Starting phenix.real_space_refine on Tue Feb 20 18:32:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi7_12920/02_2024/7oi7_12920_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi7_12920/02_2024/7oi7_12920.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi7_12920/02_2024/7oi7_12920_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi7_12920/02_2024/7oi7_12920_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi7_12920/02_2024/7oi7_12920_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi7_12920/02_2024/7oi7_12920.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi7_12920/02_2024/7oi7_12920.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi7_12920/02_2024/7oi7_12920_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi7_12920/02_2024/7oi7_12920_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1111 5.49 5 Mg 49 5.21 5 S 282 5.16 5 C 52784 2.51 5 N 16309 2.21 5 O 19210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ASP 86": "OD1" <-> "OD2" Residue "D PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 268": "OE1" <-> "OE2" Residue "E TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 309": "OD1" <-> "OD2" Residue "E TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 45": "OE1" <-> "OE2" Residue "F GLU 67": "OE1" <-> "OE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F GLU 119": "OE1" <-> "OE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F GLU 232": "OE1" <-> "OE2" Residue "F TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 292": "OD1" <-> "OD2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "I ASP 183": "OD1" <-> "OD2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K ASP 99": "OD1" <-> "OD2" Residue "K GLU 131": "OE1" <-> "OE2" Residue "L PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 101": "OD1" <-> "OD2" Residue "L PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 85": "OE1" <-> "OE2" Residue "M PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 161": "OE1" <-> "OE2" Residue "M GLU 168": "OE1" <-> "OE2" Residue "M PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 231": "OE1" <-> "OE2" Residue "M GLU 288": "OE1" <-> "OE2" Residue "N ASP 71": "OD1" <-> "OD2" Residue "N PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 23": "OE1" <-> "OE2" Residue "O TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 67": "OD1" <-> "OD2" Residue "O GLU 124": "OE1" <-> "OE2" Residue "Q PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 165": "OE1" <-> "OE2" Residue "Q GLU 173": "OE1" <-> "OE2" Residue "Q TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 234": "OE1" <-> "OE2" Residue "Q PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 266": "OE1" <-> "OE2" Residue "Q ASP 274": "OD1" <-> "OD2" Residue "Q GLU 279": "OE1" <-> "OE2" Residue "R TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "S GLU 63": "OE1" <-> "OE2" Residue "S PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 111": "OE1" <-> "OE2" Residue "S GLU 126": "OE1" <-> "OE2" Residue "S GLU 162": "OE1" <-> "OE2" Residue "S PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 126": "OD1" <-> "OD2" Residue "T GLU 135": "OE1" <-> "OE2" Residue "T GLU 187": "OE1" <-> "OE2" Residue "U PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 81": "OD1" <-> "OD2" Residue "U TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V GLU 52": "OE1" <-> "OE2" Residue "V TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 124": "OD1" <-> "OD2" Residue "V GLU 134": "OE1" <-> "OE2" Residue "V ASP 176": "OD1" <-> "OD2" Residue "V GLU 180": "OE1" <-> "OE2" Residue "V TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 200": "OE1" <-> "OE2" Residue "V GLU 206": "OE1" <-> "OE2" Residue "W TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 34": "OE1" <-> "OE2" Residue "X PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 60": "OE1" <-> "OE2" Residue "X GLU 63": "OE1" <-> "OE2" Residue "X GLU 74": "OE1" <-> "OE2" Residue "X ASP 95": "OD1" <-> "OD2" Residue "X GLU 111": "OE1" <-> "OE2" Residue "X GLU 113": "OE1" <-> "OE2" Residue "X TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 136": "OD1" <-> "OD2" Residue "X ASP 142": "OD1" <-> "OD2" Residue "X GLU 151": "OE1" <-> "OE2" Residue "X GLU 199": "OE1" <-> "OE2" Residue "X GLU 210": "OE1" <-> "OE2" Residue "X GLU 213": "OE1" <-> "OE2" Residue "X PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 150": "OE1" <-> "OE2" Residue "Y GLU 224": "OE1" <-> "OE2" Residue "Y GLU 227": "OE1" <-> "OE2" Residue "Z GLU 43": "OE1" <-> "OE2" Residue "Z PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 54": "OE1" <-> "OE2" Residue "0 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 47": "OD1" <-> "OD2" Residue "3 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 32": "OE1" <-> "OE2" Residue "5 GLU 42": "OE1" <-> "OE2" Residue "5 GLU 51": "OE1" <-> "OE2" Residue "5 TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 115": "OE1" <-> "OE2" Residue "5 GLU 130": "OE1" <-> "OE2" Residue "5 GLU 148": "OE1" <-> "OE2" Residue "5 GLU 174": "OE1" <-> "OE2" Residue "5 GLU 216": "OE1" <-> "OE2" Residue "5 GLU 246": "OE1" <-> "OE2" Residue "5 TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 272": "OD1" <-> "OD2" Residue "5 TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 307": "OD1" <-> "OD2" Residue "5 GLU 368": "OE1" <-> "OE2" Residue "5 ASP 379": "OD1" <-> "OD2" Residue "5 PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 62": "OE1" <-> "OE2" Residue "6 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 153": "OE1" <-> "OE2" Residue "6 PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 192": "OE1" <-> "OE2" Residue "6 PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 134": "OD1" <-> "OD2" Residue "7 GLU 161": "OE1" <-> "OE2" Residue "7 TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 197": "OE1" <-> "OE2" Residue "7 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 217": "OE1" <-> "OE2" Residue "7 TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 242": "OE1" <-> "OE2" Residue "7 ASP 314": "OD1" <-> "OD2" Residue "8 GLU 100": "OE1" <-> "OE2" Residue "8 PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 16": "OD1" <-> "OD2" Residue "9 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 64": "OD1" <-> "OD2" Residue "9 PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 104": "OE1" <-> "OE2" Residue "b PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 122": "OD1" <-> "OD2" Residue "c PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 71": "OE1" <-> "OE2" Residue "c TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 102": "OE1" <-> "OE2" Residue "c GLU 142": "OE1" <-> "OE2" Residue "c GLU 151": "OE1" <-> "OE2" Residue "c GLU 176": "OE1" <-> "OE2" Residue "c GLU 182": "OE1" <-> "OE2" Residue "c ASP 217": "OD1" <-> "OD2" Residue "c GLU 243": "OE1" <-> "OE2" Residue "c TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 295": "OE1" <-> "OE2" Residue "c TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 290": "OE1" <-> "OE2" Residue "e GLU 182": "OE1" <-> "OE2" Residue "f TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 43": "OD1" <-> "OD2" Residue "g ASP 59": "OD1" <-> "OD2" Residue "g ASP 77": "OD1" <-> "OD2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 72": "OE1" <-> "OE2" Residue "j ASP 48": "OD1" <-> "OD2" Residue "j GLU 83": "OE1" <-> "OE2" Residue "j ASP 85": "OD1" <-> "OD2" Residue "k ASP 70": "OD1" <-> "OD2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "o GLU 69": "OE1" <-> "OE2" Residue "o PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 72": "OE1" <-> "OE2" Residue "p ASP 46": "OD1" <-> "OD2" Residue "p ASP 56": "OD1" <-> "OD2" Residue "q TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 41": "OD1" <-> "OD2" Residue "q GLU 43": "OE1" <-> "OE2" Residue "q GLU 86": "OE1" <-> "OE2" Residue "q GLU 91": "OE1" <-> "OE2" Residue "q TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 110": "OE1" <-> "OE2" Residue "q GLU 111": "OE1" <-> "OE2" Residue "r PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 64": "OE1" <-> "OE2" Residue "s TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 103": "OD1" <-> "OD2" Residue "s GLU 214": "OE1" <-> "OE2" Residue "s TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 254": "OD1" <-> "OD2" Residue "s PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 290": "OD1" <-> "OD2" Residue "s TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 321": "OE1" <-> "OE2" Residue "s PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 348": "OE1" <-> "OE2" Residue "s ASP 350": "OD1" <-> "OD2" Residue "s PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 415": "OD1" <-> "OD2" Residue "u GLU 104": "OE1" <-> "OE2" Residue "u TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 89747 Number of models: 1 Model: "" Number of chains: 60 Chain: "D" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1706 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain breaks: 1 Chain: "E" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2258 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 22, 'TRANS': 262} Chain breaks: 1 Chain: "F" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2013 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 21, 'TRANS': 228} Chain: "H" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "I" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1283 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 11, 'TRANS': 146} Chain breaks: 1 Chain: "J" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1061 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 9, 'TRANS': 130} Chain: "K" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1451 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 15, 'TRANS': 161} Chain: "L" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 889 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "M" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2305 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 26, 'TRANS': 260} Chain: "N" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1654 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 14, 'TRANS': 190} Chain: "O" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1245 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 9, 'TRANS': 142} Chain: "P" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1148 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 134} Chain: "Q" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1805 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 14, 'TRANS': 202} Chain: "R" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1153 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "S" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1251 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "T" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1305 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 12, 'TRANS': 146} Chain breaks: 1 Chain: "U" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1154 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} Chain breaks: 1 Chain: "V" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1575 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 16, 'TRANS': 175} Chain breaks: 1 Chain: "W" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 859 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "X" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2035 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 18, 'TRANS': 224} Chain: "Y" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1517 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "Z" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 978 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 11, 'TRANS': 108} Chain: "0" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 880 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "1" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 433 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "2" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "3" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 831 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "5" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3156 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 354} Chain breaks: 1 Chain: "6" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2640 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 28, 'TRANS': 295} Chain breaks: 3 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 59 Chain: "7" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2334 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 17, 'TRANS': 269} Chain: "8" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 836 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 9, 'TRANS': 89} Chain: "9" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 107} Chain breaks: 1 Chain: "a" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 686 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 10, 'TRANS': 71} Chain breaks: 1 Chain: "b" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1178 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 9, 'TRANS': 138} Chain: "c" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2217 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 258} Chain breaks: 1 Chain: "d" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1741 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 17, 'TRANS': 193} Chain breaks: 3 Chain: "e" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1762 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Chain: "f" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 915 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "g" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1067 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 113} Chain: "h" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 827 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain breaks: 1 Chain: "i" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 827 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "j" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 684 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Chain: "k" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 627 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Chain: "l" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 221 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "m" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 372 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain: "o" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 665 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "p" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1058 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 3 Chain: "q" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1039 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 14, 'TRANS': 109} Chain: "r" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1203 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 16, 'TRANS': 129} Chain breaks: 2 Chain: "s" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3036 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain breaks: 1 Chain: "u" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 927 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "v" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 588 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "w" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "A" Number of atoms: 22369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1054, 22369 Classifications: {'RNA': 1054} Modifications used: {'rna2p_pur': 113, 'rna2p_pyr': 85, 'rna3p_pur': 447, 'rna3p_pyr': 409} Link IDs: {'rna2p': 197, 'rna3p': 856} Chain breaks: 23 Chain: "B" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1191 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 29, 'rna3p_pyr': 26} Link IDs: {'rna2p': 1, 'rna3p': 54} Chain breaks: 4 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Unusual residues: {' MG': 47} Classifications: {'undetermined': 47} Link IDs: {None: 46} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7048 SG CYS I 64 141.160 100.250 60.984 1.00 83.93 S ATOM 59958 SG CYS r 70 145.701 100.516 61.578 1.00 73.62 S ATOM 60273 SG CYS r 108 143.726 102.601 61.869 1.00 73.55 S ATOM 31693 SG CYS 0 110 164.374 86.829 174.171 1.00 28.56 S ATOM 31715 SG CYS 0 113 161.896 84.599 175.808 1.00 32.44 S ATOM 31795 SG CYS 0 123 160.599 87.637 174.650 1.00 21.08 S ATOM 31818 SG CYS 0 126 162.996 87.783 177.659 1.00 26.50 S Time building chain proxies: 34.78, per 1000 atoms: 0.39 Number of scatterers: 89747 At special positions: 0 Unit cell: (220.052, 224.388, 254.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 282 16.00 P 1111 15.00 Mg 49 11.99 O 19210 8.00 N 16309 7.00 C 52784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 30.51 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 113 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 110 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 126 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" SG CYS r 70 " pdb="ZN ZN I 301 " - pdb=" SG CYS r 108 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 64 " Number of angles added : 6 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15298 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 263 helices and 77 sheets defined 31.8% alpha, 11.6% beta 295 base pairs and 591 stacking pairs defined. Time for finding SS restraints: 31.77 Creating SS restraints... Processing helix chain 'D' and resid 184 through 186 No H-bonds generated for 'chain 'D' and resid 184 through 186' Processing helix chain 'D' and resid 260 through 266 Processing helix chain 'E' and resid 55 through 77 Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 135 through 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 154 through 156 No H-bonds generated for 'chain 'E' and resid 154 through 156' Processing helix chain 'E' and resid 159 through 168 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 218 through 221 No H-bonds generated for 'chain 'E' and resid 218 through 221' Processing helix chain 'E' and resid 305 through 307 No H-bonds generated for 'chain 'E' and resid 305 through 307' Processing helix chain 'E' and resid 321 through 323 No H-bonds generated for 'chain 'E' and resid 321 through 323' Processing helix chain 'F' and resid 84 through 87 No H-bonds generated for 'chain 'F' and resid 84 through 87' Processing helix chain 'F' and resid 93 through 106 Processing helix chain 'F' and resid 167 through 183 Processing helix chain 'F' and resid 200 through 209 Processing helix chain 'F' and resid 228 through 236 removed outlier: 4.769A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 255 Processing helix chain 'F' and resid 263 through 276 removed outlier: 4.080A pdb=" N GLN F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 77 No H-bonds generated for 'chain 'H' and resid 75 through 77' Processing helix chain 'H' and resid 86 through 88 No H-bonds generated for 'chain 'H' and resid 86 through 88' Processing helix chain 'H' and resid 116 through 121 Processing helix chain 'H' and resid 136 through 145 Processing helix chain 'I' and resid 42 through 50 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 78 through 92 Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'I' and resid 129 through 137 Proline residue: I 133 - end of helix Processing helix chain 'I' and resid 144 through 146 No H-bonds generated for 'chain 'I' and resid 144 through 146' Processing helix chain 'I' and resid 162 through 169 Processing helix chain 'I' and resid 188 through 196 Processing helix chain 'J' and resid 46 through 58 Processing helix chain 'J' and resid 88 through 94 Processing helix chain 'J' and resid 114 through 121 Processing helix chain 'J' and resid 137 through 149 Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 28 through 40 Processing helix chain 'K' and resid 70 through 74 Processing helix chain 'K' and resid 92 through 98 Processing helix chain 'K' and resid 102 through 111 Processing helix chain 'K' and resid 118 through 124 removed outlier: 3.685A pdb=" N GLU K 123 " --> pdb=" O ARG K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 138 No H-bonds generated for 'chain 'K' and resid 135 through 138' Processing helix chain 'K' and resid 160 through 165 Processing helix chain 'L' and resid 45 through 48 No H-bonds generated for 'chain 'L' and resid 45 through 48' Processing helix chain 'L' and resid 135 through 138 No H-bonds generated for 'chain 'L' and resid 135 through 138' Processing helix chain 'M' and resid 11 through 17 Processing helix chain 'M' and resid 98 through 106 Processing helix chain 'M' and resid 118 through 123 Processing helix chain 'M' and resid 132 through 134 No H-bonds generated for 'chain 'M' and resid 132 through 134' Processing helix chain 'M' and resid 161 through 169 Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 191 through 194 No H-bonds generated for 'chain 'M' and resid 191 through 194' Processing helix chain 'M' and resid 229 through 239 Processing helix chain 'M' and resid 253 through 257 Processing helix chain 'M' and resid 288 through 294 Processing helix chain 'N' and resid 69 through 71 No H-bonds generated for 'chain 'N' and resid 69 through 71' Processing helix chain 'N' and resid 99 through 110 Processing helix chain 'N' and resid 169 through 181 removed outlier: 4.575A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 207 Processing helix chain 'N' and resid 215 through 221 Processing helix chain 'N' and resid 226 through 228 No H-bonds generated for 'chain 'N' and resid 226 through 228' Processing helix chain 'N' and resid 233 through 237 removed outlier: 3.607A pdb=" N HIS N 237 " --> pdb=" O ASP N 234 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 39 Processing helix chain 'O' and resid 46 through 65 removed outlier: 3.694A pdb=" N LEU O 65 " --> pdb=" O ASP O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 79 Processing helix chain 'O' and resid 83 through 91 Proline residue: O 87 - end of helix Processing helix chain 'O' and resid 93 through 96 No H-bonds generated for 'chain 'O' and resid 93 through 96' Processing helix chain 'O' and resid 144 through 157 Processing helix chain 'P' and resid 40 through 42 No H-bonds generated for 'chain 'P' and resid 40 through 42' Processing helix chain 'P' and resid 110 through 113 No H-bonds generated for 'chain 'P' and resid 110 through 113' Processing helix chain 'P' and resid 122 through 139 Processing helix chain 'P' and resid 150 through 153 No H-bonds generated for 'chain 'P' and resid 150 through 153' Processing helix chain 'P' and resid 156 through 168 Processing helix chain 'Q' and resid 78 through 80 No H-bonds generated for 'chain 'Q' and resid 78 through 80' Processing helix chain 'Q' and resid 89 through 105 Processing helix chain 'Q' and resid 144 through 146 No H-bonds generated for 'chain 'Q' and resid 144 through 146' Processing helix chain 'Q' and resid 188 through 191 Processing helix chain 'Q' and resid 195 through 197 No H-bonds generated for 'chain 'Q' and resid 195 through 197' Processing helix chain 'Q' and resid 245 through 248 No H-bonds generated for 'chain 'Q' and resid 245 through 248' Processing helix chain 'Q' and resid 251 through 258 Processing helix chain 'Q' and resid 264 through 266 No H-bonds generated for 'chain 'Q' and resid 264 through 266' Processing helix chain 'Q' and resid 277 through 289 Processing helix chain 'R' and resid 18 through 25 Processing helix chain 'R' and resid 33 through 36 Processing helix chain 'R' and resid 39 through 78 removed outlier: 4.581A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 90 Processing helix chain 'R' and resid 99 through 108 Processing helix chain 'R' and resid 110 through 132 Processing helix chain 'S' and resid 69 through 89 Processing helix chain 'T' and resid 50 through 55 removed outlier: 3.589A pdb=" N LYS T 54 " --> pdb=" O LYS T 50 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN T 55 " --> pdb=" O TRP T 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 50 through 55' Processing helix chain 'T' and resid 87 through 93 Processing helix chain 'T' and resid 99 through 107 removed outlier: 3.697A pdb=" N GLU T 107 " --> pdb=" O LEU T 103 " (cutoff:3.500A) Processing helix chain 'T' and resid 112 through 131 Processing helix chain 'T' and resid 192 through 205 Processing helix chain 'U' and resid 50 through 60 Processing helix chain 'U' and resid 128 through 134 Processing helix chain 'U' and resid 142 through 144 No H-bonds generated for 'chain 'U' and resid 142 through 144' Processing helix chain 'V' and resid 29 through 34 Processing helix chain 'V' and resid 117 through 119 No H-bonds generated for 'chain 'V' and resid 117 through 119' Processing helix chain 'V' and resid 194 through 202 Processing helix chain 'W' and resid 111 through 119 Processing helix chain 'X' and resid 8 through 17 removed outlier: 4.564A pdb=" N LYS X 12 " --> pdb=" O TRP X 9 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 23 Processing helix chain 'X' and resid 26 through 33 Processing helix chain 'X' and resid 73 through 77 Processing helix chain 'X' and resid 129 through 138 Processing helix chain 'X' and resid 141 through 147 Processing helix chain 'X' and resid 150 through 153 No H-bonds generated for 'chain 'X' and resid 150 through 153' Processing helix chain 'X' and resid 156 through 171 Processing helix chain 'X' and resid 181 through 190 Processing helix chain 'X' and resid 198 through 203 removed outlier: 5.062A pdb=" N TRP X 203 " --> pdb=" O GLU X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 208 through 219 Processing helix chain 'X' and resid 226 through 243 Processing helix chain 'Y' and resid 64 through 67 Processing helix chain 'Y' and resid 71 through 73 No H-bonds generated for 'chain 'Y' and resid 71 through 73' Processing helix chain 'Y' and resid 87 through 90 No H-bonds generated for 'chain 'Y' and resid 87 through 90' Processing helix chain 'Y' and resid 95 through 121 Processing helix chain 'Y' and resid 130 through 157 Processing helix chain 'Y' and resid 194 through 196 No H-bonds generated for 'chain 'Y' and resid 194 through 196' Processing helix chain 'Y' and resid 206 through 237 Processing helix chain 'Z' and resid 43 through 46 Processing helix chain 'Z' and resid 50 through 55 Processing helix chain 'Z' and resid 80 through 89 Processing helix chain 'Z' and resid 104 through 112 Processing helix chain '0' and resid 87 through 94 Processing helix chain '0' and resid 124 through 145 Processing helix chain '2' and resid 57 through 64 Processing helix chain '2' and resid 66 through 71 Processing helix chain '2' and resid 73 through 85 Processing helix chain '3' and resid 108 through 113 Processing helix chain '3' and resid 138 through 144 Processing helix chain '3' and resid 152 through 159 Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '5' and resid 48 through 51 Processing helix chain '5' and resid 85 through 87 No H-bonds generated for 'chain '5' and resid 85 through 87' Processing helix chain '5' and resid 117 through 124 Processing helix chain '5' and resid 134 through 139 removed outlier: 4.404A pdb=" N LEU 5 139 " --> pdb=" O LYS 5 135 " (cutoff:3.500A) Processing helix chain '5' and resid 150 through 162 Processing helix chain '5' and resid 173 through 193 Proline residue: 5 178 - end of helix removed outlier: 4.347A pdb=" N ILE 5 192 " --> pdb=" O CYS 5 188 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU 5 193 " --> pdb=" O LYS 5 189 " (cutoff:3.500A) Processing helix chain '5' and resid 196 through 200 Processing helix chain '5' and resid 242 through 247 Processing helix chain '5' and resid 306 through 329 Processing helix chain '5' and resid 409 through 418 Processing helix chain '6' and resid 55 through 66 Processing helix chain '6' and resid 74 through 78 Processing helix chain '6' and resid 100 through 114 Processing helix chain '6' and resid 117 through 124 Processing helix chain '6' and resid 132 through 141 Processing helix chain '6' and resid 144 through 154 Processing helix chain '6' and resid 157 through 161 Processing helix chain '6' and resid 300 through 305 Processing helix chain '6' and resid 308 through 310 No H-bonds generated for 'chain '6' and resid 308 through 310' Processing helix chain '6' and resid 325 through 332 Processing helix chain '6' and resid 363 through 368 removed outlier: 3.631A pdb=" N ARG 6 368 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) Processing helix chain '7' and resid 37 through 57 Processing helix chain '7' and resid 88 through 95 Processing helix chain '7' and resid 97 through 99 No H-bonds generated for 'chain '7' and resid 97 through 99' Processing helix chain '7' and resid 108 through 110 No H-bonds generated for 'chain '7' and resid 108 through 110' Processing helix chain '7' and resid 136 through 155 Processing helix chain '7' and resid 174 through 176 No H-bonds generated for 'chain '7' and resid 174 through 176' Processing helix chain '7' and resid 196 through 211 Processing helix chain '7' and resid 223 through 229 Processing helix chain '7' and resid 234 through 244 Processing helix chain '7' and resid 272 through 274 No H-bonds generated for 'chain '7' and resid 272 through 274' Processing helix chain '7' and resid 310 through 319 Processing helix chain '8' and resid 108 through 153 Processing helix chain '9' and resid 28 through 33 Processing helix chain '9' and resid 88 through 104 Proline residue: 9 98 - end of helix Processing helix chain '9' and resid 115 through 117 No H-bonds generated for 'chain '9' and resid 115 through 117' Processing helix chain 'a' and resid 105 through 116 Processing helix chain 'a' and resid 120 through 122 No H-bonds generated for 'chain 'a' and resid 120 through 122' Processing helix chain 'a' and resid 128 through 133 Processing helix chain 'b' and resid 41 through 49 Processing helix chain 'b' and resid 51 through 57 Processing helix chain 'b' and resid 94 through 106 Processing helix chain 'b' and resid 140 through 142 No H-bonds generated for 'chain 'b' and resid 140 through 142' Processing helix chain 'c' and resid 36 through 52 Processing helix chain 'c' and resid 60 through 62 No H-bonds generated for 'chain 'c' and resid 60 through 62' Processing helix chain 'c' and resid 68 through 78 Processing helix chain 'c' and resid 85 through 92 Processing helix chain 'c' and resid 95 through 105 Processing helix chain 'c' and resid 123 through 144 Processing helix chain 'c' and resid 150 through 160 Processing helix chain 'c' and resid 163 through 172 removed outlier: 3.776A pdb=" N ASN c 172 " --> pdb=" O HIS c 168 " (cutoff:3.500A) Processing helix chain 'c' and resid 175 through 178 No H-bonds generated for 'chain 'c' and resid 175 through 178' Processing helix chain 'c' and resid 188 through 218 Proline residue: c 208 - end of helix Processing helix chain 'c' and resid 220 through 223 Processing helix chain 'c' and resid 237 through 247 Processing helix chain 'c' and resid 289 through 305 Processing helix chain 'd' and resid 53 through 63 Processing helix chain 'd' and resid 119 through 129 removed outlier: 4.875A pdb=" N TYR d 128 " --> pdb=" O ARG d 124 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP d 129 " --> pdb=" O ILE d 125 " (cutoff:3.500A) Processing helix chain 'd' and resid 137 through 154 removed outlier: 3.560A pdb=" N GLU d 147 " --> pdb=" O ASP d 143 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN d 154 " --> pdb=" O LEU d 150 " (cutoff:3.500A) Processing helix chain 'd' and resid 157 through 163 Processing helix chain 'd' and resid 166 through 173 Proline residue: d 170 - end of helix Processing helix chain 'e' and resid 65 through 80 Processing helix chain 'e' and resid 86 through 89 No H-bonds generated for 'chain 'e' and resid 86 through 89' Processing helix chain 'e' and resid 93 through 103 Processing helix chain 'e' and resid 117 through 130 Processing helix chain 'e' and resid 149 through 151 No H-bonds generated for 'chain 'e' and resid 149 through 151' Processing helix chain 'e' and resid 184 through 195 Processing helix chain 'e' and resid 258 through 263 removed outlier: 3.683A pdb=" N ASP e 262 " --> pdb=" O ASP e 258 " (cutoff:3.500A) Processing helix chain 'e' and resid 272 through 274 No H-bonds generated for 'chain 'e' and resid 272 through 274' Processing helix chain 'f' and resid 100 through 115 Processing helix chain 'f' and resid 164 through 177 Processing helix chain 'g' and resid 45 through 51 removed outlier: 3.994A pdb=" N ARG g 50 " --> pdb=" O PHE g 47 " (cutoff:3.500A) Processing helix chain 'g' and resid 117 through 131 removed outlier: 3.580A pdb=" N SER g 129 " --> pdb=" O GLU g 125 " (cutoff:3.500A) Proline residue: g 130 - end of helix Processing helix chain 'g' and resid 154 through 164 Processing helix chain 'h' and resid 66 through 77 Processing helix chain 'h' and resid 86 through 88 No H-bonds generated for 'chain 'h' and resid 86 through 88' Processing helix chain 'h' and resid 94 through 108 Processing helix chain 'h' and resid 123 through 130 Processing helix chain 'h' and resid 139 through 144 Processing helix chain 'i' and resid 49 through 52 No H-bonds generated for 'chain 'i' and resid 49 through 52' Processing helix chain 'i' and resid 70 through 72 No H-bonds generated for 'chain 'i' and resid 70 through 72' Processing helix chain 'i' and resid 78 through 80 No H-bonds generated for 'chain 'i' and resid 78 through 80' Processing helix chain 'i' and resid 87 through 101 removed outlier: 6.235A pdb=" N SER i 100 " --> pdb=" O LYS i 96 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG i 101 " --> pdb=" O MET i 97 " (cutoff:3.500A) Processing helix chain 'i' and resid 104 through 121 Processing helix chain 'j' and resid 26 through 30 Processing helix chain 'j' and resid 42 through 45 No H-bonds generated for 'chain 'j' and resid 42 through 45' Processing helix chain 'j' and resid 61 through 104 Processing helix chain 'k' and resid 28 through 36 Processing helix chain 'k' and resid 40 through 43 No H-bonds generated for 'chain 'k' and resid 40 through 43' Processing helix chain 'k' and resid 83 through 95 Processing helix chain 'l' and resid 115 through 132 Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 57 through 59 No H-bonds generated for 'chain 'o' and resid 57 through 59' Processing helix chain 'o' and resid 64 through 80 Processing helix chain 'o' and resid 88 through 98 removed outlier: 4.375A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N THR o 98 " --> pdb=" O HIS o 94 " (cutoff:3.500A) Processing helix chain 'p' and resid 45 through 48 No H-bonds generated for 'chain 'p' and resid 45 through 48' Processing helix chain 'p' and resid 56 through 58 No H-bonds generated for 'chain 'p' and resid 56 through 58' Processing helix chain 'p' and resid 113 through 122 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 143 through 162 Processing helix chain 'p' and resid 175 through 186 Processing helix chain 'q' and resid 54 through 64 Processing helix chain 'q' and resid 66 through 68 No H-bonds generated for 'chain 'q' and resid 66 through 68' Processing helix chain 'q' and resid 72 through 74 No H-bonds generated for 'chain 'q' and resid 72 through 74' Processing helix chain 'q' and resid 79 through 92 Processing helix chain 'q' and resid 96 through 147 Proline residue: q 129 - end of helix Processing helix chain 'r' and resid 73 through 75 No H-bonds generated for 'chain 'r' and resid 73 through 75' Processing helix chain 'r' and resid 87 through 92 removed outlier: 4.844A pdb=" N PHE r 92 " --> pdb=" O LEU r 88 " (cutoff:3.500A) Processing helix chain 'r' and resid 102 through 105 No H-bonds generated for 'chain 'r' and resid 102 through 105' Processing helix chain 'r' and resid 109 through 123 Processing helix chain 'r' and resid 179 through 181 No H-bonds generated for 'chain 'r' and resid 179 through 181' Processing helix chain 's' and resid 56 through 72 Processing helix chain 's' and resid 76 through 84 Processing helix chain 's' and resid 102 through 110 Processing helix chain 's' and resid 141 through 154 Processing helix chain 's' and resid 168 through 171 No H-bonds generated for 'chain 's' and resid 168 through 171' Processing helix chain 's' and resid 173 through 188 Processing helix chain 's' and resid 193 through 197 Processing helix chain 's' and resid 308 through 313 Processing helix chain 's' and resid 319 through 341 Processing helix chain 's' and resid 416 through 424 Processing helix chain 'u' and resid 95 through 103 Processing helix chain 'u' and resid 132 through 149 Processing helix chain 'u' and resid 182 through 188 Processing helix chain 'u' and resid 191 through 195 removed outlier: 3.893A pdb=" N THR u 195 " --> pdb=" O GLU u 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 191 through 195' Processing helix chain 'v' and resid 7 through 21 Processing helix chain 'v' and resid 28 through 39 Processing helix chain 'v' and resid 48 through 63 Processing helix chain 'w' and resid 76 through 88 Processing helix chain 'w' and resid 112 through 122 Processing helix chain 'w' and resid 132 through 137 removed outlier: 3.852A pdb=" N GLU w 136 " --> pdb=" O ASP w 132 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LYS w 137 " --> pdb=" O ILE w 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 132 through 137' Processing helix chain 'w' and resid 141 through 151 Processing sheet with id= A, first strand: chain 'D' and resid 162 through 165 removed outlier: 6.480A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE D 139 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= C, first strand: chain 'D' and resid 232 through 237 removed outlier: 3.632A pdb=" N ARG D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLN D 227 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU D 216 " --> pdb=" O GLN D 227 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 331 through 333 removed outlier: 6.697A pdb=" N TYR E 284 " --> pdb=" O TRP E 274 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE E 276 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE E 282 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU E 296 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS E 209 " --> pdb=" O LEU E 296 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 175 through 181 removed outlier: 6.281A pdb=" N GLY E 148 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL E 129 " --> pdb=" O GLY E 148 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 214 through 216 Processing sheet with id= G, first strand: chain 'F' and resid 62 through 65 Processing sheet with id= H, first strand: chain 'F' and resid 187 through 190 removed outlier: 6.480A pdb=" N LEU F 259 " --> pdb=" O HIS F 188 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N MET F 190 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU F 261 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 111 through 114 Processing sheet with id= J, first strand: chain 'H' and resid 54 through 58 removed outlier: 6.103A pdb=" N GLU H 57 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU H 82 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'I' and resid 122 through 124 Processing sheet with id= L, first strand: chain 'I' and resid 179 through 181 Processing sheet with id= M, first strand: chain 'J' and resid 110 through 113 Processing sheet with id= N, first strand: chain 'K' and resid 125 through 127 removed outlier: 6.328A pdb=" N VAL K 57 " --> pdb=" O HIS K 126 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU K 20 " --> pdb=" O VAL K 142 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLU K 144 " --> pdb=" O LEU K 20 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ASP K 22 " --> pdb=" O GLU K 144 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'K' and resid 76 through 80 Processing sheet with id= P, first strand: chain 'L' and resid 72 through 77 Processing sheet with id= Q, first strand: chain 'M' and resid 153 through 156 removed outlier: 6.555A pdb=" N VAL M 173 " --> pdb=" O ILE M 154 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL M 156 " --> pdb=" O VAL M 173 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N THR M 175 " --> pdb=" O VAL M 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'M' and resid 274 through 276 Processing sheet with id= S, first strand: chain 'M' and resid 92 through 97 removed outlier: 7.279A pdb=" N LYS M 94 " --> pdb=" O TYR M 136 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL M 138 " --> pdb=" O LYS M 94 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU M 96 " --> pdb=" O VAL M 138 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU M 140 " --> pdb=" O LEU M 96 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'N' and resid 87 through 91 Processing sheet with id= U, first strand: chain 'N' and resid 95 through 97 Processing sheet with id= V, first strand: chain 'N' and resid 118 through 122 Processing sheet with id= W, first strand: chain 'N' and resid 129 through 132 Processing sheet with id= X, first strand: chain 'O' and resid 41 through 45 Processing sheet with id= Y, first strand: chain 'P' and resid 80 through 85 Processing sheet with id= Z, first strand: chain 'Q' and resid 173 through 178 removed outlier: 6.757A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) removed outlier: 9.741A pdb=" N LEU Q 134 " --> pdb=" O VAL Q 154 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL Q 154 " --> pdb=" O LEU Q 134 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE Q 150 " --> pdb=" O ILE Q 138 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'S' and resid 104 through 109 removed outlier: 6.524A pdb=" N HIS S 100 " --> pdb=" O VAL S 133 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL S 133 " --> pdb=" O HIS S 100 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'S' and resid 112 through 116 Processing sheet with id= AC, first strand: chain 'S' and resid 127 through 129 removed outlier: 6.241A pdb=" N THR S 159 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE S 195 " --> pdb=" O THR S 159 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'S' and resid 169 through 175 Processing sheet with id= AE, first strand: chain 'T' and resid 72 through 77 removed outlier: 6.347A pdb=" N VAL T 179 " --> pdb=" O ILE T 142 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE T 142 " --> pdb=" O VAL T 179 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'T' and resid 153 through 155 Processing sheet with id= AG, first strand: chain 'U' and resid 26 through 28 removed outlier: 3.723A pdb=" N GLN U 27 " --> pdb=" O ARG U 43 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'V' and resid 120 through 122 removed outlier: 6.720A pdb=" N VAL V 87 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL V 79 " --> pdb=" O TRP V 85 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TRP V 85 " --> pdb=" O VAL V 79 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'V' and resid 93 through 98 Processing sheet with id= AJ, first strand: chain 'V' and resid 133 through 136 removed outlier: 3.774A pdb=" N ARG V 136 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL V 144 " --> pdb=" O ARG V 136 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'W' and resid 81 through 83 removed outlier: 6.036A pdb=" N ALA W 91 " --> pdb=" O ILE W 66 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE W 66 " --> pdb=" O ALA W 91 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'W' and resid 95 through 103 Processing sheet with id= AM, first strand: chain 'X' and resid 50 through 53 removed outlier: 3.732A pdb=" N ASN X 53 " --> pdb=" O GLN X 58 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN X 58 " --> pdb=" O ASN X 53 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'X' and resid 86 through 91 Processing sheet with id= AO, first strand: chain 'X' and resid 110 through 116 Processing sheet with id= AP, first strand: chain 'Y' and resid 166 through 170 Processing sheet with id= AQ, first strand: chain 'Z' and resid 98 through 101 Processing sheet with id= AR, first strand: chain '0' and resid 107 through 109 Processing sheet with id= AS, first strand: chain '0' and resid 156 through 159 removed outlier: 6.147A pdb=" N ARG 0 173 " --> pdb=" O VAL 0 157 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU 0 159 " --> pdb=" O ARG 0 173 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE 0 175 " --> pdb=" O LEU 0 159 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain '1' and resid 29 through 35 Processing sheet with id= AU, first strand: chain '1' and resid 16 through 18 Processing sheet with id= AV, first strand: chain '3' and resid 114 through 116 Processing sheet with id= AW, first strand: chain '5' and resid 266 through 268 removed outlier: 7.044A pdb=" N LEU 5 219 " --> pdb=" O TYR 5 105 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N PHE 5 107 " --> pdb=" O LEU 5 219 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN 5 221 " --> pdb=" O PHE 5 107 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain '5' and resid 126 through 130 removed outlier: 7.203A pdb=" N ASN 5 372 " --> pdb=" O LYS 5 127 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ILE 5 129 " --> pdb=" O ASN 5 372 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA 5 374 " --> pdb=" O ILE 5 129 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N VAL 5 341 " --> pdb=" O TYR 5 287 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N HIS 5 289 " --> pdb=" O VAL 5 341 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU 5 230 " --> pdb=" O HIS 5 289 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain '5' and resid 385 through 387 Processing sheet with id= AZ, first strand: chain '6' and resid 203 through 205 Processing sheet with id= BA, first strand: chain '6' and resid 213 through 220 removed outlier: 5.552A pdb=" N LYS 6 274 " --> pdb=" O PRO 6 313 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain '7' and resid 64 through 69 Processing sheet with id= BC, first strand: chain '7' and resid 282 through 285 removed outlier: 6.058A pdb=" N VAL 7 184 " --> pdb=" O LEU 7 166 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU 7 166 " --> pdb=" O VAL 7 184 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain '7' and resid 217 through 221 Processing sheet with id= BE, first strand: chain '7' and resid 275 through 280 removed outlier: 6.635A pdb=" N LEU 7 302 " --> pdb=" O PHE 7 276 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N TYR 7 278 " --> pdb=" O VAL 7 300 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL 7 300 " --> pdb=" O TYR 7 278 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain '9' and resid 42 through 45 Processing sheet with id= BG, first strand: chain 'a' and resid 45 through 51 Processing sheet with id= BH, first strand: chain 'b' and resid 28 through 31 removed outlier: 6.561A pdb=" N VAL b 62 " --> pdb=" O LEU b 29 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N PHE b 31 " --> pdb=" O VAL b 62 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR b 64 " --> pdb=" O PHE b 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= BH Processing sheet with id= BI, first strand: chain 'b' and resid 74 through 78 Processing sheet with id= BJ, first strand: chain 'c' and resid 254 through 259 removed outlier: 6.518A pdb=" N PHE c 271 " --> pdb=" O THR c 258 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N CYS c 276 " --> pdb=" O LEU c 280 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU c 280 " --> pdb=" O CYS c 276 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'd' and resid 184 through 186 removed outlier: 5.283A pdb=" N GLU d 249 " --> pdb=" O MET d 261 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N MET d 261 " --> pdb=" O GLU d 249 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N GLN d 251 " --> pdb=" O TRP d 259 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N TRP d 259 " --> pdb=" O GLN d 251 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'd' and resid 193 through 198 removed outlier: 6.331A pdb=" N THR d 213 " --> pdb=" O VAL d 195 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLN d 211 " --> pdb=" O VAL d 197 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'e' and resid 175 through 177 removed outlier: 6.844A pdb=" N GLY e 228 " --> pdb=" O ARG e 46 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU e 48 " --> pdb=" O GLY e 228 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS e 230 " --> pdb=" O LEU e 48 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ALA e 50 " --> pdb=" O LYS e 230 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE e 232 " --> pdb=" O ALA e 50 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'e' and resid 161 through 164 Processing sheet with id= BO, first strand: chain 'e' and resid 199 through 204 removed outlier: 6.182A pdb=" N LYS e 203 " --> pdb=" O LEU e 238 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU e 238 " --> pdb=" O LYS e 203 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'f' and resid 93 through 97 Processing sheet with id= BQ, first strand: chain 'g' and resid 96 through 101 Processing sheet with id= BR, first strand: chain 'k' and resid 50 through 55 Processing sheet with id= BS, first strand: chain 'm' and resid 52 through 56 Processing sheet with id= BT, first strand: chain 'p' and resid 77 through 80 Processing sheet with id= BU, first strand: chain 'r' and resid 36 through 41 Processing sheet with id= BV, first strand: chain 's' and resid 90 through 93 removed outlier: 6.802A pdb=" N ARG s 230 " --> pdb=" O TYR s 91 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL s 93 " --> pdb=" O ARG s 230 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLN s 232 " --> pdb=" O VAL s 93 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 's' and resid 112 through 116 removed outlier: 6.717A pdb=" N ASN s 391 " --> pdb=" O VAL s 113 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU s 115 " --> pdb=" O ASN s 391 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N CYS s 393 " --> pdb=" O LEU s 115 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 's' and resid 199 through 202 Processing sheet with id= BY, first strand: chain 'u' and resid 108 through 113 2094 hydrogen bonds defined for protein. 5949 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 713 hydrogen bonds 1226 hydrogen bond angles 0 basepair planarities 295 basepair parallelities 591 stacking parallelities Total time for adding SS restraints: 45.42 Time building geometry restraints manager: 33.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 12146 1.31 - 1.44: 31744 1.44 - 1.57: 47523 1.57 - 1.69: 2197 1.69 - 1.82: 449 Bond restraints: 94059 Sorted by residual: bond pdb=" C ARG P 173 " pdb=" N GLU P 174 " ideal model delta sigma weight residual 1.330 1.384 -0.054 1.47e-02 4.63e+03 1.34e+01 bond pdb=" C GLU E 327 " pdb=" N LEU E 328 " ideal model delta sigma weight residual 1.329 1.269 0.060 1.86e-02 2.89e+03 1.03e+01 bond pdb=" C VAL N 151 " pdb=" N THR N 152 " ideal model delta sigma weight residual 1.335 1.426 -0.092 3.04e-02 1.08e+03 9.06e+00 bond pdb=" C LYS i 68 " pdb=" N HIS i 69 " ideal model delta sigma weight residual 1.331 1.246 0.085 2.83e-02 1.25e+03 8.99e+00 bond pdb=" CG PRO 5 258 " pdb=" CD PRO 5 258 " ideal model delta sigma weight residual 1.512 1.433 0.079 2.70e-02 1.37e+03 8.63e+00 ... (remaining 94054 not shown) Histogram of bond angle deviations from ideal: 92.87 - 102.03: 1246 102.03 - 111.19: 43356 111.19 - 120.34: 51871 120.34 - 129.50: 34694 129.50 - 138.66: 1230 Bond angle restraints: 132397 Sorted by residual: angle pdb=" CA PRO r 64 " pdb=" N PRO r 64 " pdb=" CD PRO r 64 " ideal model delta sigma weight residual 112.00 99.29 12.71 1.40e+00 5.10e-01 8.25e+01 angle pdb=" CA PRO 5 258 " pdb=" N PRO 5 258 " pdb=" CD PRO 5 258 " ideal model delta sigma weight residual 111.50 99.32 12.18 1.40e+00 5.10e-01 7.57e+01 angle pdb=" C ARG X 36 " pdb=" N THR X 37 " pdb=" CA THR X 37 " ideal model delta sigma weight residual 120.49 130.66 -10.17 1.42e+00 4.96e-01 5.13e+01 angle pdb=" N VAL s 251 " pdb=" CA VAL s 251 " pdb=" C VAL s 251 " ideal model delta sigma weight residual 109.19 103.48 5.71 8.20e-01 1.49e+00 4.85e+01 angle pdb=" C LYS 9 71 " pdb=" CA LYS 9 71 " pdb=" CB LYS 9 71 " ideal model delta sigma weight residual 108.88 118.24 -9.36 1.50e+00 4.44e-01 3.90e+01 ... (remaining 132392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 54836 35.90 - 71.80: 2597 71.80 - 107.70: 360 107.70 - 143.60: 8 143.60 - 179.50: 30 Dihedral angle restraints: 57831 sinusoidal: 34222 harmonic: 23609 Sorted by residual: dihedral pdb=" O4' U A1228 " pdb=" C1' U A1228 " pdb=" N1 U A1228 " pdb=" C2 U A1228 " ideal model delta sinusoidal sigma weight residual -160.00 9.49 -169.49 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' C A 709 " pdb=" C1' C A 709 " pdb=" N1 C A 709 " pdb=" C2 C A 709 " ideal model delta sinusoidal sigma weight residual 200.00 32.00 168.00 1 1.50e+01 4.44e-03 8.44e+01 dihedral pdb=" O4' C A 143 " pdb=" C1' C A 143 " pdb=" N1 C A 143 " pdb=" C2 C A 143 " ideal model delta sinusoidal sigma weight residual -160.00 3.29 -163.29 1 1.50e+01 4.44e-03 8.35e+01 ... (remaining 57828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 13948 0.087 - 0.175: 1288 0.175 - 0.262: 83 0.262 - 0.349: 14 0.349 - 0.436: 3 Chirality restraints: 15336 Sorted by residual: chirality pdb=" CG LEU 6 218 " pdb=" CB LEU 6 218 " pdb=" CD1 LEU 6 218 " pdb=" CD2 LEU 6 218 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" C3' A A 153 " pdb=" C4' A A 153 " pdb=" O3' A A 153 " pdb=" C2' A A 153 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CB VAL s 251 " pdb=" CA VAL s 251 " pdb=" CG1 VAL s 251 " pdb=" CG2 VAL s 251 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 15333 not shown) Planarity restraints: 12900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO r 63 " -0.110 5.00e-02 4.00e+02 1.56e-01 3.88e+01 pdb=" N PRO r 64 " 0.269 5.00e-02 4.00e+02 pdb=" CA PRO r 64 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO r 64 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 113 " 0.093 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO D 114 " -0.239 5.00e-02 4.00e+02 pdb=" CA PRO D 114 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO D 114 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 108 " -0.345 9.50e-02 1.11e+02 1.55e-01 1.48e+01 pdb=" NE ARG F 108 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG F 108 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG F 108 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG F 108 " -0.010 2.00e-02 2.50e+03 ... (remaining 12897 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 1255 2.61 - 3.18: 70821 3.18 - 3.76: 154104 3.76 - 4.33: 208300 4.33 - 4.90: 316269 Nonbonded interactions: 750749 Sorted by model distance: nonbonded pdb=" OP2 G A 106 " pdb="MG MG A1634 " model vdw 2.041 2.170 nonbonded pdb=" OP2 A A 703 " pdb="MG MG A1674 " model vdw 2.064 2.170 nonbonded pdb=" O4 U A 752 " pdb="MG MG A1674 " model vdw 2.073 2.170 nonbonded pdb=" OP1 A A 623 " pdb="MG MG A1667 " model vdw 2.077 2.170 nonbonded pdb=" OP2 G A 341 " pdb="MG MG A1638 " model vdw 2.087 2.170 ... (remaining 750744 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 12.730 Check model and map are aligned: 1.000 Set scattering table: 0.600 Process input model: 223.260 Find NCS groups from input model: 2.660 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 247.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 : 0.006 0.140 94059 Z= 0.379 Angle : 0.954 14.549 132397 Z= 0.502 Chirality : 0.051 0.436 15336 Planarity : 0.008 0.156 12900 Dihedral : 18.535 179.496 42533 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 0.10 % Allowed : 0.39 % Favored : 99.51 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.19 % 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: -1.48 (0.09), residues: 7941 helix: -0.76 (0.09), residues: 2658 sheet: -0.87 (0.16), residues: 967 loop : -1.10 (0.09), residues: 4316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP V 170 HIS 0.015 0.001 HIS 7 94 PHE 0.052 0.003 PHE 6 258 TYR 0.045 0.003 TYR V 187 ARG 0.020 0.001 ARG 5 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1550 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1543 time to evaluate : 6.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 100 ILE cc_start: 0.8012 (mt) cc_final: 0.7764 (mt) REVERT: E 175 THR cc_start: 0.8368 (p) cc_final: 0.8167 (p) REVERT: E 331 ASP cc_start: 0.7778 (p0) cc_final: 0.7193 (p0) REVERT: E 333 TYR cc_start: 0.7758 (m-10) cc_final: 0.7458 (m-10) REVERT: F 232 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7510 (mm-30) REVERT: K 42 LEU cc_start: 0.8943 (mm) cc_final: 0.8695 (mt) REVERT: K 135 GLU cc_start: 0.6914 (tm-30) cc_final: 0.6603 (tm-30) REVERT: Q 243 ILE cc_start: 0.8110 (mm) cc_final: 0.7794 (mm) REVERT: S 84 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8518 (t0) REVERT: T 168 GLU cc_start: 0.6149 (pt0) cc_final: 0.5798 (pt0) REVERT: T 187 GLU cc_start: 0.5795 (tp30) cc_final: 0.5296 (tt0) REVERT: V 176 ASP cc_start: 0.7024 (m-30) cc_final: 0.6564 (t0) REVERT: X 129 MET cc_start: 0.6690 (mmm) cc_final: 0.6419 (mmm) REVERT: X 142 ASP cc_start: 0.6722 (t0) cc_final: 0.6221 (t0) REVERT: X 165 MET cc_start: 0.8093 (mmt) cc_final: 0.7606 (mmt) REVERT: X 212 ILE cc_start: 0.9268 (mt) cc_final: 0.9068 (mm) REVERT: Y 139 MET cc_start: 0.8623 (mmm) cc_final: 0.8237 (mmm) REVERT: 2 88 LYS cc_start: 0.7986 (ttmt) cc_final: 0.7636 (tttt) REVERT: 5 106 ILE cc_start: 0.8853 (mm) cc_final: 0.8647 (mm) REVERT: 5 245 ILE cc_start: 0.7646 (pt) cc_final: 0.7409 (pt) REVERT: 6 185 MET cc_start: 0.3147 (mmp) cc_final: 0.1159 (mmp) REVERT: 7 165 ASN cc_start: 0.7337 (t0) cc_final: 0.6940 (t0) REVERT: 7 193 MET cc_start: 0.7543 (mmm) cc_final: 0.7324 (mmm) REVERT: d 168 CYS cc_start: 0.7464 (t) cc_final: 0.7153 (t) REVERT: d 185 PHE cc_start: 0.7387 (t80) cc_final: 0.7068 (t80) REVERT: d 243 LEU cc_start: 0.7795 (tp) cc_final: 0.7165 (tt) REVERT: f 48 TYR cc_start: 0.7325 (t80) cc_final: 0.7114 (t80) REVERT: f 127 MET cc_start: 0.1978 (mmm) cc_final: 0.1052 (mmt) REVERT: g 45 TYR cc_start: 0.8016 (t80) cc_final: 0.7802 (t80) REVERT: h 76 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7651 (tm-30) REVERT: h 96 LEU cc_start: 0.7639 (mm) cc_final: 0.7399 (tp) REVERT: h 137 ARG cc_start: 0.6606 (ptt-90) cc_final: 0.6393 (ptt-90) REVERT: i 58 ASP cc_start: 0.7827 (m-30) cc_final: 0.7597 (m-30) REVERT: i 84 LYS cc_start: 0.8061 (ptmt) cc_final: 0.7820 (ptpp) REVERT: p 74 ASP cc_start: 0.7375 (p0) cc_final: 0.6782 (p0) REVERT: q 84 GLU cc_start: 0.6982 (tp30) cc_final: 0.6727 (tp30) REVERT: q 128 MET cc_start: 0.7162 (tmm) cc_final: 0.5693 (ttm) REVERT: r 170 ASN cc_start: 0.7700 (t0) cc_final: 0.7438 (t0) outliers start: 7 outliers final: 1 residues processed: 1548 average time/residue: 0.8681 time to fit residues: 2308.3449 Evaluate side-chains 1210 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1208 time to evaluate : 6.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 118 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 895 random chunks: chunk 755 optimal weight: 0.6980 chunk 678 optimal weight: 50.0000 chunk 376 optimal weight: 0.5980 chunk 231 optimal weight: 30.0000 chunk 457 optimal weight: 6.9990 chunk 362 optimal weight: 2.9990 chunk 701 optimal weight: 0.6980 chunk 271 optimal weight: 0.6980 chunk 426 optimal weight: 1.9990 chunk 522 optimal weight: 6.9990 chunk 812 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 GLN F 184 GLN F 257 GLN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 HIS ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 158 GLN Q 175 GLN R 89 ASN R 149 HIS T 62 GLN T 133 ASN T 210 HIS V 78 GLN V 117 HIS W 76 HIS X 177 HIS Y 89 GLN Z 53 HIS 0 118 GLN ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 163 HIS ** 7 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 84 ASN 7 284 HIS ** 7 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 143 GLN 9 123 GLN ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 107 GLN d 149 HIS ** d 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 274 GLN h 67 GLN ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 19 GLN ** o 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 143 GLN r 146 GLN ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 358 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 94059 Z= 0.178 Angle : 0.612 12.368 132397 Z= 0.310 Chirality : 0.040 0.286 15336 Planarity : 0.005 0.084 12900 Dihedral : 19.872 179.848 25439 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.55 % Rotamer: Outliers : 1.62 % Allowed : 9.20 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.19 % 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: -0.91 (0.09), residues: 7941 helix: -0.01 (0.10), residues: 2673 sheet: -0.77 (0.16), residues: 983 loop : -0.90 (0.09), residues: 4285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP 6 235 HIS 0.011 0.001 HIS 7 94 PHE 0.030 0.002 PHE Q 164 TYR 0.021 0.001 TYR 5 176 ARG 0.010 0.000 ARG v 6 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1441 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1325 time to evaluate : 6.378 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: D 263 ASN cc_start: 0.6132 (t0) cc_final: 0.5590 (m110) REVERT: E 100 ILE cc_start: 0.7892 (mt) cc_final: 0.7668 (mt) REVERT: H 59 TRP cc_start: 0.6976 (OUTLIER) cc_final: 0.5627 (m-10) REVERT: K 42 LEU cc_start: 0.9005 (mm) cc_final: 0.8779 (mt) REVERT: K 135 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6630 (tm-30) REVERT: K 144 GLU cc_start: 0.7771 (tp30) cc_final: 0.7525 (tp30) REVERT: K 153 LYS cc_start: 0.7989 (ptmt) cc_final: 0.7643 (ptmm) REVERT: M 252 LEU cc_start: 0.8007 (mm) cc_final: 0.7801 (mt) REVERT: O 52 MET cc_start: 0.7895 (tmm) cc_final: 0.7687 (tmm) REVERT: O 120 MET cc_start: 0.8313 (mmm) cc_final: 0.8037 (mmm) REVERT: P 158 MET cc_start: 0.4948 (ppp) cc_final: 0.3653 (ptp) REVERT: Q 243 ILE cc_start: 0.8092 (mm) cc_final: 0.7803 (mm) REVERT: T 168 GLU cc_start: 0.6126 (pt0) cc_final: 0.5810 (pt0) REVERT: T 187 GLU cc_start: 0.5655 (tp30) cc_final: 0.5141 (tt0) REVERT: V 176 ASP cc_start: 0.7131 (m-30) cc_final: 0.6755 (t0) REVERT: X 165 MET cc_start: 0.7985 (mmt) cc_final: 0.7306 (mmt) REVERT: 5 245 ILE cc_start: 0.7700 (pt) cc_final: 0.7445 (pt) REVERT: 6 63 GLN cc_start: 0.6518 (mp10) cc_final: 0.6248 (mp10) REVERT: 7 93 MET cc_start: 0.8240 (ppp) cc_final: 0.6825 (ptt) REVERT: 7 165 ASN cc_start: 0.7196 (t0) cc_final: 0.6913 (t0) REVERT: 7 214 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8807 (mp) REVERT: c 97 TYR cc_start: 0.8598 (t80) cc_final: 0.8316 (t80) REVERT: d 196 GLN cc_start: 0.8140 (tp-100) cc_final: 0.7769 (tp-100) REVERT: d 226 ASP cc_start: 0.7436 (m-30) cc_final: 0.7129 (m-30) REVERT: d 243 LEU cc_start: 0.7607 (tp) cc_final: 0.6924 (tt) REVERT: e 234 PHE cc_start: 0.1653 (t80) cc_final: 0.1041 (t80) REVERT: e 243 PHE cc_start: -0.2034 (t80) cc_final: -0.2464 (t80) REVERT: f 48 TYR cc_start: 0.7384 (t80) cc_final: 0.7118 (t80) REVERT: g 107 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7908 (mtp) REVERT: h 76 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7729 (tm-30) REVERT: h 153 LYS cc_start: 0.7501 (mmmm) cc_final: 0.7257 (mmmm) REVERT: i 58 ASP cc_start: 0.7777 (m-30) cc_final: 0.7538 (m-30) REVERT: i 84 LYS cc_start: 0.8064 (ptmt) cc_final: 0.7817 (ptpp) REVERT: p 74 ASP cc_start: 0.7359 (p0) cc_final: 0.6824 (p0) REVERT: p 157 MET cc_start: 0.7361 (tmm) cc_final: 0.6521 (ttm) REVERT: q 131 MET cc_start: 0.6189 (OUTLIER) cc_final: 0.3954 (ptp) outliers start: 116 outliers final: 76 residues processed: 1366 average time/residue: 0.8074 time to fit residues: 1892.0798 Evaluate side-chains 1260 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1180 time to evaluate : 6.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain H residue 59 TRP Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 26 LYS Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 117 HIS Chi-restraints excluded: chain W residue 56 MET Chi-restraints excluded: chain X residue 218 LEU Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Z residue 114 LYS Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 124 THR Chi-restraints excluded: chain 5 residue 218 LEU Chi-restraints excluded: chain 5 residue 327 LEU Chi-restraints excluded: chain 6 residue 69 HIS Chi-restraints excluded: chain 6 residue 291 TYR Chi-restraints excluded: chain 6 residue 379 ILE Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 176 SER Chi-restraints excluded: chain 7 residue 214 LEU Chi-restraints excluded: chain 9 residue 46 SER Chi-restraints excluded: chain 9 residue 65 LEU Chi-restraints excluded: chain c residue 147 ASP Chi-restraints excluded: chain d residue 221 THR Chi-restraints excluded: chain e residue 233 PHE Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain f residue 113 LEU Chi-restraints excluded: chain g residue 65 HIS Chi-restraints excluded: chain g residue 107 MET Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 90 SER Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 62 ILE Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain o residue 28 SER Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain p residue 61 VAL Chi-restraints excluded: chain p residue 78 ILE Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 131 MET Chi-restraints excluded: chain r residue 107 LEU Chi-restraints excluded: chain r residue 121 MET Chi-restraints excluded: chain r residue 180 LEU Chi-restraints excluded: chain s residue 182 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 895 random chunks: chunk 451 optimal weight: 10.0000 chunk 252 optimal weight: 0.9980 chunk 676 optimal weight: 10.0000 chunk 553 optimal weight: 9.9990 chunk 224 optimal weight: 8.9990 chunk 814 optimal weight: 10.0000 chunk 879 optimal weight: 10.0000 chunk 725 optimal weight: 4.9990 chunk 807 optimal weight: 4.9990 chunk 277 optimal weight: 5.9990 chunk 653 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 GLN E 57 ASN E 72 GLN F 184 GLN ** F 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 HIS P 97 GLN ** S 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 62 GLN U 27 GLN V 92 ASN V 117 HIS X 15 GLN X 89 GLN X 177 HIS Z 53 HIS ** Z 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 118 GLN 2 77 GLN ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 266 HIS 6 332 HIS ** 7 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 84 ASN 7 284 HIS ** 7 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 309 HIS 8 143 GLN 8 158 HIS ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 157 HIS ** d 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 274 GLN h 67 GLN h 119 GLN ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 112 HIS r 146 GLN ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 280 ASN s 315 ASN s 358 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 94059 Z= 0.447 Angle : 0.713 11.578 132397 Z= 0.359 Chirality : 0.045 0.378 15336 Planarity : 0.006 0.090 12900 Dihedral : 19.748 178.848 25435 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.89 % Rotamer: Outliers : 2.97 % Allowed : 11.98 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.09), residues: 7941 helix: 0.24 (0.10), residues: 2680 sheet: -0.78 (0.16), residues: 987 loop : -0.86 (0.09), residues: 4274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 6 235 HIS 0.018 0.002 HIS V 117 PHE 0.042 0.002 PHE 6 270 TYR 0.029 0.002 TYR 5 176 ARG 0.009 0.001 ARG F 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1454 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1242 time to evaluate : 6.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 263 ASN cc_start: 0.6496 (t0) cc_final: 0.5860 (m-40) REVERT: H 59 TRP cc_start: 0.7410 (OUTLIER) cc_final: 0.6027 (m-10) REVERT: H 81 LYS cc_start: 0.8666 (ttpt) cc_final: 0.7946 (ttpt) REVERT: K 90 VAL cc_start: 0.9239 (p) cc_final: 0.8990 (m) REVERT: K 135 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6842 (tm-30) REVERT: K 153 LYS cc_start: 0.8259 (ptmt) cc_final: 0.8022 (ptmm) REVERT: M 170 ASN cc_start: 0.7965 (m-40) cc_final: 0.7614 (m110) REVERT: N 107 LEU cc_start: 0.7649 (pp) cc_final: 0.7424 (pt) REVERT: Q 167 TYR cc_start: 0.8317 (m-80) cc_final: 0.8069 (m-80) REVERT: Q 243 ILE cc_start: 0.8179 (mm) cc_final: 0.7892 (mm) REVERT: R 16 ASP cc_start: 0.6946 (t70) cc_final: 0.6595 (t70) REVERT: S 73 THR cc_start: 0.8526 (p) cc_final: 0.8052 (m) REVERT: S 109 THR cc_start: 0.9071 (t) cc_final: 0.8807 (p) REVERT: X 89 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8076 (mp-120) REVERT: X 165 MET cc_start: 0.8124 (mmt) cc_final: 0.7875 (mmt) REVERT: 0 181 ARG cc_start: 0.8011 (tpp80) cc_final: 0.7674 (tpp-160) REVERT: 7 93 MET cc_start: 0.8176 (ppp) cc_final: 0.7016 (ptt) REVERT: c 310 ASN cc_start: 0.8727 (p0) cc_final: 0.8481 (p0) REVERT: e 217 PHE cc_start: 0.4812 (p90) cc_final: 0.4324 (m-80) REVERT: e 234 PHE cc_start: 0.1917 (t80) cc_final: 0.1318 (t80) REVERT: e 243 PHE cc_start: -0.2132 (t80) cc_final: -0.2443 (t80) REVERT: h 67 GLN cc_start: 0.7806 (mm110) cc_final: 0.7578 (mm110) REVERT: h 76 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7765 (tm-30) REVERT: i 58 ASP cc_start: 0.7858 (m-30) cc_final: 0.7632 (m-30) REVERT: j 96 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8153 (tp40) REVERT: p 74 ASP cc_start: 0.7426 (p0) cc_final: 0.6883 (p0) REVERT: p 157 MET cc_start: 0.7640 (tmm) cc_final: 0.6925 (ttm) REVERT: q 131 MET cc_start: 0.6307 (OUTLIER) cc_final: 0.3952 (ptp) REVERT: r 169 TRP cc_start: 0.7722 (p-90) cc_final: 0.7428 (p-90) REVERT: r 170 ASN cc_start: 0.7908 (t0) cc_final: 0.7701 (t0) REVERT: s 51 MET cc_start: 0.8058 (tpp) cc_final: 0.7662 (mmm) REVERT: u 96 MET cc_start: 0.6722 (pmm) cc_final: 0.6465 (pmm) outliers start: 212 outliers final: 144 residues processed: 1346 average time/residue: 0.8158 time to fit residues: 1890.1684 Evaluate side-chains 1307 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1159 time to evaluate : 6.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain H residue 59 TRP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain N residue 235 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 26 LYS Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 46 MET Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 171 ILE Chi-restraints excluded: chain W residue 56 MET Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 89 GLN Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 218 LEU Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain Y residue 90 LEU Chi-restraints excluded: chain Y residue 126 MET Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Z residue 86 ILE Chi-restraints excluded: chain Z residue 103 ILE Chi-restraints excluded: chain Z residue 114 LYS Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain 0 residue 129 LYS Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 121 LEU Chi-restraints excluded: chain 5 residue 124 THR Chi-restraints excluded: chain 5 residue 153 CYS Chi-restraints excluded: chain 5 residue 166 THR Chi-restraints excluded: chain 5 residue 180 ILE Chi-restraints excluded: chain 5 residue 218 LEU Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 327 LEU Chi-restraints excluded: chain 5 residue 345 VAL Chi-restraints excluded: chain 5 residue 365 ASP Chi-restraints excluded: chain 6 residue 69 HIS Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 366 LEU Chi-restraints excluded: chain 6 residue 379 ILE Chi-restraints excluded: chain 7 residue 160 ASP Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 176 SER Chi-restraints excluded: chain 9 residue 46 SER Chi-restraints excluded: chain 9 residue 65 LEU Chi-restraints excluded: chain 9 residue 74 VAL Chi-restraints excluded: chain 9 residue 136 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 115 MET Chi-restraints excluded: chain b residue 32 SER Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain c residue 100 SER Chi-restraints excluded: chain c residue 147 ASP Chi-restraints excluded: chain d residue 216 MET Chi-restraints excluded: chain e residue 233 PHE Chi-restraints excluded: chain g residue 101 THR Chi-restraints excluded: chain g residue 107 MET Chi-restraints excluded: chain g residue 109 VAL Chi-restraints excluded: chain g residue 146 THR Chi-restraints excluded: chain h residue 90 SER Chi-restraints excluded: chain h residue 151 ASN Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain j residue 96 GLN Chi-restraints excluded: chain m residue 74 MET Chi-restraints excluded: chain o residue 28 SER Chi-restraints excluded: chain o residue 32 LYS Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain p residue 41 SER Chi-restraints excluded: chain p residue 48 LEU Chi-restraints excluded: chain p residue 61 VAL Chi-restraints excluded: chain p residue 73 LEU Chi-restraints excluded: chain p residue 78 ILE Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 162 SER Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 88 GLU Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain q residue 131 MET Chi-restraints excluded: chain r residue 107 LEU Chi-restraints excluded: chain r residue 121 MET Chi-restraints excluded: chain r residue 180 LEU Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 362 THR Chi-restraints excluded: chain u residue 103 GLN Chi-restraints excluded: chain u residue 186 GLU Chi-restraints excluded: chain u residue 200 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 895 random chunks: chunk 804 optimal weight: 1.9990 chunk 612 optimal weight: 40.0000 chunk 422 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 388 optimal weight: 40.0000 chunk 546 optimal weight: 0.6980 chunk 817 optimal weight: 10.0000 chunk 865 optimal weight: 7.9990 chunk 426 optimal weight: 0.9990 chunk 774 optimal weight: 20.0000 chunk 233 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 GLN F 184 GLN ** F 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN I 91 GLN R 36 ASN ** S 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 62 GLN V 117 HIS X 177 HIS X 237 GLN ** Z 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 181 HIS ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 84 ASN ** 7 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 284 HIS ** 7 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 GLN ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 149 HIS ** d 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 274 GLN ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 112 HIS r 146 GLN s 152 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 94059 Z= 0.348 Angle : 0.650 11.790 132397 Z= 0.327 Chirality : 0.043 0.332 15336 Planarity : 0.005 0.076 12900 Dihedral : 19.686 178.843 25435 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.15 % Rotamer: Outliers : 3.26 % Allowed : 14.59 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.09), residues: 7941 helix: 0.41 (0.10), residues: 2714 sheet: -0.87 (0.16), residues: 996 loop : -0.76 (0.10), residues: 4231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 2 66 HIS 0.009 0.001 HIS i 69 PHE 0.033 0.002 PHE e 131 TYR 0.024 0.002 TYR 5 176 ARG 0.010 0.001 ARG g 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1461 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1228 time to evaluate : 6.370 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: D 263 ASN cc_start: 0.6582 (t0) cc_final: 0.5898 (m-40) REVERT: E 66 SER cc_start: 0.8508 (t) cc_final: 0.8284 (p) REVERT: E 184 ASN cc_start: 0.8407 (p0) cc_final: 0.7963 (p0) REVERT: H 59 TRP cc_start: 0.7403 (OUTLIER) cc_final: 0.6070 (m-10) REVERT: K 90 VAL cc_start: 0.9199 (p) cc_final: 0.8944 (m) REVERT: M 39 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6903 (ptm160) REVERT: M 170 ASN cc_start: 0.7952 (m-40) cc_final: 0.7588 (m110) REVERT: P 158 MET cc_start: 0.4943 (ppp) cc_final: 0.3479 (ptp) REVERT: P 177 ARG cc_start: 0.7402 (ttt-90) cc_final: 0.7158 (ttt-90) REVERT: S 73 THR cc_start: 0.8664 (p) cc_final: 0.8245 (m) REVERT: S 109 THR cc_start: 0.9079 (t) cc_final: 0.8854 (p) REVERT: V 78 GLN cc_start: 0.8886 (tm130) cc_final: 0.8316 (tm-30) REVERT: 0 181 ARG cc_start: 0.8080 (tpp80) cc_final: 0.7716 (tpp-160) REVERT: 7 93 MET cc_start: 0.8007 (ppp) cc_final: 0.7066 (ptt) REVERT: 7 143 TRP cc_start: 0.8970 (OUTLIER) cc_final: 0.7902 (m-90) REVERT: c 127 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: h 76 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7797 (tm-30) REVERT: h 77 VAL cc_start: 0.8682 (p) cc_final: 0.8325 (p) REVERT: i 58 ASP cc_start: 0.7925 (m-30) cc_final: 0.7672 (m-30) REVERT: j 48 ASP cc_start: 0.7679 (m-30) cc_final: 0.7414 (m-30) REVERT: p 74 ASP cc_start: 0.7408 (p0) cc_final: 0.6832 (p0) REVERT: p 109 GLU cc_start: 0.7224 (mp0) cc_final: 0.6971 (mp0) REVERT: p 133 LEU cc_start: 0.8518 (mm) cc_final: 0.8171 (mm) REVERT: p 157 MET cc_start: 0.7722 (tmm) cc_final: 0.7245 (ttm) REVERT: q 131 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.4897 (mmm) REVERT: r 120 LYS cc_start: 0.8324 (mttt) cc_final: 0.8014 (mtpt) REVERT: r 150 TYR cc_start: 0.8662 (p90) cc_final: 0.8425 (p90) REVERT: r 169 TRP cc_start: 0.7791 (p-90) cc_final: 0.7460 (p-90) REVERT: r 170 ASN cc_start: 0.8020 (t0) cc_final: 0.7772 (t0) REVERT: s 104 ARG cc_start: 0.7820 (mtp-110) cc_final: 0.7572 (mtp85) REVERT: s 150 LEU cc_start: 0.9395 (mm) cc_final: 0.9070 (mp) REVERT: s 167 GLU cc_start: 0.7189 (pt0) cc_final: 0.6966 (pt0) outliers start: 233 outliers final: 156 residues processed: 1342 average time/residue: 0.8839 time to fit residues: 2052.7399 Evaluate side-chains 1329 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1168 time to evaluate : 6.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain H residue 59 TRP Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 39 ARG Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain N residue 235 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 46 MET Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 171 ILE Chi-restraints excluded: chain V residue 176 ASP Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 88 CYS Chi-restraints excluded: chain W residue 127 TYR Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 218 LEU Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain Y residue 126 MET Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 103 ILE Chi-restraints excluded: chain Z residue 114 LYS Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 138 CYS Chi-restraints excluded: chain 0 residue 89 VAL Chi-restraints excluded: chain 0 residue 129 LYS Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 3 residue 153 THR Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 121 LEU Chi-restraints excluded: chain 5 residue 124 THR Chi-restraints excluded: chain 5 residue 153 CYS Chi-restraints excluded: chain 5 residue 180 ILE Chi-restraints excluded: chain 5 residue 218 LEU Chi-restraints excluded: chain 5 residue 250 ASN Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 327 LEU Chi-restraints excluded: chain 5 residue 345 VAL Chi-restraints excluded: chain 6 residue 271 LEU Chi-restraints excluded: chain 6 residue 366 LEU Chi-restraints excluded: chain 6 residue 379 ILE Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 160 ASP Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 176 SER Chi-restraints excluded: chain 7 residue 269 ILE Chi-restraints excluded: chain 7 residue 281 SER Chi-restraints excluded: chain 9 residue 46 SER Chi-restraints excluded: chain 9 residue 65 LEU Chi-restraints excluded: chain 9 residue 122 THR Chi-restraints excluded: chain 9 residue 136 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 115 MET Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 122 ASP Chi-restraints excluded: chain c residue 100 SER Chi-restraints excluded: chain c residue 127 GLU Chi-restraints excluded: chain c residue 147 ASP Chi-restraints excluded: chain d residue 80 CYS Chi-restraints excluded: chain e residue 233 PHE Chi-restraints excluded: chain f residue 184 LEU Chi-restraints excluded: chain g residue 109 VAL Chi-restraints excluded: chain g residue 114 GLU Chi-restraints excluded: chain h residue 90 SER Chi-restraints excluded: chain h residue 136 ASP Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 62 ILE Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 SER Chi-restraints excluded: chain o residue 32 LYS Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain p residue 41 SER Chi-restraints excluded: chain p residue 48 LEU Chi-restraints excluded: chain p residue 61 VAL Chi-restraints excluded: chain p residue 78 ILE Chi-restraints excluded: chain p residue 100 GLU Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain p residue 162 SER Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 88 GLU Chi-restraints excluded: chain q residue 131 MET Chi-restraints excluded: chain q residue 132 ILE Chi-restraints excluded: chain r residue 72 ILE Chi-restraints excluded: chain r residue 85 ASP Chi-restraints excluded: chain r residue 107 LEU Chi-restraints excluded: chain r residue 121 MET Chi-restraints excluded: chain r residue 146 GLN Chi-restraints excluded: chain r residue 180 LEU Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 301 LEU Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 362 THR Chi-restraints excluded: chain u residue 103 GLN Chi-restraints excluded: chain u residue 200 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 895 random chunks: chunk 720 optimal weight: 8.9990 chunk 491 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 644 optimal weight: 8.9990 chunk 356 optimal weight: 3.9990 chunk 738 optimal weight: 2.9990 chunk 597 optimal weight: 30.0000 chunk 1 optimal weight: 4.9990 chunk 441 optimal weight: 5.9990 chunk 776 optimal weight: 50.0000 chunk 218 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 184 GLN ** F 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 62 GLN V 117 HIS ** W 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 177 HIS ** Z 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 69 HIS 7 84 ASN ** 7 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 54 GLN ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 110 HIS ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 112 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 94059 Z= 0.494 Angle : 0.739 22.091 132397 Z= 0.370 Chirality : 0.046 0.372 15336 Planarity : 0.006 0.088 12900 Dihedral : 19.722 178.939 25435 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.05 % Favored : 94.93 % Rotamer: Outliers : 4.14 % Allowed : 15.37 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.09), residues: 7941 helix: 0.36 (0.10), residues: 2709 sheet: -0.88 (0.16), residues: 1005 loop : -0.82 (0.10), residues: 4227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP 2 66 HIS 0.013 0.001 HIS s 221 PHE 0.036 0.002 PHE d 185 TYR 0.029 0.002 TYR 5 176 ARG 0.010 0.001 ARG u 185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1516 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1220 time to evaluate : 6.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 263 ASN cc_start: 0.6671 (t0) cc_final: 0.5940 (m-40) REVERT: E 66 SER cc_start: 0.8513 (t) cc_final: 0.8286 (p) REVERT: E 184 ASN cc_start: 0.8402 (p0) cc_final: 0.8019 (p0) REVERT: F 199 ASP cc_start: 0.8181 (t0) cc_final: 0.7950 (t0) REVERT: H 59 TRP cc_start: 0.7521 (OUTLIER) cc_final: 0.6175 (m-10) REVERT: H 69 ARG cc_start: 0.5542 (mmm160) cc_final: 0.4445 (mmm160) REVERT: K 90 VAL cc_start: 0.9202 (p) cc_final: 0.8929 (m) REVERT: K 95 LEU cc_start: 0.9525 (tt) cc_final: 0.9245 (tt) REVERT: M 39 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.7033 (ptm160) REVERT: M 170 ASN cc_start: 0.8103 (m-40) cc_final: 0.7694 (m110) REVERT: P 179 TYR cc_start: 0.7853 (m-80) cc_final: 0.7349 (m-80) REVERT: Q 167 TYR cc_start: 0.8360 (m-10) cc_final: 0.8151 (m-10) REVERT: R 23 GLU cc_start: 0.7525 (tp30) cc_final: 0.7254 (tp30) REVERT: S 73 THR cc_start: 0.8673 (p) cc_final: 0.8401 (m) REVERT: S 109 THR cc_start: 0.9129 (t) cc_final: 0.8911 (p) REVERT: X 70 TYR cc_start: 0.8721 (t80) cc_final: 0.8479 (t80) REVERT: 0 181 ARG cc_start: 0.8161 (tpp80) cc_final: 0.7868 (tpp-160) REVERT: 7 93 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7137 (ptt) REVERT: 7 143 TRP cc_start: 0.9127 (OUTLIER) cc_final: 0.7949 (m-90) REVERT: a 114 LYS cc_start: 0.8344 (mttt) cc_final: 0.8066 (mttt) REVERT: c 97 TYR cc_start: 0.8637 (t80) cc_final: 0.8292 (t80) REVERT: c 127 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: c 307 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8309 (m-80) REVERT: g 68 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.8971 (t) REVERT: h 76 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7857 (tm-30) REVERT: h 77 VAL cc_start: 0.8694 (p) cc_final: 0.8363 (p) REVERT: i 58 ASP cc_start: 0.8014 (m-30) cc_final: 0.7737 (m-30) REVERT: j 48 ASP cc_start: 0.7730 (m-30) cc_final: 0.7469 (m-30) REVERT: p 74 ASP cc_start: 0.7525 (p0) cc_final: 0.7036 (p0) REVERT: p 138 GLU cc_start: 0.7019 (mp0) cc_final: 0.6474 (mp0) REVERT: p 157 MET cc_start: 0.7765 (tmm) cc_final: 0.7547 (ttm) REVERT: q 131 MET cc_start: 0.6258 (OUTLIER) cc_final: 0.4745 (mpp) REVERT: r 120 LYS cc_start: 0.8505 (mttt) cc_final: 0.8092 (mtpt) REVERT: r 146 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6545 (mp10) REVERT: r 169 TRP cc_start: 0.7825 (p-90) cc_final: 0.7471 (p-90) REVERT: r 170 ASN cc_start: 0.8072 (t0) cc_final: 0.7531 (t0) REVERT: s 104 ARG cc_start: 0.7826 (mtp-110) cc_final: 0.7549 (mtp85) REVERT: u 96 MET cc_start: 0.7103 (pmm) cc_final: 0.6616 (pmm) REVERT: u 180 MET cc_start: 0.5310 (OUTLIER) cc_final: 0.4258 (mmt) outliers start: 296 outliers final: 213 residues processed: 1375 average time/residue: 0.8174 time to fit residues: 1932.3902 Evaluate side-chains 1395 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1172 time to evaluate : 6.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain H residue 59 TRP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 93 ASN Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 166 PHE Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain M residue 39 ARG Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 267 PHE Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 235 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 52 MET Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 46 MET Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain V residue 171 ILE Chi-restraints excluded: chain V residue 176 ASP Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 88 CYS Chi-restraints excluded: chain W residue 127 TYR Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 218 LEU Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain Y residue 90 LEU Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Y residue 176 ILE Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 86 ILE Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 103 ILE Chi-restraints excluded: chain Z residue 117 ILE Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 138 CYS Chi-restraints excluded: chain 0 residue 89 VAL Chi-restraints excluded: chain 0 residue 129 LYS Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 3 residue 112 ASP Chi-restraints excluded: chain 3 residue 153 THR Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 124 THR Chi-restraints excluded: chain 5 residue 153 CYS Chi-restraints excluded: chain 5 residue 166 THR Chi-restraints excluded: chain 5 residue 180 ILE Chi-restraints excluded: chain 5 residue 218 LEU Chi-restraints excluded: chain 5 residue 250 ASN Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 315 LEU Chi-restraints excluded: chain 5 residue 327 LEU Chi-restraints excluded: chain 5 residue 344 SER Chi-restraints excluded: chain 5 residue 345 VAL Chi-restraints excluded: chain 6 residue 51 TYR Chi-restraints excluded: chain 6 residue 258 PHE Chi-restraints excluded: chain 6 residue 272 LEU Chi-restraints excluded: chain 6 residue 366 LEU Chi-restraints excluded: chain 6 residue 379 ILE Chi-restraints excluded: chain 7 residue 93 MET Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 160 ASP Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 176 SER Chi-restraints excluded: chain 7 residue 269 ILE Chi-restraints excluded: chain 7 residue 311 THR Chi-restraints excluded: chain 9 residue 46 SER Chi-restraints excluded: chain 9 residue 62 VAL Chi-restraints excluded: chain 9 residue 65 LEU Chi-restraints excluded: chain 9 residue 100 ILE Chi-restraints excluded: chain 9 residue 122 THR Chi-restraints excluded: chain 9 residue 136 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 115 MET Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain b residue 122 ASP Chi-restraints excluded: chain c residue 100 SER Chi-restraints excluded: chain c residue 122 ASN Chi-restraints excluded: chain c residue 127 GLU Chi-restraints excluded: chain c residue 147 ASP Chi-restraints excluded: chain c residue 307 PHE Chi-restraints excluded: chain d residue 80 CYS Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 176 ILE Chi-restraints excluded: chain d residue 216 MET Chi-restraints excluded: chain e residue 233 PHE Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 109 VAL Chi-restraints excluded: chain g residue 114 GLU Chi-restraints excluded: chain g residue 135 THR Chi-restraints excluded: chain g residue 146 THR Chi-restraints excluded: chain h residue 134 ILE Chi-restraints excluded: chain h residue 136 ASP Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 92 ILE Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain m residue 77 MET Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 SER Chi-restraints excluded: chain o residue 32 LYS Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain p residue 41 SER Chi-restraints excluded: chain p residue 48 LEU Chi-restraints excluded: chain p residue 61 VAL Chi-restraints excluded: chain p residue 78 ILE Chi-restraints excluded: chain p residue 100 GLU Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 162 SER Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 88 GLU Chi-restraints excluded: chain q residue 98 THR Chi-restraints excluded: chain q residue 131 MET Chi-restraints excluded: chain q residue 132 ILE Chi-restraints excluded: chain q residue 140 ARG Chi-restraints excluded: chain r residue 54 THR Chi-restraints excluded: chain r residue 85 ASP Chi-restraints excluded: chain r residue 86 VAL Chi-restraints excluded: chain r residue 107 LEU Chi-restraints excluded: chain r residue 121 MET Chi-restraints excluded: chain r residue 146 GLN Chi-restraints excluded: chain r residue 159 VAL Chi-restraints excluded: chain r residue 180 LEU Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 153 GLU Chi-restraints excluded: chain s residue 182 SER Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 286 SER Chi-restraints excluded: chain s residue 301 LEU Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 362 THR Chi-restraints excluded: chain s residue 374 LEU Chi-restraints excluded: chain u residue 103 GLN Chi-restraints excluded: chain u residue 180 MET Chi-restraints excluded: chain u residue 200 ASP Chi-restraints excluded: chain v residue 19 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 895 random chunks: chunk 291 optimal weight: 0.0970 chunk 779 optimal weight: 0.9990 chunk 171 optimal weight: 9.9990 chunk 507 optimal weight: 50.0000 chunk 213 optimal weight: 30.0000 chunk 865 optimal weight: 6.9990 chunk 718 optimal weight: 0.9990 chunk 400 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 286 optimal weight: 2.9990 chunk 454 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 GLN D 252 HIS F 184 GLN ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 22 GLN ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN T 62 GLN T 109 ASN T 133 ASN U 23 ASN V 117 HIS ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 149 GLN ** 7 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 158 HIS 9 123 GLN ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 54 GLN ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN ** j 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 112 HIS s 314 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 94059 Z= 0.190 Angle : 0.603 11.315 132397 Z= 0.302 Chirality : 0.040 0.284 15336 Planarity : 0.005 0.091 12900 Dihedral : 19.668 179.637 25435 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.15 % Rotamer: Outliers : 3.14 % Allowed : 17.88 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.09), residues: 7941 helix: 0.72 (0.10), residues: 2689 sheet: -0.80 (0.16), residues: 974 loop : -0.65 (0.10), residues: 4278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 78 HIS 0.010 0.001 HIS D 252 PHE 0.037 0.001 PHE d 185 TYR 0.032 0.001 TYR o 47 ARG 0.008 0.000 ARG g 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1486 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1262 time to evaluate : 7.258 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: D 263 ASN cc_start: 0.6550 (t0) cc_final: 0.5851 (m-40) REVERT: E 66 SER cc_start: 0.8455 (t) cc_final: 0.8246 (p) REVERT: E 184 ASN cc_start: 0.8450 (p0) cc_final: 0.7982 (p0) REVERT: E 207 THR cc_start: 0.8909 (t) cc_final: 0.8675 (m) REVERT: H 59 TRP cc_start: 0.7315 (OUTLIER) cc_final: 0.5999 (m-10) REVERT: M 170 ASN cc_start: 0.8028 (m-40) cc_final: 0.7609 (m110) REVERT: O 150 GLN cc_start: 0.8334 (tp40) cc_final: 0.8078 (tt0) REVERT: P 158 MET cc_start: 0.4973 (ppp) cc_final: 0.4296 (ptm) REVERT: Q 180 GLU cc_start: 0.7297 (tp30) cc_final: 0.6454 (tp30) REVERT: S 73 THR cc_start: 0.8613 (p) cc_final: 0.8333 (m) REVERT: T 89 TYR cc_start: 0.8928 (m-80) cc_final: 0.7635 (m-10) REVERT: U 46 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7496 (mpp) REVERT: V 78 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8289 (tm-30) REVERT: Z 144 GLU cc_start: 0.7906 (pm20) cc_final: 0.7224 (pm20) REVERT: 5 125 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7645 (pttp) REVERT: 7 93 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.6869 (ptt) REVERT: 7 94 HIS cc_start: 0.8964 (OUTLIER) cc_final: 0.7832 (t-90) REVERT: 7 143 TRP cc_start: 0.9022 (OUTLIER) cc_final: 0.8105 (m-90) REVERT: 7 193 MET cc_start: 0.7399 (mmm) cc_final: 0.7177 (mmm) REVERT: c 127 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: c 247 LYS cc_start: 0.8588 (mmmm) cc_final: 0.8274 (tttm) REVERT: d 196 GLN cc_start: 0.7799 (tp-100) cc_final: 0.7364 (tp-100) REVERT: h 76 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7801 (tm-30) REVERT: h 77 VAL cc_start: 0.8630 (p) cc_final: 0.8310 (p) REVERT: i 58 ASP cc_start: 0.7893 (m-30) cc_final: 0.7598 (m-30) REVERT: j 48 ASP cc_start: 0.7594 (m-30) cc_final: 0.7375 (m-30) REVERT: o 51 MET cc_start: 0.7473 (mtp) cc_final: 0.7270 (mtp) REVERT: p 74 ASP cc_start: 0.7475 (p0) cc_final: 0.6962 (p0) REVERT: p 157 MET cc_start: 0.7722 (tmm) cc_final: 0.7499 (ttm) REVERT: r 120 LYS cc_start: 0.8424 (mttt) cc_final: 0.8071 (mttt) REVERT: r 169 TRP cc_start: 0.7811 (p-90) cc_final: 0.7439 (p-90) REVERT: r 170 ASN cc_start: 0.7968 (t0) cc_final: 0.7599 (t0) REVERT: s 104 ARG cc_start: 0.7733 (mtp-110) cc_final: 0.7475 (mtp85) REVERT: s 304 ASP cc_start: 0.7590 (m-30) cc_final: 0.7134 (m-30) REVERT: u 96 MET cc_start: 0.6998 (pmm) cc_final: 0.6677 (pmm) REVERT: u 180 MET cc_start: 0.5840 (pmm) cc_final: 0.4712 (mmt) outliers start: 224 outliers final: 145 residues processed: 1390 average time/residue: 0.8194 time to fit residues: 1957.1132 Evaluate side-chains 1334 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1181 time to evaluate : 6.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain H residue 59 TRP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain K residue 166 PHE Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain L residue 104 ASN Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 267 PHE Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 46 MET Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain V residue 171 ILE Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain W residue 127 TYR Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 173 ASP Chi-restraints excluded: chain X residue 194 PHE Chi-restraints excluded: chain X residue 218 LEU Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 176 ILE Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 103 ILE Chi-restraints excluded: chain Z residue 114 LYS Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 138 CYS Chi-restraints excluded: chain 0 residue 129 LYS Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 3 residue 153 THR Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 121 LEU Chi-restraints excluded: chain 5 residue 124 THR Chi-restraints excluded: chain 5 residue 125 LYS Chi-restraints excluded: chain 5 residue 180 ILE Chi-restraints excluded: chain 5 residue 218 LEU Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 315 LEU Chi-restraints excluded: chain 5 residue 327 LEU Chi-restraints excluded: chain 6 residue 51 TYR Chi-restraints excluded: chain 6 residue 69 HIS Chi-restraints excluded: chain 6 residue 149 GLN Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 258 PHE Chi-restraints excluded: chain 6 residue 272 LEU Chi-restraints excluded: chain 6 residue 366 LEU Chi-restraints excluded: chain 6 residue 379 ILE Chi-restraints excluded: chain 7 residue 93 MET Chi-restraints excluded: chain 7 residue 94 HIS Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 160 ASP Chi-restraints excluded: chain 7 residue 164 VAL Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 176 SER Chi-restraints excluded: chain 7 residue 281 SER Chi-restraints excluded: chain 9 residue 65 LEU Chi-restraints excluded: chain 9 residue 136 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 115 MET Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain c residue 100 SER Chi-restraints excluded: chain c residue 122 ASN Chi-restraints excluded: chain c residue 127 GLU Chi-restraints excluded: chain c residue 277 ASP Chi-restraints excluded: chain e residue 233 PHE Chi-restraints excluded: chain h residue 90 SER Chi-restraints excluded: chain h residue 136 ASP Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 62 ILE Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain m residue 77 MET Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain p residue 48 LEU Chi-restraints excluded: chain p residue 78 ILE Chi-restraints excluded: chain p residue 100 GLU Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 132 ILE Chi-restraints excluded: chain r residue 54 THR Chi-restraints excluded: chain r residue 85 ASP Chi-restraints excluded: chain r residue 86 VAL Chi-restraints excluded: chain r residue 107 LEU Chi-restraints excluded: chain r residue 121 MET Chi-restraints excluded: chain r residue 180 LEU Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 362 THR Chi-restraints excluded: chain u residue 200 ASP Chi-restraints excluded: chain v residue 19 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 895 random chunks: chunk 834 optimal weight: 8.9990 chunk 97 optimal weight: 0.0040 chunk 493 optimal weight: 4.9990 chunk 632 optimal weight: 0.0270 chunk 489 optimal weight: 6.9990 chunk 728 optimal weight: 0.8980 chunk 483 optimal weight: 7.9990 chunk 862 optimal weight: 4.9990 chunk 539 optimal weight: 5.9990 chunk 525 optimal weight: 10.0000 chunk 398 optimal weight: 4.9990 overall best weight: 2.1854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 GLN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN M 219 ASN Q 158 GLN S 84 ASN T 62 GLN V 117 HIS ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 298 GLN ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 274 GLN e 54 GLN e 175 GLN ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 89 GLN ** j 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 19 GLN ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 112 HIS s 101 ASN s 314 GLN ** u 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 94059 Z= 0.270 Angle : 0.623 11.194 132397 Z= 0.312 Chirality : 0.041 0.315 15336 Planarity : 0.005 0.098 12900 Dihedral : 19.589 178.916 25435 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 3.30 % Allowed : 18.20 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.10), residues: 7941 helix: 0.75 (0.10), residues: 2704 sheet: -0.78 (0.16), residues: 981 loop : -0.61 (0.10), residues: 4256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP E 90 HIS 0.008 0.001 HIS D 252 PHE 0.049 0.001 PHE Q 164 TYR 0.025 0.001 TYR V 19 ARG 0.017 0.000 ARG 6 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1456 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1220 time to evaluate : 6.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 263 ASN cc_start: 0.6568 (t0) cc_final: 0.5835 (m-40) REVERT: E 66 SER cc_start: 0.8478 (t) cc_final: 0.8260 (p) REVERT: E 184 ASN cc_start: 0.8477 (p0) cc_final: 0.7995 (p0) REVERT: E 207 THR cc_start: 0.8962 (t) cc_final: 0.8746 (m) REVERT: H 69 ARG cc_start: 0.6068 (tpt170) cc_final: 0.5470 (tpt90) REVERT: H 120 ARG cc_start: 0.7701 (mmt90) cc_final: 0.7143 (mtt-85) REVERT: K 95 LEU cc_start: 0.9387 (tt) cc_final: 0.9121 (tt) REVERT: M 170 ASN cc_start: 0.8090 (m-40) cc_final: 0.7661 (m110) REVERT: O 150 GLN cc_start: 0.8313 (tp40) cc_final: 0.8056 (tt0) REVERT: P 158 MET cc_start: 0.4657 (ppp) cc_final: 0.4179 (ptp) REVERT: Q 180 GLU cc_start: 0.7355 (tp30) cc_final: 0.6481 (tp30) REVERT: S 73 THR cc_start: 0.8625 (p) cc_final: 0.8405 (m) REVERT: T 89 TYR cc_start: 0.8975 (m-80) cc_final: 0.7958 (m-80) REVERT: U 46 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7543 (mpp) REVERT: V 78 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: Z 77 ARG cc_start: 0.8738 (mtt-85) cc_final: 0.8498 (mtt90) REVERT: 5 125 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7728 (pttp) REVERT: 7 93 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.6992 (ptt) REVERT: 7 94 HIS cc_start: 0.8987 (OUTLIER) cc_final: 0.7801 (t-90) REVERT: 7 143 TRP cc_start: 0.9065 (OUTLIER) cc_final: 0.8149 (m-90) REVERT: c 81 GLU cc_start: 0.6503 (pm20) cc_final: 0.6207 (pm20) REVERT: c 97 TYR cc_start: 0.8496 (t80) cc_final: 0.8177 (t80) REVERT: c 127 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: d 259 TRP cc_start: 0.8587 (m100) cc_final: 0.8211 (m100) REVERT: e 136 ARG cc_start: -0.1345 (mtt180) cc_final: -0.5704 (ttt90) REVERT: e 162 ARG cc_start: -0.2541 (tpt170) cc_final: -0.5642 (mpt180) REVERT: h 76 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7831 (tm-30) REVERT: h 77 VAL cc_start: 0.8653 (p) cc_final: 0.8340 (p) REVERT: h 122 ARG cc_start: 0.8303 (mmm160) cc_final: 0.7895 (mmm160) REVERT: i 58 ASP cc_start: 0.7933 (m-30) cc_final: 0.7645 (m-30) REVERT: j 48 ASP cc_start: 0.7607 (m-30) cc_final: 0.7403 (m-30) REVERT: p 74 ASP cc_start: 0.7484 (p0) cc_final: 0.7016 (p0) REVERT: r 85 ASP cc_start: 0.4441 (OUTLIER) cc_final: 0.3621 (p0) REVERT: r 120 LYS cc_start: 0.8527 (mttt) cc_final: 0.8188 (mtpt) REVERT: r 169 TRP cc_start: 0.7821 (p-90) cc_final: 0.7430 (p-90) REVERT: r 170 ASN cc_start: 0.7974 (t0) cc_final: 0.7593 (t0) REVERT: s 304 ASP cc_start: 0.7681 (m-30) cc_final: 0.7204 (m-30) REVERT: u 96 MET cc_start: 0.6935 (pmm) cc_final: 0.6729 (pmm) outliers start: 236 outliers final: 185 residues processed: 1356 average time/residue: 0.8307 time to fit residues: 1935.1069 Evaluate side-chains 1364 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1171 time to evaluate : 7.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 325 GLU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain H residue 59 TRP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 166 PHE Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain L residue 104 ASN Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 267 PHE Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain N residue 235 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 25 ARG Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 198 SER Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 109 ASN Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 46 MET Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain V residue 171 ILE Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain W residue 127 TYR Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 173 ASP Chi-restraints excluded: chain X residue 194 PHE Chi-restraints excluded: chain X residue 218 LEU Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Y residue 176 ILE Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 86 ILE Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 103 ILE Chi-restraints excluded: chain Z residue 114 LYS Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 138 CYS Chi-restraints excluded: chain Z residue 148 GLN Chi-restraints excluded: chain 0 residue 89 VAL Chi-restraints excluded: chain 0 residue 129 LYS Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 3 residue 112 ASP Chi-restraints excluded: chain 3 residue 153 THR Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 121 LEU Chi-restraints excluded: chain 5 residue 124 THR Chi-restraints excluded: chain 5 residue 125 LYS Chi-restraints excluded: chain 5 residue 166 THR Chi-restraints excluded: chain 5 residue 180 ILE Chi-restraints excluded: chain 5 residue 218 LEU Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 315 LEU Chi-restraints excluded: chain 5 residue 327 LEU Chi-restraints excluded: chain 6 residue 51 TYR Chi-restraints excluded: chain 6 residue 60 ARG Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 258 PHE Chi-restraints excluded: chain 6 residue 272 LEU Chi-restraints excluded: chain 6 residue 366 LEU Chi-restraints excluded: chain 6 residue 379 ILE Chi-restraints excluded: chain 7 residue 93 MET Chi-restraints excluded: chain 7 residue 94 HIS Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 160 ASP Chi-restraints excluded: chain 7 residue 164 VAL Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 176 SER Chi-restraints excluded: chain 9 residue 62 VAL Chi-restraints excluded: chain 9 residue 65 LEU Chi-restraints excluded: chain 9 residue 100 ILE Chi-restraints excluded: chain 9 residue 122 THR Chi-restraints excluded: chain 9 residue 136 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 115 MET Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain c residue 100 SER Chi-restraints excluded: chain c residue 122 ASN Chi-restraints excluded: chain c residue 127 GLU Chi-restraints excluded: chain c residue 277 ASP Chi-restraints excluded: chain e residue 233 PHE Chi-restraints excluded: chain g residue 114 GLU Chi-restraints excluded: chain h residue 90 SER Chi-restraints excluded: chain h residue 136 ASP Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 62 ILE Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain m residue 77 MET Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain p residue 41 SER Chi-restraints excluded: chain p residue 48 LEU Chi-restraints excluded: chain p residue 78 ILE Chi-restraints excluded: chain p residue 100 GLU Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 162 SER Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 132 ILE Chi-restraints excluded: chain r residue 54 THR Chi-restraints excluded: chain r residue 85 ASP Chi-restraints excluded: chain r residue 86 VAL Chi-restraints excluded: chain r residue 96 HIS Chi-restraints excluded: chain r residue 107 LEU Chi-restraints excluded: chain r residue 121 MET Chi-restraints excluded: chain r residue 151 LEU Chi-restraints excluded: chain r residue 180 LEU Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 301 LEU Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 362 THR Chi-restraints excluded: chain u residue 200 ASP Chi-restraints excluded: chain v residue 19 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 895 random chunks: chunk 533 optimal weight: 0.9990 chunk 344 optimal weight: 0.5980 chunk 515 optimal weight: 5.9990 chunk 259 optimal weight: 0.8980 chunk 169 optimal weight: 20.0000 chunk 167 optimal weight: 3.9990 chunk 548 optimal weight: 1.9990 chunk 587 optimal weight: 0.9990 chunk 426 optimal weight: 4.9990 chunk 80 optimal weight: 30.0000 chunk 678 optimal weight: 50.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 GLN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 HIS F 184 GLN ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 GLN S 84 ASN T 62 GLN T 133 ASN V 117 HIS ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 149 GLN ** 6 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 GLN ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 102 GLN ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 77 HIS d 251 GLN d 274 GLN e 54 GLN ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 19 GLN ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 123 HIS r 112 HIS s 101 ASN s 240 GLN ** u 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 94059 Z= 0.182 Angle : 0.595 11.698 132397 Z= 0.298 Chirality : 0.039 0.285 15336 Planarity : 0.005 0.107 12900 Dihedral : 19.556 179.874 25435 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.94 % Favored : 96.03 % Rotamer: Outliers : 3.01 % Allowed : 18.86 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.10), residues: 7941 helix: 0.84 (0.10), residues: 2704 sheet: -0.72 (0.16), residues: 971 loop : -0.54 (0.10), residues: 4266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP E 90 HIS 0.010 0.001 HIS p 123 PHE 0.041 0.001 PHE Q 164 TYR 0.027 0.001 TYR V 19 ARG 0.018 0.000 ARG e 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1408 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1193 time to evaluate : 6.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 263 ASN cc_start: 0.6563 (t0) cc_final: 0.5844 (m-40) REVERT: E 184 ASN cc_start: 0.8502 (p0) cc_final: 0.8109 (p0) REVERT: E 207 THR cc_start: 0.8943 (t) cc_final: 0.8703 (m) REVERT: H 69 ARG cc_start: 0.5937 (tpt170) cc_final: 0.5340 (tpt90) REVERT: K 95 LEU cc_start: 0.9354 (tt) cc_final: 0.9085 (tt) REVERT: M 170 ASN cc_start: 0.8046 (m-40) cc_final: 0.7625 (m110) REVERT: O 150 GLN cc_start: 0.8225 (tp40) cc_final: 0.7983 (tt0) REVERT: P 158 MET cc_start: 0.4628 (ppp) cc_final: 0.4092 (ptp) REVERT: Q 167 TYR cc_start: 0.8195 (m-10) cc_final: 0.7870 (m-10) REVERT: Q 180 GLU cc_start: 0.7241 (tp30) cc_final: 0.6448 (tp30) REVERT: S 73 THR cc_start: 0.8594 (p) cc_final: 0.8392 (m) REVERT: T 89 TYR cc_start: 0.8898 (m-80) cc_final: 0.7883 (m-80) REVERT: U 46 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7526 (mpp) REVERT: V 78 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8242 (tm-30) REVERT: Y 147 GLN cc_start: 0.7911 (tp40) cc_final: 0.7665 (tp40) REVERT: Z 144 GLU cc_start: 0.7973 (pm20) cc_final: 0.7546 (pm20) REVERT: 0 136 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7582 (tm-30) REVERT: 5 125 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7742 (pttp) REVERT: 6 154 TYR cc_start: 0.6332 (t80) cc_final: 0.6031 (t80) REVERT: 7 93 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.6851 (ptt) REVERT: 7 94 HIS cc_start: 0.8934 (OUTLIER) cc_final: 0.7847 (t-90) REVERT: 7 143 TRP cc_start: 0.9038 (OUTLIER) cc_final: 0.8155 (m-90) REVERT: 7 193 MET cc_start: 0.7345 (mmm) cc_final: 0.7081 (mmm) REVERT: c 81 GLU cc_start: 0.6366 (pm20) cc_final: 0.6038 (pm20) REVERT: c 127 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: d 57 MET cc_start: 0.2290 (tpp) cc_final: 0.1948 (tpp) REVERT: d 259 TRP cc_start: 0.8614 (m100) cc_final: 0.8180 (m100) REVERT: e 136 ARG cc_start: -0.1297 (mtt180) cc_final: -0.5679 (ttt90) REVERT: e 162 ARG cc_start: -0.2539 (tpt170) cc_final: -0.5659 (mpt180) REVERT: g 98 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7623 (mttt) REVERT: h 76 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7830 (tm-30) REVERT: h 77 VAL cc_start: 0.8690 (p) cc_final: 0.8392 (p) REVERT: i 58 ASP cc_start: 0.7892 (m-30) cc_final: 0.7593 (m-30) REVERT: o 71 PHE cc_start: 0.8597 (t80) cc_final: 0.8018 (t80) REVERT: p 74 ASP cc_start: 0.7423 (p0) cc_final: 0.6914 (p0) REVERT: q 131 MET cc_start: 0.6440 (OUTLIER) cc_final: 0.5045 (mmm) REVERT: r 85 ASP cc_start: 0.4206 (OUTLIER) cc_final: 0.3469 (p0) REVERT: r 120 LYS cc_start: 0.8566 (mttt) cc_final: 0.8225 (mtpt) REVERT: r 169 TRP cc_start: 0.7833 (p-90) cc_final: 0.7458 (p-90) REVERT: r 170 ASN cc_start: 0.7953 (t0) cc_final: 0.7632 (t0) REVERT: s 104 ARG cc_start: 0.7750 (mtp-110) cc_final: 0.7530 (mtp85) REVERT: s 304 ASP cc_start: 0.7615 (m-30) cc_final: 0.7200 (m-30) REVERT: u 180 MET cc_start: 0.5822 (pmm) cc_final: 0.4511 (mmm) outliers start: 215 outliers final: 170 residues processed: 1315 average time/residue: 0.8430 time to fit residues: 1900.4577 Evaluate side-chains 1342 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1162 time to evaluate : 6.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain H residue 59 TRP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 166 PHE Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 104 ASN Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 267 PHE Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 46 MET Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain V residue 171 ILE Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain W residue 56 MET Chi-restraints excluded: chain W residue 88 CYS Chi-restraints excluded: chain W residue 127 TYR Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 173 ASP Chi-restraints excluded: chain X residue 194 PHE Chi-restraints excluded: chain X residue 218 LEU Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Y residue 176 ILE Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 103 ILE Chi-restraints excluded: chain Z residue 114 LYS Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 148 GLN Chi-restraints excluded: chain 0 residue 89 VAL Chi-restraints excluded: chain 0 residue 105 ASN Chi-restraints excluded: chain 0 residue 129 LYS Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 3 residue 133 LEU Chi-restraints excluded: chain 3 residue 153 THR Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 121 LEU Chi-restraints excluded: chain 5 residue 124 THR Chi-restraints excluded: chain 5 residue 125 LYS Chi-restraints excluded: chain 5 residue 180 ILE Chi-restraints excluded: chain 5 residue 218 LEU Chi-restraints excluded: chain 5 residue 250 ASN Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 315 LEU Chi-restraints excluded: chain 5 residue 327 LEU Chi-restraints excluded: chain 5 residue 345 VAL Chi-restraints excluded: chain 6 residue 51 TYR Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 258 PHE Chi-restraints excluded: chain 6 residue 272 LEU Chi-restraints excluded: chain 6 residue 273 PHE Chi-restraints excluded: chain 6 residue 366 LEU Chi-restraints excluded: chain 6 residue 379 ILE Chi-restraints excluded: chain 7 residue 93 MET Chi-restraints excluded: chain 7 residue 94 HIS Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 160 ASP Chi-restraints excluded: chain 7 residue 164 VAL Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 176 SER Chi-restraints excluded: chain 9 residue 65 LEU Chi-restraints excluded: chain 9 residue 100 ILE Chi-restraints excluded: chain 9 residue 122 THR Chi-restraints excluded: chain 9 residue 136 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 115 MET Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain c residue 100 SER Chi-restraints excluded: chain c residue 122 ASN Chi-restraints excluded: chain c residue 127 GLU Chi-restraints excluded: chain c residue 277 ASP Chi-restraints excluded: chain e residue 233 PHE Chi-restraints excluded: chain g residue 98 LYS Chi-restraints excluded: chain g residue 109 VAL Chi-restraints excluded: chain g residue 162 LEU Chi-restraints excluded: chain h residue 90 SER Chi-restraints excluded: chain h residue 136 ASP Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 62 ILE Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain m residue 77 MET Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain p residue 48 LEU Chi-restraints excluded: chain p residue 78 ILE Chi-restraints excluded: chain p residue 100 GLU Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 131 MET Chi-restraints excluded: chain q residue 132 ILE Chi-restraints excluded: chain r residue 54 THR Chi-restraints excluded: chain r residue 83 TYR Chi-restraints excluded: chain r residue 85 ASP Chi-restraints excluded: chain r residue 86 VAL Chi-restraints excluded: chain r residue 104 ILE Chi-restraints excluded: chain r residue 107 LEU Chi-restraints excluded: chain r residue 121 MET Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 151 LEU Chi-restraints excluded: chain r residue 180 LEU Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 362 THR Chi-restraints excluded: chain u residue 200 ASP Chi-restraints excluded: chain v residue 19 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 895 random chunks: chunk 784 optimal weight: 4.9990 chunk 826 optimal weight: 6.9990 chunk 754 optimal weight: 5.9990 chunk 803 optimal weight: 5.9990 chunk 483 optimal weight: 6.9990 chunk 350 optimal weight: 7.9990 chunk 631 optimal weight: 0.0370 chunk 246 optimal weight: 0.9990 chunk 726 optimal weight: 4.9990 chunk 760 optimal weight: 0.8980 chunk 801 optimal weight: 6.9990 overall best weight: 2.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 GLN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN F 184 GLN ** F 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 GLN S 84 ASN T 62 GLN T 101 GLN T 133 ASN V 117 HIS W 76 HIS X 177 HIS ** 7 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 298 GLN 9 123 GLN ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 274 GLN e 54 GLN ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 135 GLN ** j 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 19 GLN ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 112 HIS s 101 ASN s 358 GLN ** u 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 94059 Z= 0.289 Angle : 0.636 11.745 132397 Z= 0.318 Chirality : 0.041 0.323 15336 Planarity : 0.005 0.116 12900 Dihedral : 19.510 179.114 25435 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.45 % Favored : 95.52 % Rotamer: Outliers : 3.35 % Allowed : 19.01 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.10), residues: 7941 helix: 0.82 (0.10), residues: 2705 sheet: -0.78 (0.16), residues: 978 loop : -0.54 (0.10), residues: 4258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP E 90 HIS 0.007 0.001 HIS 5 289 PHE 0.040 0.002 PHE d 185 TYR 0.025 0.001 TYR V 19 ARG 0.012 0.001 ARG e 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1422 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1183 time to evaluate : 6.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 263 ASN cc_start: 0.6444 (t0) cc_final: 0.5715 (m-40) REVERT: E 207 THR cc_start: 0.8996 (t) cc_final: 0.8768 (m) REVERT: H 69 ARG cc_start: 0.6204 (tpt170) cc_final: 0.5597 (tpt90) REVERT: K 95 LEU cc_start: 0.9382 (tt) cc_final: 0.9131 (tt) REVERT: M 170 ASN cc_start: 0.8110 (m-40) cc_final: 0.7693 (m110) REVERT: O 150 GLN cc_start: 0.8284 (tp40) cc_final: 0.8007 (tt0) REVERT: P 158 MET cc_start: 0.4614 (ppp) cc_final: 0.4097 (ptp) REVERT: Q 167 TYR cc_start: 0.8335 (m-10) cc_final: 0.7808 (m-10) REVERT: Q 180 GLU cc_start: 0.7258 (tp30) cc_final: 0.6470 (tp30) REVERT: U 46 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7504 (mpp) REVERT: V 78 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8212 (tm-30) REVERT: Y 147 GLN cc_start: 0.7985 (tp40) cc_final: 0.7760 (tp40) REVERT: Z 144 GLU cc_start: 0.8149 (pm20) cc_final: 0.7695 (pm20) REVERT: 5 125 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7838 (pttp) REVERT: 6 154 TYR cc_start: 0.6495 (t80) cc_final: 0.6169 (t80) REVERT: 7 93 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.6974 (ptt) REVERT: 7 94 HIS cc_start: 0.8985 (OUTLIER) cc_final: 0.7755 (t-90) REVERT: 7 143 TRP cc_start: 0.9100 (OUTLIER) cc_final: 0.8126 (m-90) REVERT: 7 193 MET cc_start: 0.7463 (mmm) cc_final: 0.7229 (mmm) REVERT: c 97 TYR cc_start: 0.8476 (t80) cc_final: 0.8142 (t80) REVERT: c 127 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: c 248 ARG cc_start: 0.8138 (mmt90) cc_final: 0.7832 (mmt90) REVERT: d 259 TRP cc_start: 0.8641 (m100) cc_final: 0.8269 (m100) REVERT: e 136 ARG cc_start: -0.1366 (mtt180) cc_final: -0.5801 (ttt90) REVERT: e 162 ARG cc_start: -0.2695 (tpt170) cc_final: -0.5766 (mpt180) REVERT: g 98 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7675 (mttt) REVERT: h 76 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7834 (tm-30) REVERT: h 77 VAL cc_start: 0.8673 (p) cc_final: 0.8379 (p) REVERT: i 58 ASP cc_start: 0.7933 (m-30) cc_final: 0.7640 (m-30) REVERT: o 71 PHE cc_start: 0.8653 (t80) cc_final: 0.8068 (t80) REVERT: p 74 ASP cc_start: 0.7411 (p0) cc_final: 0.6943 (p0) REVERT: q 131 MET cc_start: 0.6316 (OUTLIER) cc_final: 0.4909 (tpp) REVERT: r 85 ASP cc_start: 0.4340 (OUTLIER) cc_final: 0.3648 (p0) REVERT: r 120 LYS cc_start: 0.8529 (mttt) cc_final: 0.8110 (mtpt) REVERT: r 169 TRP cc_start: 0.7831 (p-90) cc_final: 0.7436 (p-90) REVERT: r 170 ASN cc_start: 0.8102 (t0) cc_final: 0.7774 (t0) REVERT: s 104 ARG cc_start: 0.7816 (mtp-110) cc_final: 0.7591 (mtp85) REVERT: s 304 ASP cc_start: 0.7682 (m-30) cc_final: 0.7213 (m-30) REVERT: u 180 MET cc_start: 0.5712 (pmm) cc_final: 0.4604 (mmm) outliers start: 239 outliers final: 202 residues processed: 1311 average time/residue: 0.8375 time to fit residues: 1884.2250 Evaluate side-chains 1373 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1161 time to evaluate : 6.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 325 GLU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain H residue 59 TRP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 166 PHE Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain L residue 104 ASN Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 267 PHE Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain N residue 235 LEU Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 25 ARG Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 198 SER Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 46 MET Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain V residue 171 ILE Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain W residue 88 CYS Chi-restraints excluded: chain W residue 127 TYR Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 173 ASP Chi-restraints excluded: chain X residue 218 LEU Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Y residue 176 ILE Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 103 ILE Chi-restraints excluded: chain Z residue 114 LYS Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 138 CYS Chi-restraints excluded: chain Z residue 148 GLN Chi-restraints excluded: chain 0 residue 89 VAL Chi-restraints excluded: chain 0 residue 105 ASN Chi-restraints excluded: chain 0 residue 129 LYS Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 3 residue 133 LEU Chi-restraints excluded: chain 3 residue 153 THR Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 121 LEU Chi-restraints excluded: chain 5 residue 124 THR Chi-restraints excluded: chain 5 residue 125 LYS Chi-restraints excluded: chain 5 residue 166 THR Chi-restraints excluded: chain 5 residue 180 ILE Chi-restraints excluded: chain 5 residue 218 LEU Chi-restraints excluded: chain 5 residue 250 ASN Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 315 LEU Chi-restraints excluded: chain 5 residue 327 LEU Chi-restraints excluded: chain 5 residue 345 VAL Chi-restraints excluded: chain 6 residue 51 TYR Chi-restraints excluded: chain 6 residue 69 HIS Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 258 PHE Chi-restraints excluded: chain 6 residue 272 LEU Chi-restraints excluded: chain 6 residue 273 PHE Chi-restraints excluded: chain 6 residue 366 LEU Chi-restraints excluded: chain 6 residue 379 ILE Chi-restraints excluded: chain 7 residue 42 GLU Chi-restraints excluded: chain 7 residue 93 MET Chi-restraints excluded: chain 7 residue 94 HIS Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 160 ASP Chi-restraints excluded: chain 7 residue 164 VAL Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 176 SER Chi-restraints excluded: chain 7 residue 281 SER Chi-restraints excluded: chain 9 residue 62 VAL Chi-restraints excluded: chain 9 residue 65 LEU Chi-restraints excluded: chain 9 residue 100 ILE Chi-restraints excluded: chain 9 residue 122 THR Chi-restraints excluded: chain 9 residue 136 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 115 MET Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain b residue 90 HIS Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain c residue 100 SER Chi-restraints excluded: chain c residue 122 ASN Chi-restraints excluded: chain c residue 127 GLU Chi-restraints excluded: chain c residue 277 ASP Chi-restraints excluded: chain d residue 216 MET Chi-restraints excluded: chain e residue 233 PHE Chi-restraints excluded: chain f residue 91 LEU Chi-restraints excluded: chain f residue 178 LEU Chi-restraints excluded: chain g residue 98 LYS Chi-restraints excluded: chain g residue 109 VAL Chi-restraints excluded: chain g residue 114 GLU Chi-restraints excluded: chain g residue 162 LEU Chi-restraints excluded: chain h residue 134 ILE Chi-restraints excluded: chain h residue 135 GLN Chi-restraints excluded: chain h residue 136 ASP Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 62 ILE Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain m residue 77 MET Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 SER Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain p residue 41 SER Chi-restraints excluded: chain p residue 78 ILE Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 131 MET Chi-restraints excluded: chain q residue 132 ILE Chi-restraints excluded: chain r residue 54 THR Chi-restraints excluded: chain r residue 83 TYR Chi-restraints excluded: chain r residue 85 ASP Chi-restraints excluded: chain r residue 86 VAL Chi-restraints excluded: chain r residue 104 ILE Chi-restraints excluded: chain r residue 107 LEU Chi-restraints excluded: chain r residue 121 MET Chi-restraints excluded: chain r residue 151 LEU Chi-restraints excluded: chain r residue 180 LEU Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 153 GLU Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 362 THR Chi-restraints excluded: chain u residue 200 ASP Chi-restraints excluded: chain v residue 19 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 895 random chunks: chunk 527 optimal weight: 1.9990 chunk 850 optimal weight: 8.9990 chunk 518 optimal weight: 5.9990 chunk 403 optimal weight: 1.9990 chunk 590 optimal weight: 10.0000 chunk 891 optimal weight: 40.0000 chunk 820 optimal weight: 10.0000 chunk 710 optimal weight: 30.0000 chunk 73 optimal weight: 0.8980 chunk 548 optimal weight: 0.0070 chunk 435 optimal weight: 0.8980 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 GLN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 GLN S 84 ASN T 62 GLN T 133 ASN V 117 HIS W 76 HIS X 177 HIS ** Y 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 274 GLN e 54 GLN ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 112 HIS s 101 ASN s 358 GLN ** u 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 94059 Z= 0.188 Angle : 0.607 18.352 132397 Z= 0.303 Chirality : 0.039 0.285 15336 Planarity : 0.005 0.124 12900 Dihedral : 19.502 179.874 25435 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.87 % Favored : 96.11 % Rotamer: Outliers : 2.94 % Allowed : 19.50 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.10), residues: 7941 helix: 0.92 (0.10), residues: 2690 sheet: -0.72 (0.16), residues: 977 loop : -0.49 (0.10), residues: 4274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP h 86 HIS 0.008 0.001 HIS 5 289 PHE 0.039 0.001 PHE d 185 TYR 0.028 0.001 TYR V 19 ARG 0.011 0.000 ARG M 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15882 Ramachandran restraints generated. 7941 Oldfield, 0 Emsley, 7941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1399 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1189 time to evaluate : 7.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 263 ASN cc_start: 0.6466 (t0) cc_final: 0.5757 (m-40) REVERT: E 96 ARG cc_start: 0.6932 (ptt90) cc_final: 0.6727 (ptt90) REVERT: E 207 THR cc_start: 0.8964 (t) cc_final: 0.8713 (m) REVERT: H 69 ARG cc_start: 0.6163 (tpt170) cc_final: 0.5559 (tpt90) REVERT: K 95 LEU cc_start: 0.9347 (tt) cc_final: 0.9077 (tt) REVERT: M 170 ASN cc_start: 0.8090 (m-40) cc_final: 0.7652 (m110) REVERT: O 116 ASP cc_start: 0.8200 (p0) cc_final: 0.7949 (p0) REVERT: O 150 GLN cc_start: 0.8216 (tp40) cc_final: 0.7934 (tt0) REVERT: Q 167 TYR cc_start: 0.8255 (m-10) cc_final: 0.7909 (m-10) REVERT: Q 180 GLU cc_start: 0.7234 (tp30) cc_final: 0.6481 (tp30) REVERT: T 89 TYR cc_start: 0.8905 (m-80) cc_final: 0.7898 (m-80) REVERT: U 46 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7529 (mpp) REVERT: V 78 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: X 177 HIS cc_start: 0.7845 (OUTLIER) cc_final: 0.7537 (m170) REVERT: Z 144 GLU cc_start: 0.8171 (pm20) cc_final: 0.7700 (pm20) REVERT: 0 136 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7603 (tm-30) REVERT: 5 125 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7671 (pttp) REVERT: 5 331 ASN cc_start: 0.7316 (p0) cc_final: 0.6541 (p0) REVERT: 6 154 TYR cc_start: 0.6445 (t80) cc_final: 0.6194 (t80) REVERT: 7 93 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.6928 (ptt) REVERT: 7 94 HIS cc_start: 0.8941 (OUTLIER) cc_final: 0.7808 (t-90) REVERT: 7 143 TRP cc_start: 0.9063 (OUTLIER) cc_final: 0.8221 (m-90) REVERT: 7 193 MET cc_start: 0.7455 (mmm) cc_final: 0.7226 (mmm) REVERT: c 97 TYR cc_start: 0.8408 (t80) cc_final: 0.8146 (t80) REVERT: c 127 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: c 248 ARG cc_start: 0.8092 (mmt90) cc_final: 0.7830 (mmt90) REVERT: d 259 TRP cc_start: 0.8616 (m100) cc_final: 0.8220 (m100) REVERT: e 136 ARG cc_start: -0.1351 (mtt180) cc_final: -0.5781 (ttt90) REVERT: e 162 ARG cc_start: -0.2525 (tpt170) cc_final: -0.5682 (mpt180) REVERT: e 200 MET cc_start: -0.2371 (mpp) cc_final: -0.2897 (mpt) REVERT: g 98 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7506 (mttt) REVERT: h 76 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7891 (tm-30) REVERT: h 77 VAL cc_start: 0.8627 (p) cc_final: 0.8159 (p) REVERT: h 122 ARG cc_start: 0.7948 (mmm-85) cc_final: 0.7651 (mmm160) REVERT: i 58 ASP cc_start: 0.7907 (m-30) cc_final: 0.7579 (m-30) REVERT: o 71 PHE cc_start: 0.8517 (t80) cc_final: 0.7926 (t80) REVERT: p 74 ASP cc_start: 0.7361 (p0) cc_final: 0.6879 (p0) REVERT: q 131 MET cc_start: 0.6442 (OUTLIER) cc_final: 0.5004 (tpp) REVERT: r 120 LYS cc_start: 0.8573 (mttt) cc_final: 0.8270 (mtpt) REVERT: r 169 TRP cc_start: 0.7823 (p-90) cc_final: 0.7382 (p-90) REVERT: r 170 ASN cc_start: 0.8085 (t0) cc_final: 0.7744 (t0) REVERT: s 104 ARG cc_start: 0.7770 (mtp-110) cc_final: 0.7469 (mtp85) REVERT: s 304 ASP cc_start: 0.7680 (m-30) cc_final: 0.7250 (m-30) REVERT: u 96 MET cc_start: 0.6480 (pmm) cc_final: 0.6111 (pmm) outliers start: 210 outliers final: 182 residues processed: 1305 average time/residue: 0.8303 time to fit residues: 1856.2402 Evaluate side-chains 1359 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1167 time to evaluate : 8.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 325 GLU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain H residue 59 TRP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 166 PHE Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain L residue 104 ASN Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 267 PHE Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 25 ARG Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 198 SER Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 24 PHE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 46 MET Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain V residue 171 ILE Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain W residue 88 CYS Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 169 LEU Chi-restraints excluded: chain X residue 173 ASP Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 218 LEU Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Y residue 176 ILE Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 103 ILE Chi-restraints excluded: chain Z residue 114 LYS Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 148 GLN Chi-restraints excluded: chain 0 residue 89 VAL Chi-restraints excluded: chain 0 residue 105 ASN Chi-restraints excluded: chain 0 residue 129 LYS Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 3 residue 112 ASP Chi-restraints excluded: chain 3 residue 153 THR Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 121 LEU Chi-restraints excluded: chain 5 residue 124 THR Chi-restraints excluded: chain 5 residue 125 LYS Chi-restraints excluded: chain 5 residue 166 THR Chi-restraints excluded: chain 5 residue 180 ILE Chi-restraints excluded: chain 5 residue 218 LEU Chi-restraints excluded: chain 5 residue 250 ASN Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 315 LEU Chi-restraints excluded: chain 5 residue 327 LEU Chi-restraints excluded: chain 5 residue 347 THR Chi-restraints excluded: chain 6 residue 51 TYR Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 174 HIS Chi-restraints excluded: chain 6 residue 258 PHE Chi-restraints excluded: chain 6 residue 272 LEU Chi-restraints excluded: chain 6 residue 273 PHE Chi-restraints excluded: chain 6 residue 366 LEU Chi-restraints excluded: chain 6 residue 379 ILE Chi-restraints excluded: chain 7 residue 42 GLU Chi-restraints excluded: chain 7 residue 93 MET Chi-restraints excluded: chain 7 residue 94 HIS Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 160 ASP Chi-restraints excluded: chain 7 residue 164 VAL Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 176 SER Chi-restraints excluded: chain 7 residue 281 SER Chi-restraints excluded: chain 9 residue 62 VAL Chi-restraints excluded: chain 9 residue 65 LEU Chi-restraints excluded: chain 9 residue 100 ILE Chi-restraints excluded: chain 9 residue 122 THR Chi-restraints excluded: chain 9 residue 136 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 115 MET Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain b residue 90 HIS Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain c residue 100 SER Chi-restraints excluded: chain c residue 122 ASN Chi-restraints excluded: chain c residue 127 GLU Chi-restraints excluded: chain c residue 277 ASP Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain e residue 233 PHE Chi-restraints excluded: chain f residue 91 LEU Chi-restraints excluded: chain g residue 98 LYS Chi-restraints excluded: chain g residue 109 VAL Chi-restraints excluded: chain g residue 114 GLU Chi-restraints excluded: chain g residue 162 LEU Chi-restraints excluded: chain h residue 136 ASP Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 62 ILE Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain m residue 77 MET Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 SER Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain p residue 78 ILE Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 131 MET Chi-restraints excluded: chain q residue 132 ILE Chi-restraints excluded: chain r residue 54 THR Chi-restraints excluded: chain r residue 83 TYR Chi-restraints excluded: chain r residue 86 VAL Chi-restraints excluded: chain r residue 104 ILE Chi-restraints excluded: chain r residue 107 LEU Chi-restraints excluded: chain r residue 121 MET Chi-restraints excluded: chain r residue 151 LEU Chi-restraints excluded: chain r residue 180 LEU Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 362 THR Chi-restraints excluded: chain u residue 200 ASP Chi-restraints excluded: chain v residue 19 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 895 random chunks: chunk 563 optimal weight: 5.9990 chunk 756 optimal weight: 8.9990 chunk 217 optimal weight: 5.9990 chunk 654 optimal weight: 2.9990 chunk 104 optimal weight: 50.0000 chunk 197 optimal weight: 1.9990 chunk 711 optimal weight: 9.9990 chunk 297 optimal weight: 10.0000 chunk 730 optimal weight: 1.9990 chunk 90 optimal weight: 50.0000 chunk 130 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 GLN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** F 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 GLN S 84 ASN ** S 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 62 GLN T 101 GLN T 133 ASN V 117 HIS W 76 HIS X 177 HIS ** Y 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 GLN ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 222 GLN d 274 GLN e 54 GLN ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 123 HIS r 112 HIS s 101 ASN s 240 GLN s 358 GLN ** u 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.180573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.143526 restraints weight = 132405.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.137193 restraints weight = 196531.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132698 restraints weight = 135806.073| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 94059 Z= 0.411 Angle : 0.703 16.433 132397 Z= 0.351 Chirality : 0.044 0.351 15336 Planarity : 0.006 0.190 12900 Dihedral : 19.516 179.587 25435 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 3.30 % Allowed : 19.21 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.10), residues: 7941 helix: 0.77 (0.10), residues: 2695 sheet: -0.85 (0.16), residues: 1007 loop : -0.57 (0.10), residues: 4239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP E 90 HIS 0.032 0.001 HIS X 177 PHE 0.039 0.002 PHE d 185 TYR 0.028 0.002 TYR V 19 ARG 0.013 0.001 ARG u 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25724.13 seconds wall clock time: 450 minutes 53.43 seconds (27053.43 seconds total)