Starting phenix.real_space_refine on Fri Mar 22 16:34:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdb_4812/03_2024/6rdb_4812_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdb_4812/03_2024/6rdb_4812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdb_4812/03_2024/6rdb_4812.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdb_4812/03_2024/6rdb_4812.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdb_4812/03_2024/6rdb_4812_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdb_4812/03_2024/6rdb_4812_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 116 5.16 5 C 21563 2.51 5 N 5800 2.21 5 O 6464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "H PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 111": "OE1" <-> "OE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 86": "OE1" <-> "OE2" Residue "P ASP 127": "OD1" <-> "OD2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P GLU 142": "OE1" <-> "OE2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 54": "OD1" <-> "OD2" Residue "R GLU 32": "OE1" <-> "OE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 95": "OD1" <-> "OD2" Residue "R ASP 156": "OD1" <-> "OD2" Residue "R PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 177": "OE1" <-> "OE2" Residue "R GLU 186": "OE1" <-> "OE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 144": "OD1" <-> "OD2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S GLU 154": "OE1" <-> "OE2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 214": "OD1" <-> "OD2" Residue "S ASP 222": "OD1" <-> "OD2" Residue "S GLU 238": "OE1" <-> "OE2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S GLU 283": "OE1" <-> "OE2" Residue "S ASP 291": "OD1" <-> "OD2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ASP 92": "OD1" <-> "OD2" Residue "T ASP 135": "OD1" <-> "OD2" Residue "T ASP 142": "OD1" <-> "OD2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ASP 172": "OD1" <-> "OD2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 294": "OD1" <-> "OD2" Residue "T TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 325": "OD1" <-> "OD2" Residue "T ASP 326": "OD1" <-> "OD2" Residue "T ARG 347": "NH1" <-> "NH2" Residue "T ASP 353": "OD1" <-> "OD2" Residue "T PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 403": "OD1" <-> "OD2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 429": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 522": "OE1" <-> "OE2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ASP 46": "OD1" <-> "OD2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 107": "OE1" <-> "OE2" Residue "U ASP 112": "OD1" <-> "OD2" Residue "U ASP 125": "OD1" <-> "OD2" Residue "U TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ASP 165": "OD1" <-> "OD2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 221": "OE1" <-> "OE2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ASP 237": "OD1" <-> "OD2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 311": "OE1" <-> "OE2" Residue "U PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U ARG 342": "NH1" <-> "NH2" Residue "U ARG 343": "NH1" <-> "NH2" Residue "U ARG 364": "NH1" <-> "NH2" Residue "U PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 409": "OE1" <-> "OE2" Residue "U GLU 411": "OE1" <-> "OE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 449": "OE1" <-> "OE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 465": "OD1" <-> "OD2" Residue "U GLU 475": "OE1" <-> "OE2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 142": "OD1" <-> "OD2" Residue "V TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V ASP 210": "OD1" <-> "OD2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 266": "NH1" <-> "NH2" Residue "V PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ASP 325": "OD1" <-> "OD2" Residue "V ASP 326": "OD1" <-> "OD2" Residue "V ARG 335": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "V ARG 360": "NH1" <-> "NH2" Residue "V PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 389": "OD1" <-> "OD2" Residue "V ASP 403": "OD1" <-> "OD2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 429": "NH1" <-> "NH2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V GLU 455": "OE1" <-> "OE2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V GLU 553": "OE1" <-> "OE2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X ASP 82": "OD1" <-> "OD2" Residue "X ASP 136": "OD1" <-> "OD2" Residue "X GLU 146": "OE1" <-> "OE2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 152": "OE1" <-> "OE2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "X PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 215": "OE1" <-> "OE2" Residue "X ARG 218": "NH1" <-> "NH2" Residue "X GLU 219": "OE1" <-> "OE2" Residue "X ARG 225": "NH1" <-> "NH2" Residue "X GLU 238": "OE1" <-> "OE2" Residue "X ARG 239": "NH1" <-> "NH2" Residue "X TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 253": "OE1" <-> "OE2" Residue "X ASP 279": "OD1" <-> "OD2" Residue "X ASP 285": "OD1" <-> "OD2" Residue "X GLU 296": "OE1" <-> "OE2" Residue "X ASP 317": "OD1" <-> "OD2" Residue "X TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 378": "OD1" <-> "OD2" Residue "X TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 401": "NH1" <-> "NH2" Residue "X ASP 409": "OD1" <-> "OD2" Residue "X ASP 415": "OD1" <-> "OD2" Residue "X GLU 424": "OE1" <-> "OE2" Residue "X PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 494": "OE1" <-> "OE2" Residue "X GLU 497": "OE1" <-> "OE2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X GLU 536": "OE1" <-> "OE2" Residue "X GLU 540": "OE1" <-> "OE2" Residue "X GLU 546": "OE1" <-> "OE2" Residue "X GLU 547": "OE1" <-> "OE2" Residue "Y ASP 36": "OD1" <-> "OD2" Residue "Y GLU 64": "OE1" <-> "OE2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y ASP 82": "OD1" <-> "OD2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y ASP 139": "OD1" <-> "OD2" Residue "Y ARG 145": "NH1" <-> "NH2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 215": "OE1" <-> "OE2" Residue "Y GLU 226": "OE1" <-> "OE2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y GLU 270": "OE1" <-> "OE2" Residue "Y GLU 296": "OE1" <-> "OE2" Residue "Y TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 359": "OD1" <-> "OD2" Residue "Y ARG 366": "NH1" <-> "NH2" Residue "Y TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 378": "OD1" <-> "OD2" Residue "Y ASP 381": "OD1" <-> "OD2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 465": "OD1" <-> "OD2" Residue "Y PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 542": "OD1" <-> "OD2" Residue "Y GLU 546": "OE1" <-> "OE2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "Z ARG 98": "NH1" <-> "NH2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z ASP 130": "OD1" <-> "OD2" Residue "Z GLU 156": "OE1" <-> "OE2" Residue "Z PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 216": "NH1" <-> "NH2" Residue "Z ARG 258": "NH1" <-> "NH2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z ARG 289": "NH1" <-> "NH2" Residue "Z GLU 323": "OE1" <-> "OE2" Residue "Z PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 378": "OD1" <-> "OD2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 424": "OE1" <-> "OE2" Residue "Z ARG 435": "NH1" <-> "NH2" Residue "Z ARG 437": "NH1" <-> "NH2" Residue "Z PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 480": "OD1" <-> "OD2" Residue "Z PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 505": "OD1" <-> "OD2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z ASP 523": "OD1" <-> "OD2" Residue "Z ASP 542": "OD1" <-> "OD2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 552": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33961 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "P" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 886 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3649 Classifications: {'peptide': 483} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 461} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain breaks: 1 Chain: "V" Number of atoms: 3961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3961 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "U" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "V" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "X" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "Y" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 16.86, per 1000 atoms: 0.50 Number of scatterers: 33961 At special positions: 0 Unit cell: (160.056, 132.678, 207.441, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 13 15.00 Mg 5 11.99 O 6464 8.00 N 5800 7.00 C 21563 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.07 Conformation dependent library (CDL) restraints added in 5.8 seconds 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8168 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 176 helices and 26 sheets defined 46.0% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.66 Creating SS restraints... Processing helix chain 'A' and resid 55 through 71 removed outlier: 4.302A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 91 removed outlier: 3.818A pdb=" N GLY A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 98 through 125 removed outlier: 3.699A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 65 removed outlier: 4.376A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 91 removed outlier: 3.563A pdb=" N GLY B 73 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL B 74 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU B 78 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET B 81 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE B 82 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY B 83 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 85 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA B 89 " --> pdb=" O ILE B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 125 removed outlier: 3.917A pdb=" N LEU B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 91 removed outlier: 4.050A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C 91 " --> pdb=" O ASN C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 100 through 125 removed outlier: 4.465A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 125 " --> pdb=" O VAL C 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 65 removed outlier: 3.632A pdb=" N LYS D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 91 removed outlier: 3.550A pdb=" N GLY D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU D 78 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY D 79 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET D 81 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE D 82 " --> pdb=" O GLY D 79 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY D 83 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 85 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 89 " --> pdb=" O ILE D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 124 removed outlier: 3.524A pdb=" N LEU D 99 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL D 100 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY D 101 " --> pdb=" O GLN D 98 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU D 104 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU D 105 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA D 108 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU D 109 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA D 114 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 115 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER D 117 " --> pdb=" O ALA D 114 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU D 118 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU D 119 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 89 removed outlier: 4.372A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS E 66 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 98 through 110 removed outlier: 3.590A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 123 removed outlier: 3.575A pdb=" N LEU E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 91 removed outlier: 3.834A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS F 66 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY F 79 " --> pdb=" O GLY F 75 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 119 removed outlier: 5.402A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU F 99 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL F 100 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU F 104 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU F 105 " --> pdb=" O TYR F 102 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA F 108 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU F 109 " --> pdb=" O GLY F 106 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU F 111 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU F 118 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU F 119 " --> pdb=" O PHE F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 126 No H-bonds generated for 'chain 'F' and resid 123 through 126' Processing helix chain 'G' and resid 55 through 91 removed outlier: 3.734A pdb=" N LYS G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS G 66 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 123 removed outlier: 3.739A pdb=" N VAL G 100 " --> pdb=" O ALA G 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA G 114 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 91 removed outlier: 3.500A pdb=" N GLY H 65 " --> pdb=" O MET H 61 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA H 70 " --> pdb=" O CYS H 66 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA H 72 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 125 removed outlier: 3.909A pdb=" N VAL H 100 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY H 101 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU H 111 " --> pdb=" O PHE H 107 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE H 122 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU H 125 " --> pdb=" O VAL H 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 65 removed outlier: 4.499A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 91 removed outlier: 3.757A pdb=" N GLY I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL I 74 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA I 76 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY I 79 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N MET I 81 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE I 82 " --> pdb=" O GLY I 79 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER I 84 " --> pdb=" O MET I 81 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU I 85 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG I 91 " --> pdb=" O GLY I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 95 No H-bonds generated for 'chain 'I' and resid 93 through 95' Processing helix chain 'I' and resid 98 through 123 removed outlier: 4.127A pdb=" N LEU I 109 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE I 122 " --> pdb=" O LEU I 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 89 removed outlier: 3.899A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS J 66 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 108 removed outlier: 5.414A pdb=" N LYS J 97 " --> pdb=" O ASN J 94 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN J 98 " --> pdb=" O ILE J 95 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU J 99 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU J 104 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU J 105 " --> pdb=" O TYR J 102 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE J 107 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA J 108 " --> pdb=" O LEU J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 125 Processing helix chain 'P' and resid 51 through 63 Processing helix chain 'P' and resid 69 through 83 removed outlier: 3.740A pdb=" N LYS P 82 " --> pdb=" O ILE P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 92 removed outlier: 3.774A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 108 removed outlier: 3.904A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 118 through 127 Processing helix chain 'P' and resid 131 through 148 removed outlier: 4.289A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL P 137 " --> pdb=" O LEU P 134 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU P 143 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU P 146 " --> pdb=" O GLU P 143 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA P 147 " --> pdb=" O LEU P 144 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 11 No H-bonds generated for 'chain 'Q' and resid 8 through 11' Processing helix chain 'Q' and resid 16 through 30 removed outlier: 3.974A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 39 removed outlier: 3.901A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 37 removed outlier: 3.587A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 54 removed outlier: 3.648A pdb=" N TYR R 54 " --> pdb=" O PRO R 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 51 through 54' Processing helix chain 'R' and resid 152 through 154 No H-bonds generated for 'chain 'R' and resid 152 through 154' Processing helix chain 'R' and resid 159 through 167 removed outlier: 3.860A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 196 removed outlier: 3.638A pdb=" N TYR R 188 " --> pdb=" O ALA R 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 69 removed outlier: 3.728A pdb=" N ILE S 47 " --> pdb=" O VAL S 43 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN S 52 " --> pdb=" O ARG S 48 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 78 No H-bonds generated for 'chain 'S' and resid 75 through 78' Processing helix chain 'S' and resid 80 through 88 Proline residue: S 84 - end of helix Processing helix chain 'S' and resid 115 through 129 removed outlier: 3.545A pdb=" N ILE S 119 " --> pdb=" O LEU S 115 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR S 120 " --> pdb=" O ASN S 116 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 153 removed outlier: 3.869A pdb=" N THR S 151 " --> pdb=" O ARG S 147 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ARG S 152 " --> pdb=" O SER S 148 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE S 153 " --> pdb=" O GLN S 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 147 through 153' Processing helix chain 'S' and resid 172 through 184 removed outlier: 3.765A pdb=" N LEU S 182 " --> pdb=" O ILE S 178 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS S 184 " --> pdb=" O GLU S 180 " (cutoff:3.500A) Processing helix chain 'S' and resid 217 through 220 No H-bonds generated for 'chain 'S' and resid 217 through 220' Processing helix chain 'S' and resid 239 through 274 removed outlier: 3.617A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP S 245 " --> pdb=" O ASP S 241 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA S 268 " --> pdb=" O CYS S 264 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) Processing helix chain 'S' and resid 276 through 312 removed outlier: 4.061A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 137 No H-bonds generated for 'chain 'T' and resid 135 through 137' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 192 through 194 No H-bonds generated for 'chain 'T' and resid 192 through 194' Processing helix chain 'T' and resid 207 through 212 removed outlier: 3.609A pdb=" N LEU T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 231 through 246 removed outlier: 3.655A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN T 244 " --> pdb=" O ILE T 240 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 279 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 296 through 300 Processing helix chain 'T' and resid 302 through 315 removed outlier: 3.557A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 340 removed outlier: 3.569A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 347 through 349 No H-bonds generated for 'chain 'T' and resid 347 through 349' Processing helix chain 'T' and resid 352 through 364 removed outlier: 4.536A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER T 359 " --> pdb=" O TYR T 356 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG T 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU T 362 " --> pdb=" O SER T 359 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU T 363 " --> pdb=" O ARG T 360 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 401 Processing helix chain 'T' and resid 410 through 414 Processing helix chain 'T' and resid 431 through 434 removed outlier: 3.765A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 431 through 434' Processing helix chain 'T' and resid 437 through 440 No H-bonds generated for 'chain 'T' and resid 437 through 440' Processing helix chain 'T' and resid 443 through 459 removed outlier: 4.207A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA T 458 " --> pdb=" O ARG T 454 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 470 through 483 removed outlier: 3.814A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 505 Processing helix chain 'T' and resid 517 through 526 removed outlier: 5.092A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA T 523 " --> pdb=" O ALA T 519 " (cutoff:3.500A) Processing helix chain 'T' and resid 532 through 539 Processing helix chain 'T' and resid 544 through 551 removed outlier: 3.660A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS T 551 " --> pdb=" O ASP T 547 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 48 removed outlier: 4.099A pdb=" N GLU U 47 " --> pdb=" O LYS U 43 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU U 48 " --> pdb=" O ALA U 44 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 63 Processing helix chain 'U' and resid 66 through 72 removed outlier: 3.659A pdb=" N GLU U 72 " --> pdb=" O PRO U 68 " (cutoff:3.500A) Processing helix chain 'U' and resid 135 through 137 No H-bonds generated for 'chain 'U' and resid 135 through 137' Processing helix chain 'U' and resid 207 through 212 Processing helix chain 'U' and resid 231 through 248 removed outlier: 3.556A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN U 242 " --> pdb=" O ALA U 238 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS U 243 " --> pdb=" O ILE U 239 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLN U 248 " --> pdb=" O ASN U 244 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 279 Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 296 through 314 Proline residue: U 303 - end of helix removed outlier: 3.576A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 removed outlier: 3.543A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 354 through 364 removed outlier: 3.617A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG U 364 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 393 through 399 Processing helix chain 'U' and resid 410 through 414 Processing helix chain 'U' and resid 437 through 459 removed outlier: 3.547A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) Processing helix chain 'U' and resid 471 through 484 removed outlier: 3.507A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU U 482 " --> pdb=" O ALA U 478 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 505 removed outlier: 3.613A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 517 through 527 removed outlier: 3.530A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 531 through 539 removed outlier: 3.707A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 544 through 553 removed outlier: 3.575A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) Processing helix chain 'V' and resid 46 through 48 No H-bonds generated for 'chain 'V' and resid 46 through 48' Processing helix chain 'V' and resid 59 through 69 removed outlier: 3.885A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Proline residue: V 68 - end of helix Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 212 Processing helix chain 'V' and resid 231 through 247 removed outlier: 3.954A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 266 through 279 Processing helix chain 'V' and resid 281 through 283 No H-bonds generated for 'chain 'V' and resid 281 through 283' Processing helix chain 'V' and resid 296 through 315 Proline residue: V 303 - end of helix removed outlier: 3.592A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG V 314 " --> pdb=" O ALA V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 340 Processing helix chain 'V' and resid 352 through 364 removed outlier: 4.221A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER V 359 " --> pdb=" O TYR V 356 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU V 363 " --> pdb=" O ARG V 360 " (cutoff:3.500A) Processing helix chain 'V' and resid 370 through 372 No H-bonds generated for 'chain 'V' and resid 370 through 372' Processing helix chain 'V' and resid 393 through 401 Processing helix chain 'V' and resid 410 through 413 No H-bonds generated for 'chain 'V' and resid 410 through 413' Processing helix chain 'V' and resid 431 through 434 removed outlier: 3.591A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 431 through 434' Processing helix chain 'V' and resid 440 through 456 removed outlier: 3.638A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU V 448 " --> pdb=" O GLY V 444 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 481 Processing helix chain 'V' and resid 494 through 505 Processing helix chain 'V' and resid 514 through 516 No H-bonds generated for 'chain 'V' and resid 514 through 516' Processing helix chain 'V' and resid 531 through 539 removed outlier: 3.539A pdb=" N ILE V 535 " --> pdb=" O ALA V 531 " (cutoff:3.500A) Processing helix chain 'V' and resid 544 through 553 removed outlier: 3.812A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS V 551 " --> pdb=" O ASP V 547 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 117 No H-bonds generated for 'chain 'X' and resid 115 through 117' Processing helix chain 'X' and resid 150 through 152 No H-bonds generated for 'chain 'X' and resid 150 through 152' Processing helix chain 'X' and resid 165 through 170 Processing helix chain 'X' and resid 189 through 203 removed outlier: 3.551A pdb=" N ALA X 201 " --> pdb=" O ILE X 197 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA X 203 " --> pdb=" O ASN X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 228 Processing helix chain 'X' and resid 236 through 241 removed outlier: 3.500A pdb=" N ARG X 239 " --> pdb=" O GLY X 236 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 255 through 258 No H-bonds generated for 'chain 'X' and resid 255 through 258' Processing helix chain 'X' and resid 261 through 274 removed outlier: 3.562A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 298 removed outlier: 3.540A pdb=" N ALA X 293 " --> pdb=" O PHE X 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN X 294 " --> pdb=" O THR X 291 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER X 298 " --> pdb=" O SER X 295 " (cutoff:3.500A) Processing helix chain 'X' and resid 307 through 309 No H-bonds generated for 'chain 'X' and resid 307 through 309' Processing helix chain 'X' and resid 314 through 324 removed outlier: 4.319A pdb=" N ARG X 324 " --> pdb=" O GLY X 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 351 through 357 removed outlier: 4.586A pdb=" N ALA X 356 " --> pdb=" O ALA X 352 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N HIS X 357 " --> pdb=" O THR X 353 " (cutoff:3.500A) Processing helix chain 'X' and resid 366 through 370 Processing helix chain 'X' and resid 389 through 392 No H-bonds generated for 'chain 'X' and resid 389 through 392' Processing helix chain 'X' and resid 394 through 419 removed outlier: 4.690A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE X 419 " --> pdb=" O ASP X 415 " (cutoff:3.500A) Processing helix chain 'X' and resid 422 through 424 No H-bonds generated for 'chain 'X' and resid 422 through 424' Processing helix chain 'X' and resid 427 through 442 removed outlier: 3.535A pdb=" N THR X 432 " --> pdb=" O GLU X 428 " (cutoff:3.500A) Processing helix chain 'X' and resid 451 through 454 No H-bonds generated for 'chain 'X' and resid 451 through 454' Processing helix chain 'X' and resid 463 through 475 Processing helix chain 'X' and resid 492 through 506 removed outlier: 3.645A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS X 501 " --> pdb=" O GLU X 497 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 532 removed outlier: 3.524A pdb=" N VAL X 531 " --> pdb=" O LEU X 527 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 527 through 532' Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 165 through 170 Processing helix chain 'Y' and resid 189 through 200 Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 4.857A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 258 No H-bonds generated for 'chain 'Y' and resid 255 through 258' Processing helix chain 'Y' and resid 261 through 274 Processing helix chain 'Y' and resid 288 through 296 Processing helix chain 'Y' and resid 314 through 324 removed outlier: 4.225A pdb=" N ARG Y 324 " --> pdb=" O GLY Y 320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 349 through 357 removed outlier: 3.716A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS Y 357 " --> pdb=" O THR Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 370 Processing helix chain 'Y' and resid 389 through 392 No H-bonds generated for 'chain 'Y' and resid 389 through 392' Processing helix chain 'Y' and resid 394 through 417 removed outlier: 4.090A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS Y 411 " --> pdb=" O LEU Y 407 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) Processing helix chain 'Y' and resid 429 through 443 Processing helix chain 'Y' and resid 463 through 474 removed outlier: 3.522A pdb=" N GLY Y 472 " --> pdb=" O SER Y 468 " (cutoff:3.500A) Processing helix chain 'Y' and resid 492 through 507 removed outlier: 3.522A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP Y 500 " --> pdb=" O LYS Y 496 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS Y 501 " --> pdb=" O GLU Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 509 through 511 No H-bonds generated for 'chain 'Y' and resid 509 through 511' Processing helix chain 'Y' and resid 527 through 532 Processing helix chain 'Y' and resid 545 through 554 removed outlier: 3.580A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 117 No H-bonds generated for 'chain 'Z' and resid 115 through 117' Processing helix chain 'Z' and resid 165 through 169 Processing helix chain 'Z' and resid 189 through 202 Processing helix chain 'Z' and resid 217 through 229 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 4.650A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 259 Processing helix chain 'Z' and resid 261 through 274 removed outlier: 3.510A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 300 Processing helix chain 'Z' and resid 307 through 309 No H-bonds generated for 'chain 'Z' and resid 307 through 309' Processing helix chain 'Z' and resid 314 through 322 removed outlier: 3.860A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 349 through 355 Processing helix chain 'Z' and resid 366 through 369 No H-bonds generated for 'chain 'Z' and resid 366 through 369' Processing helix chain 'Z' and resid 393 through 411 Processing helix chain 'Z' and resid 414 through 417 No H-bonds generated for 'chain 'Z' and resid 414 through 417' Processing helix chain 'Z' and resid 429 through 440 removed outlier: 3.525A pdb=" N LYS Z 438 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) Processing helix chain 'Z' and resid 448 through 454 removed outlier: 3.619A pdb=" N GLU Z 451 " --> pdb=" O GLN Z 448 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL Z 452 " --> pdb=" O VAL Z 449 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE Z 453 " --> pdb=" O ALA Z 450 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR Z 454 " --> pdb=" O GLU Z 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 448 through 454' Processing helix chain 'Z' and resid 463 through 475 removed outlier: 3.622A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 492 through 506 removed outlier: 4.104A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) Processing helix chain 'Z' and resid 509 through 511 No H-bonds generated for 'chain 'Z' and resid 509 through 511' Processing helix chain 'Z' and resid 527 through 531 Processing sheet with id= A, first strand: chain 'Q' and resid 45 through 49 Processing sheet with id= B, first strand: chain 'R' and resid 72 through 75 removed outlier: 6.692A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE R 144 " --> pdb=" O TYR R 75 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'R' and resid 97 through 100 removed outlier: 6.637A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 203 through 211 removed outlier: 3.609A pdb=" N LYS S 204 " --> pdb=" O LYS S 196 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA S 161 " --> pdb=" O SER S 141 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'T' and resid 84 through 86 removed outlier: 3.766A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS T 116 " --> pdb=" O PHE T 132 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY T 128 " --> pdb=" O LEU T 120 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N TYR T 98 " --> pdb=" O VAL T 87 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N VAL T 87 " --> pdb=" O TYR T 98 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'T' and resid 152 through 155 Processing sheet with id= G, first strand: chain 'T' and resid 404 through 407 removed outlier: 3.612A pdb=" N LEU T 222 " --> pdb=" O GLY T 404 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'T' and resid 376 through 381 Processing sheet with id= I, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.650A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= K, first strand: chain 'U' and resid 404 through 408 removed outlier: 3.965A pdb=" N ASP U 226 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'U' and resid 285 through 290 removed outlier: 8.788A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE U 380 " --> pdb=" O TYR U 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'V' and resid 143 through 145 removed outlier: 6.525A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLN V 149 " --> pdb=" O LEU V 108 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N CYS V 110 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR V 147 " --> pdb=" O CYS V 110 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= O, first strand: chain 'V' and resid 404 through 408 Processing sheet with id= P, first strand: chain 'V' and resid 285 through 290 removed outlier: 8.977A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE V 380 " --> pdb=" O TYR V 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'X' and resid 37 through 39 removed outlier: 6.595A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ARG X 51 " --> pdb=" O VAL X 40 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL X 40 " --> pdb=" O ARG X 51 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'X' and resid 110 through 113 Processing sheet with id= S, first strand: chain 'X' and resid 360 through 363 removed outlier: 7.559A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLY X 183 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL X 339 " --> pdb=" O GLY X 183 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE X 207 " --> pdb=" O LEU X 281 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N PHE X 283 " --> pdb=" O PHE X 207 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL X 209 " --> pdb=" O PHE X 283 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ASP X 285 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ALA X 211 " --> pdb=" O ASP X 285 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= U, first strand: chain 'Y' and resid 39 through 44 removed outlier: 6.439A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'Y' and resid 360 through 363 removed outlier: 7.502A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N GLY Y 183 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL Y 339 " --> pdb=" O GLY Y 183 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE Y 207 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N PHE Y 283 " --> pdb=" O PHE Y 207 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ALA Y 211 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Z' and resid 38 through 44 removed outlier: 6.244A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id= Y, first strand: chain 'Z' and resid 360 through 362 removed outlier: 8.541A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL Z 284 " --> pdb=" O VAL Z 336 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL Z 213 " --> pdb=" O ASP Z 285 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Z' and resid 559 through 561 1300 hydrogen bonds defined for protein. 3552 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.76 Time building geometry restraints manager: 13.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8590 1.33 - 1.45: 5891 1.45 - 1.57: 19739 1.57 - 1.69: 23 1.69 - 1.81: 200 Bond restraints: 34443 Sorted by residual: bond pdb=" N PRO X 349 " pdb=" CA PRO X 349 " ideal model delta sigma weight residual 1.469 1.689 -0.220 1.28e-02 6.10e+03 2.95e+02 bond pdb=" C4 ADP Y 601 " pdb=" C5 ADP Y 601 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C4 ADP X 601 " pdb=" C5 ADP X 601 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C ASP X 348 " pdb=" N PRO X 349 " ideal model delta sigma weight residual 1.334 1.448 -0.114 2.34e-02 1.83e+03 2.38e+01 bond pdb=" C5 ADP Y 601 " pdb=" C6 ADP Y 601 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 ... (remaining 34438 not shown) Histogram of bond angle deviations from ideal: 97.25 - 105.56: 717 105.56 - 113.87: 20032 113.87 - 122.18: 19964 122.18 - 130.49: 5875 130.49 - 138.80: 91 Bond angle restraints: 46679 Sorted by residual: angle pdb=" C ASP X 348 " pdb=" N PRO X 349 " pdb=" CA PRO X 349 " ideal model delta sigma weight residual 119.84 138.80 -18.96 1.25e+00 6.40e-01 2.30e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 130.61 9.26 1.00e+00 1.00e+00 8.58e+01 angle pdb=" CA PRO X 349 " pdb=" N PRO X 349 " pdb=" CD PRO X 349 " ideal model delta sigma weight residual 112.00 99.71 12.29 1.40e+00 5.10e-01 7.70e+01 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 131.53 8.34 1.00e+00 1.00e+00 6.96e+01 angle pdb=" N GLU J 111 " pdb=" CA GLU J 111 " pdb=" C GLU J 111 " ideal model delta sigma weight residual 112.23 102.58 9.65 1.26e+00 6.30e-01 5.87e+01 ... (remaining 46674 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.60: 19623 24.60 - 49.19: 1040 49.19 - 73.79: 142 73.79 - 98.38: 32 98.38 - 122.98: 2 Dihedral angle restraints: 20839 sinusoidal: 8071 harmonic: 12768 Sorted by residual: dihedral pdb=" O1B ADP X 601 " pdb=" O3A ADP X 601 " pdb=" PB ADP X 601 " pdb=" PA ADP X 601 " ideal model delta sinusoidal sigma weight residual 300.00 177.02 122.98 1 2.00e+01 2.50e-03 3.71e+01 dihedral pdb=" C5' ADP Y 601 " pdb=" O5' ADP Y 601 " pdb=" PA ADP Y 601 " pdb=" O2A ADP Y 601 " ideal model delta sinusoidal sigma weight residual -60.00 59.62 -119.62 1 2.00e+01 2.50e-03 3.59e+01 dihedral pdb=" CA ASP T 326 " pdb=" C ASP T 326 " pdb=" N LEU T 327 " pdb=" CA LEU T 327 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 20836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4534 0.078 - 0.155: 865 0.155 - 0.233: 109 0.233 - 0.310: 16 0.310 - 0.388: 2 Chirality restraints: 5526 Sorted by residual: chirality pdb=" CA ASP S 83 " pdb=" N ASP S 83 " pdb=" C ASP S 83 " pdb=" CB ASP S 83 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CB VAL U 180 " pdb=" CA VAL U 180 " pdb=" CG1 VAL U 180 " pdb=" CG2 VAL U 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA PRO X 349 " pdb=" N PRO X 349 " pdb=" C PRO X 349 " pdb=" CB PRO X 349 " both_signs ideal model delta sigma weight residual False 2.72 3.02 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 5523 not shown) Planarity restraints: 5999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS T 415 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.93e+00 pdb=" C LYS T 415 " 0.052 2.00e-02 2.50e+03 pdb=" O LYS T 415 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY T 416 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU Q 33 " -0.049 5.00e-02 4.00e+02 7.43e-02 8.82e+00 pdb=" N PRO Q 34 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO Q 34 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO Q 34 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP Z 348 " -0.047 5.00e-02 4.00e+02 7.19e-02 8.26e+00 pdb=" N PRO Z 349 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO Z 349 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO Z 349 " -0.040 5.00e-02 4.00e+02 ... (remaining 5996 not shown) Histogram of nonbonded interaction distances: 0.35 - 1.26: 3 1.26 - 2.17: 20 2.17 - 3.08: 21212 3.08 - 3.99: 94241 3.99 - 4.90: 180261 Warning: very small nonbonded interaction distances. Nonbonded interactions: 295737 Sorted by model distance: nonbonded pdb="MG MG X 602 " pdb=" O HOH X 703 " model vdw 0.351 2.170 nonbonded pdb=" OH TYR V 259 " pdb=" OD2 ASP V 325 " model vdw 0.928 2.440 nonbonded pdb=" CZ TYR V 259 " pdb=" OD2 ASP V 325 " model vdw 1.165 3.260 nonbonded pdb=" OH TYR V 259 " pdb=" CG ASP V 325 " model vdw 1.597 3.270 nonbonded pdb=" OE1 GLU X 215 " pdb=" O HOH X 701 " model vdw 1.599 2.440 ... (remaining 295732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 80 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 80 through 562 or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 25.780 Check model and map are aligned: 0.500 Set scattering table: 0.260 Process input model: 84.410 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.200 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:13.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 : 0.008 0.220 34443 Z= 0.539 Angle : 0.997 18.960 46679 Z= 0.583 Chirality : 0.062 0.388 5526 Planarity : 0.007 0.074 5999 Dihedral : 15.160 122.975 12671 Min Nonbonded Distance : 0.351 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.08 % Favored : 95.79 % Rotamer: Outliers : 1.23 % Allowed : 7.88 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -4.44 (0.10), residues: 4463 helix: -4.11 (0.06), residues: 2130 sheet: -1.12 (0.21), residues: 571 loop : -1.69 (0.13), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP X 141 HIS 0.009 0.002 HIS S 250 PHE 0.027 0.002 PHE S 249 TYR 0.017 0.002 TYR U 57 ARG 0.008 0.001 ARG U 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 600 time to evaluate : 3.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 97 LYS cc_start: 0.8632 (mppt) cc_final: 0.8423 (mttp) REVERT: E 56 LEU cc_start: 0.7670 (pt) cc_final: 0.6850 (mt) REVERT: E 60 LYS cc_start: 0.7275 (mtmt) cc_final: 0.7011 (ptpp) REVERT: E 100 VAL cc_start: 0.7164 (t) cc_final: 0.6850 (m) REVERT: G 61 MET cc_start: 0.7353 (mtm) cc_final: 0.7036 (mmt) REVERT: I 81 MET cc_start: 0.7282 (ttp) cc_final: 0.6745 (ppp) REVERT: I 119 LEU cc_start: 0.6734 (mp) cc_final: 0.6371 (pp) REVERT: J 66 CYS cc_start: 0.7471 (m) cc_final: 0.7014 (m) REVERT: P 63 LYS cc_start: 0.8457 (tppt) cc_final: 0.8164 (tppp) REVERT: P 69 LYS cc_start: 0.7885 (tttm) cc_final: 0.7652 (tptp) REVERT: P 72 ASP cc_start: 0.8056 (t0) cc_final: 0.7654 (t0) REVERT: P 73 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7771 (mt-10) REVERT: P 119 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8348 (mmmm) REVERT: P 140 ASN cc_start: 0.8995 (m-40) cc_final: 0.8788 (m110) REVERT: P 145 MET cc_start: 0.8481 (mmm) cc_final: 0.8144 (mmm) REVERT: Q 10 ARG cc_start: 0.7827 (tpp-160) cc_final: 0.7391 (ttt90) REVERT: S 62 MET cc_start: 0.7486 (ptp) cc_final: 0.7226 (ptt) REVERT: S 219 GLN cc_start: 0.6956 (mt0) cc_final: 0.6698 (tp-100) REVERT: T 475 GLU cc_start: 0.7255 (tp30) cc_final: 0.6822 (tp30) REVERT: U 71 LYS cc_start: 0.8422 (tppt) cc_final: 0.8178 (tppp) REVERT: V 61 HIS cc_start: 0.7750 (t70) cc_final: 0.7378 (m170) REVERT: X 189 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8194 (mtmm) REVERT: X 385 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7282 (tpt90) REVERT: X 415 ASP cc_start: 0.7598 (t70) cc_final: 0.7363 (t0) REVERT: X 484 MET cc_start: 0.8069 (mmt) cc_final: 0.7622 (tpp) REVERT: X 573 LYS cc_start: 0.7823 (mtmt) cc_final: 0.7491 (mmtm) REVERT: Y 243 LYS cc_start: 0.8299 (mtpt) cc_final: 0.7957 (mmtm) REVERT: Y 313 THR cc_start: 0.9236 (p) cc_final: 0.9010 (p) REVERT: Y 385 ARG cc_start: 0.8042 (mmt90) cc_final: 0.7789 (mmm-85) REVERT: Y 437 ARG cc_start: 0.7709 (mtt-85) cc_final: 0.7466 (mmm-85) REVERT: Y 484 MET cc_start: 0.8116 (tpp) cc_final: 0.7877 (tpt) REVERT: Y 501 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6646 (tmmm) REVERT: Z 493 LYS cc_start: 0.7809 (mtmt) cc_final: 0.7600 (mttt) outliers start: 44 outliers final: 20 residues processed: 641 average time/residue: 1.5256 time to fit residues: 1158.4299 Evaluate side-chains 452 residues out of total 3569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 429 time to evaluate : 3.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain T residue 267 SER Chi-restraints excluded: chain T residue 268 THR Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 345 PRO Chi-restraints excluded: chain U residue 348 GLU Chi-restraints excluded: chain V residue 267 SER Chi-restraints excluded: chain V residue 268 THR Chi-restraints excluded: chain V residue 323 ILE Chi-restraints excluded: chain V residue 325 ASP Chi-restraints excluded: chain V residue 329 LYS Chi-restraints excluded: chain V residue 417 ILE Chi-restraints excluded: chain V residue 487 LYS Chi-restraints excluded: chain X residue 189 LYS Chi-restraints excluded: chain X residue 287 ILE Chi-restraints excluded: chain X residue 385 ARG Chi-restraints excluded: chain Y residue 306 SER Chi-restraints excluded: chain Y residue 501 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 374 optimal weight: 0.9990 chunk 335 optimal weight: 0.9980 chunk 186 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 226 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 chunk 347 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 211 optimal weight: 2.9990 chunk 258 optimal weight: 0.8980 chunk 402 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN H 98 GLN ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN J 98 GLN Q 21 ASN R 73 ASN R 85 GLN R 104 HIS R 137 HIS R 181 ASN S 174 GLN S 186 ASN S 293 ASN S 297 GLN T 264 GLN T 386 GLN T 435 GLN T 441 GLN T 488 GLN T 497 GLN T 529 ASN U 121 ASN U 196 GLN U 242 GLN U 246 ASN U 248 GLN U 319 HIS U 441 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 527 GLN V 104 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 126 HIS V 139 HIS ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 244 ASN V 264 GLN V 271 GLN V 486 GLN V 488 GLN V 497 GLN X 199 ASN X 241 ASN X 278 GLN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 337 GLN X 398 ASN X 408 GLN ** X 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 241 ASN Y 398 ASN Z 144 HIS Z 199 ASN Z 278 GLN Z 448 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34443 Z= 0.219 Angle : 0.603 9.270 46679 Z= 0.311 Chirality : 0.044 0.284 5526 Planarity : 0.005 0.051 5999 Dihedral : 8.024 115.416 4969 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.64 % Rotamer: Outliers : 2.72 % Allowed : 15.41 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -2.76 (0.11), residues: 4463 helix: -2.32 (0.09), residues: 2182 sheet: -0.87 (0.21), residues: 572 loop : -1.16 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 37 HIS 0.004 0.001 HIS S 237 PHE 0.021 0.001 PHE B 107 TYR 0.014 0.001 TYR V 414 ARG 0.007 0.000 ARG S 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 480 time to evaluate : 3.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7333 (mpp) cc_final: 0.7010 (mtm) REVERT: C 97 LYS cc_start: 0.8740 (mppt) cc_final: 0.8445 (mttm) REVERT: E 92 ASN cc_start: 0.7707 (p0) cc_final: 0.7175 (p0) REVERT: F 81 MET cc_start: 0.7922 (ttp) cc_final: 0.7592 (ttp) REVERT: G 95 ILE cc_start: 0.7826 (mm) cc_final: 0.7435 (mm) REVERT: H 61 MET cc_start: 0.7133 (tpp) cc_final: 0.6865 (mmp) REVERT: H 105 LEU cc_start: 0.8235 (tm) cc_final: 0.8025 (tt) REVERT: I 81 MET cc_start: 0.7347 (ttp) cc_final: 0.7068 (ppp) REVERT: I 119 LEU cc_start: 0.6626 (mp) cc_final: 0.6245 (pp) REVERT: J 66 CYS cc_start: 0.7504 (m) cc_final: 0.7155 (m) REVERT: P 49 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7955 (t) REVERT: P 63 LYS cc_start: 0.8518 (tppt) cc_final: 0.8072 (tppp) REVERT: P 69 LYS cc_start: 0.7699 (tttm) cc_final: 0.7473 (tptp) REVERT: P 71 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: P 72 ASP cc_start: 0.7979 (t0) cc_final: 0.7610 (t70) REVERT: P 122 PHE cc_start: 0.7940 (m-80) cc_final: 0.7687 (m-80) REVERT: P 136 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7616 (tp30) REVERT: Q 10 ARG cc_start: 0.7898 (tpp-160) cc_final: 0.7498 (ttm-80) REVERT: Q 40 GLN cc_start: 0.7583 (mm-40) cc_final: 0.7274 (tm130) REVERT: S 62 MET cc_start: 0.7437 (ptp) cc_final: 0.7214 (ptt) REVERT: S 169 ARG cc_start: 0.7679 (ptm160) cc_final: 0.7322 (ptm160) REVERT: S 219 GLN cc_start: 0.6836 (mt0) cc_final: 0.6614 (tp-100) REVERT: T 237 ASP cc_start: 0.7657 (m-30) cc_final: 0.7428 (m-30) REVERT: U 45 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7696 (mp) REVERT: U 71 LYS cc_start: 0.8336 (tppt) cc_final: 0.8067 (tppp) REVERT: U 84 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8908 (mp) REVERT: U 282 MET cc_start: 0.8953 (tpt) cc_final: 0.8452 (tpt) REVERT: U 482 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7386 (mm-30) REVERT: U 511 LYS cc_start: 0.7918 (mttt) cc_final: 0.7633 (mmtm) REVERT: V 61 HIS cc_start: 0.7777 (t70) cc_final: 0.7574 (t-170) REVERT: V 471 GLN cc_start: 0.6576 (pp30) cc_final: 0.6335 (tm130) REVERT: X 484 MET cc_start: 0.8073 (mmt) cc_final: 0.7590 (tpp) REVERT: X 573 LYS cc_start: 0.7550 (mtmt) cc_final: 0.7211 (mmtm) REVERT: Y 51 ARG cc_start: 0.8294 (ttt-90) cc_final: 0.7923 (ttt-90) REVERT: Y 243 LYS cc_start: 0.8291 (mtpt) cc_final: 0.7912 (mmtm) REVERT: Y 385 ARG cc_start: 0.7975 (mmt90) cc_final: 0.7742 (mmm-85) REVERT: Y 437 ARG cc_start: 0.7293 (mtt-85) cc_final: 0.7071 (mmm-85) REVERT: Y 484 MET cc_start: 0.8185 (tpp) cc_final: 0.7915 (tpt) REVERT: Z 292 GLN cc_start: 0.7861 (tt0) cc_final: 0.7592 (tt0) REVERT: Z 493 LYS cc_start: 0.7760 (mtmt) cc_final: 0.7446 (mttt) outliers start: 97 outliers final: 30 residues processed: 540 average time/residue: 1.3862 time to fit residues: 902.2556 Evaluate side-chains 452 residues out of total 3569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 417 time to evaluate : 3.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 71 GLN Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain S residue 86 VAL Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 267 SER Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 207 LYS Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 323 ILE Chi-restraints excluded: chain V residue 326 ASP Chi-restraints excluded: chain V residue 529 ASN Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 492 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 223 optimal weight: 0.8980 chunk 124 optimal weight: 0.0670 chunk 334 optimal weight: 7.9990 chunk 273 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 403 optimal weight: 3.9990 chunk 435 optimal weight: 0.3980 chunk 358 optimal weight: 4.9990 chunk 399 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 323 optimal weight: 0.0000 overall best weight: 0.8724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN G 87 ASN ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN P 83 GLN P 140 ASN R 38 ASN R 181 ASN S 186 ASN T 515 GLN T 529 ASN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 515 GLN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34443 Z= 0.210 Angle : 0.561 9.635 46679 Z= 0.284 Chirality : 0.043 0.214 5526 Planarity : 0.004 0.043 5999 Dihedral : 7.174 102.240 4924 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 3.17 % Allowed : 17.10 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -1.78 (0.12), residues: 4463 helix: -1.29 (0.10), residues: 2173 sheet: -0.84 (0.21), residues: 601 loop : -0.86 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 37 HIS 0.004 0.001 HIS V 241 PHE 0.025 0.001 PHE B 107 TYR 0.016 0.001 TYR U 502 ARG 0.007 0.000 ARG T 496 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 424 time to evaluate : 4.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7283 (mpp) cc_final: 0.7008 (mtm) REVERT: E 92 ASN cc_start: 0.7569 (p0) cc_final: 0.7155 (p0) REVERT: F 81 MET cc_start: 0.7902 (ttp) cc_final: 0.7507 (ttp) REVERT: G 87 ASN cc_start: 0.6974 (m-40) cc_final: 0.6764 (m110) REVERT: G 95 ILE cc_start: 0.7961 (mm) cc_final: 0.7579 (mm) REVERT: I 81 MET cc_start: 0.7283 (ttp) cc_final: 0.7074 (ppp) REVERT: I 119 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6199 (pp) REVERT: J 66 CYS cc_start: 0.7548 (m) cc_final: 0.7230 (m) REVERT: P 63 LYS cc_start: 0.8542 (tppt) cc_final: 0.8317 (tptm) REVERT: P 71 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: P 72 ASP cc_start: 0.7825 (t0) cc_final: 0.7515 (t0) REVERT: P 73 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7763 (mt-10) REVERT: P 122 PHE cc_start: 0.8028 (m-80) cc_final: 0.7775 (m-80) REVERT: P 136 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7576 (tp30) REVERT: Q 10 ARG cc_start: 0.7778 (tpp-160) cc_final: 0.7331 (ttm-80) REVERT: R 127 PHE cc_start: 0.7840 (m-80) cc_final: 0.7544 (m-80) REVERT: S 62 MET cc_start: 0.7201 (ptp) cc_final: 0.6918 (mtp) REVERT: S 232 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.7014 (m-30) REVERT: T 237 ASP cc_start: 0.7607 (m-30) cc_final: 0.7355 (m-30) REVERT: U 71 LYS cc_start: 0.8333 (tppt) cc_final: 0.8081 (tppp) REVERT: U 84 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8861 (mp) REVERT: U 511 LYS cc_start: 0.7885 (mttt) cc_final: 0.7675 (mmpt) REVERT: V 449 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7336 (mt-10) REVERT: V 455 GLU cc_start: 0.7589 (pt0) cc_final: 0.7172 (pp20) REVERT: X 573 LYS cc_start: 0.7428 (mtmt) cc_final: 0.7183 (mtpt) REVERT: Y 243 LYS cc_start: 0.8289 (mtpt) cc_final: 0.7871 (mmtm) REVERT: Y 385 ARG cc_start: 0.7968 (mmt90) cc_final: 0.7733 (mmm-85) REVERT: Y 437 ARG cc_start: 0.7404 (mtt-85) cc_final: 0.7202 (mmm-85) REVERT: Y 484 MET cc_start: 0.8179 (tpp) cc_final: 0.7873 (tpt) REVERT: Z 292 GLN cc_start: 0.7730 (tt0) cc_final: 0.7508 (tt0) REVERT: Z 493 LYS cc_start: 0.7729 (mtmt) cc_final: 0.7369 (mttt) outliers start: 113 outliers final: 52 residues processed: 491 average time/residue: 1.4210 time to fit residues: 837.9438 Evaluate side-chains 452 residues out of total 3569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 394 time to evaluate : 3.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 71 GLN Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 86 VAL Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 279 THR Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain T residue 556 LYS Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 207 LYS Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 326 ASP Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 449 GLU Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 481 THR Chi-restraints excluded: chain V residue 515 GLN Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 492 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 398 optimal weight: 2.9990 chunk 303 optimal weight: 0.6980 chunk 209 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 270 optimal weight: 7.9990 chunk 404 optimal weight: 4.9990 chunk 428 optimal weight: 0.9990 chunk 211 optimal weight: 0.6980 chunk 383 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN J 98 GLN P 83 GLN P 140 ASN ** Q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN S 174 GLN S 186 ASN T 529 ASN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN U 549 HIS ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34443 Z= 0.202 Angle : 0.546 9.515 46679 Z= 0.277 Chirality : 0.043 0.182 5526 Planarity : 0.004 0.041 5999 Dihedral : 6.899 96.999 4920 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.39 % Rotamer: Outliers : 3.59 % Allowed : 17.88 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -1.18 (0.13), residues: 4463 helix: -0.70 (0.11), residues: 2150 sheet: -0.73 (0.21), residues: 601 loop : -0.63 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 37 HIS 0.004 0.001 HIS V 241 PHE 0.030 0.001 PHE B 107 TYR 0.015 0.001 TYR V 414 ARG 0.007 0.000 ARG T 496 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 430 time to evaluate : 3.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7296 (mpp) cc_final: 0.7075 (mtm) REVERT: A 95 ILE cc_start: 0.7371 (OUTLIER) cc_final: 0.7133 (mt) REVERT: D 61 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7574 (mmt) REVERT: E 60 LYS cc_start: 0.7022 (mtmp) cc_final: 0.6577 (ptpp) REVERT: E 92 ASN cc_start: 0.7497 (p0) cc_final: 0.7073 (p0) REVERT: F 81 MET cc_start: 0.7845 (ttp) cc_final: 0.7517 (ttp) REVERT: G 59 SER cc_start: 0.8301 (t) cc_final: 0.7981 (p) REVERT: G 62 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7762 (p) REVERT: I 119 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6130 (pp) REVERT: J 59 SER cc_start: 0.7527 (p) cc_final: 0.7167 (p) REVERT: J 66 CYS cc_start: 0.7588 (m) cc_final: 0.7275 (m) REVERT: P 63 LYS cc_start: 0.8579 (tppt) cc_final: 0.8160 (tppp) REVERT: P 69 LYS cc_start: 0.7873 (tptm) cc_final: 0.7497 (tptp) REVERT: P 72 ASP cc_start: 0.7658 (t0) cc_final: 0.7452 (t0) REVERT: P 73 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7797 (mt-10) REVERT: P 103 LYS cc_start: 0.8326 (mmmm) cc_final: 0.7626 (mmmt) REVERT: P 122 PHE cc_start: 0.8056 (m-80) cc_final: 0.7732 (m-80) REVERT: P 136 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7579 (tp30) REVERT: Q 10 ARG cc_start: 0.7857 (tpp-160) cc_final: 0.7435 (ttt90) REVERT: R 127 PHE cc_start: 0.7737 (m-80) cc_final: 0.7451 (m-80) REVERT: S 68 MET cc_start: 0.7552 (ttp) cc_final: 0.7337 (ttp) REVERT: S 232 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.7038 (m-30) REVERT: T 237 ASP cc_start: 0.7611 (m-30) cc_final: 0.7354 (m-30) REVERT: U 71 LYS cc_start: 0.8305 (tppt) cc_final: 0.8053 (tppp) REVERT: U 84 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8806 (mp) REVERT: U 511 LYS cc_start: 0.7890 (mttt) cc_final: 0.7683 (mmpt) REVERT: V 149 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7682 (mm-40) REVERT: V 449 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: V 482 GLU cc_start: 0.7733 (mp0) cc_final: 0.7332 (mp0) REVERT: V 512 VAL cc_start: 0.8468 (t) cc_final: 0.8245 (m) REVERT: X 430 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7817 (ttmt) REVERT: Y 51 ARG cc_start: 0.8296 (ttt-90) cc_final: 0.7922 (ttt-90) REVERT: Y 243 LYS cc_start: 0.8289 (mtpt) cc_final: 0.7877 (mmtm) REVERT: Y 385 ARG cc_start: 0.8002 (mmt90) cc_final: 0.7794 (mmm-85) REVERT: Y 411 LYS cc_start: 0.8486 (mtpp) cc_final: 0.8257 (mtpt) REVERT: Y 484 MET cc_start: 0.8186 (tpp) cc_final: 0.7909 (tpt) REVERT: Z 359 ASP cc_start: 0.7550 (m-30) cc_final: 0.7188 (m-30) REVERT: Z 493 LYS cc_start: 0.7738 (mtmt) cc_final: 0.7342 (mttt) outliers start: 128 outliers final: 57 residues processed: 508 average time/residue: 1.4074 time to fit residues: 869.5601 Evaluate side-chains 477 residues out of total 3569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 410 time to evaluate : 3.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 86 VAL Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 279 THR Chi-restraints excluded: chain T residue 429 ARG Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 207 LYS Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 497 GLN Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 298 LEU Chi-restraints excluded: chain V residue 326 ASP Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 449 GLU Chi-restraints excluded: chain V residue 481 THR Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 286 ASN Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 430 LYS Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 557 GLU Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 452 VAL Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 426 SER Chi-restraints excluded: chain Z residue 492 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 356 optimal weight: 2.9990 chunk 243 optimal weight: 0.0070 chunk 6 optimal weight: 0.6980 chunk 318 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 365 optimal weight: 0.6980 chunk 295 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 218 optimal weight: 1.9990 chunk 384 optimal weight: 0.3980 chunk 108 optimal weight: 2.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN P 140 ASN R 181 ASN S 186 ASN T 529 ASN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 440 GLN Y 83 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 34443 Z= 0.161 Angle : 0.525 11.125 46679 Z= 0.264 Chirality : 0.042 0.182 5526 Planarity : 0.004 0.049 5999 Dihedral : 6.555 93.264 4920 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.55 % Rotamer: Outliers : 3.50 % Allowed : 18.86 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.75 (0.13), residues: 4463 helix: -0.32 (0.11), residues: 2158 sheet: -0.57 (0.22), residues: 546 loop : -0.46 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP R 37 HIS 0.004 0.001 HIS V 241 PHE 0.037 0.001 PHE H 116 TYR 0.012 0.001 TYR V 414 ARG 0.008 0.000 ARG T 496 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 452 time to evaluate : 3.842 Fit side-chains revert: symmetry clash REVERT: A 95 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7154 (mt) REVERT: D 61 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7636 (mmt) REVERT: D 113 ILE cc_start: 0.5542 (OUTLIER) cc_final: 0.5211 (mp) REVERT: E 60 LYS cc_start: 0.7010 (mtmp) cc_final: 0.6525 (ptpp) REVERT: E 92 ASN cc_start: 0.7459 (p0) cc_final: 0.7043 (p0) REVERT: F 81 MET cc_start: 0.7780 (ttp) cc_final: 0.7546 (ttp) REVERT: G 59 SER cc_start: 0.8280 (t) cc_final: 0.7966 (p) REVERT: G 62 VAL cc_start: 0.7856 (OUTLIER) cc_final: 0.7629 (p) REVERT: G 95 ILE cc_start: 0.7785 (mm) cc_final: 0.7370 (mm) REVERT: H 61 MET cc_start: 0.6858 (mmp) cc_final: 0.6653 (mmt) REVERT: I 102 TYR cc_start: 0.5667 (m-80) cc_final: 0.5446 (m-80) REVERT: I 119 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6154 (pp) REVERT: J 59 SER cc_start: 0.7480 (p) cc_final: 0.7136 (p) REVERT: J 66 CYS cc_start: 0.7547 (m) cc_final: 0.7237 (m) REVERT: J 107 PHE cc_start: 0.6934 (t80) cc_final: 0.6333 (t80) REVERT: P 63 LYS cc_start: 0.8574 (tppt) cc_final: 0.8155 (tppp) REVERT: P 69 LYS cc_start: 0.7865 (tptm) cc_final: 0.7631 (tptp) REVERT: P 103 LYS cc_start: 0.8337 (mmmm) cc_final: 0.7696 (mmmt) REVERT: P 136 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7460 (tp30) REVERT: Q 10 ARG cc_start: 0.7836 (tpp-160) cc_final: 0.7422 (ttt90) REVERT: Q 40 GLN cc_start: 0.7136 (tp-100) cc_final: 0.6791 (tp40) REVERT: R 127 PHE cc_start: 0.7587 (m-80) cc_final: 0.7294 (m-80) REVERT: R 182 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.7154 (ttt180) REVERT: S 234 GLU cc_start: 0.7659 (tm-30) cc_final: 0.6733 (tm-30) REVERT: S 242 VAL cc_start: 0.7494 (t) cc_final: 0.7092 (t) REVERT: S 303 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7254 (mm-30) REVERT: T 237 ASP cc_start: 0.7614 (m-30) cc_final: 0.7352 (m-30) REVERT: U 71 LYS cc_start: 0.8311 (tppt) cc_final: 0.8062 (tppp) REVERT: U 511 LYS cc_start: 0.7826 (mttt) cc_final: 0.7606 (mmpt) REVERT: V 67 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8162 (mt) REVERT: V 149 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7605 (mm-40) REVERT: V 449 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7356 (mt-10) REVERT: V 482 GLU cc_start: 0.7665 (mp0) cc_final: 0.7464 (mp0) REVERT: X 484 MET cc_start: 0.8145 (mmt) cc_final: 0.7854 (mmp) REVERT: Y 51 ARG cc_start: 0.8281 (ttt-90) cc_final: 0.7895 (ttt-90) REVERT: Y 243 LYS cc_start: 0.8271 (mtpt) cc_final: 0.7875 (mmtm) REVERT: Y 401 ARG cc_start: 0.7801 (mmm160) cc_final: 0.6930 (mmt180) REVERT: Y 484 MET cc_start: 0.8233 (tpp) cc_final: 0.8016 (tpt) REVERT: Z 359 ASP cc_start: 0.7500 (m-30) cc_final: 0.7080 (m-30) REVERT: Z 493 LYS cc_start: 0.7595 (mtmt) cc_final: 0.7283 (mttt) outliers start: 125 outliers final: 49 residues processed: 535 average time/residue: 1.3120 time to fit residues: 855.7391 Evaluate side-chains 482 residues out of total 3569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 423 time to evaluate : 4.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain S residue 86 VAL Chi-restraints excluded: chain S residue 186 ASN Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 279 THR Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 207 LYS Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 298 LEU Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 449 GLU Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 468 SER Chi-restraints excluded: chain X residue 557 GLU Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 426 SER Chi-restraints excluded: chain Z residue 492 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 144 optimal weight: 0.7980 chunk 385 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 251 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 428 optimal weight: 6.9990 chunk 355 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 141 optimal weight: 0.0970 chunk 225 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN Q 21 ASN R 181 ASN T 529 ASN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN ** V 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 121 ASN V 152 ASN V 515 GLN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 ASN Z 440 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34443 Z= 0.185 Angle : 0.536 9.919 46679 Z= 0.269 Chirality : 0.043 0.180 5526 Planarity : 0.004 0.060 5999 Dihedral : 6.421 92.961 4920 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.24 % Rotamer: Outliers : 3.36 % Allowed : 19.65 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.56 (0.13), residues: 4463 helix: -0.11 (0.11), residues: 2155 sheet: -0.51 (0.21), residues: 583 loop : -0.42 (0.16), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 37 HIS 0.004 0.001 HIS U 549 PHE 0.034 0.001 PHE A 107 TYR 0.015 0.001 TYR V 414 ARG 0.009 0.000 ARG T 496 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 437 time to evaluate : 3.693 Fit side-chains revert: symmetry clash REVERT: A 95 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7186 (mt) REVERT: C 85 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7824 (tt) REVERT: D 61 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7639 (mmt) REVERT: D 113 ILE cc_start: 0.5564 (OUTLIER) cc_final: 0.5226 (mp) REVERT: E 60 LYS cc_start: 0.6985 (mtmp) cc_final: 0.6486 (ptpp) REVERT: E 92 ASN cc_start: 0.7527 (p0) cc_final: 0.7052 (p0) REVERT: F 61 MET cc_start: 0.6710 (mmp) cc_final: 0.6425 (mmm) REVERT: G 59 SER cc_start: 0.8224 (t) cc_final: 0.7872 (p) REVERT: G 62 VAL cc_start: 0.7855 (OUTLIER) cc_final: 0.7631 (p) REVERT: G 95 ILE cc_start: 0.7775 (mm) cc_final: 0.7379 (mm) REVERT: H 61 MET cc_start: 0.6830 (mmp) cc_final: 0.6630 (mmt) REVERT: I 102 TYR cc_start: 0.6064 (m-80) cc_final: 0.5377 (m-80) REVERT: I 119 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6232 (pp) REVERT: J 59 SER cc_start: 0.7612 (p) cc_final: 0.7289 (p) REVERT: J 66 CYS cc_start: 0.7526 (m) cc_final: 0.7224 (m) REVERT: J 107 PHE cc_start: 0.6778 (t80) cc_final: 0.6172 (t80) REVERT: P 63 LYS cc_start: 0.8570 (tppt) cc_final: 0.8145 (tppp) REVERT: P 73 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7809 (mt-10) REVERT: P 103 LYS cc_start: 0.8183 (mmmm) cc_final: 0.7567 (mmmt) REVERT: P 136 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7514 (tp30) REVERT: Q 10 ARG cc_start: 0.7871 (tpp-160) cc_final: 0.7452 (ttm-80) REVERT: R 127 PHE cc_start: 0.7596 (m-80) cc_final: 0.7335 (m-80) REVERT: S 234 GLU cc_start: 0.7602 (tm-30) cc_final: 0.6687 (tm-30) REVERT: S 242 VAL cc_start: 0.7573 (t) cc_final: 0.7184 (t) REVERT: S 303 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7277 (mm-30) REVERT: T 237 ASP cc_start: 0.7642 (m-30) cc_final: 0.7392 (m-30) REVERT: U 71 LYS cc_start: 0.8310 (tppt) cc_final: 0.8054 (tppp) REVERT: V 149 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7618 (mm-40) REVERT: V 449 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: V 455 GLU cc_start: 0.7683 (pt0) cc_final: 0.7388 (pp20) REVERT: V 482 GLU cc_start: 0.7663 (mp0) cc_final: 0.7200 (mp0) REVERT: X 484 MET cc_start: 0.8149 (mmt) cc_final: 0.7938 (mmp) REVERT: Y 243 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7886 (mmtm) REVERT: Y 401 ARG cc_start: 0.7795 (mmm160) cc_final: 0.6950 (mmt180) REVERT: Y 484 MET cc_start: 0.8225 (tpp) cc_final: 0.8022 (tpt) REVERT: Z 437 ARG cc_start: 0.8126 (mtm110) cc_final: 0.7875 (mtp85) REVERT: Z 441 ARG cc_start: 0.7705 (mtt90) cc_final: 0.7290 (mtt90) REVERT: Z 493 LYS cc_start: 0.7570 (mtmt) cc_final: 0.7326 (mttt) outliers start: 120 outliers final: 58 residues processed: 510 average time/residue: 1.3359 time to fit residues: 828.2196 Evaluate side-chains 476 residues out of total 3569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 409 time to evaluate : 3.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 86 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 279 THR Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 207 LYS Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 298 LEU Chi-restraints excluded: chain V residue 326 ASP Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 449 GLU Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 286 ASN Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 468 SER Chi-restraints excluded: chain X residue 557 GLU Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 426 SER Chi-restraints excluded: chain Z residue 492 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 413 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 244 optimal weight: 0.2980 chunk 313 optimal weight: 0.4980 chunk 242 optimal weight: 2.9990 chunk 360 optimal weight: 0.7980 chunk 239 optimal weight: 1.9990 chunk 426 optimal weight: 0.5980 chunk 267 optimal weight: 2.9990 chunk 260 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 148 HIS Q 21 ASN R 181 ASN T 241 HIS T 529 ASN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 152 ASN V 515 GLN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 ASN Z 440 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34443 Z= 0.170 Angle : 0.535 9.528 46679 Z= 0.266 Chirality : 0.043 0.276 5526 Planarity : 0.004 0.055 5999 Dihedral : 6.203 93.108 4920 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.63 % Favored : 96.35 % Rotamer: Outliers : 3.05 % Allowed : 20.60 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.36 (0.13), residues: 4463 helix: 0.07 (0.12), residues: 2152 sheet: -0.47 (0.22), residues: 573 loop : -0.32 (0.16), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 37 HIS 0.005 0.001 HIS P 148 PHE 0.039 0.001 PHE A 107 TYR 0.013 0.001 TYR U 502 ARG 0.008 0.000 ARG T 496 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 431 time to evaluate : 3.843 Fit side-chains REVERT: D 61 MET cc_start: 0.7964 (mpt) cc_final: 0.7671 (mmt) REVERT: E 92 ASN cc_start: 0.7513 (p0) cc_final: 0.7022 (p0) REVERT: F 61 MET cc_start: 0.6666 (mmp) cc_final: 0.6426 (mmm) REVERT: G 59 SER cc_start: 0.8231 (t) cc_final: 0.7882 (p) REVERT: G 62 VAL cc_start: 0.7780 (OUTLIER) cc_final: 0.7568 (p) REVERT: G 95 ILE cc_start: 0.7754 (mm) cc_final: 0.7380 (mm) REVERT: I 119 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6266 (pp) REVERT: J 59 SER cc_start: 0.7452 (p) cc_final: 0.7105 (p) REVERT: J 66 CYS cc_start: 0.7510 (m) cc_final: 0.7212 (m) REVERT: P 63 LYS cc_start: 0.8499 (tppt) cc_final: 0.8000 (mmmm) REVERT: P 73 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7827 (mt-10) REVERT: P 101 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7354 (ttp-110) REVERT: Q 10 ARG cc_start: 0.7833 (tpp-160) cc_final: 0.7409 (ttm-80) REVERT: Q 40 GLN cc_start: 0.7136 (tp-100) cc_final: 0.6709 (tp40) REVERT: S 234 GLU cc_start: 0.7550 (tm-30) cc_final: 0.6657 (tm-30) REVERT: S 242 VAL cc_start: 0.7541 (t) cc_final: 0.7145 (t) REVERT: T 237 ASP cc_start: 0.7641 (m-30) cc_final: 0.7399 (m-30) REVERT: T 535 ILE cc_start: 0.8603 (mt) cc_final: 0.8376 (mp) REVERT: U 71 LYS cc_start: 0.8343 (tppt) cc_final: 0.8081 (tppp) REVERT: V 149 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7601 (mm-40) REVERT: V 449 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: V 482 GLU cc_start: 0.7692 (mp0) cc_final: 0.7220 (mp0) REVERT: Y 51 ARG cc_start: 0.8285 (ttt-90) cc_final: 0.7902 (ttt-90) REVERT: Y 243 LYS cc_start: 0.8271 (mtpt) cc_final: 0.7874 (mmtm) REVERT: Y 401 ARG cc_start: 0.7835 (mmm160) cc_final: 0.6954 (mmt180) REVERT: Y 484 MET cc_start: 0.8217 (tpp) cc_final: 0.7993 (tpt) REVERT: Z 426 SER cc_start: 0.7561 (OUTLIER) cc_final: 0.7115 (p) REVERT: Z 437 ARG cc_start: 0.8217 (mtm110) cc_final: 0.7930 (mtp85) REVERT: Z 441 ARG cc_start: 0.7684 (mtt90) cc_final: 0.7268 (mtt90) REVERT: Z 493 LYS cc_start: 0.7558 (mtmt) cc_final: 0.7313 (mttt) outliers start: 109 outliers final: 58 residues processed: 503 average time/residue: 1.3275 time to fit residues: 812.2478 Evaluate side-chains 464 residues out of total 3569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 401 time to evaluate : 3.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain S residue 86 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 279 THR Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 298 LEU Chi-restraints excluded: chain V residue 326 ASP Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 449 GLU Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 512 VAL Chi-restraints excluded: chain V residue 515 GLN Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 468 SER Chi-restraints excluded: chain X residue 557 GLU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 426 SER Chi-restraints excluded: chain Z residue 492 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 264 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 255 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 271 optimal weight: 1.9990 chunk 290 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 335 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 98 GLN ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN T 435 GLN T 529 ASN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 152 ASN V 515 GLN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 ASN Z 440 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34443 Z= 0.214 Angle : 0.561 10.239 46679 Z= 0.280 Chirality : 0.044 0.193 5526 Planarity : 0.004 0.055 5999 Dihedral : 6.287 94.565 4920 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.92 % Favored : 96.06 % Rotamer: Outliers : 3.14 % Allowed : 20.71 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.31 (0.13), residues: 4463 helix: 0.14 (0.12), residues: 2150 sheet: -0.53 (0.21), residues: 591 loop : -0.32 (0.16), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 37 HIS 0.003 0.001 HIS S 250 PHE 0.034 0.002 PHE A 107 TYR 0.014 0.001 TYR V 414 ARG 0.009 0.000 ARG T 496 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 415 time to evaluate : 3.795 Fit side-chains REVERT: B 115 LEU cc_start: 0.6631 (mt) cc_final: 0.6372 (mt) REVERT: C 97 LYS cc_start: 0.8646 (mttp) cc_final: 0.8311 (mttm) REVERT: D 61 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7682 (mmt) REVERT: E 92 ASN cc_start: 0.7516 (p0) cc_final: 0.7033 (p0) REVERT: F 98 GLN cc_start: 0.7077 (tt0) cc_final: 0.6828 (tm-30) REVERT: G 59 SER cc_start: 0.8236 (t) cc_final: 0.7887 (p) REVERT: G 62 VAL cc_start: 0.7809 (OUTLIER) cc_final: 0.7579 (p) REVERT: G 95 ILE cc_start: 0.7735 (mm) cc_final: 0.7358 (mm) REVERT: I 119 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6331 (pp) REVERT: J 59 SER cc_start: 0.7392 (p) cc_final: 0.7035 (p) REVERT: J 66 CYS cc_start: 0.7672 (m) cc_final: 0.7424 (m) REVERT: J 107 PHE cc_start: 0.6705 (t80) cc_final: 0.6487 (t80) REVERT: P 63 LYS cc_start: 0.8500 (tppt) cc_final: 0.7976 (mmmm) REVERT: P 73 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7849 (mt-10) REVERT: P 101 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7640 (mtm-85) REVERT: Q 10 ARG cc_start: 0.7855 (tpp-160) cc_final: 0.7394 (ttm-80) REVERT: Q 40 GLN cc_start: 0.7099 (tp-100) cc_final: 0.6730 (tp40) REVERT: S 156 GLN cc_start: 0.5635 (pm20) cc_final: 0.5372 (pm20) REVERT: S 234 GLU cc_start: 0.7665 (tm-30) cc_final: 0.6769 (tm-30) REVERT: S 242 VAL cc_start: 0.7569 (t) cc_final: 0.7179 (t) REVERT: T 237 ASP cc_start: 0.7628 (m-30) cc_final: 0.7415 (m-30) REVERT: T 535 ILE cc_start: 0.8597 (mt) cc_final: 0.8359 (mp) REVERT: U 71 LYS cc_start: 0.8340 (tppt) cc_final: 0.8080 (tppp) REVERT: V 149 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7552 (mm-40) REVERT: V 449 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7366 (mt-10) REVERT: Y 243 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7882 (mmtm) REVERT: Y 401 ARG cc_start: 0.7868 (mmm160) cc_final: 0.6925 (mmt180) REVERT: Z 82 ASP cc_start: 0.7600 (t0) cc_final: 0.7065 (t0) REVERT: Z 426 SER cc_start: 0.7595 (OUTLIER) cc_final: 0.7134 (p) REVERT: Z 437 ARG cc_start: 0.8295 (mtm110) cc_final: 0.8056 (mtp85) REVERT: Z 441 ARG cc_start: 0.7718 (mtt90) cc_final: 0.7345 (mtt90) REVERT: Z 493 LYS cc_start: 0.7556 (mtmt) cc_final: 0.7307 (mttt) outliers start: 112 outliers final: 72 residues processed: 488 average time/residue: 1.3210 time to fit residues: 781.5748 Evaluate side-chains 483 residues out of total 3569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 405 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain S residue 86 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 304 LEU Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 279 THR Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain T residue 556 LYS Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 207 LYS Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 298 LEU Chi-restraints excluded: chain V residue 326 ASP Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 449 GLU Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 481 THR Chi-restraints excluded: chain V residue 515 GLN Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 286 ASN Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 468 SER Chi-restraints excluded: chain X residue 557 GLU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 452 VAL Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 426 SER Chi-restraints excluded: chain Z residue 492 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 388 optimal weight: 0.3980 chunk 409 optimal weight: 0.9990 chunk 373 optimal weight: 7.9990 chunk 397 optimal weight: 0.6980 chunk 408 optimal weight: 0.9980 chunk 239 optimal weight: 3.9990 chunk 173 optimal weight: 0.1980 chunk 312 optimal weight: 0.8980 chunk 122 optimal weight: 0.4980 chunk 359 optimal weight: 1.9990 chunk 376 optimal weight: 10.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN T 529 ASN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 152 ASN V 219 GLN V 515 GLN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 398 ASN Y 83 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34443 Z= 0.167 Angle : 0.551 14.489 46679 Z= 0.272 Chirality : 0.043 0.227 5526 Planarity : 0.004 0.050 5999 Dihedral : 6.070 94.488 4920 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.72 % Allowed : 21.61 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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 (0.13), residues: 4463 helix: 0.26 (0.12), residues: 2156 sheet: -0.47 (0.22), residues: 573 loop : -0.27 (0.16), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 37 HIS 0.003 0.001 HIS S 237 PHE 0.031 0.001 PHE H 107 TYR 0.015 0.001 TYR S 231 ARG 0.009 0.000 ARG T 496 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 416 time to evaluate : 3.351 Fit side-chains REVERT: A 92 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.7983 (p0) REVERT: B 115 LEU cc_start: 0.6622 (mt) cc_final: 0.6373 (mt) REVERT: C 81 MET cc_start: 0.7866 (tpp) cc_final: 0.7516 (ttt) REVERT: D 61 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7716 (mmt) REVERT: D 92 ASN cc_start: 0.6758 (OUTLIER) cc_final: 0.6464 (p0) REVERT: E 92 ASN cc_start: 0.7466 (p0) cc_final: 0.7008 (p0) REVERT: F 61 MET cc_start: 0.6667 (mmp) cc_final: 0.6416 (mmm) REVERT: G 59 SER cc_start: 0.8231 (t) cc_final: 0.7878 (p) REVERT: G 62 VAL cc_start: 0.7742 (OUTLIER) cc_final: 0.7518 (p) REVERT: G 95 ILE cc_start: 0.7750 (mm) cc_final: 0.7381 (mm) REVERT: I 119 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6248 (pp) REVERT: J 59 SER cc_start: 0.7373 (p) cc_final: 0.7010 (p) REVERT: J 66 CYS cc_start: 0.7582 (m) cc_final: 0.7286 (m) REVERT: P 63 LYS cc_start: 0.8543 (tppt) cc_final: 0.8085 (mmmm) REVERT: P 72 ASP cc_start: 0.7563 (t0) cc_final: 0.6967 (t70) REVERT: P 73 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7687 (mt-10) REVERT: P 84 HIS cc_start: 0.7832 (m90) cc_final: 0.7524 (m90) REVERT: P 101 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7616 (mtm-85) REVERT: Q 10 ARG cc_start: 0.7852 (tpp-160) cc_final: 0.7398 (ttm-80) REVERT: Q 40 GLN cc_start: 0.7080 (tp-100) cc_final: 0.6752 (tp40) REVERT: S 156 GLN cc_start: 0.5670 (pm20) cc_final: 0.5449 (pm20) REVERT: S 203 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7758 (m-80) REVERT: S 234 GLU cc_start: 0.7522 (tm-30) cc_final: 0.6677 (tm-30) REVERT: S 242 VAL cc_start: 0.7539 (t) cc_final: 0.7152 (t) REVERT: T 237 ASP cc_start: 0.7641 (m-30) cc_final: 0.7402 (m-30) REVERT: T 535 ILE cc_start: 0.8578 (mt) cc_final: 0.8345 (mp) REVERT: U 71 LYS cc_start: 0.8337 (tppt) cc_final: 0.8036 (tppp) REVERT: V 149 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7568 (mm-40) REVERT: V 418 ARG cc_start: 0.8146 (mpt-90) cc_final: 0.7908 (mtt90) REVERT: V 449 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: Y 243 LYS cc_start: 0.8266 (mtpt) cc_final: 0.7854 (mmtm) REVERT: Y 401 ARG cc_start: 0.7875 (mmm160) cc_final: 0.7057 (mmt180) REVERT: Z 82 ASP cc_start: 0.7548 (t0) cc_final: 0.7010 (t0) REVERT: Z 426 SER cc_start: 0.7582 (OUTLIER) cc_final: 0.7139 (p) REVERT: Z 493 LYS cc_start: 0.7542 (mtmt) cc_final: 0.7290 (mttt) outliers start: 97 outliers final: 62 residues processed: 484 average time/residue: 1.3655 time to fit residues: 805.0657 Evaluate side-chains 468 residues out of total 3569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 397 time to evaluate : 3.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain S residue 86 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 279 THR Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 207 LYS Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 298 LEU Chi-restraints excluded: chain V residue 326 ASP Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 449 GLU Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 512 VAL Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 468 SER Chi-restraints excluded: chain X residue 557 GLU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 426 SER Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 492 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 396 optimal weight: 0.9990 chunk 261 optimal weight: 0.6980 chunk 420 optimal weight: 3.9990 chunk 256 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 292 optimal weight: 0.5980 chunk 441 optimal weight: 0.6980 chunk 406 optimal weight: 0.9980 chunk 351 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 271 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 529 ASN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 152 ASN V 471 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 ASN Z 440 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 34443 Z= 0.198 Angle : 0.652 59.188 46679 Z= 0.346 Chirality : 0.043 0.353 5526 Planarity : 0.004 0.054 5999 Dihedral : 6.084 94.613 4920 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.30 % Allowed : 22.45 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.13), residues: 4463 helix: 0.27 (0.12), residues: 2156 sheet: -0.46 (0.22), residues: 573 loop : -0.27 (0.16), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 37 HIS 0.003 0.001 HIS S 250 PHE 0.028 0.001 PHE H 107 TYR 0.017 0.001 TYR F 102 ARG 0.008 0.000 ARG T 496 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 397 time to evaluate : 4.130 Fit side-chains REVERT: A 92 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.7494 (p0) REVERT: B 115 LEU cc_start: 0.6636 (mt) cc_final: 0.6388 (mt) REVERT: C 81 MET cc_start: 0.7869 (tpp) cc_final: 0.7509 (ttt) REVERT: D 61 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7717 (mmt) REVERT: D 92 ASN cc_start: 0.6754 (OUTLIER) cc_final: 0.6463 (p0) REVERT: E 92 ASN cc_start: 0.7478 (p0) cc_final: 0.7009 (p0) REVERT: F 61 MET cc_start: 0.6665 (mmp) cc_final: 0.6424 (mmm) REVERT: G 59 SER cc_start: 0.8231 (t) cc_final: 0.7879 (p) REVERT: G 62 VAL cc_start: 0.7742 (OUTLIER) cc_final: 0.7520 (p) REVERT: G 95 ILE cc_start: 0.7750 (mm) cc_final: 0.7381 (mm) REVERT: I 119 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6251 (pp) REVERT: J 59 SER cc_start: 0.7369 (p) cc_final: 0.7023 (p) REVERT: J 66 CYS cc_start: 0.7587 (m) cc_final: 0.7289 (m) REVERT: P 63 LYS cc_start: 0.8549 (tppt) cc_final: 0.8084 (mmmm) REVERT: P 72 ASP cc_start: 0.7565 (t0) cc_final: 0.6965 (t70) REVERT: P 73 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7687 (mt-10) REVERT: P 101 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7618 (mtm-85) REVERT: Q 10 ARG cc_start: 0.7851 (tpp-160) cc_final: 0.7398 (ttm-80) REVERT: Q 40 GLN cc_start: 0.7080 (tp-100) cc_final: 0.6748 (tp40) REVERT: S 156 GLN cc_start: 0.5666 (pm20) cc_final: 0.5451 (pm20) REVERT: S 203 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7759 (m-80) REVERT: S 234 GLU cc_start: 0.7527 (tm-30) cc_final: 0.6678 (tm-30) REVERT: S 242 VAL cc_start: 0.7537 (t) cc_final: 0.7156 (t) REVERT: T 237 ASP cc_start: 0.7645 (m-30) cc_final: 0.7400 (m-30) REVERT: T 535 ILE cc_start: 0.8585 (mt) cc_final: 0.8345 (mp) REVERT: U 71 LYS cc_start: 0.8338 (tppt) cc_final: 0.8036 (tppp) REVERT: V 149 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7562 (mm-40) REVERT: V 418 ARG cc_start: 0.8147 (mpt-90) cc_final: 0.7914 (mtt90) REVERT: V 449 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: Y 243 LYS cc_start: 0.8267 (mtpt) cc_final: 0.7855 (mmtm) REVERT: Y 401 ARG cc_start: 0.7875 (mmm160) cc_final: 0.7058 (mmt180) REVERT: Z 82 ASP cc_start: 0.7583 (t0) cc_final: 0.7048 (t0) REVERT: Z 426 SER cc_start: 0.7584 (OUTLIER) cc_final: 0.7137 (p) REVERT: Z 493 LYS cc_start: 0.7543 (mtmt) cc_final: 0.7290 (mttt) outliers start: 82 outliers final: 64 residues processed: 454 average time/residue: 1.3951 time to fit residues: 766.0030 Evaluate side-chains 468 residues out of total 3569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 395 time to evaluate : 3.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain S residue 86 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 279 THR Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 207 LYS Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 522 GLU Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 298 LEU Chi-restraints excluded: chain V residue 326 ASP Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 449 GLU Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 512 VAL Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 468 SER Chi-restraints excluded: chain X residue 557 GLU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 426 SER Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 492 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 215 optimal weight: 0.9990 chunk 279 optimal weight: 0.9990 chunk 374 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 324 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 97 optimal weight: 0.4980 chunk 352 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 361 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 529 ASN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 471 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 ASN Z 440 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.145971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.102760 restraints weight = 44725.836| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.73 r_work: 0.3064 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 34443 Z= 0.198 Angle : 0.652 59.199 46679 Z= 0.346 Chirality : 0.043 0.354 5526 Planarity : 0.004 0.054 5999 Dihedral : 6.084 94.614 4920 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.13 % Allowed : 22.67 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.13), residues: 4463 helix: 0.27 (0.12), residues: 2156 sheet: -0.46 (0.22), residues: 573 loop : -0.27 (0.16), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 37 HIS 0.003 0.001 HIS S 250 PHE 0.028 0.001 PHE H 107 TYR 0.017 0.001 TYR F 102 ARG 0.008 0.000 ARG T 496 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13553.84 seconds wall clock time: 240 minutes 28.06 seconds (14428.06 seconds total)