Starting phenix.real_space_refine on Thu Feb 22 11:06:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rde_4815/02_2024/6rde_4815_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rde_4815/02_2024/6rde_4815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rde_4815/02_2024/6rde_4815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rde_4815/02_2024/6rde_4815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rde_4815/02_2024/6rde_4815_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rde_4815/02_2024/6rde_4815_updated.pdb" } resolution = 2.9 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 21548 2.51 5 N 5795 2.21 5 O 6449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 111": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "P GLU 64": "OE1" <-> "OE2" Residue "P ASP 111": "OD1" <-> "OD2" Residue "P PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 123": "OE1" <-> "OE2" Residue "P ASP 127": "OD1" <-> "OD2" Residue "P GLU 142": "OE1" <-> "OE2" Residue "P GLU 143": "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 GLU 64": "OE1" <-> "OE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 62": "OE1" <-> "OE2" Residue "R PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 148": "OE1" <-> "OE2" Residue "R GLU 175": "OE1" <-> "OE2" Residue "R PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 164": "OD1" <-> "OD2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 222": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S GLU 283": "OE1" <-> "OE2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 303": "OE1" <-> "OE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ASP 112": "OD1" <-> "OD2" Residue "T ASP 125": "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 ASP 237": "OD1" <-> "OD2" Residue "T TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 325": "OD1" <-> "OD2" Residue "T ASP 353": "OD1" <-> "OD2" Residue "T ASP 403": "OD1" <-> "OD2" Residue "T GLU 411": "OE1" <-> "OE2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 418": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 475": "OE1" <-> "OE2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 510": "OD1" <-> "OD2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ASP 46": "OD1" <-> "OD2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 92": "OD1" <-> "OD2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 112": "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 ARG 227": "NH1" <-> "NH2" 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 GLU 371": "OE1" <-> "OE2" Residue "U PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 389": "OD1" <-> "OD2" Residue "U PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 510": "OD1" <-> "OD2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U GLU 521": "OE1" <-> "OE2" Residue "U GLU 522": "OE1" <-> "OE2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 74": "OE1" <-> "OE2" Residue "V PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 142": "OD1" <-> "OD2" 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 ARG 335": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "V ARG 347": "NH1" <-> "NH2" Residue "V ARG 360": "NH1" <-> "NH2" 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 PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 465": "OD1" <-> "OD2" Residue "V ASP 467": "OD1" <-> "OD2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V GLU 521": "OE1" <-> "OE2" Residue "V GLU 553": "OE1" <-> "OE2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X ARG 71": "NH1" <-> "NH2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X ASP 104": "OD1" <-> "OD2" Residue "X ARG 120": "NH1" <-> "NH2" Residue "X ASP 130": "OD1" <-> "OD2" Residue "X GLU 131": "OE1" <-> "OE2" Residue "X GLU 152": "OE1" <-> "OE2" Residue "X PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "X GLU 229": "OE1" <-> "OE2" Residue "X ARG 258": "NH1" <-> "NH2" Residue "X GLU 270": "OE1" <-> "OE2" Residue "X PHE 283": "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 ARG 385": "NH1" <-> "NH2" Residue "X ARG 401": "NH1" <-> "NH2" Residue "X ASP 409": "OD1" <-> "OD2" Residue "X TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 428": "OE1" <-> "OE2" Residue "X ARG 435": "NH1" <-> "NH2" Residue "X ARG 437": "NH1" <-> "NH2" Residue "X PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X GLU 519": "OE1" <-> "OE2" Residue "X GLU 520": "OE1" <-> "OE2" Residue "X GLU 533": "OE1" <-> "OE2" Residue "X ASP 543": "OD1" <-> "OD2" Residue "X PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 564": "OE1" <-> "OE2" Residue "Y TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y ASP 104": "OD1" <-> "OD2" Residue "Y GLU 146": "OE1" <-> "OE2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 156": "OE1" <-> "OE2" Residue "Y ASP 168": "OD1" <-> "OD2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 218": "NH1" <-> "NH2" Residue "Y ARG 225": "NH1" <-> "NH2" Residue "Y ARG 239": "NH1" <-> "NH2" Residue "Y TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 279": "OD1" <-> "OD2" Residue "Y GLU 296": "OE1" <-> "OE2" Residue "Y ASP 317": "OD1" <-> "OD2" Residue "Y ASP 348": "OD1" <-> "OD2" Residue "Y TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 401": "NH1" <-> "NH2" Residue "Y ASP 415": "OD1" <-> "OD2" Residue "Y ASP 429": "OD1" <-> "OD2" Residue "Y PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 479": "OD1" <-> "OD2" Residue "Y PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 494": "OE1" <-> "OE2" Residue "Y ARG 509": "NH1" <-> "NH2" Residue "Y GLU 533": "OE1" <-> "OE2" Residue "Y GLU 540": "OE1" <-> "OE2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "Z ARG 115": "NH1" <-> "NH2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z ASP 136": "OD1" <-> "OD2" Residue "Z ASP 139": "OD1" <-> "OD2" Residue "Z ARG 145": "NH1" <-> "NH2" Residue "Z PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 215": "OE1" <-> "OE2" Residue "Z GLU 238": "OE1" <-> "OE2" Residue "Z ARG 258": "NH1" <-> "NH2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z ASP 279": "OD1" <-> "OD2" Residue "Z GLU 296": "OE1" <-> "OE2" Residue "Z TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 359": "OD1" <-> "OD2" Residue "Z ARG 366": "NH1" <-> "NH2" Residue "Z GLU 370": "OE1" <-> "OE2" Residue "Z TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 378": "OD1" <-> "OD2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z GLU 424": "OE1" <-> "OE2" Residue "Z GLU 428": "OE1" <-> "OE2" Residue "Z ASP 429": "OD1" <-> "OD2" Residue "Z GLU 451": "OE1" <-> "OE2" Residue "Z PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 462": "OD1" <-> "OD2" Residue "Z PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 505": "OD1" <-> "OD2" Residue "Z GLU 511": "OE1" <-> "OE2" Residue "Z ASP 523": "OD1" <-> "OD2" Residue "Z ASP 543": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33926 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: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 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: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "Y" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3952 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 497} Chain: "Z" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain breaks: 1 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: "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: "Z" 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: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "U" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 17.38, per 1000 atoms: 0.51 Number of scatterers: 33926 At special positions: 0 Unit cell: (164.268, 129.519, 208.494, 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 6449 8.00 N 5795 7.00 C 21548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.26 Conformation dependent library (CDL) restraints added in 6.0 seconds 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8158 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 181 helices and 28 sheets defined 46.9% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.88 Creating SS restraints... Processing helix chain 'A' and resid 55 through 91 removed outlier: 3.872A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ALA A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.649A pdb=" N LEU A 99 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL A 100 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 103 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 124 removed outlier: 3.751A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.544A pdb=" N LYS B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 111 Processing helix chain 'B' and resid 114 through 125 removed outlier: 4.017A pdb=" N LEU B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 65 removed outlier: 3.752A pdb=" N LYS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 64 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 91 removed outlier: 4.145A pdb=" N GLY C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL C 74 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY C 77 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 78 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY C 79 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET C 81 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE C 82 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 85 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C 89 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG C 91 " --> pdb=" O GLY C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 125 removed outlier: 5.733A pdb=" N LYS C 97 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU C 104 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 105 " --> pdb=" O TYR C 102 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 109 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU C 111 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU C 115 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER C 117 " --> pdb=" O ALA C 114 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU C 118 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C 119 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE C 124 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 125 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 91 removed outlier: 4.531A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY D 65 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 125 removed outlier: 4.928A pdb=" N LYS D 97 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 99 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 100 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY D 101 " --> pdb=" O GLN D 98 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU D 104 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU D 105 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA D 108 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR D 110 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU D 111 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE D 116 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N SER D 117 " --> pdb=" O ALA D 114 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 119 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL D 121 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE D 122 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE D 124 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 91 removed outlier: 3.514A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA E 64 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU E 85 " --> pdb=" O MET E 81 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 124 removed outlier: 3.988A pdb=" N VAL E 100 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY E 101 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 91 removed outlier: 3.918A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY F 79 " --> pdb=" O GLY F 75 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 95 No H-bonds generated for 'chain 'F' and resid 93 through 95' Processing helix chain 'F' and resid 98 through 125 removed outlier: 3.596A pdb=" N LEU F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU F 111 " --> pdb=" O PHE F 107 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU F 118 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU F 119 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 67 removed outlier: 4.201A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 91 removed outlier: 3.949A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY G 79 " --> pdb=" O GLY G 75 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG G 91 " --> pdb=" O ASN G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 125 removed outlier: 5.275A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL G 100 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU G 104 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU G 105 " --> pdb=" O TYR G 102 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA G 108 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU G 109 " --> pdb=" O GLY G 106 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU G 111 " --> pdb=" O ALA G 108 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER G 112 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU G 115 " --> pdb=" O SER G 112 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER G 117 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL G 121 " --> pdb=" O LEU G 118 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE G 122 " --> pdb=" O LEU G 119 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE G 124 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU G 125 " --> pdb=" O PHE G 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 62 removed outlier: 4.340A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 89 removed outlier: 3.933A pdb=" N ALA H 70 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL H 74 " --> pdb=" O LEU H 71 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY H 75 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU H 78 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY H 79 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET H 81 " --> pdb=" O LEU H 78 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE H 82 " --> pdb=" O GLY H 79 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU H 85 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA H 89 " --> pdb=" O ILE H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 125 removed outlier: 5.100A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL H 100 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU H 104 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE H 107 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR H 110 " --> pdb=" O PHE H 107 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE H 113 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER H 117 " --> pdb=" O ALA H 114 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU H 118 " --> pdb=" O LEU H 115 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE H 124 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU H 125 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 91 removed outlier: 3.621A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA I 70 " --> pdb=" O CYS I 66 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ALA I 72 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY I 79 " --> pdb=" O GLY I 75 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 125 removed outlier: 5.684A pdb=" N LYS I 97 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL I 100 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU I 104 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU I 105 " --> pdb=" O TYR I 102 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE I 107 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR I 110 " --> pdb=" O PHE I 107 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU I 111 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER I 112 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER I 117 " --> pdb=" O ALA I 114 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL I 121 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE I 124 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU I 125 " --> pdb=" O PHE I 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 91 removed outlier: 3.517A pdb=" N SER J 59 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 95 No H-bonds generated for 'chain 'J' and resid 93 through 95' Processing helix chain 'J' and resid 98 through 124 removed outlier: 3.697A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER J 112 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 63 Processing helix chain 'P' and resid 69 through 83 Processing helix chain 'P' and resid 85 through 92 removed outlier: 4.106A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 108 Processing helix chain 'P' and resid 116 through 127 Processing helix chain 'P' and resid 131 through 148 removed outlier: 3.849A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU P 142 " --> pdb=" O VAL P 139 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU P 143 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU P 144 " --> pdb=" O TYR P 141 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU P 146 " --> pdb=" O GLU P 143 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA P 147 " --> pdb=" O LEU P 144 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 12 No H-bonds generated for 'chain 'Q' and resid 10 through 12' Processing helix chain 'Q' and resid 16 through 30 removed outlier: 3.543A pdb=" N LEU Q 27 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN Q 29 " --> pdb=" O ASP Q 25 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 39 removed outlier: 3.658A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 43 No H-bonds generated for 'chain 'Q' and resid 41 through 43' Processing helix chain 'R' and resid 32 through 40 removed outlier: 3.753A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 54 Processing helix chain 'R' and resid 160 through 169 removed outlier: 3.712A pdb=" N LEU R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA R 165 " --> pdb=" O LYS R 161 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 192 removed outlier: 3.534A pdb=" N GLU R 186 " --> pdb=" O ARG R 182 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU R 187 " --> pdb=" O ALA R 183 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA R 190 " --> pdb=" O GLU R 186 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 88 removed outlier: 3.646A pdb=" N ARG S 48 " --> pdb=" O LYS S 44 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS S 55 " --> pdb=" O LYS S 51 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN S 70 " --> pdb=" O SER S 66 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU S 76 " --> pdb=" O GLN S 72 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN S 77 " --> pdb=" O ILE S 73 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY S 80 " --> pdb=" O GLU S 76 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU S 81 " --> pdb=" O GLN S 77 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL S 82 " --> pdb=" O SER S 78 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP S 83 " --> pdb=" O ARG S 79 " (cutoff:3.500A) Proline residue: S 84 - end of helix Processing helix chain 'S' and resid 118 through 126 Processing helix chain 'S' and resid 144 through 150 removed outlier: 3.556A pdb=" N SER S 148 " --> pdb=" O ASP S 144 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN S 149 " --> pdb=" O LYS S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 184 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 273 removed outlier: 3.791A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 314 removed outlier: 3.572A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU S 314 " --> pdb=" O GLY S 310 " (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 207 through 212 Processing helix chain 'T' and resid 231 through 246 removed outlier: 3.532A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN T 244 " --> pdb=" O ILE T 240 " (cutoff:3.500A) Processing helix chain 'T' and resid 251 through 253 No H-bonds generated for 'chain 'T' and resid 251 through 253' 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 315 Proline residue: T 303 - end of helix removed outlier: 4.412A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 340 removed outlier: 3.550A 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 354 through 362 removed outlier: 3.853A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 399 Processing helix chain 'T' and resid 410 through 414 Processing helix chain 'T' and resid 431 through 434 Processing helix chain 'T' and resid 437 through 442 removed outlier: 3.579A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 444 through 459 removed outlier: 3.611A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 470 through 484 removed outlier: 3.652A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU T 482 " --> pdb=" O ALA T 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 505 removed outlier: 3.831A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 527 removed outlier: 3.555A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 539 Processing helix chain 'T' and resid 544 through 555 removed outlier: 3.573A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA T 552 " --> pdb=" O ALA T 548 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 48 No H-bonds generated for 'chain 'U' and resid 46 through 48' Processing helix chain 'U' and resid 59 through 64 removed outlier: 3.632A pdb=" N SER U 63 " --> pdb=" O ILE U 59 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 59 through 64' Processing helix chain 'U' and resid 66 through 73 removed outlier: 3.938A pdb=" N TRP U 73 " --> pdb=" O ALA U 69 " (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 157 through 159 No H-bonds generated for 'chain 'U' and resid 157 through 159' Processing helix chain 'U' and resid 207 through 212 Processing helix chain 'U' and resid 231 through 246 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 315 Proline residue: U 303 - end of helix removed outlier: 3.610A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG U 314 " --> pdb=" O ALA U 310 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 removed outlier: 3.928A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 347 through 349 No H-bonds generated for 'chain 'U' and resid 347 through 349' Processing helix chain 'U' and resid 354 through 364 removed outlier: 3.555A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARG U 364 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 370 through 372 No H-bonds generated for 'chain 'U' and resid 370 through 372' Processing helix chain 'U' and resid 393 through 401 Processing helix chain 'U' and resid 410 through 414 removed outlier: 3.617A pdb=" N TYR U 414 " --> pdb=" O THR U 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 410 through 414' Processing helix chain 'U' and resid 437 through 449 removed outlier: 4.078A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) Processing helix chain 'U' and resid 451 through 459 removed outlier: 3.824A pdb=" N GLU U 455 " --> pdb=" O ALA U 451 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL U 456 " --> pdb=" O GLN U 452 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA U 458 " --> pdb=" O ARG U 454 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE U 459 " --> pdb=" O GLU U 455 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 484 removed outlier: 3.555A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU U 482 " --> pdb=" O ALA U 478 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET U 483 " --> pdb=" O ARG U 479 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU U 484 " --> pdb=" O LEU U 480 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 505 removed outlier: 3.781A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 517 through 527 removed outlier: 3.739A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 532 through 539 Processing helix chain 'U' and resid 544 through 553 Processing helix chain 'V' and resid 45 through 48 Processing helix chain 'V' and resid 58 through 66 removed outlier: 3.864A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) 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 210 No H-bonds generated for 'chain 'V' and resid 207 through 210' Processing helix chain 'V' and resid 231 through 248 removed outlier: 3.548A pdb=" N GLN V 242 " --> pdb=" O ALA V 238 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS V 243 " --> pdb=" O ILE V 239 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLN V 248 " --> pdb=" O ASN V 244 " (cutoff:3.500A) Processing helix chain 'V' and resid 251 through 253 No H-bonds generated for 'chain 'V' and resid 251 through 253' Processing helix chain 'V' and resid 266 through 279 Processing helix chain 'V' and resid 281 through 284 Processing helix chain 'V' and resid 296 through 315 Proline residue: V 303 - end of helix removed outlier: 3.571A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) removed outlier: 3.535A 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 347 through 349 No H-bonds generated for 'chain 'V' and resid 347 through 349' Processing helix chain 'V' and resid 352 through 364 removed outlier: 4.369A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR V 356 " --> pdb=" O ASP V 353 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER V 359 " --> pdb=" O TYR V 356 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU V 361 " --> pdb=" O HIS V 358 " (cutoff:3.500A) removed outlier: 4.578A 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: 3.511A 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 439 through 456 removed outlier: 3.888A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 483 removed outlier: 3.877A pdb=" N ALA V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) Processing helix chain 'V' and resid 494 through 505 removed outlier: 3.608A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) Processing helix chain 'V' and resid 508 through 510 No H-bonds generated for 'chain 'V' and resid 508 through 510' 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 518 through 527 removed outlier: 3.698A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN V 527 " --> pdb=" O ALA V 523 " (cutoff:3.500A) Processing helix chain 'V' and resid 532 through 539 removed outlier: 3.558A pdb=" N ALA V 538 " --> pdb=" O LYS V 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 549 through 553 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 Processing helix chain 'X' and resid 217 through 230 Processing helix chain 'X' and resid 236 through 241 removed outlier: 4.766A 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: 3.727A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 300 Processing helix chain 'X' and resid 314 through 324 removed outlier: 4.406A pdb=" N ARG X 324 " --> pdb=" O GLY X 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 342 through 344 No H-bonds generated for 'chain 'X' and resid 342 through 344' Processing helix chain 'X' and resid 349 through 354 Processing helix chain 'X' and resid 366 through 370 Processing helix chain 'X' and resid 394 through 412 removed outlier: 3.545A pdb=" N VAL X 399 " --> pdb=" O GLU X 395 " (cutoff:3.500A) Processing helix chain 'X' and resid 414 through 417 No H-bonds generated for 'chain 'X' and resid 414 through 417' Processing helix chain 'X' and resid 427 through 440 removed outlier: 4.006A pdb=" N LEU X 431 " --> pdb=" O GLU X 427 " (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 474 removed outlier: 3.517A pdb=" N SER X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY X 472 " --> pdb=" O SER X 468 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL X 473 " --> pdb=" O GLY X 469 " (cutoff:3.500A) Processing helix chain 'X' and resid 483 through 485 No H-bonds generated for 'chain 'X' and resid 483 through 485' Processing helix chain 'X' and resid 492 through 502 removed outlier: 4.160A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) Processing helix chain 'X' and resid 504 through 506 No H-bonds generated for 'chain 'X' and resid 504 through 506' Processing helix chain 'X' and resid 527 through 531 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 150 through 152 No H-bonds generated for 'chain 'Y' and resid 150 through 152' Processing helix chain 'Y' and resid 165 through 170 Processing helix chain 'Y' and resid 191 through 199 Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 3.909A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 5.053A 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 removed outlier: 3.546A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 288 through 298 Processing helix chain 'Y' and resid 314 through 322 Processing helix chain 'Y' and resid 342 through 344 No H-bonds generated for 'chain 'Y' and resid 342 through 344' Processing helix chain 'Y' and resid 349 through 357 removed outlier: 3.637A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N HIS Y 357 " --> pdb=" O THR Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 371 removed outlier: 3.674A pdb=" N LEU Y 371 " --> pdb=" O SER Y 367 " (cutoff:3.500A) Processing helix chain 'Y' and resid 394 through 412 Processing helix chain 'Y' and resid 414 through 419 Processing helix chain 'Y' and resid 422 through 424 No H-bonds generated for 'chain 'Y' and resid 422 through 424' Processing helix chain 'Y' and resid 427 through 442 removed outlier: 3.648A pdb=" N THR Y 432 " --> pdb=" O GLU Y 428 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA Y 434 " --> pdb=" O LYS Y 430 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG Y 441 " --> pdb=" O ARG Y 437 " (cutoff:3.500A) Processing helix chain 'Y' and resid 451 through 454 No H-bonds generated for 'chain 'Y' and resid 451 through 454' Processing helix chain 'Y' and resid 463 through 475 removed outlier: 3.840A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU Y 474 " --> pdb=" O PHE Y 470 " (cutoff:3.500A) Processing helix chain 'Y' and resid 484 through 486 No H-bonds generated for 'chain 'Y' and resid 484 through 486' Processing helix chain 'Y' and resid 492 through 507 removed outlier: 3.867A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) Processing helix chain 'Y' and resid 527 through 532 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 170 Processing helix chain 'Z' and resid 189 through 199 Processing helix chain 'Z' and resid 217 through 229 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 3.629A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 274 removed outlier: 3.619A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 288 through 298 removed outlier: 3.847A pdb=" N VAL Z 297 " --> pdb=" O ALA Z 293 " (cutoff:3.500A) Processing helix chain 'Z' and resid 314 through 322 Processing helix chain 'Z' and resid 342 through 344 No H-bonds generated for 'chain 'Z' and resid 342 through 344' Processing helix chain 'Z' and resid 349 through 353 Processing helix chain 'Z' and resid 366 through 370 Processing helix chain 'Z' and resid 385 through 387 No H-bonds generated for 'chain 'Z' and resid 385 through 387' Processing helix chain 'Z' and resid 389 through 392 No H-bonds generated for 'chain 'Z' and resid 389 through 392' Processing helix chain 'Z' and resid 394 through 417 removed outlier: 3.849A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) Processing helix chain 'Z' and resid 431 through 443 removed outlier: 3.723A pdb=" N LYS Z 438 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG Z 441 " --> pdb=" O ARG Z 437 " (cutoff:3.500A) Processing helix chain 'Z' and resid 449 through 451 No H-bonds generated for 'chain 'Z' and resid 449 through 451' Processing helix chain 'Z' and resid 463 through 475 removed outlier: 3.716A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 483 through 485 No H-bonds generated for 'chain 'Z' and resid 483 through 485' Processing helix chain 'Z' and resid 492 through 507 removed outlier: 3.892A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS Z 501 " --> pdb=" O GLU Z 497 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 533 removed outlier: 4.088A pdb=" N VAL Z 531 " --> pdb=" O LEU Z 527 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) 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: 7.026A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.501A 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: 3.582A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.356A 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: 3.651A pdb=" N SER S 189 " --> pdb=" O LYS S 99 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ALA S 161 " --> pdb=" O SER S 141 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'T' and resid 94 through 97 removed outlier: 6.769A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (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 408 removed outlier: 3.711A pdb=" N LEU T 222 " --> pdb=" O GLY T 404 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'T' and resid 285 through 290 removed outlier: 8.949A pdb=" N ILE T 286 " --> pdb=" O VAL T 255 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N CYS T 257 " --> pdb=" O ILE T 286 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL T 288 " --> pdb=" O CYS T 257 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR T 259 " --> pdb=" O VAL T 288 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ALA T 290 " --> pdb=" O TYR T 259 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA T 261 " --> pdb=" O ALA T 290 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER T 376 " --> pdb=" O GLY T 320 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE T 322 " --> pdb=" O SER T 376 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE T 380 " --> pdb=" O TYR T 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.746A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 6.237A 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 163 through 165 removed outlier: 8.236A pdb=" N THR U 164 " --> pdb=" O THR U 285 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N MET U 287 " --> pdb=" O THR U 164 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN U 264 " --> pdb=" O ASP U 325 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE U 380 " --> pdb=" O TYR U 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'U' and resid 405 through 408 removed outlier: 6.568A pdb=" N LEU U 222 " --> pdb=" O ILE U 406 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU U 408 " --> pdb=" O LEU U 222 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE U 224 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'U' and resid 107 through 111 removed outlier: 4.583A pdb=" N GLN U 149 " --> pdb=" O LEU U 108 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N CYS U 110 " --> pdb=" O THR U 147 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR U 147 " --> pdb=" O CYS U 110 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'V' and resid 143 through 145 removed outlier: 6.561A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLN V 149 " --> pdb=" O LEU V 108 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N CYS V 110 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR V 147 " --> pdb=" O CYS V 110 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= P, first strand: chain 'V' and resid 404 through 408 Processing sheet with id= Q, first strand: chain 'V' and resid 285 through 290 removed outlier: 8.716A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N PHE V 380 " --> pdb=" O TYR V 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'X' and resid 38 through 44 removed outlier: 6.353A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'X' and resid 110 through 113 Processing sheet with id= T, first strand: chain 'X' and resid 244 through 250 removed outlier: 6.916A pdb=" N SER X 208 " --> pdb=" O THR X 245 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL X 247 " --> pdb=" O SER X 208 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE X 210 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLY X 249 " --> pdb=" O PHE X 210 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLY X 212 " --> pdb=" O GLY X 249 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL X 209 " --> pdb=" O ASP X 279 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU X 281 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA X 211 " --> pdb=" O LEU X 281 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N PHE X 283 " --> pdb=" O ALA X 211 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL X 213 " --> pdb=" O PHE X 283 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ASP X 285 " --> pdb=" O VAL X 213 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLU X 215 " --> pdb=" O ASP X 285 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER X 332 " --> pdb=" O VAL X 280 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU X 282 " --> pdb=" O SER X 332 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR X 334 " --> pdb=" O LEU X 282 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL X 284 " --> pdb=" O THR X 334 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL X 336 " --> pdb=" O VAL X 284 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLY X 180 " --> pdb=" O ASP X 359 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR X 361 " --> pdb=" O GLY X 180 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N PHE X 182 " --> pdb=" O THR X 361 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL X 363 " --> pdb=" O PHE X 182 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= V, first strand: chain 'Y' and resid 37 through 39 removed outlier: 6.496A pdb=" N ARG Y 86 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N HIS Y 79 " --> pdb=" O THR Y 84 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR Y 84 " --> pdb=" O HIS Y 79 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ARG Y 51 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N VAL Y 40 " --> pdb=" O ARG Y 51 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Y' and resid 110 through 113 Processing sheet with id= X, first strand: chain 'Y' and resid 360 through 363 removed outlier: 7.326A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY Y 183 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N VAL Y 339 " --> pdb=" O GLY Y 183 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE Y 207 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N PHE Y 283 " --> pdb=" O PHE Y 207 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA Y 211 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Z' and resid 38 through 44 removed outlier: 6.527A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id= AA, first strand: chain 'Z' and resid 360 through 363 removed outlier: 7.466A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N GLY Z 183 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VAL Z 339 " --> pdb=" O GLY Z 183 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Z' and resid 559 through 561 1275 hydrogen bonds defined for protein. 3399 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: 12.24 Time building geometry restraints manager: 13.25 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: 10105 1.33 - 1.45: 5348 1.45 - 1.57: 18742 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34416 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.40e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.89e+01 bond pdb=" C5 ATP U1001 " pdb=" N7 ATP U1001 " ideal model delta sigma weight residual 1.387 1.334 0.053 1.00e-02 1.00e+04 2.78e+01 bond pdb=" C4 ATP U1001 " pdb=" N9 ATP U1001 " ideal model delta sigma weight residual 1.374 1.331 0.043 1.00e-02 1.00e+04 1.87e+01 bond pdb=" C8 ATP U1001 " pdb=" N7 ATP U1001 " ideal model delta sigma weight residual 1.310 1.348 -0.038 1.00e-02 1.00e+04 1.42e+01 ... (remaining 34411 not shown) Histogram of bond angle deviations from ideal: 93.39 - 101.90: 100 101.90 - 110.42: 9318 110.42 - 118.94: 19012 118.94 - 127.45: 17980 127.45 - 135.97: 232 Bond angle restraints: 46642 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 119.67 20.20 1.00e+00 1.00e+00 4.08e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 126.00 10.83 1.00e+00 1.00e+00 1.17e+02 angle pdb=" C5 ATP U1001 " pdb=" C4 ATP U1001 " pdb=" N3 ATP U1001 " ideal model delta sigma weight residual 126.80 118.34 8.46 1.00e+00 1.00e+00 7.16e+01 angle pdb=" N3 ATP U1001 " pdb=" C4 ATP U1001 " pdb=" N9 ATP U1001 " ideal model delta sigma weight residual 127.04 135.33 -8.29 1.15e+00 7.59e-01 5.21e+01 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 132.66 7.21 1.00e+00 1.00e+00 5.20e+01 ... (remaining 46637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.15: 20184 32.15 - 64.31: 575 64.31 - 96.46: 58 96.46 - 128.62: 2 128.62 - 160.77: 1 Dihedral angle restraints: 20820 sinusoidal: 8066 harmonic: 12754 Sorted by residual: dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -127.83 -52.17 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -129.31 -50.69 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" C5' ADP Z 601 " pdb=" O5' ADP Z 601 " pdb=" PA ADP Z 601 " pdb=" O2A ADP Z 601 " ideal model delta sinusoidal sigma weight residual 300.00 139.23 160.77 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 20817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 4221 0.068 - 0.137: 1153 0.137 - 0.205: 127 0.205 - 0.273: 17 0.273 - 0.341: 2 Chirality restraints: 5520 Sorted by residual: chirality pdb=" CB VAL T 180 " pdb=" CA VAL T 180 " pdb=" CG1 VAL T 180 " pdb=" CG2 VAL T 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.91e+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 -2.35 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ASP Y 513 " pdb=" N ASP Y 513 " pdb=" C ASP Y 513 " pdb=" CB ASP Y 513 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 5517 not shown) Planarity restraints: 5995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 6.01e-02 3.61e+01 pdb=" C ALA Z 503 " -0.104 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA X 307 " 0.016 2.00e-02 2.50e+03 3.08e-02 9.46e+00 pdb=" C ALA X 307 " -0.053 2.00e-02 2.50e+03 pdb=" O ALA X 307 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL X 308 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU Q 33 " -0.048 5.00e-02 4.00e+02 7.22e-02 8.33e+00 pdb=" N PRO Q 34 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO Q 34 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO Q 34 " -0.040 5.00e-02 4.00e+02 ... (remaining 5992 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 47 2.33 - 2.97: 15751 2.97 - 3.62: 50800 3.62 - 4.26: 88083 4.26 - 4.90: 141629 Nonbonded interactions: 296310 Sorted by model distance: nonbonded pdb="MG MG U1002 " pdb=" O HOH U1104 " model vdw 1.688 2.170 nonbonded pdb="MG MG V1002 " pdb=" O HOH V1104 " model vdw 1.706 2.170 nonbonded pdb=" OG1 THR V 232 " pdb="MG MG V1002 " model vdw 2.046 2.170 nonbonded pdb=" O3B ADP Y 601 " pdb="MG MG Y 602 " model vdw 2.053 2.170 nonbonded pdb=" OG1 THR Y 190 " pdb="MG MG Y 602 " model vdw 2.057 2.170 ... (remaining 296305 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 562 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 552) selection = (chain 'Y' and resid 37 through 552) selection = (chain 'Z' and resid 37 through 552) } 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: 6.400 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: 25.530 Check model and map are aligned: 0.460 Set scattering table: 0.270 Process input model: 88.170 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.190 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: 0.000 Load rotamer database and sin/cos tables:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 0.010 0.121 34416 Z= 0.675 Angle : 0.992 20.204 46642 Z= 0.555 Chirality : 0.060 0.341 5520 Planarity : 0.007 0.072 5995 Dihedral : 14.980 160.771 12662 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.69 % Favored : 95.16 % Rotamer: Outliers : 0.39 % Allowed : 5.53 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.10), residues: 4459 helix: -4.19 (0.05), residues: 2128 sheet: -1.42 (0.20), residues: 616 loop : -1.93 (0.13), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP R 37 HIS 0.008 0.002 HIS Z 144 PHE 0.031 0.003 PHE S 249 TYR 0.021 0.003 TYR X 310 ARG 0.014 0.001 ARG U 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 582 time to evaluate : 3.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 117 SER cc_start: 0.8546 (p) cc_final: 0.8333 (p) REVERT: G 61 MET cc_start: 0.7264 (mmt) cc_final: 0.7051 (mmm) REVERT: G 113 ILE cc_start: 0.7666 (mt) cc_final: 0.7276 (mt) REVERT: J 61 MET cc_start: 0.7676 (mpp) cc_final: 0.7198 (mtp) REVERT: J 119 LEU cc_start: 0.7307 (tt) cc_final: 0.7037 (tp) REVERT: S 68 MET cc_start: 0.7606 (ttp) cc_final: 0.7312 (ttt) REVERT: S 271 MET cc_start: 0.7645 (ttp) cc_final: 0.7407 (ttt) REVERT: T 479 ARG cc_start: 0.8372 (mtt90) cc_final: 0.8077 (mtt90) REVERT: T 489 PHE cc_start: 0.8270 (m-80) cc_final: 0.8005 (m-80) REVERT: T 537 LYS cc_start: 0.8041 (tptt) cc_final: 0.7595 (ttpp) REVERT: U 309 MET cc_start: 0.8712 (mtt) cc_final: 0.8395 (mtt) REVERT: U 509 LEU cc_start: 0.7876 (mt) cc_final: 0.7656 (mp) REVERT: X 90 MET cc_start: 0.8912 (mmt) cc_final: 0.8709 (mmt) REVERT: X 408 GLN cc_start: 0.7372 (tp40) cc_final: 0.7138 (tp40) REVERT: X 412 ASN cc_start: 0.8213 (m-40) cc_final: 0.7940 (m-40) REVERT: Y 359 ASP cc_start: 0.7662 (m-30) cc_final: 0.7430 (m-30) REVERT: Y 415 ASP cc_start: 0.7484 (p0) cc_final: 0.7265 (p0) REVERT: Y 451 GLU cc_start: 0.7166 (pt0) cc_final: 0.6961 (pt0) REVERT: Y 501 LYS cc_start: 0.7764 (tptt) cc_final: 0.7376 (mtpm) REVERT: Z 317 ASP cc_start: 0.7610 (m-30) cc_final: 0.7134 (m-30) REVERT: Z 401 ARG cc_start: 0.7652 (mmm160) cc_final: 0.7303 (mtp180) REVERT: Z 405 LYS cc_start: 0.8541 (tptt) cc_final: 0.7676 (mtpt) outliers start: 14 outliers final: 5 residues processed: 591 average time/residue: 1.4907 time to fit residues: 1049.1858 Evaluate side-chains 406 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 401 time to evaluate : 3.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain Y residue 371 LEU Chi-restraints excluded: chain Z residue 280 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 0.8980 chunk 335 optimal weight: 0.0270 chunk 185 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 225 optimal weight: 0.3980 chunk 178 optimal weight: 0.8980 chunk 346 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 210 optimal weight: 0.9990 chunk 257 optimal weight: 1.9990 chunk 401 optimal weight: 6.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 94 ASN B 92 ASN B 98 GLN C 94 ASN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 ASN E 98 GLN I 98 GLN J 87 ASN J 92 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 46 HIS Q 49 GLN R 38 ASN R 73 ASN R 83 GLN R 137 HIS R 154 GLN R 178 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 98 ASN ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 257 ASN S 262 ASN S 267 HIS T 121 ASN T 152 ASN ** T 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 248 GLN T 386 GLN T 435 GLN T 441 GLN T 539 ASN T 549 HIS U 152 ASN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 ASN U 248 GLN U 264 GLN U 271 GLN U 319 HIS U 386 GLN U 422 ASN V 64 GLN V 121 ASN V 126 HIS V 139 HIS V 242 GLN V 271 GLN V 386 GLN V 486 GLN V 497 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 199 ASN X 278 GLN X 294 ASN X 398 ASN X 448 GLN X 514 ASN Y 157 GLN Y 174 GLN ** Y 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 278 GLN ** Y 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 83 ASN Z 100 GLN Z 123 ASN Z 174 GLN Z 294 ASN Z 398 ASN Z 408 GLN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34416 Z= 0.174 Angle : 0.564 8.628 46642 Z= 0.295 Chirality : 0.042 0.173 5520 Planarity : 0.005 0.063 5995 Dihedral : 7.564 134.244 4922 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.03 % Favored : 96.82 % Rotamer: Outliers : 2.08 % Allowed : 12.29 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.87 (0.11), residues: 4459 helix: -2.34 (0.09), residues: 2120 sheet: -1.03 (0.21), residues: 579 loop : -1.35 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP U 73 HIS 0.007 0.001 HIS V 83 PHE 0.021 0.001 PHE U 508 TYR 0.017 0.001 TYR E 102 ARG 0.004 0.000 ARG S 198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 492 time to evaluate : 3.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7305 (ppp) cc_final: 0.7078 (ppp) REVERT: C 61 MET cc_start: 0.7004 (OUTLIER) cc_final: 0.6770 (mtp) REVERT: D 109 LEU cc_start: 0.7816 (mm) cc_final: 0.7518 (tt) REVERT: E 95 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7933 (mt) REVERT: G 113 ILE cc_start: 0.7840 (mt) cc_final: 0.7529 (mt) REVERT: P 68 ASP cc_start: 0.7432 (t70) cc_final: 0.7206 (t0) REVERT: P 82 LYS cc_start: 0.8517 (mtmm) cc_final: 0.8311 (mtmp) REVERT: P 149 LYS cc_start: 0.7240 (ptpp) cc_final: 0.6581 (pptt) REVERT: Q 61 LYS cc_start: 0.8014 (tttm) cc_final: 0.7757 (tttm) REVERT: S 271 MET cc_start: 0.7440 (ttp) cc_final: 0.7202 (ttt) REVERT: T 537 LYS cc_start: 0.8096 (tptt) cc_final: 0.7573 (ttpp) REVERT: U 309 MET cc_start: 0.8651 (mtt) cc_final: 0.8319 (mtt) REVERT: X 408 GLN cc_start: 0.7390 (tp40) cc_final: 0.7017 (tp40) REVERT: X 412 ASN cc_start: 0.8185 (m-40) cc_final: 0.7828 (m-40) REVERT: X 448 GLN cc_start: 0.7674 (tt0) cc_final: 0.7376 (mt0) REVERT: Y 501 LYS cc_start: 0.7526 (tptt) cc_final: 0.7198 (mtpm) REVERT: Z 405 LYS cc_start: 0.8538 (tptt) cc_final: 0.8301 (tptm) REVERT: Z 502 MET cc_start: 0.6351 (mtp) cc_final: 0.5727 (tpp) outliers start: 74 outliers final: 20 residues processed: 531 average time/residue: 1.3837 time to fit residues: 888.7764 Evaluate side-chains 430 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 408 time to evaluate : 4.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 326 ASP Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 395 GLU Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Z residue 414 GLN Chi-restraints excluded: chain Z residue 488 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 223 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 334 optimal weight: 5.9990 chunk 273 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 402 optimal weight: 3.9990 chunk 434 optimal weight: 0.7980 chunk 358 optimal weight: 0.6980 chunk 398 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 322 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN C 94 ASN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 ASN F 87 ASN G 98 GLN I 98 GLN J 87 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN ** R 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN S 41 GLN ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 405 GLN T 539 ASN U 152 ASN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 422 ASN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 152 ASN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 241 ASN X 278 GLN ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 123 ASN Z 294 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 34416 Z= 0.273 Angle : 0.579 8.424 46642 Z= 0.298 Chirality : 0.044 0.208 5520 Planarity : 0.004 0.057 5995 Dihedral : 7.165 117.384 4918 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.92 % Favored : 95.92 % Rotamer: Outliers : 2.89 % Allowed : 14.78 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.00 (0.12), residues: 4459 helix: -1.39 (0.10), residues: 2127 sheet: -0.93 (0.21), residues: 603 loop : -1.12 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP U 73 HIS 0.005 0.001 HIS Z 144 PHE 0.017 0.001 PHE A 107 TYR 0.018 0.002 TYR X 310 ARG 0.006 0.000 ARG X 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 429 time to evaluate : 3.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 109 LEU cc_start: 0.7858 (mm) cc_final: 0.7472 (tt) REVERT: E 61 MET cc_start: 0.7490 (ttm) cc_final: 0.7017 (ttp) REVERT: E 95 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7997 (mt) REVERT: F 111 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6378 (mm-30) REVERT: G 60 LYS cc_start: 0.7243 (ptpt) cc_final: 0.6933 (ptpt) REVERT: J 126 PHE cc_start: 0.7148 (m-80) cc_final: 0.6932 (m-80) REVERT: P 68 ASP cc_start: 0.7518 (t70) cc_final: 0.7295 (t0) REVERT: Q 31 LEU cc_start: 0.5876 (OUTLIER) cc_final: 0.5561 (mt) REVERT: S 271 MET cc_start: 0.7495 (ttp) cc_final: 0.7201 (ttt) REVERT: T 199 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6314 (mpp80) REVERT: T 508 PHE cc_start: 0.8582 (m-80) cc_final: 0.8336 (m-80) REVERT: T 537 LYS cc_start: 0.8043 (tptt) cc_final: 0.7706 (ttpp) REVERT: T 541 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7866 (tttp) REVERT: U 309 MET cc_start: 0.8706 (mtt) cc_final: 0.8379 (mtt) REVERT: X 408 GLN cc_start: 0.7398 (tp40) cc_final: 0.7042 (tp40) REVERT: X 412 ASN cc_start: 0.8147 (m-40) cc_final: 0.7794 (m-40) REVERT: X 448 GLN cc_start: 0.7755 (tt0) cc_final: 0.7452 (mt0) REVERT: Y 66 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: Y 501 LYS cc_start: 0.7496 (tptt) cc_final: 0.7146 (mtpm) REVERT: Z 401 ARG cc_start: 0.7514 (mmm160) cc_final: 0.6949 (mmp80) REVERT: Z 405 LYS cc_start: 0.8555 (tptt) cc_final: 0.8278 (tptm) outliers start: 103 outliers final: 40 residues processed: 486 average time/residue: 1.4110 time to fit residues: 825.5435 Evaluate side-chains 440 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 394 time to evaluate : 4.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 199 ARG Chi-restraints excluded: chain T residue 326 ASP Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 140 ILE Chi-restraints excluded: chain X residue 306 SER Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 395 GLU Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 414 GLN Chi-restraints excluded: chain Z residue 415 ASP Chi-restraints excluded: chain Z residue 432 THR Chi-restraints excluded: chain Z residue 488 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 397 optimal weight: 4.9990 chunk 302 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 270 optimal weight: 0.1980 chunk 403 optimal weight: 7.9990 chunk 427 optimal weight: 0.0570 chunk 210 optimal weight: 0.7980 chunk 382 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN C 94 ASN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN J 87 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN ** R 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN S 98 ASN ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 549 HIS V 61 HIS V 152 ASN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34416 Z= 0.160 Angle : 0.521 9.563 46642 Z= 0.265 Chirality : 0.042 0.170 5520 Planarity : 0.004 0.052 5995 Dihedral : 6.463 94.123 4918 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.21 % Favored : 96.66 % Rotamer: Outliers : 2.61 % Allowed : 16.27 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.34 (0.12), residues: 4459 helix: -0.78 (0.11), residues: 2140 sheet: -0.77 (0.21), residues: 614 loop : -0.81 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP U 73 HIS 0.004 0.001 HIS R 66 PHE 0.020 0.001 PHE U 508 TYR 0.017 0.001 TYR Z 487 ARG 0.008 0.000 ARG S 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 452 time to evaluate : 3.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 109 LEU cc_start: 0.7727 (mm) cc_final: 0.7389 (tt) REVERT: D 113 ILE cc_start: 0.6828 (mm) cc_final: 0.6518 (OUTLIER) REVERT: E 78 LEU cc_start: 0.7252 (pp) cc_final: 0.6784 (mt) REVERT: J 119 LEU cc_start: 0.7078 (tt) cc_final: 0.6859 (tp) REVERT: J 126 PHE cc_start: 0.7174 (m-80) cc_final: 0.6945 (m-80) REVERT: P 68 ASP cc_start: 0.7521 (t70) cc_final: 0.7280 (t0) REVERT: P 149 LYS cc_start: 0.7094 (ptpp) cc_final: 0.6466 (pptt) REVERT: S 271 MET cc_start: 0.7455 (ttp) cc_final: 0.7158 (ttt) REVERT: T 237 ASP cc_start: 0.6902 (m-30) cc_final: 0.6645 (m-30) REVERT: T 508 PHE cc_start: 0.8550 (m-80) cc_final: 0.8321 (m-80) REVERT: T 537 LYS cc_start: 0.8006 (tptt) cc_final: 0.7741 (ttpp) REVERT: T 541 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7520 (tttp) REVERT: U 309 MET cc_start: 0.8683 (mtt) cc_final: 0.8376 (mtt) REVERT: V 502 TYR cc_start: 0.7156 (t80) cc_final: 0.6690 (t80) REVERT: V 521 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6650 (tt0) REVERT: V 547 ASP cc_start: 0.7236 (p0) cc_final: 0.6569 (t0) REVERT: V 549 HIS cc_start: 0.6816 (OUTLIER) cc_final: 0.5851 (m170) REVERT: X 408 GLN cc_start: 0.7355 (tp40) cc_final: 0.6971 (tp40) REVERT: X 412 ASN cc_start: 0.8066 (m-40) cc_final: 0.7713 (m-40) REVERT: X 448 GLN cc_start: 0.7709 (tt0) cc_final: 0.7416 (mt0) REVERT: Y 266 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8259 (tt) REVERT: Y 501 LYS cc_start: 0.7512 (tptt) cc_final: 0.7094 (mtpm) outliers start: 93 outliers final: 30 residues processed: 513 average time/residue: 1.4198 time to fit residues: 878.9441 Evaluate side-chains 437 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 404 time to evaluate : 3.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 446 LEU Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 521 GLU Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 88 ILE Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 367 SER Chi-restraints excluded: chain Z residue 488 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 355 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 318 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 364 optimal weight: 0.6980 chunk 295 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 218 optimal weight: 1.9990 chunk 383 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN C 94 ASN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN ** R 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 253 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 152 ASN ** Y 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 398 ASN Z 412 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34416 Z= 0.171 Angle : 0.526 8.671 46642 Z= 0.268 Chirality : 0.042 0.238 5520 Planarity : 0.004 0.047 5995 Dihedral : 6.311 90.975 4918 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 2.55 % Allowed : 17.08 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.13), residues: 4459 helix: -0.44 (0.11), residues: 2139 sheet: -0.67 (0.21), residues: 613 loop : -0.65 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP U 73 HIS 0.003 0.001 HIS S 267 PHE 0.024 0.001 PHE U 508 TYR 0.018 0.001 TYR Z 487 ARG 0.004 0.000 ARG Y 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 425 time to evaluate : 3.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 LEU cc_start: 0.7021 (tt) cc_final: 0.6662 (tp) REVERT: D 109 LEU cc_start: 0.7712 (mm) cc_final: 0.7359 (tt) REVERT: D 113 ILE cc_start: 0.6735 (mm) cc_final: 0.6473 (OUTLIER) REVERT: E 78 LEU cc_start: 0.7290 (pp) cc_final: 0.6835 (mt) REVERT: E 95 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7892 (tt) REVERT: E 115 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7069 (pt) REVERT: J 119 LEU cc_start: 0.7138 (tt) cc_final: 0.6916 (tp) REVERT: J 126 PHE cc_start: 0.7188 (m-80) cc_final: 0.6961 (m-80) REVERT: P 68 ASP cc_start: 0.7533 (t70) cc_final: 0.7280 (t0) REVERT: P 149 LYS cc_start: 0.7051 (ptpp) cc_final: 0.6425 (pptt) REVERT: Q 31 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5391 (mt) REVERT: Q 48 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6549 (ptm-80) REVERT: S 271 MET cc_start: 0.7462 (ttp) cc_final: 0.7179 (ttt) REVERT: T 237 ASP cc_start: 0.6905 (m-30) cc_final: 0.6615 (m-30) REVERT: T 407 PHE cc_start: 0.7510 (t80) cc_final: 0.7067 (m-80) REVERT: T 537 LYS cc_start: 0.8044 (tptt) cc_final: 0.7734 (ttpp) REVERT: T 541 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7758 (tttp) REVERT: U 309 MET cc_start: 0.8691 (mtt) cc_final: 0.8359 (mtt) REVERT: V 502 TYR cc_start: 0.7096 (t80) cc_final: 0.6683 (t80) REVERT: V 547 ASP cc_start: 0.7158 (p0) cc_final: 0.6609 (t0) REVERT: V 549 HIS cc_start: 0.6832 (OUTLIER) cc_final: 0.5859 (m170) REVERT: X 408 GLN cc_start: 0.7355 (tp40) cc_final: 0.6992 (tp40) REVERT: X 412 ASN cc_start: 0.8254 (m-40) cc_final: 0.7927 (m-40) REVERT: X 448 GLN cc_start: 0.7718 (tt0) cc_final: 0.7424 (mt0) REVERT: Y 66 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6400 (mp0) REVERT: Y 266 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8301 (tt) REVERT: Y 415 ASP cc_start: 0.7521 (p0) cc_final: 0.7287 (p0) REVERT: Y 501 LYS cc_start: 0.7415 (tptt) cc_final: 0.7034 (mtpm) REVERT: Z 401 ARG cc_start: 0.7489 (mmm160) cc_final: 0.6860 (mmp80) outliers start: 91 outliers final: 41 residues processed: 481 average time/residue: 1.3845 time to fit residues: 802.5368 Evaluate side-chains 441 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 393 time to evaluate : 3.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 48 ARG Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 326 ASP Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 88 ILE Chi-restraints excluded: chain X residue 298 SER Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 395 GLU Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 495 VAL Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 367 SER Chi-restraints excluded: chain Z residue 415 ASP Chi-restraints excluded: chain Z residue 488 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 143 optimal weight: 2.9990 chunk 384 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 250 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 427 optimal weight: 0.0570 chunk 355 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 224 optimal weight: 4.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN C 94 ASN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN I 98 GLN J 87 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN S 98 ASN ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 422 ASN V 61 HIS V 244 ASN ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 278 GLN ** Y 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 34416 Z= 0.289 Angle : 0.580 8.511 46642 Z= 0.296 Chirality : 0.044 0.244 5520 Planarity : 0.004 0.044 5995 Dihedral : 6.681 99.723 4918 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.77 % Favored : 96.10 % Rotamer: Outliers : 3.23 % Allowed : 17.08 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.93 (0.13), residues: 4459 helix: -0.39 (0.11), residues: 2136 sheet: -0.69 (0.21), residues: 613 loop : -0.64 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP V 73 HIS 0.004 0.001 HIS Z 144 PHE 0.020 0.001 PHE U 508 TYR 0.020 0.002 TYR Z 487 ARG 0.007 0.000 ARG Y 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 401 time to evaluate : 3.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 109 LEU cc_start: 0.7691 (mm) cc_final: 0.7342 (tt) REVERT: D 113 ILE cc_start: 0.6967 (mm) cc_final: 0.6630 (OUTLIER) REVERT: E 61 MET cc_start: 0.7335 (ttm) cc_final: 0.7031 (ttp) REVERT: E 95 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7939 (tt) REVERT: E 115 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7090 (pt) REVERT: I 61 MET cc_start: 0.7252 (mmp) cc_final: 0.6949 (mmt) REVERT: J 119 LEU cc_start: 0.7195 (tt) cc_final: 0.6990 (tp) REVERT: J 126 PHE cc_start: 0.7221 (m-80) cc_final: 0.6999 (m-80) REVERT: Q 31 LEU cc_start: 0.5828 (OUTLIER) cc_final: 0.5383 (mt) REVERT: Q 48 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6583 (ptm-80) REVERT: S 271 MET cc_start: 0.7444 (ttp) cc_final: 0.7190 (ttt) REVERT: S 274 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7510 (mpm) REVERT: T 237 ASP cc_start: 0.6950 (m-30) cc_final: 0.6732 (m-30) REVERT: T 407 PHE cc_start: 0.7655 (t80) cc_final: 0.7132 (m-80) REVERT: T 418 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8023 (mtt90) REVERT: T 537 LYS cc_start: 0.8085 (tptt) cc_final: 0.7753 (ttpp) REVERT: T 541 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7793 (tttp) REVERT: V 502 TYR cc_start: 0.7176 (t80) cc_final: 0.6733 (t80) REVERT: V 547 ASP cc_start: 0.7220 (p0) cc_final: 0.6568 (t0) REVERT: V 549 HIS cc_start: 0.6810 (OUTLIER) cc_final: 0.5782 (m170) REVERT: X 408 GLN cc_start: 0.7384 (tp40) cc_final: 0.7038 (tp40) REVERT: X 412 ASN cc_start: 0.8153 (m-40) cc_final: 0.7824 (m-40) REVERT: X 441 ARG cc_start: 0.7915 (mpp-170) cc_final: 0.7706 (mpt180) REVERT: X 448 GLN cc_start: 0.7763 (tt0) cc_final: 0.7441 (mt0) REVERT: Y 66 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6457 (mp0) REVERT: Y 266 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8399 (tt) REVERT: Y 501 LYS cc_start: 0.7534 (tptt) cc_final: 0.7127 (mtpm) REVERT: Z 401 ARG cc_start: 0.7483 (mmm160) cc_final: 0.6946 (mmp80) outliers start: 115 outliers final: 60 residues processed: 474 average time/residue: 1.3944 time to fit residues: 798.0911 Evaluate side-chains 453 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 384 time to evaluate : 3.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 48 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 83 GLN Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 274 MET Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 326 ASP Chi-restraints excluded: chain T residue 418 ARG Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 446 LEU Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 407 PHE Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 88 ILE Chi-restraints excluded: chain X residue 157 GLN Chi-restraints excluded: chain X residue 298 SER Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 495 VAL Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 367 SER Chi-restraints excluded: chain Z residue 414 GLN Chi-restraints excluded: chain Z residue 415 ASP Chi-restraints excluded: chain Z residue 417 ILE Chi-restraints excluded: chain Z residue 432 THR Chi-restraints excluded: chain Z residue 488 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 412 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 243 optimal weight: 7.9990 chunk 312 optimal weight: 0.8980 chunk 241 optimal weight: 1.9990 chunk 359 optimal weight: 0.6980 chunk 238 optimal weight: 1.9990 chunk 426 optimal weight: 0.9980 chunk 266 optimal weight: 2.9990 chunk 259 optimal weight: 0.7980 chunk 196 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN C 94 ASN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN I 98 GLN J 87 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN S 98 ASN ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 515 GLN V 61 HIS V 152 ASN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34416 Z= 0.191 Angle : 0.542 9.836 46642 Z= 0.274 Chirality : 0.043 0.308 5520 Planarity : 0.004 0.046 5995 Dihedral : 6.405 100.243 4918 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.34 % Favored : 96.52 % Rotamer: Outliers : 2.78 % Allowed : 18.12 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.13), residues: 4459 helix: -0.14 (0.11), residues: 2135 sheet: -0.65 (0.21), residues: 619 loop : -0.51 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP V 73 HIS 0.003 0.001 HIS R 66 PHE 0.022 0.001 PHE A 107 TYR 0.020 0.001 TYR Z 487 ARG 0.006 0.000 ARG Y 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 419 time to evaluate : 3.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 109 LEU cc_start: 0.7683 (mm) cc_final: 0.7357 (tt) REVERT: D 113 ILE cc_start: 0.6919 (mm) cc_final: 0.6591 (OUTLIER) REVERT: E 61 MET cc_start: 0.7224 (ttm) cc_final: 0.6916 (ttp) REVERT: E 95 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7979 (tt) REVERT: E 115 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7080 (pt) REVERT: G 119 LEU cc_start: 0.7692 (tp) cc_final: 0.7294 (pp) REVERT: I 61 MET cc_start: 0.7275 (mmp) cc_final: 0.6995 (mmt) REVERT: J 126 PHE cc_start: 0.7143 (m-80) cc_final: 0.6924 (m-80) REVERT: Q 31 LEU cc_start: 0.5803 (OUTLIER) cc_final: 0.5378 (mt) REVERT: Q 48 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6553 (ptm-80) REVERT: S 271 MET cc_start: 0.7530 (ttp) cc_final: 0.7291 (ttt) REVERT: T 237 ASP cc_start: 0.6928 (m-30) cc_final: 0.6650 (m-30) REVERT: T 407 PHE cc_start: 0.7658 (t80) cc_final: 0.7146 (m-80) REVERT: T 537 LYS cc_start: 0.8067 (tptt) cc_final: 0.7739 (ttpp) REVERT: T 541 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7733 (tttp) REVERT: V 502 TYR cc_start: 0.7136 (t80) cc_final: 0.6749 (t80) REVERT: V 521 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6700 (tt0) REVERT: V 547 ASP cc_start: 0.7185 (p0) cc_final: 0.6568 (t0) REVERT: V 550 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7158 (pp) REVERT: X 408 GLN cc_start: 0.7369 (tp40) cc_final: 0.7113 (tp40) REVERT: X 412 ASN cc_start: 0.8126 (m-40) cc_final: 0.7806 (m-40) REVERT: X 441 ARG cc_start: 0.7876 (mpp-170) cc_final: 0.7657 (mpt180) REVERT: X 448 GLN cc_start: 0.7747 (tt0) cc_final: 0.7439 (mt0) REVERT: Y 66 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6451 (mp0) REVERT: Y 266 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8383 (tt) REVERT: Y 415 ASP cc_start: 0.7594 (p0) cc_final: 0.7365 (p0) REVERT: Y 501 LYS cc_start: 0.7512 (tptt) cc_final: 0.7099 (mtpm) REVERT: Z 401 ARG cc_start: 0.7409 (mmm160) cc_final: 0.6934 (mmp80) outliers start: 99 outliers final: 49 residues processed: 484 average time/residue: 1.3914 time to fit residues: 815.1749 Evaluate side-chains 444 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 387 time to evaluate : 3.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 48 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 83 GLN Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 326 ASP Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 446 LEU Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 521 GLU Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 88 ILE Chi-restraints excluded: chain X residue 157 GLN Chi-restraints excluded: chain X residue 298 SER Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 495 VAL Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 365 SER Chi-restraints excluded: chain Z residue 367 SER Chi-restraints excluded: chain Z residue 432 THR Chi-restraints excluded: chain Z residue 488 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 263 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 254 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 270 optimal weight: 4.9990 chunk 290 optimal weight: 0.9980 chunk 210 optimal weight: 0.5980 chunk 39 optimal weight: 0.0980 chunk 334 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN C 94 ASN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN S 98 ASN ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 188 GLN ** T 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 515 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 152 ASN V 471 GLN ** Y 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34416 Z= 0.171 Angle : 0.534 11.995 46642 Z= 0.270 Chirality : 0.042 0.316 5520 Planarity : 0.003 0.046 5995 Dihedral : 6.178 98.448 4918 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.45 % Favored : 96.41 % Rotamer: Outliers : 2.50 % Allowed : 18.82 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.13), residues: 4459 helix: 0.03 (0.11), residues: 2147 sheet: -0.50 (0.21), residues: 602 loop : -0.44 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP V 73 HIS 0.004 0.001 HIS R 66 PHE 0.027 0.001 PHE U 508 TYR 0.021 0.001 TYR Z 487 ARG 0.006 0.000 ARG Y 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 409 time to evaluate : 3.707 Fit side-chains revert: symmetry clash REVERT: D 113 ILE cc_start: 0.6696 (mm) cc_final: 0.6420 (OUTLIER) REVERT: E 61 MET cc_start: 0.7269 (ttm) cc_final: 0.6946 (ttp) REVERT: E 78 LEU cc_start: 0.7294 (pp) cc_final: 0.6942 (mt) REVERT: E 115 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7083 (pt) REVERT: G 119 LEU cc_start: 0.7687 (tp) cc_final: 0.7322 (pp) REVERT: I 61 MET cc_start: 0.7472 (mmp) cc_final: 0.7186 (mmp) REVERT: J 126 PHE cc_start: 0.7136 (m-80) cc_final: 0.6899 (m-80) REVERT: P 75 TYR cc_start: 0.8526 (m-10) cc_final: 0.7845 (m-10) REVERT: Q 31 LEU cc_start: 0.5752 (OUTLIER) cc_final: 0.5359 (mt) REVERT: Q 48 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6540 (ptm-80) REVERT: S 271 MET cc_start: 0.7487 (ttp) cc_final: 0.7198 (ttt) REVERT: T 237 ASP cc_start: 0.6872 (m-30) cc_final: 0.6643 (m-30) REVERT: T 407 PHE cc_start: 0.7636 (t80) cc_final: 0.7189 (m-80) REVERT: T 537 LYS cc_start: 0.8056 (tptt) cc_final: 0.7735 (ttpp) REVERT: T 541 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7725 (tttp) REVERT: U 76 SER cc_start: 0.8375 (OUTLIER) cc_final: 0.7991 (t) REVERT: V 502 TYR cc_start: 0.7178 (t80) cc_final: 0.6832 (t80) REVERT: V 521 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6674 (tt0) REVERT: V 547 ASP cc_start: 0.7063 (p0) cc_final: 0.6552 (t0) REVERT: V 550 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7160 (pp) REVERT: X 408 GLN cc_start: 0.7369 (tp40) cc_final: 0.7120 (tp40) REVERT: X 412 ASN cc_start: 0.8086 (m-40) cc_final: 0.7789 (m-40) REVERT: X 441 ARG cc_start: 0.7864 (mpp-170) cc_final: 0.7637 (mpt180) REVERT: X 448 GLN cc_start: 0.7718 (tt0) cc_final: 0.7416 (mt0) REVERT: Y 66 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6396 (mp0) REVERT: Y 266 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8312 (tt) REVERT: Y 279 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7618 (m-30) REVERT: Y 415 ASP cc_start: 0.7585 (p0) cc_final: 0.7349 (p0) REVERT: Y 501 LYS cc_start: 0.7498 (tptt) cc_final: 0.7088 (mtpm) REVERT: Z 401 ARG cc_start: 0.7371 (mmm160) cc_final: 0.6898 (mmp80) REVERT: Z 484 MET cc_start: 0.7343 (mmm) cc_final: 0.6816 (pmm) outliers start: 89 outliers final: 47 residues processed: 470 average time/residue: 1.4391 time to fit residues: 822.2805 Evaluate side-chains 433 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 377 time to evaluate : 3.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 48 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 326 ASP Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 446 LEU Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 521 GLU Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 88 ILE Chi-restraints excluded: chain X residue 157 GLN Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 279 ASP Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 495 VAL Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 365 SER Chi-restraints excluded: chain Z residue 432 THR Chi-restraints excluded: chain Z residue 488 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 387 optimal weight: 2.9990 chunk 408 optimal weight: 0.1980 chunk 372 optimal weight: 0.9990 chunk 396 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 311 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 358 optimal weight: 0.5980 chunk 375 optimal weight: 0.0980 chunk 395 optimal weight: 0.7980 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 C 94 ASN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN I 98 GLN J 87 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 149 GLN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 398 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 34416 Z= 0.157 Angle : 0.531 11.969 46642 Z= 0.269 Chirality : 0.042 0.319 5520 Planarity : 0.004 0.076 5995 Dihedral : 6.021 96.648 4918 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.39 % Favored : 96.48 % Rotamer: Outliers : 2.10 % Allowed : 19.66 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.13), residues: 4459 helix: 0.17 (0.12), residues: 2144 sheet: -0.42 (0.21), residues: 593 loop : -0.38 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP V 73 HIS 0.005 0.001 HIS V 83 PHE 0.031 0.001 PHE A 107 TYR 0.017 0.001 TYR S 231 ARG 0.005 0.000 ARG Y 435 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 409 time to evaluate : 3.642 Fit side-chains revert: symmetry clash REVERT: D 113 ILE cc_start: 0.6608 (mm) cc_final: 0.6350 (OUTLIER) REVERT: E 61 MET cc_start: 0.7238 (ttm) cc_final: 0.6914 (ttp) REVERT: G 119 LEU cc_start: 0.7657 (tp) cc_final: 0.7328 (pp) REVERT: I 81 MET cc_start: 0.7581 (ttp) cc_final: 0.7310 (ttt) REVERT: J 126 PHE cc_start: 0.7272 (m-80) cc_final: 0.6980 (m-80) REVERT: P 149 LYS cc_start: 0.7113 (ptpp) cc_final: 0.6474 (pptt) REVERT: Q 31 LEU cc_start: 0.5661 (OUTLIER) cc_final: 0.5324 (mp) REVERT: Q 48 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6419 (ptm-80) REVERT: S 271 MET cc_start: 0.7450 (ttp) cc_final: 0.7192 (ttt) REVERT: T 237 ASP cc_start: 0.6856 (m-30) cc_final: 0.6615 (m-30) REVERT: T 407 PHE cc_start: 0.7637 (t80) cc_final: 0.7180 (m-80) REVERT: T 537 LYS cc_start: 0.8046 (tptt) cc_final: 0.7738 (ttpp) REVERT: U 76 SER cc_start: 0.8366 (OUTLIER) cc_final: 0.7973 (t) REVERT: V 502 TYR cc_start: 0.7186 (t80) cc_final: 0.6894 (t80) REVERT: V 521 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6650 (tt0) REVERT: V 547 ASP cc_start: 0.7058 (p0) cc_final: 0.6561 (t0) REVERT: V 549 HIS cc_start: 0.6733 (OUTLIER) cc_final: 0.5703 (m170) REVERT: V 550 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7154 (pp) REVERT: X 408 GLN cc_start: 0.7363 (tp40) cc_final: 0.7117 (tp40) REVERT: X 412 ASN cc_start: 0.8046 (m-40) cc_final: 0.7759 (m-40) REVERT: X 441 ARG cc_start: 0.7856 (mpp-170) cc_final: 0.7629 (mpt180) REVERT: X 448 GLN cc_start: 0.7702 (tt0) cc_final: 0.7411 (mt0) REVERT: Y 266 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8291 (tt) REVERT: Y 279 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: Y 501 LYS cc_start: 0.7600 (tptt) cc_final: 0.7135 (mtpm) REVERT: Z 401 ARG cc_start: 0.7322 (mmm160) cc_final: 0.6976 (mmp80) REVERT: Z 484 MET cc_start: 0.7320 (mmm) cc_final: 0.6755 (pmm) outliers start: 75 outliers final: 47 residues processed: 463 average time/residue: 1.3438 time to fit residues: 754.0388 Evaluate side-chains 432 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 378 time to evaluate : 3.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 48 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 326 ASP Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 446 LEU Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 521 GLU Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 88 ILE Chi-restraints excluded: chain X residue 157 GLN Chi-restraints excluded: chain X residue 278 GLN Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 298 SER Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 279 ASP Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 495 VAL Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 365 SER Chi-restraints excluded: chain Z residue 432 THR Chi-restraints excluded: chain Z residue 488 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 260 optimal weight: 0.5980 chunk 419 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 291 optimal weight: 0.6980 chunk 440 optimal weight: 2.9990 chunk 405 optimal weight: 0.7980 chunk 350 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 270 optimal weight: 4.9990 chunk 215 optimal weight: 0.2980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN C 94 ASN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN J 87 ASN Q 40 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 188 GLN T 196 GLN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 61 HIS V 488 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34416 Z= 0.195 Angle : 0.546 11.097 46642 Z= 0.277 Chirality : 0.043 0.307 5520 Planarity : 0.004 0.068 5995 Dihedral : 6.108 97.369 4918 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.70 % Favored : 96.14 % Rotamer: Outliers : 1.82 % Allowed : 20.53 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.13), residues: 4459 helix: 0.18 (0.11), residues: 2148 sheet: -0.45 (0.21), residues: 604 loop : -0.39 (0.16), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP V 73 HIS 0.004 0.001 HIS V 83 PHE 0.031 0.001 PHE A 107 TYR 0.022 0.001 TYR Z 487 ARG 0.009 0.000 ARG X 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8918 Ramachandran restraints generated. 4459 Oldfield, 0 Emsley, 4459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 388 time to evaluate : 4.236 Fit side-chains revert: symmetry clash REVERT: D 113 ILE cc_start: 0.6781 (mm) cc_final: 0.6495 (OUTLIER) REVERT: E 61 MET cc_start: 0.7284 (ttm) cc_final: 0.6710 (ttp) REVERT: G 119 LEU cc_start: 0.7712 (tp) cc_final: 0.7390 (pp) REVERT: I 81 MET cc_start: 0.7586 (ttp) cc_final: 0.7312 (ttt) REVERT: J 126 PHE cc_start: 0.7305 (m-80) cc_final: 0.7029 (m-80) REVERT: P 149 LYS cc_start: 0.7181 (ptpp) cc_final: 0.6489 (pptt) REVERT: Q 31 LEU cc_start: 0.5606 (OUTLIER) cc_final: 0.5319 (mp) REVERT: Q 48 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6448 (ptm-80) REVERT: S 271 MET cc_start: 0.7511 (ttp) cc_final: 0.7251 (ttt) REVERT: T 237 ASP cc_start: 0.6868 (m-30) cc_final: 0.6602 (m-30) REVERT: T 407 PHE cc_start: 0.7641 (t80) cc_final: 0.7177 (m-80) REVERT: T 537 LYS cc_start: 0.8053 (tptt) cc_final: 0.7744 (ttpp) REVERT: U 76 SER cc_start: 0.8377 (OUTLIER) cc_final: 0.7988 (t) REVERT: U 152 ASN cc_start: 0.8057 (OUTLIER) cc_final: 0.7484 (m-40) REVERT: V 502 TYR cc_start: 0.7201 (t80) cc_final: 0.6912 (t80) REVERT: V 547 ASP cc_start: 0.7066 (p0) cc_final: 0.6578 (t0) REVERT: V 549 HIS cc_start: 0.6804 (OUTLIER) cc_final: 0.5777 (m170) REVERT: V 550 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7058 (pp) REVERT: X 408 GLN cc_start: 0.7372 (tp40) cc_final: 0.7135 (tp40) REVERT: X 412 ASN cc_start: 0.8073 (m-40) cc_final: 0.7781 (m-40) REVERT: X 441 ARG cc_start: 0.7884 (mpp-170) cc_final: 0.7651 (mpt180) REVERT: X 448 GLN cc_start: 0.7717 (tt0) cc_final: 0.7418 (mt0) REVERT: Y 266 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8387 (tt) REVERT: Y 279 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7620 (m-30) REVERT: Y 415 ASP cc_start: 0.7579 (p0) cc_final: 0.7353 (p0) REVERT: Y 501 LYS cc_start: 0.7581 (tptt) cc_final: 0.7111 (mtpm) REVERT: Z 401 ARG cc_start: 0.7315 (mmm160) cc_final: 0.7045 (mmp80) REVERT: Z 484 MET cc_start: 0.7430 (mmm) cc_final: 0.6834 (pmm) outliers start: 65 outliers final: 48 residues processed: 434 average time/residue: 1.3827 time to fit residues: 727.0795 Evaluate side-chains 428 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 373 time to evaluate : 4.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 48 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 152 ASN Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 446 LEU Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 88 ILE Chi-restraints excluded: chain X residue 157 GLN Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 298 SER Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 279 ASP Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 495 VAL Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 365 SER Chi-restraints excluded: chain Z residue 432 THR Chi-restraints excluded: chain Z residue 488 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 278 optimal weight: 5.9990 chunk 373 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 323 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 97 optimal weight: 0.0670 chunk 351 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 360 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN C 94 ASN C 98 GLN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN J 87 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 HIS R 154 GLN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 149 GLN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 471 GLN V 488 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.141904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.104046 restraints weight = 46319.804| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.64 r_work: 0.3065 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 34416 Z= 0.294 Angle : 0.602 10.268 46642 Z= 0.306 Chirality : 0.045 0.275 5520 Planarity : 0.004 0.062 5995 Dihedral : 6.543 103.934 4918 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.99 % Favored : 95.85 % Rotamer: Outliers : 2.02 % Allowed : 20.45 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.50 (0.13), residues: 4459 helix: -0.01 (0.11), residues: 2154 sheet: -0.54 (0.21), residues: 605 loop : -0.43 (0.16), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP V 73 HIS 0.005 0.001 HIS Z 144 PHE 0.035 0.002 PHE U 508 TYR 0.023 0.002 TYR Z 487 ARG 0.009 0.000 ARG X 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13321.43 seconds wall clock time: 238 minutes 42.31 seconds (14322.31 seconds total)