded: chain Y residue 204 VAL Chi-restraints excluded: chain Y residue 246 LEU Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain Y residue 260 LEU Chi-restraints excluded: chain Z residue 99 SER Chi-restraints excluded: chain Z residue 179 PHE Chi-restraints excluded: chain Z residue 194 ASP Chi-restraints excluded: chain Z residue 229 MET Chi-restraints excluded: chain Z residue 263 ILE Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain U residue 289 THR Chi-restraints excluded: chain U residue 304 ASP Chi-restraints excluded: chain U residue 324 LYS Chi-restraints excluded: chain U residue 370 HIS Chi-restraints excluded: chain U residue 385 VAL Chi-restraints excluded: chain U residue 430 LEU Chi-restraints excluded: chain U residue 441 THR Chi-restraints excluded: chain U residue 447 ILE Chi-restraints excluded: chain U residue 454 ASP Chi-restraints excluded: chain U residue 455 ARG Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 36 ASP Chi-restraints excluded: chain 0 residue 69 ILE Chi-restraints excluded: chain 0 residue 98 GLU Chi-restraints excluded: chain 0 residue 147 SER Chi-restraints excluded: chain 0 residue 151 CYS Chi-restraints excluded: chain 0 residue 181 ILE Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 102 SER Chi-restraints excluded: chain 1 residue 121 THR Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 1 residue 146 LEU Chi-restraints excluded: chain 2 residue 10 TYR Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 2 residue 44 MET Chi-restraints excluded: chain 2 residue 53 MET Chi-restraints excluded: chain 2 residue 83 ASP Chi-restraints excluded: chain 2 residue 112 ILE Chi-restraints excluded: chain 2 residue 141 LEU Chi-restraints excluded: chain 3 residue 78 ASN Chi-restraints excluded: chain 3 residue 81 ASN Chi-restraints excluded: chain 3 residue 110 ILE Chi-restraints excluded: chain 3 residue 140 VAL Chi-restraints excluded: chain 4 residue 34 THR Chi-restraints excluded: chain 4 residue 36 LYS Chi-restraints excluded: chain 4 residue 110 ILE Chi-restraints excluded: chain 4 residue 121 THR Chi-restraints excluded: chain 4 residue 127 LEU Chi-restraints excluded: chain 5 residue 110 ILE Chi-restraints excluded: chain 5 residue 134 ILE Chi-restraints excluded: chain 6 residue 28 LEU Chi-restraints excluded: chain 6 residue 98 SER Chi-restraints excluded: chain 6 residue 102 SER Chi-restraints excluded: chain 6 residue 110 ILE Chi-restraints excluded: chain 6 residue 118 VAL Chi-restraints excluded: chain 6 residue 121 THR Chi-restraints excluded: chain 6 residue 129 VAL Chi-restraints excluded: chain 7 residue 115 ASP Chi-restraints excluded: chain 7 residue 118 VAL Chi-restraints excluded: chain 8 residue 9 GLU Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain 8 residue 92 GLN Chi-restraints excluded: chain 8 residue 115 ASP Chi-restraints excluded: chain 9 residue 26 SER Chi-restraints excluded: chain 9 residue 135 LEU Chi-restraints excluded: chain Q residue 6 GLU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain Q residue 174 ASP Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 321 LEU Chi-restraints excluded: chain Q residue 336 ILE Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 126 PHE Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 151 TRP Chi-restraints excluded: chain P residue 293 LEU Chi-restraints excluded: chain P residue 331 ILE Chi-restraints excluded: chain P residue 391 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 797 optimal weight: 0.8980 chunk 840 optimal weight: 6.9990 chunk 766 optimal weight: 7.9990 chunk 817 optimal weight: 0.7980 chunk 491 optimal weight: 10.0000 chunk 356 optimal weight: 4.9990 chunk 641 optimal weight: 0.9990 chunk 250 optimal weight: 9.9990 chunk 738 optimal weight: 8.9990 chunk 773 optimal weight: 0.0370 chunk 814 optimal weight: 7.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 4 HIS ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN D 421 GLN ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 84 HIS ** P 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 73651 Z= 0.188 Angle : 0.606 13.499 99547 Z= 0.306 Chirality : 0.041 0.259 11312 Planarity : 0.004 0.079 12746 Dihedral : 4.792 75.057 10151 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.28 % Favored : 94.69 % Rotamer: Outliers : 2.46 % Allowed : 21.60 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: -0.30 (0.09), residues: 9131 helix: 1.18 (0.07), residues: 5182 sheet: -1.67 (0.19), residues: 726 loop : -2.18 (0.10), residues: 3223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP S 52 HIS 0.007 0.001 HIS I 14 PHE 0.027 0.001 PHE Z 213 TYR 0.032 0.001 TYR 0 8 ARG 0.014 0.000 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 993 time to evaluate : 6.335 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: R 10 MET cc_start: 0.6894 (mmm) cc_final: 0.6616 (tpp) REVERT: R 61 MET cc_start: 0.8838 (tpp) cc_final: 0.8521 (mmt) REVERT: R 423 MET cc_start: 0.8635 (mtm) cc_final: 0.8218 (mtp) REVERT: R 484 MET cc_start: 0.4342 (mtp) cc_final: 0.3599 (mpp) REVERT: R 627 MET cc_start: 0.8540 (mmm) cc_final: 0.8077 (mmt) REVERT: R 717 MET cc_start: 0.8130 (tmm) cc_final: 0.7793 (tmm) REVERT: O 92 LEU cc_start: 0.7968 (mt) cc_final: 0.7721 (mt) REVERT: O 107 TRP cc_start: 0.7374 (t-100) cc_final: 0.6868 (t-100) REVERT: O 258 MET cc_start: 0.4515 (mtp) cc_final: 0.3946 (mtm) REVERT: O 298 LYS cc_start: 0.8970 (mmtm) cc_final: 0.8525 (mmtp) REVERT: O 319 MET cc_start: 0.5783 (mmm) cc_final: 0.5234 (mmm) REVERT: O 354 MET cc_start: 0.0381 (mtm) cc_final: 0.0116 (mtm) REVERT: O 369 TYR cc_start: 0.8310 (p90) cc_final: 0.7831 (p90) REVERT: M 66 ARG cc_start: 0.7095 (tmm160) cc_final: 0.6848 (tmt170) REVERT: H 24 ASN cc_start: 0.9025 (m-40) cc_final: 0.8166 (m-40) REVERT: H 28 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7953 (mm-30) REVERT: K 29 LYS cc_start: 0.9412 (tmtt) cc_final: 0.9167 (mptt) REVERT: K 34 LYS cc_start: 0.9107 (mmtp) cc_final: 0.8417 (mttt) REVERT: K 75 LYS cc_start: 0.8759 (ttpt) cc_final: 0.8531 (pttm) REVERT: K 93 ASP cc_start: 0.8114 (t0) cc_final: 0.7511 (t0) REVERT: K 97 ASP cc_start: 0.8079 (m-30) cc_final: 0.7575 (m-30) REVERT: S 19 PHE cc_start: 0.8331 (t80) cc_final: 0.7926 (t80) REVERT: S 30 LYS cc_start: 0.5998 (OUTLIER) cc_final: 0.5685 (ttpt) REVERT: S 76 LEU cc_start: 0.7551 (pp) cc_final: 0.6954 (mm) REVERT: T 71 PHE cc_start: 0.6924 (OUTLIER) cc_final: 0.5666 (m-80) REVERT: B 18 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8484 (t80) REVERT: B 347 MET cc_start: 0.8722 (tpp) cc_final: 0.8079 (tpp) REVERT: B 393 LYS cc_start: 0.9032 (ttmt) cc_final: 0.8811 (ttmt) REVERT: B 451 LEU cc_start: 0.8626 (mt) cc_final: 0.8412 (mt) REVERT: B 540 MET cc_start: 0.7012 (mtp) cc_final: 0.6694 (mtp) REVERT: C 55 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8830 (pt) REVERT: C 360 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7433 (mt-10) REVERT: C 487 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7928 (tm-30) REVERT: A 18 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7887 (t80) REVERT: E 141 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7685 (ttp-110) REVERT: E 456 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7507 (tm-30) REVERT: F 170 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8324 (tt) REVERT: F 215 LYS cc_start: 0.2583 (pptt) cc_final: 0.2068 (pptt) REVERT: F 242 ARG cc_start: 0.7919 (tpp80) cc_final: 0.7543 (ttm-80) REVERT: F 359 ASP cc_start: 0.7630 (t0) cc_final: 0.7346 (t0) REVERT: F 456 GLN cc_start: 0.8113 (tp-100) cc_final: 0.7859 (tt0) REVERT: F 474 PHE cc_start: 0.5661 (t80) cc_final: 0.5444 (t80) REVERT: D 360 ASP cc_start: 0.8126 (t0) cc_final: 0.7734 (p0) REVERT: D 457 LYS cc_start: 0.9044 (mttm) cc_final: 0.8752 (mttp) REVERT: Y 33 MET cc_start: 0.8186 (tpp) cc_final: 0.7941 (tpt) REVERT: Y 61 ARG cc_start: 0.8490 (mmm-85) cc_final: 0.8130 (tpp80) REVERT: Y 74 CYS cc_start: 0.7471 (m) cc_final: 0.7132 (m) REVERT: X 33 MET cc_start: 0.7989 (tpp) cc_final: 0.7673 (tpp) REVERT: X 151 PHE cc_start: 0.7222 (m-10) cc_final: 0.6889 (m-80) REVERT: X 153 ARG cc_start: 0.7535 (tpp80) cc_final: 0.7300 (tpp80) REVERT: X 197 TYR cc_start: 0.8202 (m-80) cc_final: 0.7974 (t80) REVERT: N 29 ASN cc_start: 0.8458 (t0) cc_final: 0.7946 (t0) REVERT: N 30 LYS cc_start: 0.9368 (ptpp) cc_final: 0.8721 (mmtm) REVERT: N 31 ASN cc_start: 0.8501 (p0) cc_final: 0.7710 (p0) REVERT: N 32 ARG cc_start: 0.8937 (mmm160) cc_final: 0.8484 (tpp-160) REVERT: N 33 HIS cc_start: 0.8620 (m170) cc_final: 0.8309 (m90) REVERT: N 47 GLU cc_start: 0.9276 (tp30) cc_final: 0.8816 (pt0) REVERT: N 73 MET cc_start: 0.9170 (mtm) cc_final: 0.8960 (ttt) REVERT: U 293 GLN cc_start: 0.9056 (mp10) cc_final: 0.8496 (mp-120) REVERT: U 373 TYR cc_start: 0.8322 (m-10) cc_final: 0.8068 (m-80) REVERT: U 430 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8553 (mt) REVERT: V 302 GLU cc_start: 0.7547 (pm20) cc_final: 0.7249 (pm20) REVERT: 0 103 TYR cc_start: 0.8468 (m-10) cc_final: 0.8068 (m-80) REVERT: 0 107 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8234 (mpp) REVERT: 1 97 LEU cc_start: 0.8855 (tt) cc_final: 0.8594 (tp) REVERT: 3 139 GLU cc_start: 0.7974 (tp30) cc_final: 0.7432 (tm-30) REVERT: 4 44 MET cc_start: 0.8507 (ppp) cc_final: 0.8158 (ppp) REVERT: 5 44 MET cc_start: 0.5224 (tpp) cc_final: 0.4932 (mmt) REVERT: 5 137 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7868 (t80) REVERT: 6 131 MET cc_start: 0.7384 (ttp) cc_final: 0.7183 (ttm) REVERT: 6 135 LEU cc_start: 0.8756 (mp) cc_final: 0.8092 (mp) REVERT: 7 10 TYR cc_start: 0.4438 (m-80) cc_final: 0.3323 (m-80) REVERT: 9 53 MET cc_start: 0.8059 (mmt) cc_final: 0.7337 (ptt) REVERT: Q 150 LEU cc_start: 0.8534 (tp) cc_final: 0.8239 (tt) REVERT: Q 208 MET cc_start: 0.8467 (mmm) cc_final: 0.8067 (tpp) REVERT: Q 236 ASP cc_start: 0.8165 (t0) cc_final: 0.7609 (t0) REVERT: P 30 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8783 (mmmt) REVERT: P 81 MET cc_start: 0.8140 (ptp) cc_final: 0.7887 (ptp) REVERT: P 92 TYR cc_start: 0.8212 (m-80) cc_final: 0.7459 (m-80) REVERT: P 101 LEU cc_start: 0.8837 (mt) cc_final: 0.8526 (tt) REVERT: P 140 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8485 (tmm) REVERT: P 151 TRP cc_start: 0.5825 (OUTLIER) cc_final: 0.5449 (m-90) REVERT: P 249 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9159 (mp) REVERT: P 331 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8885 (mm) REVERT: P 398 LEU cc_start: 0.8657 (tp) cc_final: 0.8432 (tp) outliers start: 192 outliers final: 156 residues processed: 1133 average time/residue: 0.6640 time to fit residues: 1317.9445 Evaluate side-chains 1120 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 951 time to evaluate : 6.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 GLU Chi-restraints excluded: chain R residue 120 ARG Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain R residue 355 MET Chi-restraints excluded: chain R residue 363 THR Chi-restraints excluded: chain R residue 395 THR Chi-restraints excluded: chain R residue 488 ASN Chi-restraints excluded: chain R residue 518 ILE Chi-restraints excluded: chain R residue 532 LEU Chi-restraints excluded: chain R residue 580 THR Chi-restraints excluded: chain R residue 594 TRP Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 118 LEU Chi-restraints excluded: chain O residue 123 GLU Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 324 ASN Chi-restraints excluded: chain O residue 341 HIS Chi-restraints excluded: chain O residue 363 GLN Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 226 ASP Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain L residue 69 CYS Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 88 PHE Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain K residue 32 ARG Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain T residue 55 ILE Chi-restraints excluded: chain T residue 71 PHE Chi-restraints excluded: chain T residue 80 ILE Chi-restraints excluded: chain T residue 82 ASP Chi-restraints excluded: chain T residue 105 SER Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 112 CYS Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain Y residue 98 ILE Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 246 LEU Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain Z residue 99 SER Chi-restraints excluded: chain Z residue 179 PHE Chi-restraints excluded: chain Z residue 263 ILE Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain U residue 289 THR Chi-restraints excluded: chain U residue 297 LEU Chi-restraints excluded: chain U residue 324 LYS Chi-restraints excluded: chain U residue 385 VAL Chi-restraints excluded: chain U residue 430 LEU Chi-restraints excluded: chain U residue 447 ILE Chi-restraints excluded: chain U residue 454 ASP Chi-restraints excluded: chain U residue 455 ARG Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 36 ASP Chi-restraints excluded: chain 0 residue 98 GLU Chi-restraints excluded: chain 0 residue 107 MET Chi-restraints excluded: chain 0 residue 147 SER Chi-restraints excluded: chain 0 residue 151 CYS Chi-restraints excluded: chain 1 residue 102 SER Chi-restraints excluded: chain 1 residue 121 THR Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 1 residue 146 LEU Chi-restraints excluded: chain 2 residue 10 TYR Chi-restraints excluded: chain 2 residue 44 MET Chi-restraints excluded: chain 2 residue 112 ILE Chi-restraints excluded: chain 2 residue 141 LEU Chi-restraints excluded: chain 3 residue 78 ASN Chi-restraints excluded: chain 3 residue 81 ASN Chi-restraints excluded: chain 3 residue 140 VAL Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 4 residue 36 LYS Chi-restraints excluded: chain 4 residue 110 ILE Chi-restraints excluded: chain 5 residue 110 ILE Chi-restraints excluded: chain 5 residue 137 PHE Chi-restraints excluded: chain 6 residue 98 SER Chi-restraints excluded: chain 6 residue 118 VAL Chi-restraints excluded: chain 6 residue 129 VAL Chi-restraints excluded: chain 7 residue 115 ASP Chi-restraints excluded: chain 7 residue 118 VAL Chi-restraints excluded: chain 8 residue 9 GLU Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 92 GLN Chi-restraints excluded: chain 8 residue 115 ASP Chi-restraints excluded: chain 9 residue 135 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain Q residue 174 ASP Chi-restraints excluded: chain Q residue 321 LEU Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 126 PHE Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 151 TRP Chi-restraints excluded: chain P residue 249 LEU Chi-restraints excluded: chain P residue 293 LEU Chi-restraints excluded: chain P residue 331 ILE Chi-restraints excluded: chain P residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 536 optimal weight: 7.9990 chunk 864 optimal weight: 0.9990 chunk 527 optimal weight: 1.9990 chunk 410 optimal weight: 7.9990 chunk 600 optimal weight: 10.0000 chunk 906 optimal weight: 20.0000 chunk 834 optimal weight: 6.9990 chunk 721 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 557 optimal weight: 9.9990 chunk 442 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 76 ASN R 194 ASN ** R 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 GLN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 GLN ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 GLN F 421 GLN ** Z 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 84 HIS ** P 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 233 ASN P 238 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 73651 Z= 0.308 Angle : 0.652 14.436 99547 Z= 0.330 Chirality : 0.043 0.264 11312 Planarity : 0.004 0.083 12746 Dihedral : 4.875 75.121 10151 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.02 % Favored : 93.93 % Rotamer: Outliers : 2.55 % Allowed : 21.91 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: -0.37 (0.09), residues: 9131 helix: 1.10 (0.07), residues: 5213 sheet: -1.57 (0.19), residues: 782 loop : -2.23 (0.11), residues: 3136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP S 52 HIS 0.011 0.001 HIS I 14 PHE 0.039 0.001 PHE I 38 TYR 0.048 0.001 TYR O 75 ARG 0.012 0.000 ARG H 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18262 Ramachandran restraints generated. 9131 Oldfield, 0 Emsley, 9131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 946 time to evaluate : 6.412 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: R 10 MET cc_start: 0.6890 (mmm) cc_final: 0.6623 (tpp) REVERT: R 423 MET cc_start: 0.8642 (mtm) cc_final: 0.8237 (mtp) REVERT: R 627 MET cc_start: 0.8544 (mmm) cc_final: 0.8022 (mmt) REVERT: R 717 MET cc_start: 0.8139 (tmm) cc_final: 0.7810 (tmm) REVERT: O 107 TRP cc_start: 0.7470 (t-100) cc_final: 0.6982 (t-100) REVERT: O 258 MET cc_start: 0.4547 (mtp) cc_final: 0.3984 (mtm) REVERT: O 298 LYS cc_start: 0.8977 (mmtm) cc_final: 0.8538 (mmtp) REVERT: O 319 MET cc_start: 0.5745 (mmm) cc_final: 0.5526 (mmp) REVERT: O 354 MET cc_start: 0.0317 (mtm) cc_final: 0.0022 (mtm) REVERT: O 369 TYR cc_start: 0.8372 (p90) cc_final: 0.7972 (p90) REVERT: J 50 ARG cc_start: 0.8600 (ttt180) cc_final: 0.8349 (tpp-160) REVERT: J 184 TYR cc_start: 0.8911 (m-80) cc_final: 0.8622 (m-80) REVERT: M 66 ARG cc_start: 0.7108 (tmm160) cc_final: 0.6859 (tmt170) REVERT: L 102 PHE cc_start: 0.8054 (m-80) cc_final: 0.7833 (t80) REVERT: H 24 ASN cc_start: 0.9044 (m-40) cc_final: 0.8205 (m-40) REVERT: H 28 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7975 (mm-30) REVERT: K 75 LYS cc_start: 0.8780 (ttpt) cc_final: 0.8562 (pttm) REVERT: K 93 ASP cc_start: 0.8166 (t0) cc_final: 0.7555 (t0) REVERT: K 97 ASP cc_start: 0.8110 (m-30) cc_final: 0.7616 (m-30) REVERT: S 19 PHE cc_start: 0.8365 (t80) cc_final: 0.7941 (t80) REVERT: S 30 LYS cc_start: 0.6026 (OUTLIER) cc_final: 0.5715 (ttpt) REVERT: T 71 PHE cc_start: 0.6994 (OUTLIER) cc_final: 0.5794 (m-80) REVERT: B 347 MET cc_start: 0.8713 (tpp) cc_final: 0.8175 (tpp) REVERT: B 540 MET cc_start: 0.7179 (mtp) cc_final: 0.6874 (mtp) REVERT: C 283 GLU cc_start: 0.7053 (mp0) cc_final: 0.6824 (mp0) REVERT: C 306 MET cc_start: 0.8714 (tpt) cc_final: 0.8441 (tpt) REVERT: C 360 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7420 (mt-10) REVERT: C 487 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7937 (tm-30) REVERT: A 18 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7892 (t80) REVERT: E 161 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8481 (tp40) REVERT: E 456 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7515 (tm-30) REVERT: F 170 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8382 (tt) REVERT: F 215 LYS cc_start: 0.2685 (pptt) cc_final: 0.2183 (pptt) REVERT: F 242 ARG cc_start: 0.7955 (tpp80) cc_final: 0.7594 (ttm-80) REVERT: F 359 ASP cc_start: 0.7678 (t0) cc_final: 0.7383 (t0) REVERT: F 456 GLN cc_start: 0.8162 (tp-100) cc_final: 0.7887 (tt0) REVERT: F 474 PHE cc_start: 0.5797 (t80) cc_final: 0.5570 (t80) REVERT: D 360 ASP cc_start: 0.8179 (t0) cc_final: 0.7792 (p0) REVERT: Y 33 MET cc_start: 0.8209 (tpp) cc_final: 0.7990 (tpt) REVERT: Y 61 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8114 (tpp80) REVERT: Y 74 CYS cc_start: 0.7607 (m) cc_final: 0.7243 (m) REVERT: X 33 MET cc_start: 0.8144 (tpp) cc_final: 0.7887 (tpp) REVERT: X 103 MET cc_start: 0.6599 (mmm) cc_final: 0.6255 (mmp) REVERT: X 151 PHE cc_start: 0.7270 (m-10) cc_final: 0.6832 (m-80) REVERT: X 153 ARG cc_start: 0.7541 (tpp80) cc_final: 0.7291 (tpp80) REVERT: X 197 TYR cc_start: 0.8241 (m-80) cc_final: 0.7993 (t80) REVERT: G 186 TYR cc_start: 0.8654 (t80) cc_final: 0.8307 (t80) REVERT: G 206 GLN cc_start: 0.8821 (tp40) cc_final: 0.8327 (tp40) REVERT: N 29 ASN cc_start: 0.8506 (t0) cc_final: 0.8015 (t0) REVERT: N 30 LYS cc_start: 0.9377 (ptpp) cc_final: 0.8724 (mmtm) REVERT: N 31 ASN cc_start: 0.8529 (p0) cc_final: 0.7776 (p0) REVERT: N 32 ARG cc_start: 0.8992 (mmm160) cc_final: 0.8537 (tpp-160) REVERT: N 33 HIS cc_start: 0.8650 (m170) cc_final: 0.8328 (m90) REVERT: N 73 MET cc_start: 0.9162 (mtm) cc_final: 0.8887 (ttt) REVERT: U 293 GLN cc_start: 0.9073 (mp10) cc_final: 0.8473 (mp-120) REVERT: U 373 TYR cc_start: 0.8374 (m-10) cc_final: 0.8137 (m-80) REVERT: U 428 MET cc_start: 0.8936 (mtt) cc_final: 0.8569 (mtt) REVERT: V 302 GLU cc_start: 0.7603 (pm20) cc_final: 0.7324 (pm20) REVERT: V 314 MET cc_start: 0.8547 (tpp) cc_final: 0.7242 (ttt) REVERT: 0 103 TYR cc_start: 0.8513 (m-10) cc_final: 0.8114 (m-80) REVERT: 0 107 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8298 (mpp) REVERT: 1 97 LEU cc_start: 0.8930 (tt) cc_final: 0.8657 (tp) REVERT: 3 75 LEU cc_start: 0.8356 (tp) cc_final: 0.7982 (tp) REVERT: 3 139 GLU cc_start: 0.8033 (tp30) cc_final: 0.7459 (tm-30) REVERT: 5 44 MET cc_start: 0.5383 (tpp) cc_final: 0.5109 (mmt) REVERT: 5 115 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8625 (t0) REVERT: 5 139 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8294 (tm-30) REVERT: 6 44 MET cc_start: 0.7594 (tmm) cc_final: 0.7221 (tmm) REVERT: 7 10 TYR cc_start: 0.4541 (m-80) cc_final: 0.3326 (m-80) REVERT: 9 53 MET cc_start: 0.8162 (mmt) cc_final: 0.7390 (ptt) REVERT: 9 84 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.9008 (mt) REVERT: Q 150 LEU cc_start: 0.8618 (tp) cc_final: 0.8269 (tt) REVERT: Q 208 MET cc_start: 0.8489 (mmm) cc_final: 0.8031 (tpp) REVERT: Q 236 ASP cc_start: 0.8164 (t0) cc_final: 0.7591 (t0) REVERT: P 30 LYS cc_start: 0.9051 (mmmm) cc_final: 0.8802 (mmmt) REVERT: P 92 TYR cc_start: 0.8189 (m-80) cc_final: 0.7456 (m-80) REVERT: P 101 LEU cc_start: 0.8861 (mt) cc_final: 0.8573 (tt) REVERT: P 140 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8548 (tmm) REVERT: P 205 LEU cc_start: 0.9529 (tp) cc_final: 0.9311 (mm) REVERT: P 249 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9176 (mp) REVERT: P 331 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8925 (mm) REVERT: P 398 LEU cc_start: 0.8663 (tp) cc_final: 0.8440 (tp) outliers start: 199 outliers final: 174 residues processed: 1090 average time/residue: 0.6645 time to fit residues: 1254.1857 Evaluate side-chains 1121 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 936 time to evaluate : 6.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 GLU Chi-restraints excluded: chain R residue 120 ARG Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain R residue 363 THR Chi-restraints excluded: chain R residue 488 ASN Chi-restraints excluded: chain R residue 497 ASN Chi-restraints excluded: chain R residue 529 LEU Chi-restraints excluded: chain R residue 532 LEU Chi-restraints excluded: chain R residue 580 THR Chi-restraints excluded: chain R residue 594 TRP Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 118 LEU Chi-restraints excluded: chain O residue 123 GLU Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 324 ASN Chi-restraints excluded: chain O residue 341 HIS Chi-restraints excluded: chain O residue 363 GLN Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 226 ASP Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain L residue 69 CYS Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 88 PHE Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain K residue 32 ARG Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain T residue 55 ILE Chi-restraints excluded: chain T residue 71 PHE Chi-restraints excluded: chain T residue 80 ILE Chi-restraints excluded: chain T residue 82 ASP Chi-restraints excluded: chain T residue 105 SER Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 112 CYS Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain Y residue 98 ILE Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 246 LEU Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain Z residue 99 SER Chi-restraints excluded: chain Z residue 194 ASP Chi-restraints excluded: chain Z residue 263 ILE Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain U residue 289 THR Chi-restraints excluded: chain U residue 297 LEU Chi-restraints excluded: chain U residue 324 LYS Chi-restraints excluded: chain U residue 370 HIS Chi-restraints excluded: chain U residue 385 VAL Chi-restraints excluded: chain U residue 430 LEU Chi-restraints excluded: chain U residue 447 ILE Chi-restraints excluded: chain U residue 454 ASP Chi-restraints excluded: chain U residue 455 ARG Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 36 ASP Chi-restraints excluded: chain 0 residue 69 ILE Chi-restraints excluded: chain 0 residue 98 GLU Chi-restraints excluded: chain 0 residue 107 MET Chi-restraints excluded: chain 0 residue 147 SER Chi-restraints excluded: chain 0 residue 151 CYS Chi-restraints excluded: chain 0 residue 181 ILE Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 102 SER Chi-restraints excluded: chain 1 residue 121 THR Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 1 residue 146 LEU Chi-restraints excluded: chain 2 residue 10 TYR Chi-restraints excluded: chain 2 residue 44 MET Chi-restraints excluded: chain 2 residue 53 MET Chi-restraints excluded: chain 2 residue 112 ILE Chi-restraints excluded: chain 2 residue 141 LEU Chi-restraints excluded: chain 2 residue 154 THR Chi-restraints excluded: chain 3 residue 78 ASN Chi-restraints excluded: chain 3 residue 81 ASN Chi-restraints excluded: chain 3 residue 110 ILE Chi-restraints excluded: chain 3 residue 140 VAL Chi-restraints excluded: chain 4 residue 36 LYS Chi-restraints excluded: chain 4 residue 110 ILE Chi-restraints excluded: chain 5 residue 110 ILE Chi-restraints excluded: chain 5 residue 115 ASP Chi-restraints excluded: chain 6 residue 28 LEU Chi-restraints excluded: chain 6 residue 98 SER Chi-restraints excluded: chain 6 residue 118 VAL Chi-restraints excluded: chain 6 residue 129 VAL Chi-restraints excluded: chain 7 residue 115 ASP Chi-restraints excluded: chain 7 residue 118 VAL Chi-restraints excluded: chain 8 residue 9 GLU Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain 8 residue 92 GLN Chi-restraints excluded: chain 8 residue 115 ASP Chi-restraints excluded: chain 9 residue 26 SER Chi-restraints excluded: chain 9 residue 84 ILE Chi-restraints excluded: chain 9 residue 135 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain Q residue 174 ASP Chi-restraints excluded: chain Q residue 321 LEU Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 126 PHE Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 151 TRP Chi-restraints excluded: chain P residue 249 LEU Chi-restraints excluded: chain P residue 293 LEU Chi-restraints excluded: chain P residue 331 ILE Chi-restraints excluded: chain P residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 573 optimal weight: 5.9990 chunk 769 optimal weight: 10.0000 chunk 221 optimal weight: 7.9990 chunk 665 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 chunk 200 optimal weight: 30.0000 chunk 723 optimal weight: 2.9990 chunk 302 optimal weight: 0.4980 chunk 742 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 GLN F 421 GLN ** Z 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 84 HIS ** P 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.122886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.088229 restraints weight = 157808.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.087302 restraints weight = 90740.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.087753 restraints weight = 74937.440| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.235 73651 Z= 0.340 Angle : 0.696 59.176 99547 Z= 0.366 Chirality : 0.043 0.472 11312 Planarity : 0.004 0.081 12746 Dihedral : 4.872 75.096 10151 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.98 % Favored : 93.98 % Rotamer: Outliers : 2.68 % Allowed : 22.00 % Favored : 75.32 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: -0.37 (0.09), residues: 9131 helix: 1.10 (0.07), residues: 5211 sheet: -1.57 (0.19), residues: 782 loop : -2.23 (0.11), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP S 52 HIS 0.010 0.001 HIS P 139 PHE 0.038 0.002 PHE 7 13 TYR 0.026 0.001 TYR 0 8 ARG 0.011 0.000 ARG H 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18944.32 seconds wall clock time: 332 minutes 44.33 seconds (19964.33 seconds total)