Starting phenix.real_space_refine on Fri Mar 22 15:58:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdj_4820/03_2024/6rdj_4820_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdj_4820/03_2024/6rdj_4820.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/6rdj_4820/03_2024/6rdj_4820.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdj_4820/03_2024/6rdj_4820.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdj_4820/03_2024/6rdj_4820_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdj_4820/03_2024/6rdj_4820_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 21541 2.51 5 N 5795 2.21 5 O 6421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "H PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 93": "OD1" <-> "OD2" Residue "P ASP 111": "OD1" <-> "OD2" Residue "P PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 127": "OD1" <-> "OD2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P GLU 142": "OE1" <-> "OE2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 54": "OD1" <-> "OD2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 95": "OD1" <-> "OD2" Residue "R PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 143": "OD1" <-> "OD2" Residue "R ASP 153": "OD1" <-> "OD2" Residue "R GLU 186": "OE1" <-> "OE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 83": "OD1" <-> "OD2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S ASP 108": "OD1" <-> "OD2" 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 GLU 181": "OE1" <-> "OE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 229": "OD1" <-> "OD2" Residue "S ASP 232": "OD1" <-> "OD2" Residue "S ASP 241": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S ASP 245": "OD1" <-> "OD2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ASP 142": "OD1" <-> "OD2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ASP 172": "OD1" <-> "OD2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 325": "OD1" <-> "OD2" Residue "T PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 403": "OD1" <-> "OD2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 429": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T ASP 465": "OD1" <-> "OD2" Residue "T ASP 467": "OD1" <-> "OD2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 221": "OE1" <-> "OE2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 311": "OE1" <-> "OE2" Residue "U PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U ARG 342": "NH1" <-> "NH2" Residue "U ARG 343": "NH1" <-> "NH2" Residue "U ARG 364": "NH1" <-> "NH2" Residue "U PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 409": "OE1" <-> "OE2" Residue "U GLU 411": "OE1" <-> "OE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 449": "OE1" <-> "OE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 467": "OD1" <-> "OD2" Residue "U GLU 475": "OE1" <-> "OE2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 112": "OD1" <-> "OD2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V GLU 186": "OE1" <-> "OE2" 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 PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 403": "OD1" <-> "OD2" Residue "V GLU 409": "OE1" <-> "OE2" 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 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 TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 510": "OD1" <-> "OD2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V ASP 516": "OD1" <-> "OD2" 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 ASP 53": "OD1" <-> "OD2" Residue "X GLU 146": "OE1" <-> "OE2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 215": "OE1" <-> "OE2" Residue "X ARG 218": "NH1" <-> "NH2" Residue "X GLU 219": "OE1" <-> "OE2" Residue "X ASP 222": "OD1" <-> "OD2" Residue "X ARG 225": "NH1" <-> "NH2" Residue "X ARG 239": "NH1" <-> "NH2" Residue "X TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 253": "OE1" <-> "OE2" Residue "X GLU 296": "OE1" <-> "OE2" Residue "X ASP 317": "OD1" <-> "OD2" Residue "X TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 378": "OD1" <-> "OD2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 401": "NH1" <-> "NH2" Residue "X ASP 409": "OD1" <-> "OD2" Residue "X PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 494": "OE1" <-> "OE2" Residue "X ASP 505": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X ASP 523": "OD1" <-> "OD2" Residue "X GLU 533": "OE1" <-> "OE2" Residue "X GLU 541": "OE1" <-> "OE2" Residue "X GLU 547": "OE1" <-> "OE2" Residue "Y TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 53": "OD1" <-> "OD2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y ARG 145": "NH1" <-> "NH2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 156": "OE1" <-> "OE2" Residue "Y ASP 168": "OD1" <-> "OD2" Residue "Y TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 215": "OE1" <-> "OE2" Residue "Y ASP 222": "OD1" <-> "OD2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y GLU 270": "OE1" <-> "OE2" Residue "Y ASP 279": "OD1" <-> "OD2" Residue "Y GLU 296": "OE1" <-> "OE2" Residue "Y TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 359": "OD1" <-> "OD2" Residue "Y ARG 366": "NH1" <-> "NH2" Residue "Y ASP 378": "OD1" <-> "OD2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y GLU 427": "OE1" <-> "OE2" Residue "Y ASP 429": "OD1" <-> "OD2" Residue "Y PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 491": "OD1" <-> "OD2" Residue "Y GLU 497": "OE1" <-> "OE2" Residue "Y ASP 500": "OD1" <-> "OD2" Residue "Y GLU 519": "OE1" <-> "OE2" Residue "Y ASP 528": "OD1" <-> "OD2" Residue "Y GLU 547": "OE1" <-> "OE2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "Z ASP 53": "OD1" <-> "OD2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z ASP 82": "OD1" <-> "OD2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "Z ARG 98": "NH1" <-> "NH2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z GLU 127": "OE1" <-> "OE2" Residue "Z ASP 136": "OD1" <-> "OD2" Residue "Z PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 216": "NH1" <-> "NH2" Residue "Z GLU 226": "OE1" <-> "OE2" Residue "Z ARG 258": "NH1" <-> "NH2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 289": "NH1" <-> "NH2" Residue "Z GLU 323": "OE1" <-> "OE2" Residue "Z PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 359": "OD1" <-> "OD2" Residue "Z GLU 370": "OE1" <-> "OE2" Residue "Z TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 381": "OD1" <-> "OD2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 415": "OD1" <-> "OD2" Residue "Z GLU 427": "OE1" <-> "OE2" Residue "Z ARG 435": "NH1" <-> "NH2" Residue "Z ARG 437": "NH1" <-> "NH2" Residue "Z PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 500": "OD1" <-> "OD2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z ASP 513": "OD1" <-> "OD2" Residue "Z GLU 520": "OE1" <-> "OE2" Residue "Z ASP 528": "OD1" <-> "OD2" Residue "Z ASP 548": "OD1" <-> "OD2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33891 Number of models: 1 Model: "" Number of chains: 25 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: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 895 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} 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: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3609 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 456} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.82, per 1000 atoms: 0.56 Number of scatterers: 33891 At special positions: 0 Unit cell: (159.003, 132.678, 207.441, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 13 15.00 Mg 5 11.99 O 6421 8.00 N 5795 7.00 C 21541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.18 Conformation dependent library (CDL) restraints added in 6.8 seconds 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 160 helices and 26 sheets defined 46.6% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.36 Creating SS restraints... Processing helix chain 'A' and resid 56 through 91 removed outlier: 4.640A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 125 removed outlier: 3.634A pdb=" N ALA A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LYS A 97 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 99 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 100 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU A 111 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 112 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 113 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 118 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 125 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.727A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 125 removed outlier: 5.751A pdb=" N LYS B 97 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 99 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL B 100 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY B 106 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 111 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 91 removed outlier: 3.841A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 125 removed outlier: 3.502A pdb=" N ALA C 96 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LYS C 97 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C 99 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C 106 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER C 112 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 122 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU C 125 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 65 removed outlier: 4.205A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 91 removed outlier: 3.508A pdb=" N PHE D 82 " --> pdb=" O GLY D 79 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 85 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG D 91 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 125 removed outlier: 4.485A pdb=" N LYS D 97 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 99 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL D 100 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE D 124 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 91 removed outlier: 3.533A pdb=" N CYS E 66 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 125 removed outlier: 3.609A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 91 removed outlier: 3.524A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS F 66 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 118 removed outlier: 5.175A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL F 100 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR F 110 " --> pdb=" O PHE F 107 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE F 113 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 123 No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain 'G' and resid 55 through 91 removed outlier: 4.111A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 126 removed outlier: 5.334A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU G 99 " --> pdb=" O ALA G 96 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY G 106 " --> pdb=" O ALA G 103 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER G 112 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE G 113 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE G 122 " --> pdb=" O LEU G 119 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE G 124 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU G 125 " --> pdb=" O PHE G 122 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE G 126 " --> pdb=" O LEU G 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 91 removed outlier: 3.818A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ALA H 70 " --> pdb=" O CYS H 66 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA H 72 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 126 removed outlier: 5.846A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA H 108 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU H 119 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE H 126 " --> pdb=" O LEU H 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 66 Processing helix chain 'I' and resid 68 through 91 removed outlier: 3.500A pdb=" N ALA I 76 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE I 82 " --> pdb=" O GLY I 79 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU I 85 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY I 88 " --> pdb=" O LEU I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 124 removed outlier: 3.611A pdb=" N ALA I 96 " --> pdb=" O PRO I 93 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS I 97 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU I 99 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL I 100 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU I 109 " --> pdb=" O GLY I 106 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU I 111 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER I 112 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU I 119 " --> pdb=" O PHE I 116 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL I 120 " --> pdb=" O SER I 117 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE I 124 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 89 removed outlier: 3.580A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 125 removed outlier: 3.540A pdb=" N ALA J 96 " --> pdb=" O PRO J 93 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LYS J 97 " --> pdb=" O ASN J 94 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN J 98 " --> pdb=" O ILE J 95 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLU J 111 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER J 112 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU J 125 " --> pdb=" O PHE J 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 61 Processing helix chain 'P' and resid 67 through 83 removed outlier: 3.708A pdb=" N GLN P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 92 removed outlier: 4.133A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 106 removed outlier: 4.025A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER P 106 " --> pdb=" O THR P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 126 Processing helix chain 'P' and resid 130 through 148 removed outlier: 4.139A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU P 143 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU P 146 " --> pdb=" O GLU P 143 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA P 147 " --> pdb=" O LEU P 144 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 11 No H-bonds generated for 'chain 'Q' and resid 8 through 11' Processing helix chain 'Q' and resid 16 through 30 removed outlier: 3.769A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 39 removed outlier: 3.578A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 39 removed outlier: 3.760A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN R 38 " --> pdb=" O THR R 34 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 154 No H-bonds generated for 'chain 'R' and resid 152 through 154' Processing helix chain 'R' and resid 159 through 167 Processing helix chain 'R' and resid 175 through 195 Processing helix chain 'S' and resid 42 through 78 removed outlier: 3.612A pdb=" N LYS S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU S 76 " --> pdb=" O GLN S 72 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN S 77 " --> pdb=" O ILE S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 88 Proline residue: S 84 - end of helix Processing helix chain 'S' and resid 115 through 127 Processing helix chain 'S' and resid 144 through 147 No H-bonds generated for 'chain 'S' and resid 144 through 147' Processing helix chain 'S' and resid 150 through 153 No H-bonds generated for 'chain 'S' and resid 150 through 153' Processing helix chain 'S' and resid 172 through 184 Processing helix chain 'S' and resid 217 through 221 Processing helix chain 'S' and resid 239 through 312 removed outlier: 3.579A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR S 278 " --> pdb=" O MET S 274 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE S 307 " --> pdb=" O GLU S 303 " (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 removed outlier: 3.551A pdb=" N LEU T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 231 through 246 removed outlier: 3.508A pdb=" N ALA T 235 " --> pdb=" O LYS T 231 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 279 Processing helix chain 'T' and resid 281 through 284 Processing helix chain 'T' and resid 296 through 314 removed outlier: 3.726A pdb=" N LEU T 301 " --> pdb=" O PRO T 297 " (cutoff:3.500A) Proline residue: T 303 - end of helix removed outlier: 3.688A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 340 Processing helix chain 'T' and resid 352 through 364 removed outlier: 4.158A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER T 359 " --> pdb=" O TYR T 356 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG T 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU T 362 " --> pdb=" O SER T 359 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU T 363 " --> pdb=" O ARG T 360 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 401 removed outlier: 3.687A pdb=" N SER T 400 " --> pdb=" O THR T 396 " (cutoff:3.500A) Processing helix chain 'T' and resid 410 through 414 Processing helix chain 'T' and resid 431 through 434 removed outlier: 3.930A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 431 through 434' Processing helix chain 'T' and resid 437 through 440 No H-bonds generated for 'chain 'T' and resid 437 through 440' Processing helix chain 'T' and resid 446 through 459 removed outlier: 3.621A pdb=" N ALA T 451 " --> pdb=" O LYS T 447 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA T 458 " --> pdb=" O ARG T 454 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 470 through 483 removed outlier: 3.692A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) Processing helix chain 'T' and resid 495 through 505 removed outlier: 3.525A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 514 through 527 removed outlier: 4.000A pdb=" N ILE T 517 " --> pdb=" O VAL T 514 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N VAL T 518 " --> pdb=" O GLN T 515 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU T 521 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU T 522 " --> pdb=" O ALA T 519 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL T 524 " --> pdb=" O GLU T 521 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLN T 527 " --> pdb=" O VAL T 524 " (cutoff:3.500A) Processing helix chain 'T' and resid 531 through 539 Processing helix chain 'T' and resid 544 through 553 removed outlier: 4.249A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 48 removed outlier: 4.913A pdb=" N LEU U 48 " --> pdb=" O ALA U 44 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 62 No H-bonds generated for 'chain 'U' and resid 59 through 62' Processing helix chain 'U' and resid 66 through 72 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 248 removed outlier: 3.819A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLN U 248 " --> pdb=" O ASN U 244 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 278 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: 3.638A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 removed outlier: 3.762A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 354 through 364 removed outlier: 3.665A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG U 364 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 393 through 399 Processing helix chain 'U' and resid 410 through 414 Processing helix chain 'U' and resid 437 through 458 removed outlier: 3.631A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 484 removed outlier: 3.614A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 505 removed outlier: 3.523A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 517 through 527 Processing helix chain 'U' and resid 531 through 539 Processing helix chain 'U' and resid 544 through 555 removed outlier: 3.970A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG U 555 " --> pdb=" O LYS U 551 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 66 removed outlier: 3.553A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (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 211 Processing helix chain 'V' and resid 231 through 246 Processing helix chain 'V' and resid 266 through 279 Processing helix chain 'V' and resid 281 through 283 No H-bonds generated for 'chain 'V' and resid 281 through 283' Processing helix chain 'V' and resid 296 through 315 Proline residue: V 303 - end of helix removed outlier: 3.724A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG V 314 " --> pdb=" O ALA V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 340 Processing helix chain 'V' and resid 352 through 364 removed outlier: 4.419A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER V 359 " --> pdb=" O TYR V 356 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 4.400A 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 414 Processing helix chain 'V' and resid 431 through 434 removed outlier: 3.589A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 431 through 434' Processing helix chain 'V' and resid 440 through 455 removed outlier: 3.880A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU V 448 " --> pdb=" O GLY V 444 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 481 Processing helix chain 'V' and resid 494 through 506 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 522 through 525 No H-bonds generated for 'chain 'V' and resid 522 through 525' Processing helix chain 'V' and resid 532 through 539 Processing helix chain 'V' and resid 544 through 553 removed outlier: 4.318A pdb=" N LYS V 551 " --> pdb=" O ASP V 547 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 117 No H-bonds generated for 'chain 'X' and resid 115 through 117' Processing helix chain 'X' and resid 165 through 170 Processing helix chain 'X' and resid 189 through 200 Processing helix chain 'X' and resid 217 through 228 Processing helix chain 'X' and resid 236 through 241 removed outlier: 4.835A 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: 3.602A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 288 through 298 Processing helix chain 'X' and resid 314 through 322 Processing helix chain 'X' and resid 349 through 357 removed outlier: 4.677A pdb=" N ALA X 356 " --> pdb=" O ALA X 352 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N HIS X 357 " --> pdb=" O THR X 353 " (cutoff:3.500A) Processing helix chain 'X' and resid 366 through 371 Processing helix chain 'X' and resid 389 through 392 No H-bonds generated for 'chain 'X' and resid 389 through 392' Processing helix chain 'X' and resid 394 through 420 removed outlier: 4.691A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE X 419 " --> pdb=" O ASP X 415 " (cutoff:3.500A) Processing helix chain 'X' and resid 422 through 424 No H-bonds generated for 'chain 'X' and resid 422 through 424' Processing helix chain 'X' and resid 427 through 443 Processing helix chain 'X' and resid 451 through 454 No H-bonds generated for 'chain 'X' and resid 451 through 454' Processing helix chain 'X' and resid 463 through 475 Processing helix chain 'X' and resid 492 through 505 removed outlier: 3.920A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP X 505 " --> pdb=" O LYS X 501 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 533 removed outlier: 3.573A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU X 533 " --> pdb=" O LYS X 529 " (cutoff:3.500A) Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 165 through 170 Processing helix chain 'Y' and resid 189 through 200 Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 4.509A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 258 No H-bonds generated for 'chain 'Y' and resid 255 through 258' Processing helix chain 'Y' and resid 261 through 274 Processing helix chain 'Y' and resid 288 through 295 Processing helix chain 'Y' and resid 314 through 324 removed outlier: 4.443A pdb=" N ARG Y 324 " --> pdb=" O GLY Y 320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 349 through 357 removed outlier: 4.537A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N HIS Y 357 " --> pdb=" O THR Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 370 Processing helix chain 'Y' and resid 389 through 392 No H-bonds generated for 'chain 'Y' and resid 389 through 392' Processing helix chain 'Y' and resid 394 through 420 removed outlier: 4.134A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 429 through 443 Processing helix chain 'Y' and resid 463 through 475 Processing helix chain 'Y' and resid 483 through 485 No H-bonds generated for 'chain 'Y' and resid 483 through 485' Processing helix chain 'Y' and resid 492 through 506 removed outlier: 3.593A pdb=" N ASP Y 500 " --> pdb=" O LYS Y 496 " (cutoff:3.500A) Processing helix chain 'Y' and resid 527 through 533 Processing helix chain 'Y' and resid 545 through 554 Processing helix chain 'Z' and resid 115 through 117 No H-bonds generated for 'chain 'Z' and resid 115 through 117' Processing helix chain 'Z' and resid 165 through 169 Processing helix chain 'Z' and resid 189 through 203 Processing helix chain 'Z' and resid 217 through 228 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 4.594A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 258 No H-bonds generated for 'chain 'Z' and resid 255 through 258' Processing helix chain 'Z' and resid 261 through 274 removed outlier: 3.715A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 300 Processing helix chain 'Z' and resid 314 through 322 removed outlier: 3.827A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 349 through 354 Processing helix chain 'Z' and resid 366 through 369 No H-bonds generated for 'chain 'Z' and resid 366 through 369' Processing helix chain 'Z' and resid 393 through 410 Processing helix chain 'Z' and resid 414 through 420 removed outlier: 4.610A pdb=" N ILE Z 419 " --> pdb=" O ASP Z 415 " (cutoff:3.500A) Processing helix chain 'Z' and resid 427 through 442 removed outlier: 3.611A pdb=" N LEU Z 431 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS Z 438 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) Processing helix chain 'Z' and resid 448 through 454 removed outlier: 3.701A pdb=" N GLU Z 451 " --> pdb=" O GLN Z 448 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL Z 452 " --> pdb=" O VAL Z 449 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR Z 454 " --> pdb=" O GLU Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 463 through 475 Processing helix chain 'Z' and resid 492 through 508 removed outlier: 4.149A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER Z 508 " --> pdb=" O LYS Z 504 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 533 removed outlier: 3.762A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU Z 533 " --> pdb=" O LYS Z 529 " (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: 6.568A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.634A 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: 3.957A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU R 125 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 203 through 211 removed outlier: 5.129A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA S 161 " --> pdb=" O SER S 141 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'T' and resid 86 through 91 removed outlier: 6.612A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 6.056A 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: 3.705A 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: 8.809A pdb=" N ILE T 286 " --> pdb=" O VAL T 255 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N CYS T 257 " --> pdb=" O ILE T 286 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL T 288 " --> pdb=" O CYS T 257 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TYR T 259 " --> pdb=" O VAL T 288 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ALA T 290 " --> pdb=" O TYR T 259 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA T 261 " --> pdb=" O ALA T 290 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER T 376 " --> pdb=" O GLY T 320 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE T 322 " --> pdb=" O SER T 376 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) removed outlier: 6.776A 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: 6.786A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= K, first strand: chain 'U' and resid 404 through 408 Processing sheet with id= L, first strand: chain 'U' and resid 285 through 290 removed outlier: 8.810A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE U 380 " --> pdb=" O TYR U 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'V' and resid 85 through 89 removed outlier: 6.544A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= O, first strand: chain 'V' and resid 404 through 408 Processing sheet with id= P, first strand: chain 'V' and resid 285 through 290 removed outlier: 8.818A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE V 380 " --> pdb=" O TYR V 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'X' and resid 37 through 39 removed outlier: 4.757A pdb=" N LEU X 72 " --> pdb=" O VAL X 65 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG X 51 " --> pdb=" O VAL X 40 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL X 40 " --> pdb=" O ARG X 51 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'X' and resid 110 through 113 removed outlier: 3.516A pdb=" N ASP X 139 " --> pdb=" O VAL X 113 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'X' and resid 360 through 363 removed outlier: 7.462A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLY X 183 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL X 339 " --> pdb=" O GLY X 183 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE X 207 " --> pdb=" O LEU X 281 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N PHE X 283 " --> pdb=" O PHE X 207 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL X 209 " --> pdb=" O PHE X 283 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ASP X 285 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA X 211 " --> pdb=" O ASP X 285 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= U, first strand: chain 'Y' and resid 38 through 44 removed outlier: 6.449A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'Y' and resid 360 through 362 removed outlier: 7.428A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL Y 280 " --> pdb=" O THR Y 334 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL Y 336 " --> pdb=" O VAL Y 280 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU Y 282 " --> pdb=" O VAL Y 336 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA Y 338 " --> pdb=" O LEU Y 282 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL Y 284 " --> pdb=" O ALA Y 338 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N PHE Y 207 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE Y 283 " --> pdb=" O PHE Y 207 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA Y 211 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Z' and resid 38 through 44 removed outlier: 6.301A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id= Y, first strand: chain 'Z' and resid 360 through 362 removed outlier: 8.536A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL Z 284 " --> pdb=" O VAL Z 336 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL Z 213 " --> pdb=" O ASP Z 285 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Z' and resid 559 through 561 1422 hydrogen bonds defined for protein. 3423 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: 12.65 Time building geometry restraints manager: 15.35 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: 9920 1.33 - 1.45: 5365 1.45 - 1.57: 18906 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34412 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.20e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.82e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.80e+01 bond pdb=" C ILE V 67 " pdb=" N PRO V 68 " ideal model delta sigma weight residual 1.331 1.382 -0.051 7.90e-03 1.60e+04 4.14e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.46e+01 ... (remaining 34407 not shown) Histogram of bond angle deviations from ideal: 97.95 - 105.59: 717 105.59 - 113.22: 19193 113.22 - 120.86: 16750 120.86 - 128.49: 9835 128.49 - 136.13: 143 Bond angle restraints: 46638 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 119.48 20.39 1.00e+00 1.00e+00 4.16e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 121.58 18.29 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 123.31 16.56 1.00e+00 1.00e+00 2.74e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 123.51 13.32 1.00e+00 1.00e+00 1.77e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 125.43 11.40 1.00e+00 1.00e+00 1.30e+02 ... (remaining 46633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.73: 20339 33.73 - 67.46: 450 67.46 - 101.18: 31 101.18 - 134.91: 1 134.91 - 168.64: 2 Dihedral angle restraints: 20823 sinusoidal: 8066 harmonic: 12757 Sorted by residual: 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 -120.82 -59.18 0 5.00e+00 4.00e-02 1.40e+02 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 -124.13 -55.87 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA GLU V 348 " pdb=" C GLU V 348 " pdb=" N ALA V 349 " pdb=" CA ALA V 349 " ideal model delta harmonic sigma weight residual 180.00 124.85 55.15 0 5.00e+00 4.00e-02 1.22e+02 ... (remaining 20820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4169 0.070 - 0.141: 1179 0.141 - 0.211: 147 0.211 - 0.282: 19 0.282 - 0.352: 5 Chirality restraints: 5519 Sorted by residual: chirality pdb=" CB VAL Z 113 " pdb=" CA VAL Z 113 " pdb=" CG1 VAL Z 113 " pdb=" CG2 VAL Z 113 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.10e+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 -2.28 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA PRO U 201 " pdb=" N PRO U 201 " pdb=" C PRO U 201 " pdb=" CB PRO U 201 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 5516 not shown) Planarity restraints: 5997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 6.02e-02 3.62e+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 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA U 296 " 0.062 5.00e-02 4.00e+02 9.30e-02 1.39e+01 pdb=" N PRO U 297 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO U 297 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO U 297 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL X 341 " -0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO X 342 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO X 342 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO X 342 " -0.045 5.00e-02 4.00e+02 ... (remaining 5994 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 361 2.60 - 3.17: 28217 3.17 - 3.75: 54597 3.75 - 4.32: 81075 4.32 - 4.90: 130694 Nonbonded interactions: 294944 Sorted by model distance: nonbonded pdb=" OG1 THR V 232 " pdb="MG MG V1002 " model vdw 2.025 2.170 nonbonded pdb=" O2B ATP T1001 " pdb="MG MG T1002 " model vdw 2.025 2.170 nonbonded pdb=" OE1 GLN U 228 " pdb=" NH1 ARG Z 385 " model vdw 2.044 2.520 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.056 2.170 nonbonded pdb=" O2B ATP U1001 " pdb="MG MG U1002 " model vdw 2.085 2.170 ... (remaining 294939 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 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.400 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: 0.030 Extract box with map and model: 25.800 Check model and map are aligned: 0.550 Set scattering table: 0.300 Process input model: 93.850 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.170 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:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 : 0.011 0.135 34412 Z= 0.703 Angle : 1.039 20.392 46638 Z= 0.596 Chirality : 0.064 0.352 5519 Planarity : 0.008 0.093 5997 Dihedral : 14.455 168.639 12663 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.95 % Favored : 94.75 % Rotamer: Outliers : 0.31 % Allowed : 7.94 % Favored : 91.75 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.10), residues: 4461 helix: -2.93 (0.08), residues: 2184 sheet: -1.34 (0.20), residues: 596 loop : -1.97 (0.13), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP X 141 HIS 0.013 0.002 HIS Y 79 PHE 0.036 0.003 PHE S 249 TYR 0.021 0.003 TYR X 340 ARG 0.010 0.001 ARG Z 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 675 time to evaluate : 3.488 Fit side-chains revert: symmetry clash REVERT: A 109 LEU cc_start: 0.8444 (mp) cc_final: 0.8213 (mt) REVERT: C 107 PHE cc_start: 0.8281 (t80) cc_final: 0.8063 (t80) REVERT: D 123 LEU cc_start: 0.7367 (tt) cc_final: 0.7114 (mm) REVERT: E 95 ILE cc_start: 0.8871 (tp) cc_final: 0.8517 (tp) REVERT: H 56 LEU cc_start: 0.7739 (tt) cc_final: 0.7465 (tm) REVERT: I 61 MET cc_start: 0.8014 (mmt) cc_final: 0.7640 (mmm) REVERT: J 56 LEU cc_start: 0.6617 (tt) cc_final: 0.6350 (mp) REVERT: J 107 PHE cc_start: 0.8577 (t80) cc_final: 0.8056 (t80) REVERT: J 115 LEU cc_start: 0.6296 (mt) cc_final: 0.5852 (pp) REVERT: P 59 GLN cc_start: 0.8367 (mt0) cc_final: 0.8006 (mm-40) REVERT: P 63 LYS cc_start: 0.8562 (tppt) cc_final: 0.8084 (tttm) REVERT: P 76 GLN cc_start: 0.8558 (mt0) cc_final: 0.8140 (mt0) REVERT: P 150 LYS cc_start: 0.6743 (mttm) cc_final: 0.6440 (tptt) REVERT: Q 19 TYR cc_start: 0.8754 (t80) cc_final: 0.8397 (t80) REVERT: R 58 LYS cc_start: 0.7770 (mptt) cc_final: 0.7496 (mmtm) REVERT: R 117 GLU cc_start: 0.7194 (pm20) cc_final: 0.6985 (pm20) REVERT: S 68 MET cc_start: 0.8150 (ttp) cc_final: 0.7822 (tmm) REVERT: S 218 LYS cc_start: 0.8629 (tmtt) cc_final: 0.8323 (tmtm) REVERT: S 275 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7553 (tm-30) REVERT: T 237 ASP cc_start: 0.7237 (m-30) cc_final: 0.7009 (m-30) REVERT: T 440 LYS cc_start: 0.8358 (ttpt) cc_final: 0.7969 (ttmt) REVERT: T 467 ASP cc_start: 0.7111 (m-30) cc_final: 0.5918 (t0) REVERT: T 471 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7286 (tm-30) REVERT: T 482 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7966 (mp0) REVERT: T 535 ILE cc_start: 0.8779 (mt) cc_final: 0.8530 (mp) REVERT: T 555 ARG cc_start: 0.7535 (mtt-85) cc_final: 0.7170 (mmt90) REVERT: U 118 MET cc_start: 0.8901 (ttt) cc_final: 0.8629 (ttp) REVERT: U 472 TYR cc_start: 0.7307 (t80) cc_final: 0.6928 (t80) REVERT: U 553 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7633 (mm-30) REVERT: V 50 LYS cc_start: 0.7758 (tppt) cc_final: 0.7481 (tptt) REVERT: V 447 LYS cc_start: 0.8411 (ptpt) cc_final: 0.8151 (mtpt) REVERT: V 461 GLN cc_start: 0.8196 (mp-120) cc_final: 0.7996 (mm-40) REVERT: V 535 ILE cc_start: 0.8999 (mt) cc_final: 0.8777 (mm) REVERT: X 484 MET cc_start: 0.8310 (mmt) cc_final: 0.8065 (mmm) REVERT: Y 227 MET cc_start: 0.8723 (mtp) cc_final: 0.8451 (mtt) REVERT: Y 424 GLU cc_start: 0.7111 (mp0) cc_final: 0.6904 (pm20) REVERT: Y 548 ASP cc_start: 0.7665 (t0) cc_final: 0.7461 (t0) REVERT: Z 292 GLN cc_start: 0.7879 (mt0) cc_final: 0.7672 (mt0) REVERT: Z 430 LYS cc_start: 0.7143 (tppp) cc_final: 0.6844 (mttt) outliers start: 11 outliers final: 7 residues processed: 685 average time/residue: 1.4108 time to fit residues: 1157.4450 Evaluate side-chains 456 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 449 time to evaluate : 3.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 431 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 0.5980 chunk 335 optimal weight: 0.8980 chunk 185 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 225 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 chunk 346 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 257 optimal weight: 0.8980 chunk 401 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 94 ASN I 98 GLN J 92 ASN J 98 GLN P 71 GLN P 140 ASN Q 40 GLN Q 46 HIS ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 73 ASN ** R 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 HIS R 137 HIS ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 297 GLN T 104 GLN T 196 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 386 GLN T 435 GLN T 441 GLN T 461 GLN T 497 GLN T 539 ASN T 549 HIS U 83 HIS U 134 ASN U 149 GLN U 241 HIS U 246 ASN U 319 HIS U 386 GLN U 441 GLN U 497 GLN U 539 ASN V 60 GLN V 78 GLN V 126 HIS V 139 HIS ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 242 GLN V 244 ASN V 246 ASN V 271 GLN V 461 GLN V 486 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 157 GLN X 198 ASN X 199 ASN X 241 ASN X 278 GLN X 322 GLN X 337 GLN X 398 ASN X 414 GLN Y 123 ASN Y 144 HIS Y 174 GLN Y 278 GLN Y 414 GLN Y 440 GLN Z 144 HIS Z 199 ASN Z 250 GLN Z 278 GLN Z 294 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34412 Z= 0.201 Angle : 0.590 10.688 46638 Z= 0.309 Chirality : 0.043 0.274 5519 Planarity : 0.005 0.066 5997 Dihedral : 7.704 179.016 4929 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.54 % Favored : 96.21 % Rotamer: Outliers : 2.83 % Allowed : 14.73 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.06 (0.12), residues: 4461 helix: -1.27 (0.10), residues: 2176 sheet: -1.24 (0.21), residues: 599 loop : -1.28 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 37 HIS 0.004 0.001 HIS V 549 PHE 0.019 0.001 PHE F 107 TYR 0.012 0.001 TYR Y 310 ARG 0.008 0.000 ARG S 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 514 time to evaluate : 3.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 PHE cc_start: 0.7941 (t80) cc_final: 0.7731 (t80) REVERT: E 95 ILE cc_start: 0.8735 (tp) cc_final: 0.8448 (tp) REVERT: F 81 MET cc_start: 0.7623 (ttp) cc_final: 0.7297 (ttp) REVERT: G 97 LYS cc_start: 0.7819 (ttmm) cc_final: 0.7134 (mmmt) REVERT: H 61 MET cc_start: 0.7747 (mmm) cc_final: 0.7213 (tpp) REVERT: I 61 MET cc_start: 0.7849 (mmt) cc_final: 0.7533 (mmm) REVERT: I 82 PHE cc_start: 0.7674 (m-80) cc_final: 0.7202 (m-10) REVERT: J 56 LEU cc_start: 0.6581 (tt) cc_final: 0.6303 (mp) REVERT: J 61 MET cc_start: 0.7564 (mmm) cc_final: 0.7356 (mtt) REVERT: J 92 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7902 (p0) REVERT: J 95 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7662 (tt) REVERT: P 59 GLN cc_start: 0.8450 (mt0) cc_final: 0.8050 (mm-40) REVERT: P 83 GLN cc_start: 0.7874 (pp30) cc_final: 0.7630 (pp30) REVERT: P 142 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7632 (mt-10) REVERT: P 150 LYS cc_start: 0.6790 (mttm) cc_final: 0.6461 (tptt) REVERT: Q 19 TYR cc_start: 0.8666 (t80) cc_final: 0.8416 (t80) REVERT: R 58 LYS cc_start: 0.7616 (mptt) cc_final: 0.7409 (mmtm) REVERT: S 68 MET cc_start: 0.8029 (ttp) cc_final: 0.7536 (tmm) REVERT: S 198 ARG cc_start: 0.6708 (mmm-85) cc_final: 0.6503 (mmm160) REVERT: T 237 ASP cc_start: 0.6916 (m-30) cc_final: 0.6713 (m-30) REVERT: T 411 GLU cc_start: 0.7616 (pm20) cc_final: 0.7293 (mp0) REVERT: T 440 LYS cc_start: 0.8357 (ttpt) cc_final: 0.7965 (ttmt) REVERT: T 471 GLN cc_start: 0.7751 (tm-30) cc_final: 0.7297 (tm-30) REVERT: T 487 LYS cc_start: 0.8456 (ptmt) cc_final: 0.8220 (mtmt) REVERT: T 496 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7878 (mtt90) REVERT: T 502 TYR cc_start: 0.7848 (t80) cc_final: 0.7400 (t80) REVERT: T 535 ILE cc_start: 0.8630 (mt) cc_final: 0.8364 (mp) REVERT: T 555 ARG cc_start: 0.7594 (mtt-85) cc_final: 0.7213 (mmt90) REVERT: U 118 MET cc_start: 0.9053 (ttt) cc_final: 0.8837 (ttp) REVERT: U 472 TYR cc_start: 0.7087 (t80) cc_final: 0.6824 (t80) REVERT: V 50 LYS cc_start: 0.7756 (tppt) cc_final: 0.7407 (tptt) REVERT: V 64 GLN cc_start: 0.8054 (mt0) cc_final: 0.7842 (mt0) REVERT: V 429 ARG cc_start: 0.7991 (mtt-85) cc_final: 0.7593 (mtt-85) REVERT: V 476 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7657 (tpt170) REVERT: V 509 LEU cc_start: 0.8435 (mm) cc_final: 0.8097 (mp) REVERT: X 158 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7481 (mm-30) REVERT: Y 227 MET cc_start: 0.8749 (mtp) cc_final: 0.8464 (mtt) REVERT: Y 528 ASP cc_start: 0.6683 (p0) cc_final: 0.6379 (p0) REVERT: Z 88 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8821 (pt) REVERT: Z 430 LYS cc_start: 0.7163 (tppp) cc_final: 0.6940 (mttp) outliers start: 101 outliers final: 39 residues processed: 580 average time/residue: 1.2624 time to fit residues: 895.3037 Evaluate side-chains 484 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 439 time to evaluate : 3.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 118 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 117 SER Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 251 LYS Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 448 LEU Chi-restraints excluded: chain V residue 476 ARG Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 466 THR Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 475 THR Chi-restraints excluded: chain Y residue 531 VAL Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 417 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 223 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 334 optimal weight: 0.0980 chunk 273 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 402 optimal weight: 0.6980 chunk 434 optimal weight: 0.8980 chunk 358 optimal weight: 0.8980 chunk 398 optimal weight: 0.9980 chunk 137 optimal weight: 0.0570 chunk 322 optimal weight: 1.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 GLN H 98 GLN I 98 GLN P 66 GLN ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 ASN T 140 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 405 GLN T 539 ASN U 134 ASN U 539 ASN U 549 HIS V 78 GLN V 152 ASN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS V 244 ASN V 461 GLN X 83 ASN X 414 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 34412 Z= 0.160 Angle : 0.541 10.362 46638 Z= 0.278 Chirality : 0.042 0.243 5519 Planarity : 0.004 0.057 5997 Dihedral : 6.898 151.747 4921 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.77 % Favored : 96.03 % Rotamer: Outliers : 3.17 % Allowed : 16.61 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 4461 helix: -0.62 (0.11), residues: 2186 sheet: -1.01 (0.21), residues: 601 loop : -0.96 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 37 HIS 0.003 0.001 HIS S 237 PHE 0.031 0.001 PHE E 107 TYR 0.016 0.001 TYR X 487 ARG 0.005 0.000 ARG S 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 499 time to evaluate : 3.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 LYS cc_start: 0.7440 (mttm) cc_final: 0.7209 (mttt) REVERT: C 95 ILE cc_start: 0.8982 (tt) cc_final: 0.8781 (tt) REVERT: D 123 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6989 (mm) REVERT: E 87 ASN cc_start: 0.7684 (m-40) cc_final: 0.7057 (t0) REVERT: E 95 ILE cc_start: 0.8681 (tp) cc_final: 0.8401 (tp) REVERT: F 81 MET cc_start: 0.7584 (ttp) cc_final: 0.7205 (ttp) REVERT: G 82 PHE cc_start: 0.7988 (m-10) cc_final: 0.7453 (m-10) REVERT: G 97 LYS cc_start: 0.8031 (ttmm) cc_final: 0.7206 (mmmt) REVERT: H 61 MET cc_start: 0.7662 (mmm) cc_final: 0.6929 (tpp) REVERT: I 61 MET cc_start: 0.7747 (mmt) cc_final: 0.7471 (mmm) REVERT: I 82 PHE cc_start: 0.7569 (m-80) cc_final: 0.7242 (m-10) REVERT: I 107 PHE cc_start: 0.7645 (t80) cc_final: 0.7414 (t80) REVERT: J 56 LEU cc_start: 0.6540 (tt) cc_final: 0.6238 (mp) REVERT: J 107 PHE cc_start: 0.7964 (t80) cc_final: 0.7630 (t80) REVERT: P 59 GLN cc_start: 0.8403 (mt0) cc_final: 0.8072 (mm-40) REVERT: P 83 GLN cc_start: 0.7947 (pp30) cc_final: 0.7668 (pp30) REVERT: P 150 LYS cc_start: 0.6596 (mttm) cc_final: 0.6354 (tptt) REVERT: Q 19 TYR cc_start: 0.8661 (t80) cc_final: 0.8418 (t80) REVERT: Q 72 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7713 (p) REVERT: R 58 LYS cc_start: 0.7579 (mptt) cc_final: 0.7345 (mmtm) REVERT: R 117 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: S 68 MET cc_start: 0.7938 (ttp) cc_final: 0.7596 (ttp) REVERT: S 220 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7612 (mm) REVERT: T 149 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7429 (pt0) REVERT: T 237 ASP cc_start: 0.6987 (m-30) cc_final: 0.6774 (m-30) REVERT: T 411 GLU cc_start: 0.7609 (pm20) cc_final: 0.7295 (mp0) REVERT: T 440 LYS cc_start: 0.8327 (ttpt) cc_final: 0.7921 (ttmt) REVERT: T 471 GLN cc_start: 0.7619 (tm-30) cc_final: 0.7342 (tm-30) REVERT: T 475 GLU cc_start: 0.7476 (tp30) cc_final: 0.7216 (tp30) REVERT: T 496 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7952 (mtt90) REVERT: T 522 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: T 535 ILE cc_start: 0.8535 (mt) cc_final: 0.8330 (mp) REVERT: T 549 HIS cc_start: 0.6746 (OUTLIER) cc_final: 0.6399 (t70) REVERT: T 555 ARG cc_start: 0.7600 (mtt-85) cc_final: 0.7276 (mmt90) REVERT: U 515 GLN cc_start: 0.7715 (mp10) cc_final: 0.7410 (mp10) REVERT: V 50 LYS cc_start: 0.7665 (tppt) cc_final: 0.7322 (tptt) REVERT: V 429 ARG cc_start: 0.8115 (mtt-85) cc_final: 0.7647 (mtt-85) REVERT: Y 123 ASN cc_start: 0.7934 (t0) cc_final: 0.7731 (t0) REVERT: Y 227 MET cc_start: 0.8749 (mtp) cc_final: 0.8428 (mtt) REVERT: Y 409 ASP cc_start: 0.7876 (m-30) cc_final: 0.7620 (m-30) REVERT: Y 422 MET cc_start: 0.6539 (OUTLIER) cc_final: 0.6236 (tpp) REVERT: Y 441 ARG cc_start: 0.7833 (mmt-90) cc_final: 0.7549 (mpt-90) REVERT: Y 528 ASP cc_start: 0.6656 (p0) cc_final: 0.6364 (p0) REVERT: Z 88 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8848 (pt) REVERT: Z 429 ASP cc_start: 0.6821 (m-30) cc_final: 0.6492 (m-30) REVERT: Z 430 LYS cc_start: 0.7038 (tppp) cc_final: 0.6661 (mttp) outliers start: 113 outliers final: 51 residues processed: 570 average time/residue: 1.3078 time to fit residues: 909.0238 Evaluate side-chains 489 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 428 time to evaluate : 3.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 118 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain S residue 117 SER Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 522 GLU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 251 LYS Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 411 GLU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 417 ILE Chi-restraints excluded: chain Y residue 422 MET Chi-restraints excluded: chain Y residue 475 THR Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 415 ASP Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 417 ILE Chi-restraints excluded: chain Z residue 484 MET Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 397 optimal weight: 3.9990 chunk 302 optimal weight: 0.6980 chunk 208 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 chunk 270 optimal weight: 3.9990 chunk 403 optimal weight: 5.9990 chunk 427 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 382 optimal weight: 0.5980 chunk 115 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN G 98 GLN I 98 GLN J 92 ASN P 66 GLN P 71 GLN Q 43 GLN ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 185 HIS ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 405 GLN T 497 GLN T 539 ASN U 134 ASN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 78 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 358 HIS V 461 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 414 GLN Z 448 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 34412 Z= 0.243 Angle : 0.565 10.265 46638 Z= 0.289 Chirality : 0.044 0.249 5519 Planarity : 0.004 0.056 5997 Dihedral : 6.703 109.644 4921 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.88 % Favored : 95.88 % Rotamer: Outliers : 3.54 % Allowed : 17.48 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.07 (0.13), residues: 4461 helix: -0.37 (0.11), residues: 2192 sheet: -0.91 (0.21), residues: 601 loop : -0.87 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 37 HIS 0.004 0.001 HIS U 319 PHE 0.033 0.002 PHE E 107 TYR 0.017 0.001 TYR J 102 ARG 0.005 0.000 ARG X 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 447 time to evaluate : 3.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 ILE cc_start: 0.9025 (tt) cc_final: 0.8578 (tt) REVERT: E 87 ASN cc_start: 0.7678 (m-40) cc_final: 0.7025 (t0) REVERT: E 95 ILE cc_start: 0.8730 (tp) cc_final: 0.8443 (tp) REVERT: F 81 MET cc_start: 0.7689 (ttp) cc_final: 0.7397 (ttp) REVERT: G 82 PHE cc_start: 0.8042 (m-10) cc_final: 0.7545 (m-10) REVERT: G 97 LYS cc_start: 0.8016 (ttmm) cc_final: 0.7214 (mmmt) REVERT: H 61 MET cc_start: 0.7700 (mmm) cc_final: 0.6982 (tpp) REVERT: I 61 MET cc_start: 0.7695 (mmt) cc_final: 0.7425 (mmm) REVERT: I 82 PHE cc_start: 0.7734 (m-80) cc_final: 0.7371 (m-10) REVERT: J 56 LEU cc_start: 0.6580 (tt) cc_final: 0.6260 (mt) REVERT: P 59 GLN cc_start: 0.8418 (mt0) cc_final: 0.7961 (mm-40) REVERT: P 83 GLN cc_start: 0.8111 (pp30) cc_final: 0.7808 (pp30) REVERT: Q 19 TYR cc_start: 0.8720 (t80) cc_final: 0.8486 (t80) REVERT: Q 49 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8214 (pt0) REVERT: Q 72 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7720 (p) REVERT: R 117 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: R 178 GLN cc_start: 0.8021 (tp40) cc_final: 0.7508 (mp10) REVERT: S 68 MET cc_start: 0.7966 (ttp) cc_final: 0.7444 (tmm) REVERT: S 164 ASP cc_start: 0.7441 (m-30) cc_final: 0.6898 (t0) REVERT: S 220 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7603 (mm) REVERT: T 149 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7451 (pt0) REVERT: T 237 ASP cc_start: 0.7131 (m-30) cc_final: 0.6890 (m-30) REVERT: T 411 GLU cc_start: 0.7584 (pm20) cc_final: 0.7366 (mp0) REVERT: T 440 LYS cc_start: 0.8410 (ttpt) cc_final: 0.7989 (ttmt) REVERT: T 471 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7477 (tm-30) REVERT: T 496 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8016 (mtt90) REVERT: T 522 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6652 (mp0) REVERT: T 549 HIS cc_start: 0.6764 (OUTLIER) cc_final: 0.6417 (t70) REVERT: T 555 ARG cc_start: 0.7617 (mtt-85) cc_final: 0.7258 (mmt90) REVERT: V 50 LYS cc_start: 0.7838 (tppt) cc_final: 0.7445 (tptt) REVERT: V 429 ARG cc_start: 0.8131 (mtt-85) cc_final: 0.7682 (mtt-85) REVERT: V 509 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8202 (mp) REVERT: Y 409 ASP cc_start: 0.7880 (m-30) cc_final: 0.7640 (m-30) REVERT: Y 441 ARG cc_start: 0.7940 (mmt-90) cc_final: 0.7652 (mpt-90) REVERT: Y 528 ASP cc_start: 0.6705 (p0) cc_final: 0.6395 (p0) outliers start: 126 outliers final: 61 residues processed: 527 average time/residue: 1.2761 time to fit residues: 822.6992 Evaluate side-chains 491 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 421 time to evaluate : 3.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 118 THR Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain S residue 117 SER Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 243 LYS Chi-restraints excluded: chain T residue 353 ASP Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 522 GLU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 251 LYS Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 482 GLU Chi-restraints excluded: chain V residue 509 LEU Chi-restraints excluded: chain V residue 512 VAL Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 466 THR Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 531 VAL Chi-restraints excluded: chain Z residue 41 SER Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 415 ASP Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 355 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 318 optimal weight: 5.9990 chunk 176 optimal weight: 0.6980 chunk 364 optimal weight: 0.6980 chunk 295 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 218 optimal weight: 1.9990 chunk 383 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN E 94 ASN I 98 GLN P 66 GLN P 71 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 61 HIS U 134 ASN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 461 GLN ** V 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 414 GLN Y 204 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34412 Z= 0.194 Angle : 0.545 10.230 46638 Z= 0.277 Chirality : 0.043 0.295 5519 Planarity : 0.004 0.054 5997 Dihedral : 6.341 107.740 4921 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.77 % Favored : 96.03 % Rotamer: Outliers : 3.54 % Allowed : 18.74 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.78 (0.13), residues: 4461 helix: -0.13 (0.11), residues: 2186 sheet: -0.81 (0.21), residues: 600 loop : -0.69 (0.16), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 37 HIS 0.008 0.001 HIS Y 204 PHE 0.034 0.001 PHE E 107 TYR 0.015 0.001 TYR J 102 ARG 0.006 0.000 ARG T 199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 481 time to evaluate : 4.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 95 ILE cc_start: 0.9054 (tt) cc_final: 0.8844 (tt) REVERT: D 61 MET cc_start: 0.7122 (ppp) cc_final: 0.6776 (ppp) REVERT: D 118 LEU cc_start: 0.8220 (mt) cc_final: 0.7744 (mt) REVERT: D 123 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6992 (mm) REVERT: E 61 MET cc_start: 0.7051 (mmt) cc_final: 0.6641 (mmm) REVERT: E 87 ASN cc_start: 0.7637 (m-40) cc_final: 0.6977 (t0) REVERT: E 95 ILE cc_start: 0.8770 (tp) cc_final: 0.8439 (tp) REVERT: F 81 MET cc_start: 0.7593 (ttp) cc_final: 0.7277 (ttp) REVERT: G 82 PHE cc_start: 0.8030 (m-10) cc_final: 0.7489 (m-10) REVERT: H 61 MET cc_start: 0.7664 (mmm) cc_final: 0.6971 (tpp) REVERT: I 61 MET cc_start: 0.7578 (mmt) cc_final: 0.7317 (mmm) REVERT: I 82 PHE cc_start: 0.7704 (m-80) cc_final: 0.7396 (m-10) REVERT: J 56 LEU cc_start: 0.6517 (tt) cc_final: 0.6214 (mt) REVERT: J 95 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7617 (mp) REVERT: P 66 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8142 (pm20) REVERT: P 83 GLN cc_start: 0.8050 (pp30) cc_final: 0.7754 (pp30) REVERT: Q 19 TYR cc_start: 0.8715 (t80) cc_final: 0.8513 (t80) REVERT: R 117 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: S 68 MET cc_start: 0.7956 (ttp) cc_final: 0.7446 (tmm) REVERT: S 164 ASP cc_start: 0.7339 (m-30) cc_final: 0.6833 (t0) REVERT: S 220 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7611 (mm) REVERT: T 149 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7394 (pt0) REVERT: T 237 ASP cc_start: 0.7084 (m-30) cc_final: 0.6853 (m-30) REVERT: T 411 GLU cc_start: 0.7654 (pm20) cc_final: 0.7377 (mp0) REVERT: T 440 LYS cc_start: 0.8379 (ttpt) cc_final: 0.7963 (ttmt) REVERT: T 487 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7858 (mtmt) REVERT: T 496 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7974 (mtt90) REVERT: T 522 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6653 (mp0) REVERT: T 549 HIS cc_start: 0.6915 (OUTLIER) cc_final: 0.6556 (t70) REVERT: T 555 ARG cc_start: 0.7674 (mtt-85) cc_final: 0.7335 (mmt90) REVERT: V 50 LYS cc_start: 0.7739 (tppt) cc_final: 0.7413 (tptt) REVERT: V 357 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8952 (tp) REVERT: V 429 ARG cc_start: 0.8136 (mtt-85) cc_final: 0.7672 (mtt-85) REVERT: Y 51 ARG cc_start: 0.8283 (ttm110) cc_final: 0.8030 (ttp-110) REVERT: Y 409 ASP cc_start: 0.7815 (m-30) cc_final: 0.7573 (m-30) REVERT: Y 441 ARG cc_start: 0.7936 (mmt-90) cc_final: 0.7620 (mpt-90) REVERT: Y 528 ASP cc_start: 0.6710 (p0) cc_final: 0.6371 (p0) REVERT: Z 429 ASP cc_start: 0.6865 (m-30) cc_final: 0.6541 (m-30) REVERT: Z 542 ASP cc_start: 0.6384 (OUTLIER) cc_final: 0.6079 (p0) outliers start: 126 outliers final: 66 residues processed: 561 average time/residue: 1.2801 time to fit residues: 878.6978 Evaluate side-chains 505 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 427 time to evaluate : 3.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 69 LYS Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 118 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 117 SER Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 353 ASP Chi-restraints excluded: chain T residue 487 LYS Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 522 GLU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 251 LYS Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 411 GLU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 531 VAL Chi-restraints excluded: chain Z residue 41 SER Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 415 ASP Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 542 ASP Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 143 optimal weight: 1.9990 chunk 384 optimal weight: 0.0980 chunk 84 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 chunk 105 optimal weight: 0.0980 chunk 427 optimal weight: 5.9990 chunk 355 optimal weight: 0.9990 chunk 198 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 98 GLN E 94 ASN P 66 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 461 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 414 GLN Y 198 ASN Y 414 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 34412 Z= 0.166 Angle : 0.540 10.237 46638 Z= 0.273 Chirality : 0.042 0.276 5519 Planarity : 0.004 0.053 5997 Dihedral : 6.017 102.375 4921 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.54 % Favored : 96.28 % Rotamer: Outliers : 3.42 % Allowed : 19.92 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.54 (0.13), residues: 4461 helix: 0.08 (0.11), residues: 2177 sheet: -0.74 (0.21), residues: 603 loop : -0.58 (0.16), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 37 HIS 0.006 0.001 HIS U 61 PHE 0.035 0.001 PHE E 107 TYR 0.013 0.001 TYR J 102 ARG 0.007 0.000 ARG T 479 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 448 time to evaluate : 3.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 ILE cc_start: 0.9072 (tt) cc_final: 0.8844 (tt) REVERT: C 109 LEU cc_start: 0.8645 (mt) cc_final: 0.8346 (mp) REVERT: D 61 MET cc_start: 0.7121 (ppp) cc_final: 0.6794 (ppp) REVERT: D 118 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7715 (mt) REVERT: D 123 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6910 (mm) REVERT: E 61 MET cc_start: 0.7111 (mmt) cc_final: 0.6722 (mmm) REVERT: E 87 ASN cc_start: 0.7542 (m-40) cc_final: 0.6941 (t0) REVERT: E 95 ILE cc_start: 0.8808 (tp) cc_final: 0.8503 (tp) REVERT: G 82 PHE cc_start: 0.7929 (m-10) cc_final: 0.7415 (m-10) REVERT: H 61 MET cc_start: 0.7654 (mmm) cc_final: 0.6959 (tpp) REVERT: H 119 LEU cc_start: 0.6171 (pt) cc_final: 0.5739 (mm) REVERT: J 56 LEU cc_start: 0.6564 (tt) cc_final: 0.6258 (mt) REVERT: P 83 GLN cc_start: 0.7972 (pp30) cc_final: 0.7694 (pp30) REVERT: P 112 SER cc_start: 0.3979 (OUTLIER) cc_final: 0.3745 (t) REVERT: Q 19 TYR cc_start: 0.8712 (t80) cc_final: 0.8482 (t80) REVERT: Q 72 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7676 (p) REVERT: S 68 MET cc_start: 0.7942 (ttp) cc_final: 0.7432 (tmm) REVERT: S 164 ASP cc_start: 0.7300 (m-30) cc_final: 0.6763 (t0) REVERT: S 220 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7560 (mm) REVERT: T 149 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7289 (pt0) REVERT: T 237 ASP cc_start: 0.7032 (m-30) cc_final: 0.6800 (m-30) REVERT: T 411 GLU cc_start: 0.7632 (pm20) cc_final: 0.7363 (mp0) REVERT: T 440 LYS cc_start: 0.8350 (ttpt) cc_final: 0.7931 (ttmt) REVERT: T 522 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6762 (mp0) REVERT: T 549 HIS cc_start: 0.6923 (OUTLIER) cc_final: 0.6448 (t70) REVERT: T 555 ARG cc_start: 0.7658 (mtt-85) cc_final: 0.7334 (mmt90) REVERT: U 515 GLN cc_start: 0.7963 (mp10) cc_final: 0.7605 (mp10) REVERT: V 50 LYS cc_start: 0.7731 (tppt) cc_final: 0.7397 (tptt) REVERT: V 357 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8962 (tp) REVERT: X 440 GLN cc_start: 0.8464 (mt0) cc_final: 0.8228 (mt0) REVERT: Y 51 ARG cc_start: 0.8266 (ttm110) cc_final: 0.8061 (ttp-110) REVERT: Y 123 ASN cc_start: 0.7924 (t0) cc_final: 0.7707 (t0) REVERT: Y 441 ARG cc_start: 0.7857 (mmt-90) cc_final: 0.7505 (mpt-90) REVERT: Y 528 ASP cc_start: 0.6630 (p0) cc_final: 0.6293 (p0) REVERT: Y 548 ASP cc_start: 0.8090 (t0) cc_final: 0.7764 (t0) REVERT: Z 429 ASP cc_start: 0.6999 (m-30) cc_final: 0.6665 (m-30) outliers start: 122 outliers final: 58 residues processed: 537 average time/residue: 1.2269 time to fit residues: 812.5024 Evaluate side-chains 491 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 424 time to evaluate : 3.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 112 SER Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 522 GLU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 360 ARG Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 411 GLU Chi-restraints excluded: chain V residue 509 LEU Chi-restraints excluded: chain V residue 512 VAL Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Z residue 41 SER Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 415 ASP Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 559 VAL Chi-restraints excluded: chain Z residue 573 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 412 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 243 optimal weight: 3.9990 chunk 312 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 359 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 426 optimal weight: 0.9990 chunk 266 optimal weight: 0.0470 chunk 259 optimal weight: 0.0970 chunk 196 optimal weight: 0.3980 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 98 GLN B 98 GLN E 94 ASN H 98 GLN I 98 GLN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 219 GLN V 461 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 414 GLN Y 198 ASN Y 204 HIS Y 250 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34412 Z= 0.159 Angle : 0.539 12.047 46638 Z= 0.271 Chirality : 0.042 0.314 5519 Planarity : 0.004 0.052 5997 Dihedral : 5.850 96.555 4921 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.70 % Favored : 96.17 % Rotamer: Outliers : 2.92 % Allowed : 21.07 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.41 (0.13), residues: 4461 helix: 0.20 (0.12), residues: 2180 sheet: -0.71 (0.21), residues: 603 loop : -0.52 (0.16), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 37 HIS 0.004 0.001 HIS U 61 PHE 0.037 0.001 PHE E 107 TYR 0.018 0.001 TYR E 102 ARG 0.007 0.000 ARG Z 435 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 450 time to evaluate : 3.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 LYS cc_start: 0.7267 (mttt) cc_final: 0.7029 (mmtt) REVERT: C 95 ILE cc_start: 0.8991 (tt) cc_final: 0.8744 (tt) REVERT: D 61 MET cc_start: 0.7147 (ppp) cc_final: 0.6785 (ppp) REVERT: D 95 ILE cc_start: 0.8107 (tp) cc_final: 0.7771 (tp) REVERT: D 118 LEU cc_start: 0.8126 (mt) cc_final: 0.7692 (mt) REVERT: E 61 MET cc_start: 0.7089 (mmt) cc_final: 0.6791 (mmm) REVERT: E 87 ASN cc_start: 0.7570 (m-40) cc_final: 0.6983 (t0) REVERT: E 95 ILE cc_start: 0.8895 (tp) cc_final: 0.8574 (tp) REVERT: H 61 MET cc_start: 0.7637 (mmm) cc_final: 0.6951 (tpp) REVERT: H 119 LEU cc_start: 0.6086 (pt) cc_final: 0.5695 (mm) REVERT: I 61 MET cc_start: 0.7329 (mmt) cc_final: 0.7067 (mmm) REVERT: J 56 LEU cc_start: 0.6543 (tt) cc_final: 0.6228 (mt) REVERT: P 83 GLN cc_start: 0.7960 (pp30) cc_final: 0.7657 (pp30) REVERT: P 142 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7380 (mt-10) REVERT: Q 19 TYR cc_start: 0.8730 (t80) cc_final: 0.8478 (t80) REVERT: Q 72 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7705 (p) REVERT: S 68 MET cc_start: 0.7918 (ttp) cc_final: 0.7404 (tmm) REVERT: S 164 ASP cc_start: 0.7282 (m-30) cc_final: 0.6746 (t0) REVERT: S 220 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7625 (mm) REVERT: T 237 ASP cc_start: 0.7021 (m-30) cc_final: 0.6804 (m-30) REVERT: T 411 GLU cc_start: 0.7630 (pm20) cc_final: 0.7405 (mp0) REVERT: T 440 LYS cc_start: 0.8363 (ttpt) cc_final: 0.7936 (ttmt) REVERT: T 549 HIS cc_start: 0.6936 (OUTLIER) cc_final: 0.6453 (t70) REVERT: T 555 ARG cc_start: 0.7667 (mtt-85) cc_final: 0.7330 (mmt90) REVERT: V 50 LYS cc_start: 0.7722 (tppt) cc_final: 0.7412 (tptt) REVERT: V 357 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8964 (tp) REVERT: V 559 LEU cc_start: 0.8382 (mt) cc_final: 0.8177 (mt) REVERT: X 440 GLN cc_start: 0.8451 (mt0) cc_final: 0.8216 (mt0) REVERT: Y 123 ASN cc_start: 0.7908 (t0) cc_final: 0.7691 (t0) REVERT: Y 441 ARG cc_start: 0.7826 (mmt-90) cc_final: 0.7479 (mpt-90) REVERT: Z 429 ASP cc_start: 0.6947 (m-30) cc_final: 0.6618 (m-30) REVERT: Z 573 LYS cc_start: 0.6052 (OUTLIER) cc_final: 0.5514 (mmpt) outliers start: 104 outliers final: 62 residues processed: 528 average time/residue: 1.1996 time to fit residues: 782.5386 Evaluate side-chains 482 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 415 time to evaluate : 4.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 112 SER Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 117 SER Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 360 ARG Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 411 GLU Chi-restraints excluded: chain V residue 512 VAL Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 198 ASN Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 417 ILE Chi-restraints excluded: chain Z residue 41 SER Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 140 ILE Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 559 VAL Chi-restraints excluded: chain Z residue 573 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 263 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 254 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 270 optimal weight: 2.9990 chunk 290 optimal weight: 0.7980 chunk 210 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 334 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 98 GLN B 98 GLN C 98 GLN E 94 ASN J 98 GLN P 71 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 461 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 549 HIS X 414 GLN Y 198 ASN Y 414 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34412 Z= 0.200 Angle : 0.567 11.006 46638 Z= 0.283 Chirality : 0.043 0.343 5519 Planarity : 0.004 0.053 5997 Dihedral : 5.910 94.457 4921 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.65 % Favored : 96.14 % Rotamer: Outliers : 2.75 % Allowed : 21.83 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.13), residues: 4461 helix: 0.24 (0.12), residues: 2178 sheet: -0.70 (0.21), residues: 614 loop : -0.48 (0.16), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 37 HIS 0.004 0.001 HIS U 61 PHE 0.039 0.001 PHE E 107 TYR 0.022 0.001 TYR E 102 ARG 0.007 0.000 ARG X 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 432 time to evaluate : 3.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 LYS cc_start: 0.7307 (mttt) cc_final: 0.7021 (mmtt) REVERT: C 95 ILE cc_start: 0.9001 (tt) cc_final: 0.8746 (tt) REVERT: D 61 MET cc_start: 0.7156 (ppp) cc_final: 0.6792 (ppp) REVERT: D 95 ILE cc_start: 0.8107 (tp) cc_final: 0.7767 (tp) REVERT: D 118 LEU cc_start: 0.8183 (mt) cc_final: 0.7823 (mt) REVERT: E 87 ASN cc_start: 0.7577 (m-40) cc_final: 0.6968 (t0) REVERT: E 95 ILE cc_start: 0.8969 (tp) cc_final: 0.8652 (tp) REVERT: H 60 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7530 (mttm) REVERT: H 61 MET cc_start: 0.7660 (mmm) cc_final: 0.6973 (tpp) REVERT: H 119 LEU cc_start: 0.6100 (pt) cc_final: 0.5683 (mm) REVERT: I 61 MET cc_start: 0.7324 (mmt) cc_final: 0.7071 (mmm) REVERT: J 56 LEU cc_start: 0.6537 (tt) cc_final: 0.6246 (mt) REVERT: P 83 GLN cc_start: 0.8070 (pp30) cc_final: 0.7777 (pp30) REVERT: P 142 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7356 (mt-10) REVERT: Q 19 TYR cc_start: 0.8693 (t80) cc_final: 0.8474 (t80) REVERT: S 68 MET cc_start: 0.7944 (ttp) cc_final: 0.7451 (tmm) REVERT: S 164 ASP cc_start: 0.7326 (m-30) cc_final: 0.6835 (t0) REVERT: S 220 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7638 (mm) REVERT: S 274 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8266 (mmt) REVERT: T 237 ASP cc_start: 0.7053 (m-30) cc_final: 0.6820 (m-30) REVERT: T 411 GLU cc_start: 0.7570 (pm20) cc_final: 0.7362 (mp0) REVERT: T 427 VAL cc_start: 0.8638 (p) cc_final: 0.8363 (p) REVERT: T 440 LYS cc_start: 0.8372 (ttpt) cc_final: 0.7945 (ttmt) REVERT: T 549 HIS cc_start: 0.6946 (OUTLIER) cc_final: 0.6584 (t70) REVERT: T 555 ARG cc_start: 0.7632 (mtt-85) cc_final: 0.7265 (mmt90) REVERT: V 50 LYS cc_start: 0.7743 (tppt) cc_final: 0.7443 (tptt) REVERT: V 357 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8972 (tp) REVERT: V 518 VAL cc_start: 0.8495 (p) cc_final: 0.8118 (t) REVERT: X 440 GLN cc_start: 0.8467 (mt0) cc_final: 0.8237 (mt0) REVERT: Y 441 ARG cc_start: 0.7902 (mmt-90) cc_final: 0.7554 (mpt-90) REVERT: Y 548 ASP cc_start: 0.8058 (t0) cc_final: 0.7744 (t0) REVERT: Z 429 ASP cc_start: 0.6916 (m-30) cc_final: 0.6590 (m-30) REVERT: Z 542 ASP cc_start: 0.6288 (OUTLIER) cc_final: 0.5934 (p0) REVERT: Z 573 LYS cc_start: 0.6093 (OUTLIER) cc_final: 0.5552 (mmpt) outliers start: 98 outliers final: 67 residues processed: 499 average time/residue: 1.2161 time to fit residues: 754.9826 Evaluate side-chains 488 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 415 time to evaluate : 3.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 112 SER Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 117 SER Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 274 MET Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 411 GLU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 198 ASN Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Z residue 41 SER Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 158 GLU Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 417 ILE Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 542 ASP Chi-restraints excluded: chain Z residue 559 VAL Chi-restraints excluded: chain Z residue 573 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 387 optimal weight: 9.9990 chunk 408 optimal weight: 3.9990 chunk 372 optimal weight: 0.8980 chunk 396 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 172 optimal weight: 0.0970 chunk 311 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 358 optimal weight: 0.9980 chunk 375 optimal weight: 0.0060 chunk 395 optimal weight: 0.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 98 GLN B 98 GLN C 98 GLN E 94 ASN H 98 GLN P 66 GLN P 71 GLN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 64 GLN V 219 GLN V 461 GLN V 549 HIS ** X 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 414 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34412 Z= 0.167 Angle : 0.557 12.299 46638 Z= 0.277 Chirality : 0.043 0.330 5519 Planarity : 0.004 0.052 5997 Dihedral : 5.783 89.266 4921 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.79 % Favored : 96.08 % Rotamer: Outliers : 2.78 % Allowed : 22.25 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.13), residues: 4461 helix: 0.27 (0.12), residues: 2190 sheet: -0.66 (0.21), residues: 615 loop : -0.41 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 37 HIS 0.003 0.001 HIS S 237 PHE 0.042 0.001 PHE B 82 TYR 0.020 0.001 TYR E 102 ARG 0.007 0.000 ARG X 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 431 time to evaluate : 3.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 LYS cc_start: 0.7352 (mttt) cc_final: 0.7090 (mmtt) REVERT: C 95 ILE cc_start: 0.8954 (tt) cc_final: 0.8663 (tt) REVERT: D 61 MET cc_start: 0.7172 (ppp) cc_final: 0.6782 (ppp) REVERT: D 95 ILE cc_start: 0.8116 (tp) cc_final: 0.7761 (tp) REVERT: D 118 LEU cc_start: 0.8067 (mt) cc_final: 0.7716 (mt) REVERT: E 87 ASN cc_start: 0.7602 (m-40) cc_final: 0.6978 (t0) REVERT: E 95 ILE cc_start: 0.8931 (tp) cc_final: 0.8635 (tp) REVERT: H 60 LYS cc_start: 0.8031 (mtpt) cc_final: 0.7510 (mttm) REVERT: H 61 MET cc_start: 0.7655 (mmm) cc_final: 0.6976 (tpp) REVERT: H 119 LEU cc_start: 0.6218 (pt) cc_final: 0.5795 (mm) REVERT: I 61 MET cc_start: 0.7326 (mmt) cc_final: 0.7073 (mmm) REVERT: J 56 LEU cc_start: 0.6530 (tt) cc_final: 0.6241 (mt) REVERT: P 83 GLN cc_start: 0.8076 (pp30) cc_final: 0.7751 (pp30) REVERT: P 142 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7313 (mt-10) REVERT: Q 19 TYR cc_start: 0.8683 (t80) cc_final: 0.8438 (t80) REVERT: S 68 MET cc_start: 0.7938 (ttp) cc_final: 0.7456 (tmm) REVERT: S 117 SER cc_start: 0.8747 (OUTLIER) cc_final: 0.8388 (p) REVERT: S 164 ASP cc_start: 0.7283 (m-30) cc_final: 0.6773 (t0) REVERT: S 220 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7704 (mm) REVERT: T 237 ASP cc_start: 0.7010 (m-30) cc_final: 0.6793 (m-30) REVERT: T 411 GLU cc_start: 0.7559 (pm20) cc_final: 0.7346 (mp0) REVERT: T 427 VAL cc_start: 0.8511 (p) cc_final: 0.8246 (p) REVERT: T 440 LYS cc_start: 0.8332 (ttpt) cc_final: 0.7902 (ttmt) REVERT: T 471 GLN cc_start: 0.8233 (tp40) cc_final: 0.7978 (tp40) REVERT: T 549 HIS cc_start: 0.6920 (OUTLIER) cc_final: 0.6413 (t70) REVERT: T 555 ARG cc_start: 0.7638 (mtt-85) cc_final: 0.7270 (mmt90) REVERT: V 50 LYS cc_start: 0.7638 (tppt) cc_final: 0.7329 (tptt) REVERT: V 357 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8940 (tp) REVERT: V 518 VAL cc_start: 0.8511 (p) cc_final: 0.8152 (t) REVERT: X 440 GLN cc_start: 0.8463 (mt0) cc_final: 0.8216 (mt0) REVERT: X 531 VAL cc_start: 0.7588 (t) cc_final: 0.7091 (p) REVERT: Y 430 LYS cc_start: 0.7625 (mttt) cc_final: 0.7310 (mtmm) REVERT: Y 441 ARG cc_start: 0.7837 (mmt-90) cc_final: 0.7504 (mpt-90) REVERT: Y 548 ASP cc_start: 0.8034 (t0) cc_final: 0.7709 (t0) REVERT: Z 429 ASP cc_start: 0.6904 (m-30) cc_final: 0.6638 (m-30) REVERT: Z 542 ASP cc_start: 0.6407 (OUTLIER) cc_final: 0.6065 (p0) REVERT: Z 573 LYS cc_start: 0.5995 (OUTLIER) cc_final: 0.5451 (mmpt) outliers start: 99 outliers final: 60 residues processed: 500 average time/residue: 1.2430 time to fit residues: 763.3820 Evaluate side-chains 483 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 417 time to evaluate : 3.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 69 LYS Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 117 SER Chi-restraints excluded: chain S residue 153 ILE Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 411 GLU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 41 SER Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 158 GLU Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 417 ILE Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 542 ASP Chi-restraints excluded: chain Z residue 559 VAL Chi-restraints excluded: chain Z residue 573 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 260 optimal weight: 0.7980 chunk 419 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 199 optimal weight: 0.6980 chunk 291 optimal weight: 0.1980 chunk 440 optimal weight: 2.9990 chunk 405 optimal weight: 2.9990 chunk 350 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 270 optimal weight: 4.9990 chunk 215 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 A 98 GLN B 98 GLN C 98 GLN E 94 ASN H 98 GLN P 71 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 73 ASN R 178 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 461 GLN V 549 HIS ** X 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 414 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34412 Z= 0.202 Angle : 0.583 12.444 46638 Z= 0.290 Chirality : 0.043 0.355 5519 Planarity : 0.004 0.053 5997 Dihedral : 5.868 87.259 4921 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.83 % Favored : 95.99 % Rotamer: Outliers : 2.24 % Allowed : 23.18 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.13), residues: 4461 helix: 0.25 (0.12), residues: 2196 sheet: -0.66 (0.21), residues: 615 loop : -0.40 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 37 HIS 0.004 0.001 HIS U 61 PHE 0.043 0.001 PHE B 82 TYR 0.018 0.001 TYR E 102 ARG 0.009 0.000 ARG S 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 426 time to evaluate : 3.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 LYS cc_start: 0.7326 (mttt) cc_final: 0.7047 (mmtt) REVERT: C 81 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8160 (mmm) REVERT: D 61 MET cc_start: 0.7211 (ppp) cc_final: 0.6788 (ppp) REVERT: D 95 ILE cc_start: 0.8105 (tp) cc_final: 0.7732 (tp) REVERT: D 118 LEU cc_start: 0.8036 (mt) cc_final: 0.7703 (mt) REVERT: E 87 ASN cc_start: 0.7627 (m-40) cc_final: 0.6966 (t0) REVERT: E 95 ILE cc_start: 0.9011 (tp) cc_final: 0.8710 (tp) REVERT: F 107 PHE cc_start: 0.7818 (t80) cc_final: 0.7607 (t80) REVERT: G 109 LEU cc_start: 0.8260 (mt) cc_final: 0.8013 (mt) REVERT: H 60 LYS cc_start: 0.7964 (mtpt) cc_final: 0.7412 (mttt) REVERT: H 61 MET cc_start: 0.7652 (mmm) cc_final: 0.6989 (tpp) REVERT: H 119 LEU cc_start: 0.6212 (pt) cc_final: 0.5772 (mm) REVERT: I 61 MET cc_start: 0.7339 (mmt) cc_final: 0.7074 (mmm) REVERT: J 56 LEU cc_start: 0.6594 (tt) cc_final: 0.6320 (mt) REVERT: J 107 PHE cc_start: 0.7514 (t80) cc_final: 0.7151 (t80) REVERT: P 83 GLN cc_start: 0.8043 (pp30) cc_final: 0.7706 (pp30) REVERT: P 142 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7305 (mt-10) REVERT: Q 19 TYR cc_start: 0.8712 (t80) cc_final: 0.8486 (t80) REVERT: S 68 MET cc_start: 0.7950 (ttp) cc_final: 0.7481 (tmm) REVERT: S 164 ASP cc_start: 0.7341 (m-30) cc_final: 0.6853 (t0) REVERT: T 237 ASP cc_start: 0.7035 (m-30) cc_final: 0.6818 (m-30) REVERT: T 411 GLU cc_start: 0.7569 (pm20) cc_final: 0.7358 (mp0) REVERT: T 427 VAL cc_start: 0.8539 (p) cc_final: 0.8287 (p) REVERT: T 440 LYS cc_start: 0.8384 (ttpt) cc_final: 0.7964 (ttmt) REVERT: T 549 HIS cc_start: 0.6974 (OUTLIER) cc_final: 0.6580 (t70) REVERT: T 555 ARG cc_start: 0.7649 (mtt-85) cc_final: 0.7283 (mmt90) REVERT: U 357 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.8951 (tp) REVERT: U 515 GLN cc_start: 0.7952 (mp10) cc_final: 0.7695 (mp10) REVERT: V 50 LYS cc_start: 0.7707 (tppt) cc_final: 0.7384 (tptt) REVERT: V 357 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8969 (tp) REVERT: V 518 VAL cc_start: 0.8638 (p) cc_final: 0.8312 (t) REVERT: X 440 GLN cc_start: 0.8477 (mt0) cc_final: 0.8265 (mt0) REVERT: Y 430 LYS cc_start: 0.7621 (mttt) cc_final: 0.7284 (mtmm) REVERT: Y 441 ARG cc_start: 0.7929 (mmt-90) cc_final: 0.7650 (mpt-90) REVERT: Z 429 ASP cc_start: 0.6914 (m-30) cc_final: 0.6683 (m-30) REVERT: Z 542 ASP cc_start: 0.6392 (OUTLIER) cc_final: 0.6029 (p0) REVERT: Z 573 LYS cc_start: 0.6061 (OUTLIER) cc_final: 0.5522 (mmpt) outliers start: 80 outliers final: 62 residues processed: 481 average time/residue: 1.2469 time to fit residues: 738.5490 Evaluate side-chains 478 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 410 time to evaluate : 3.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 69 LYS Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 112 SER Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 117 SER Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 353 ASP Chi-restraints excluded: chain T residue 475 GLU Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 411 GLU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 41 SER Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 417 ILE Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 542 ASP Chi-restraints excluded: chain Z residue 559 VAL Chi-restraints excluded: chain Z residue 573 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 278 optimal weight: 3.9990 chunk 373 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 323 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 351 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 360 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 98 GLN B 98 GLN C 98 GLN E 94 ASN P 66 GLN P 71 GLN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 461 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 549 HIS X 414 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.137485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.106304 restraints weight = 48245.836| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.71 r_work: 0.3109 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 34412 Z= 0.231 Angle : 0.592 12.141 46638 Z= 0.295 Chirality : 0.044 0.356 5519 Planarity : 0.004 0.053 5997 Dihedral : 5.954 87.630 4921 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.97 % Favored : 95.83 % Rotamer: Outliers : 2.47 % Allowed : 22.87 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 4461 helix: 0.23 (0.11), residues: 2196 sheet: -0.59 (0.21), residues: 592 loop : -0.43 (0.16), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP V 73 HIS 0.004 0.001 HIS U 61 PHE 0.043 0.002 PHE B 82 TYR 0.019 0.001 TYR E 102 ARG 0.007 0.000 ARG X 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13645.82 seconds wall clock time: 241 minutes 44.82 seconds (14504.82 seconds total)