Starting phenix.real_space_refine (version: 1.21rc1) on Sun May 14 12:27:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi7_12920/05_2023/7oi7_12920_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi7_12920/05_2023/7oi7_12920.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi7_12920/05_2023/7oi7_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_12920/05_2023/7oi7_12920_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi7_12920/05_2023/7oi7_12920_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi7_12920/05_2023/7oi7_12920.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi7_12920/05_2023/7oi7_12920.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi7_12920/05_2023/7oi7_12920_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi7_12920/05_2023/7oi7_12920_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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: 35.17, 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: 32.26 Conformation dependent library (CDL) restraints added in 7.3 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: 23.33 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: 47.10 Time building geometry restraints manager: 35.06 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: 53223 35.90 - 71.80: 1305 71.80 - 107.70: 105 107.70 - 143.60: 8 143.60 - 179.50: 30 Dihedral angle restraints: 54671 sinusoidal: 31062 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 54668 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: 2.070 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: 0.070 Extract box with map and model: 15.560 Check model and map are aligned: 1.060 Set scattering table: 0.610 Process input model: 219.710 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.280 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: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 244.550 ------------------------------------------------------------------------------- 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 : 15.046 179.496 39373 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 % 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 *********************** 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 : 6.927 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 outliers start: 7 outliers final: 1 residues processed: 1548 average time/residue: 0.8925 time to fit residues: 2375.9915 Evaluate side-chains 1206 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1205 time to evaluate : 6.771 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6996 time to fit residues: 10.3425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 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 S 84 ASN 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: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 94059 Z= 0.178 Angle : 0.614 12.225 132397 Z= 0.311 Chirality : 0.040 0.305 15336 Planarity : 0.005 0.084 12900 Dihedral : 14.197 179.856 22275 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.56 % Rotamer Outliers : 1.67 % 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: -0.92 (0.09), residues: 7941 helix: -0.03 (0.10), residues: 2674 sheet: -0.75 (0.16), residues: 979 loop : -0.91 (0.09), residues: 4288 *********************** 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 1444 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1325 time to evaluate : 7.016 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 outliers start: 119 outliers final: 79 residues processed: 1366 average time/residue: 0.8384 time to fit residues: 1960.0519 Evaluate side-chains 1261 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1182 time to evaluate : 6.811 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 0 residues processed: 79 average time/residue: 0.6589 time to fit residues: 106.6787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 895 random chunks: chunk 451 optimal weight: 2.9990 chunk 252 optimal weight: 0.9990 chunk 676 optimal weight: 40.0000 chunk 553 optimal weight: 9.9990 chunk 224 optimal weight: 8.9990 chunk 814 optimal weight: 8.9990 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: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 263 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** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 HIS P 97 GLN R 36 ASN S 84 ASN T 62 GLN U 27 GLN V 92 ASN X 89 GLN 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 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** 8 143 GLN 8 158 HIS ** 8 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 149 HIS ** d 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 274 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** s 280 ASN s 315 ASN s 358 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.082 94059 Z= 0.364 Angle : 0.674 11.677 132397 Z= 0.339 Chirality : 0.043 0.361 15336 Planarity : 0.005 0.092 12900 Dihedral : 14.165 179.733 22275 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.90 % Favored : 96.07 % Rotamer Outliers : 1.90 % 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: -0.69 (0.09), residues: 7941 helix: 0.30 (0.10), residues: 2676 sheet: -0.74 (0.16), residues: 1001 loop : -0.82 (0.09), residues: 4264 *********************** 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 1392 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1256 time to evaluate : 6.830 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 outliers start: 136 outliers final: 83 residues processed: 1328 average time/residue: 0.8971 time to fit residues: 2048.4114 Evaluate side-chains 1253 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1170 time to evaluate : 6.887 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 0 residues processed: 83 average time/residue: 0.6735 time to fit residues: 115.0497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.8857 > 50: distance: 26 - 60: 24.367 distance: 29 - 57: 29.414 distance: 41 - 49: 29.001 distance: 49 - 50: 24.796 distance: 50 - 51: 25.196 distance: 50 - 53: 34.997 distance: 51 - 52: 17.564 distance: 51 - 57: 46.217 distance: 52 - 174: 30.506 distance: 53 - 54: 26.227 distance: 54 - 55: 21.078 distance: 54 - 56: 17.788 distance: 57 - 58: 30.946 distance: 58 - 59: 41.993 distance: 58 - 61: 30.190 distance: 59 - 60: 15.195 distance: 59 - 63: 36.086 distance: 61 - 62: 20.066 distance: 63 - 64: 16.190 distance: 63 - 161: 23.881 distance: 64 - 65: 41.136 distance: 64 - 67: 36.208 distance: 65 - 66: 15.388 distance: 65 - 70: 16.462 distance: 66 - 158: 12.802 distance: 67 - 68: 5.602 distance: 67 - 69: 9.843 distance: 70 - 71: 28.041 distance: 71 - 72: 13.898 distance: 71 - 74: 38.743 distance: 72 - 73: 32.640 distance: 72 - 79: 10.705 distance: 74 - 75: 11.524 distance: 75 - 76: 12.195 distance: 76 - 77: 10.025 distance: 79 - 80: 24.635 distance: 80 - 81: 46.096 distance: 80 - 83: 60.469 distance: 81 - 82: 35.039 distance: 81 - 87: 42.872 distance: 83 - 84: 38.955 distance: 84 - 85: 16.543 distance: 84 - 86: 16.961 distance: 87 - 88: 53.450 distance: 87 - 93: 53.167 distance: 88 - 89: 22.370 distance: 88 - 91: 34.028 distance: 89 - 90: 46.173 distance: 89 - 94: 21.505 distance: 91 - 92: 9.021 distance: 92 - 93: 20.602 distance: 94 - 95: 39.339 distance: 95 - 96: 48.256 distance: 95 - 98: 38.831 distance: 96 - 97: 16.715 distance: 96 - 102: 43.897 distance: 98 - 99: 44.440 distance: 99 - 100: 38.799 distance: 99 - 101: 21.597 distance: 102 - 103: 39.642 distance: 102 - 108: 61.618 distance: 103 - 104: 25.751 distance: 103 - 106: 16.953 distance: 104 - 105: 5.210 distance: 104 - 109: 13.806 distance: 106 - 107: 6.644 distance: 107 - 108: 31.850 distance: 109 - 110: 16.801 distance: 110 - 111: 17.462 distance: 110 - 113: 9.025 distance: 111 - 112: 12.971 distance: 111 - 116: 39.157 distance: 113 - 114: 6.911 distance: 113 - 115: 13.295 distance: 116 - 117: 62.886 distance: 117 - 118: 57.921 distance: 117 - 120: 53.754 distance: 118 - 119: 45.266 distance: 118 - 124: 27.800 distance: 120 - 121: 22.229 distance: 120 - 122: 25.503 distance: 121 - 123: 15.050