Starting phenix.real_space_refine on Fri Mar 22 14:44:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdp_4826/03_2024/6rdp_4826_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdp_4826/03_2024/6rdp_4826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdp_4826/03_2024/6rdp_4826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdp_4826/03_2024/6rdp_4826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdp_4826/03_2024/6rdp_4826_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdp_4826/03_2024/6rdp_4826_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 GLU 111": "OE1" <-> "OE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "I GLU 111": "OE1" <-> "OE2" Residue "P PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 81": "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 ASP 25": "OD1" <-> "OD2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 95": "OD1" <-> "OD2" Residue "R GLU 117": "OE1" <-> "OE2" Residue "R ASP 156": "OD1" <-> "OD2" Residue "R ASP 174": "OD1" <-> "OD2" Residue "R PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S GLU 131": "OE1" <-> "OE2" Residue "S GLU 133": "OE1" <-> "OE2" Residue "S ASP 136": "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 PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 180": "OE1" <-> "OE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 214": "OD1" <-> "OD2" Residue "S ASP 232": "OD1" <-> "OD2" Residue "S GLU 238": "OE1" <-> "OE2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 303": "OE1" <-> "OE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ASP 135": "OD1" <-> "OD2" Residue "T ASP 142": "OD1" <-> "OD2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ASP 165": "OD1" <-> "OD2" 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 TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 294": "OD1" <-> "OD2" Residue "T TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 325": "OD1" <-> "OD2" Residue "T ASP 353": "OD1" <-> "OD2" Residue "T ASP 403": "OD1" <-> "OD2" Residue "T GLU 409": "OE1" <-> "OE2" Residue "T GLU 411": "OE1" <-> "OE2" 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 GLU 482": "OE1" <-> "OE2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 547": "OD1" <-> "OD2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 74": "OE1" <-> "OE2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 112": "OD1" <-> "OD2" Residue "U TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ASP 165": "OD1" <-> "OD2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 221": "OE1" <-> "OE2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ASP 237": "OD1" <-> "OD2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 311": "OE1" <-> "OE2" Residue "U PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U ASP 325": "OD1" <-> "OD2" 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 GLU 409": "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 GLU 455": "OE1" <-> "OE2" Residue "U PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 547": "OD1" <-> "OD2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 72": "OE1" <-> "OE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 142": "OD1" <-> "OD2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V ASP 210": "OD1" <-> "OD2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 259": "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 PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 429": "NH1" <-> "NH2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V GLU 455": "OE1" <-> "OE2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 465": "OD1" <-> "OD2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V GLU 521": "OE1" <-> "OE2" Residue "V ASP 547": "OD1" <-> "OD2" Residue "V GLU 553": "OE1" <-> "OE2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X GLU 55": "OE1" <-> "OE2" Residue "X ASP 82": "OD1" <-> "OD2" Residue "X GLU 146": "OE1" <-> "OE2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 152": "OE1" <-> "OE2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "X PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 215": "OE1" <-> "OE2" Residue "X ARG 218": "NH1" <-> "NH2" Residue "X GLU 219": "OE1" <-> "OE2" Residue "X ARG 225": "NH1" <-> "NH2" Residue "X GLU 226": "OE1" <-> "OE2" Residue "X GLU 238": "OE1" <-> "OE2" Residue "X ARG 239": "NH1" <-> "NH2" Residue "X TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 253": "OE1" <-> "OE2" Residue "X PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 285": "OD1" <-> "OD2" Residue "X GLU 296": "OE1" <-> "OE2" 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 415": "OD1" <-> "OD2" Residue "X ASP 429": "OD1" <-> "OD2" Residue "X GLU 451": "OE1" <-> "OE2" 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 GLU 511": "OE1" <-> "OE2" Residue "X GLU 520": "OE1" <-> "OE2" Residue "X ASP 528": "OD1" <-> "OD2" Residue "X GLU 533": "OE1" <-> "OE2" Residue "X ASP 548": "OD1" <-> "OD2" Residue "Y TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ASP 94": "OD1" <-> "OD2" Residue "Y ASP 104": "OD1" <-> "OD2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y ASP 139": "OD1" <-> "OD2" Residue "Y ARG 145": "NH1" <-> "NH2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 215": "OE1" <-> "OE2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y GLU 270": "OE1" <-> "OE2" Residue "Y TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 348": "OD1" <-> "OD2" Residue "Y ASP 359": "OD1" <-> "OD2" Residue "Y ARG 366": "NH1" <-> "NH2" Residue "Y TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y ASP 423": "OD1" <-> "OD2" Residue "Y PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 479": "OD1" <-> "OD2" Residue "Y PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 528": "OD1" <-> "OD2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 552": "OE1" <-> "OE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "Z GLU 66": "OE1" <-> "OE2" 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 ASP 130": "OD1" <-> "OD2" Residue "Z GLU 156": "OE1" <-> "OE2" Residue "Z PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 216": "NH1" <-> "NH2" Residue "Z ARG 258": "NH1" <-> "NH2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z ARG 289": "NH1" <-> "NH2" Residue "Z GLU 323": "OE1" <-> "OE2" Residue "Z PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 378": "OD1" <-> "OD2" Residue "Z ASP 381": "OD1" <-> "OD2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z ASP 409": "OD1" <-> "OD2" Residue "Z TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 435": "NH1" <-> "NH2" Residue "Z ARG 437": "NH1" <-> "NH2" Residue "Z TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 480": "OD1" <-> "OD2" Residue "Z GLU 483": "OE1" <-> "OE2" Residue "Z ASP 500": "OD1" <-> "OD2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z ASP 513": "OD1" <-> "OD2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 552": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 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: 17.43, per 1000 atoms: 0.51 Number of scatterers: 33891 At special positions: 0 Unit cell: (159.003, 134.784, 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: 14.45 Conformation dependent library (CDL) restraints added in 6.6 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: 162 helices and 26 sheets defined 46.0% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.82 Creating SS restraints... Processing helix chain 'A' and resid 56 through 91 removed outlier: 4.684A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 98 through 125 removed outlier: 3.570A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 91 removed outlier: 4.387A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 123 removed outlier: 3.948A pdb=" N VAL B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 89 removed outlier: 3.787A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 126 removed outlier: 3.754A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 67 through 91 removed outlier: 3.663A pdb=" N ALA D 70 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU D 78 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY D 79 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU D 85 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG D 91 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 126 removed outlier: 3.920A pdb=" N GLY D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 89 removed outlier: 4.751A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 125 removed outlier: 3.778A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 65 Processing helix chain 'F' and resid 68 through 91 removed outlier: 3.595A pdb=" N LEU F 71 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL F 74 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY F 77 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU F 85 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY F 88 " --> pdb=" O LEU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 123 removed outlier: 5.558A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU F 104 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU F 105 " --> pdb=" O TYR F 102 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU F 111 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 118 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU F 119 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL F 121 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE F 122 " --> pdb=" O LEU F 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 91 removed outlier: 4.443A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS G 66 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 123 removed outlier: 4.311A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 91 removed outlier: 3.855A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA H 70 " --> pdb=" O CYS H 66 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LEU H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA H 72 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 110 removed outlier: 3.665A pdb=" N LEU H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 125 removed outlier: 4.220A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 65 removed outlier: 3.829A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 91 removed outlier: 3.591A pdb=" N PHE I 82 " --> pdb=" O GLY I 79 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU I 85 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA I 89 " --> pdb=" O ILE I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 95 No H-bonds generated for 'chain 'I' and resid 93 through 95' Processing helix chain 'I' and resid 98 through 126 removed outlier: 3.699A pdb=" N SER I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 89 removed outlier: 4.210A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 95 No H-bonds generated for 'chain 'J' and resid 93 through 95' Processing helix chain 'J' and resid 98 through 108 removed outlier: 3.646A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 125 Processing helix chain 'P' and resid 51 through 57 removed outlier: 3.511A pdb=" N LEU P 56 " --> pdb=" O GLN P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 83 removed outlier: 3.574A pdb=" N PHE P 77 " --> pdb=" O GLU P 73 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS P 82 " --> pdb=" O ILE P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 92 removed outlier: 3.923A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 104 Processing helix chain 'P' and resid 118 through 127 removed outlier: 3.749A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 146 removed outlier: 4.050A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL P 137 " --> pdb=" O LEU P 134 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU P 143 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU P 146 " --> pdb=" O GLU P 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 30 removed outlier: 4.166A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 36 No H-bonds generated for 'chain 'Q' and resid 33 through 36' Processing helix chain 'Q' and resid 41 through 43 No H-bonds generated for 'chain 'Q' and resid 41 through 43' Processing helix chain 'R' and resid 30 through 40 removed outlier: 4.364A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 54 removed outlier: 3.725A pdb=" N TYR R 54 " --> pdb=" O PRO R 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 51 through 54' Processing helix chain 'R' and resid 152 through 154 No H-bonds generated for 'chain 'R' and resid 152 through 154' Processing helix chain 'R' and resid 159 through 167 removed outlier: 4.125A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 195 Processing helix chain 'S' and resid 40 through 72 removed outlier: 3.841A pdb=" N LYS S 44 " --> pdb=" O ASN S 40 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 78 No H-bonds generated for 'chain 'S' and resid 75 through 78' Processing helix chain 'S' and resid 81 through 89 removed outlier: 4.342A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 127 removed outlier: 3.617A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) 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 172 through 184 Processing helix chain 'S' and resid 228 through 230 No H-bonds generated for 'chain 'S' and resid 228 through 230' Processing helix chain 'S' and resid 239 through 312 removed outlier: 3.650A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN S 276 " --> pdb=" O SER S 272 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 137 No H-bonds generated for 'chain 'T' and resid 135 through 137' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 207 through 212 removed outlier: 3.708A pdb=" N LEU T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 231 through 246 removed outlier: 3.535A pdb=" N GLN T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 279 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 296 through 315 Proline residue: T 303 - end of helix removed outlier: 3.610A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 340 removed outlier: 3.816A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET T 337 " --> pdb=" O ALA T 333 " (cutoff:3.500A) Processing helix chain 'T' and resid 352 through 364 removed outlier: 4.207A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU T 357 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER T 359 " --> pdb=" O TYR T 356 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG T 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU T 362 " --> pdb=" O SER T 359 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU T 363 " --> pdb=" O ARG T 360 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 401 Processing helix chain 'T' and resid 410 through 414 removed outlier: 3.525A pdb=" N TYR T 414 " --> pdb=" O THR T 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 410 through 414' Processing helix chain 'T' and resid 431 through 433 No H-bonds generated for 'chain 'T' and resid 431 through 433' Processing helix chain 'T' and resid 437 through 460 removed outlier: 3.774A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL T 442 " --> pdb=" O GLY T 438 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY T 444 " --> pdb=" O LYS T 440 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N THR T 445 " --> pdb=" O GLN T 441 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN T 452 " --> pdb=" O LEU T 448 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG T 454 " --> pdb=" O LEU T 450 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA T 458 " --> pdb=" O ARG T 454 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 470 through 483 removed outlier: 3.949A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) Processing helix chain 'T' and resid 495 through 505 removed outlier: 3.563A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 514 through 526 removed outlier: 3.647A pdb=" N ILE T 517 " --> pdb=" O VAL T 514 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL T 518 " --> pdb=" O GLN T 515 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU T 521 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU T 522 " --> pdb=" O ALA T 519 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL T 524 " --> pdb=" O GLU T 521 " (cutoff:3.500A) Processing helix chain 'T' and resid 532 through 538 removed outlier: 3.551A pdb=" N LEU T 536 " --> pdb=" O VAL T 532 " (cutoff:3.500A) Processing helix chain 'T' and resid 544 through 553 removed outlier: 3.920A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA T 552 " --> pdb=" O ALA T 548 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 46 Processing helix chain 'U' and resid 59 through 63 Processing helix chain 'U' and resid 66 through 71 Processing helix chain 'U' and resid 135 through 137 No H-bonds generated for 'chain 'U' and resid 135 through 137' Processing helix chain 'U' and resid 207 through 212 Processing helix chain 'U' and resid 231 through 246 removed outlier: 3.749A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (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: 3.603A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 removed outlier: 3.734A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 354 through 364 removed outlier: 3.797A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG U 364 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 370 through 372 No H-bonds generated for 'chain 'U' and resid 370 through 372' Processing helix chain 'U' and resid 393 through 399 Processing helix chain 'U' and resid 410 through 414 Processing helix chain 'U' and resid 437 through 459 removed outlier: 4.000A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 484 Processing helix chain 'U' and resid 494 through 505 removed outlier: 3.570A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 517 through 527 removed outlier: 3.664A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 531 through 539 Processing helix chain 'U' and resid 544 through 553 Processing helix chain 'V' and resid 46 through 48 No H-bonds generated for 'chain 'V' and resid 46 through 48' Processing helix chain 'V' and resid 59 through 69 removed outlier: 3.973A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Proline residue: V 68 - end of helix Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 212 Processing helix chain 'V' and resid 231 through 247 removed outlier: 3.981A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 266 through 279 Processing helix chain 'V' and resid 281 through 283 No H-bonds generated for 'chain 'V' and resid 281 through 283' Processing helix chain 'V' and resid 296 through 315 Proline residue: V 303 - end of helix removed outlier: 3.733A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 340 Processing helix chain 'V' and resid 352 through 364 removed outlier: 4.118A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER V 359 " --> pdb=" O TYR V 356 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 4.167A 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 removed outlier: 3.998A pdb=" N TYR V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 410 through 414' Processing helix chain 'V' and resid 431 through 434 Processing helix chain 'V' and resid 439 through 455 removed outlier: 3.706A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU V 448 " --> pdb=" O GLY V 444 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 483 removed outlier: 3.681A pdb=" N GLU V 482 " --> pdb=" O ALA V 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 494 through 505 Processing helix chain 'V' and resid 514 through 525 removed outlier: 4.213A pdb=" N ILE V 517 " --> pdb=" O VAL V 514 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N VAL V 518 " --> pdb=" O GLN V 515 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA V 519 " --> pdb=" O ASP V 516 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU V 521 " --> pdb=" O VAL V 518 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU V 522 " --> pdb=" O ALA V 519 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA V 523 " --> pdb=" O ALA V 520 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE V 525 " --> pdb=" O GLU V 522 " (cutoff:3.500A) Processing helix chain 'V' and resid 531 through 539 Processing helix chain 'V' and resid 544 through 553 removed outlier: 4.168A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (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 203 removed outlier: 4.679A pdb=" N LYS X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA X 203 " --> pdb=" O ASN X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 229 Processing helix chain 'X' and resid 236 through 241 removed outlier: 4.675A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 255 through 274 removed outlier: 3.528A pdb=" N ARG X 260 " --> pdb=" O GLY X 256 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA X 262 " --> pdb=" O ARG X 258 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LEU X 263 " --> pdb=" O ALA X 259 " (cutoff:3.500A) removed outlier: 3.656A 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 324 removed outlier: 4.033A pdb=" N ARG X 324 " --> pdb=" O GLY X 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 349 through 357 removed outlier: 4.568A pdb=" N ALA X 356 " --> pdb=" O ALA X 352 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N HIS X 357 " --> pdb=" O THR X 353 " (cutoff:3.500A) Processing helix chain 'X' and resid 366 through 370 Processing helix chain 'X' and resid 389 through 392 No H-bonds generated for 'chain 'X' and resid 389 through 392' Processing helix chain 'X' and resid 394 through 420 removed outlier: 4.548A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE X 419 " --> pdb=" O ASP X 415 " (cutoff:3.500A) 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 Processing helix chain 'X' and resid 527 through 532 Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 165 through 170 Processing helix chain 'Y' and resid 189 through 200 Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 4.794A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 258 No H-bonds generated for 'chain 'Y' and resid 255 through 258' Processing helix chain 'Y' and resid 261 through 274 Processing helix chain 'Y' and resid 288 through 296 Processing helix chain 'Y' and resid 314 through 324 removed outlier: 4.256A pdb=" N ARG Y 324 " --> pdb=" O GLY Y 320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 349 through 357 removed outlier: 3.707A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N HIS Y 357 " --> pdb=" O THR Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 370 Processing helix chain 'Y' and resid 389 through 392 No H-bonds generated for 'chain 'Y' and resid 389 through 392' Processing helix chain 'Y' and resid 394 through 417 removed outlier: 3.902A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS Y 411 " --> pdb=" O LEU Y 407 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) Processing helix chain 'Y' and resid 429 through 443 Processing helix chain 'Y' and resid 463 through 474 Processing helix chain 'Y' and resid 483 through 486 Processing helix chain 'Y' and resid 492 through 507 removed outlier: 3.795A pdb=" N LYS Y 501 " --> pdb=" O GLU Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 527 through 532 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 230 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 3.571A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 274 removed outlier: 3.510A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.566A 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: 4.080A 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 371 removed outlier: 3.614A pdb=" N LEU Z 371 " --> pdb=" O SER Z 367 " (cutoff:3.500A) Processing helix chain 'Z' and resid 393 through 420 removed outlier: 3.963A pdb=" N LEU Z 413 " --> pdb=" O ASP Z 409 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN Z 414 " --> pdb=" O TYR Z 410 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE Z 419 " --> pdb=" O ASP Z 415 " (cutoff:3.500A) Processing helix chain 'Z' and resid 427 through 442 Processing helix chain 'Z' and resid 451 through 454 No H-bonds generated for 'chain 'Z' and resid 451 through 454' Processing helix chain 'Z' and resid 463 through 475 removed outlier: 3.615A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) Processing helix chain 'Z' and resid 483 through 486 Processing helix chain 'Z' and resid 492 through 507 removed outlier: 3.986A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 531 Processing sheet with id= A, first strand: chain 'Q' and resid 45 through 50 Processing sheet with id= B, first strand: chain 'R' and resid 97 through 100 removed outlier: 3.958A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'R' and resid 107 through 109 Processing sheet with id= D, first strand: chain 'S' and resid 203 through 211 removed outlier: 3.713A pdb=" N LYS S 204 " --> pdb=" O LYS S 196 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.461A 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: 6.680A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN T 121 " --> pdb=" O GLY T 128 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (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: 3.650A 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: 8.883A pdb=" N ILE T 286 " --> pdb=" O VAL T 255 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS T 257 " --> pdb=" O ILE T 286 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL T 288 " --> pdb=" O CYS T 257 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR T 259 " --> pdb=" O VAL T 288 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ALA T 290 " --> pdb=" O TYR T 259 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ALA T 261 " --> pdb=" O ALA T 290 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER T 376 " --> pdb=" O GLY T 320 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE T 322 " --> pdb=" O SER T 376 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) removed outlier: 6.677A 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: 6.587A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 5.874A 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: 8.682A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.618A 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 84 through 86 removed outlier: 3.804A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY V 128 " --> pdb=" O LEU V 120 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU V 122 " --> pdb=" O HIS V 126 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N HIS V 126 " --> pdb=" O LEU V 122 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N TYR V 98 " --> pdb=" O VAL V 87 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL V 87 " --> pdb=" O TYR V 98 " (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 removed outlier: 3.511A pdb=" N LEU V 222 " --> pdb=" O GLY V 404 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'V' and resid 285 through 290 removed outlier: 8.975A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE V 380 " --> pdb=" O TYR V 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'X' and resid 37 through 39 removed outlier: 6.550A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ARG X 51 " --> pdb=" O VAL X 40 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL X 40 " --> pdb=" O ARG X 51 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'X' and resid 110 through 113 Processing sheet with id= S, first strand: chain 'X' and resid 360 through 363 removed outlier: 7.481A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLY X 183 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL X 339 " --> pdb=" O GLY X 183 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE X 207 " --> pdb=" O LEU X 281 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N PHE X 283 " --> pdb=" O PHE X 207 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL X 209 " --> pdb=" O PHE X 283 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ASP X 285 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 7.272A 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: 6.429A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'Y' and resid 360 through 363 removed outlier: 7.478A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N GLY Y 183 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL Y 339 " --> pdb=" O GLY Y 183 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE Y 207 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N PHE Y 283 " --> pdb=" O PHE Y 207 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.161A 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: 6.428A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.733A 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: 8.328A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 3.554A 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 1411 hydrogen bonds defined for protein. 3882 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: 11.13 Time building geometry restraints manager: 15.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8056 1.33 - 1.45: 7063 1.45 - 1.58: 19072 1.58 - 1.70: 21 1.70 - 1.83: 200 Bond restraints: 34412 Sorted by residual: bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.86e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.76e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.452 -0.064 1.00e-02 1.00e+04 4.09e+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 3.53e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.45e+01 ... (remaining 34407 not shown) Histogram of bond angle deviations from ideal: 96.12 - 104.11: 509 104.11 - 112.11: 16686 112.11 - 120.10: 15430 120.10 - 128.10: 13846 128.10 - 136.09: 167 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 139.87 120.79 19.08 1.00e+00 1.00e+00 3.64e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 120.87 19.00 1.00e+00 1.00e+00 3.61e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 121.99 17.88 1.00e+00 1.00e+00 3.20e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 121.69 15.14 1.00e+00 1.00e+00 2.29e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 123.61 13.22 1.00e+00 1.00e+00 1.75e+02 ... (remaining 46633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.28: 19548 23.28 - 46.57: 1121 46.57 - 69.85: 113 69.85 - 93.14: 39 93.14 - 116.42: 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 -119.14 -60.86 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual -180.00 -120.34 -59.66 0 5.00e+00 4.00e-02 1.42e+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 -123.11 -56.89 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 20820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4868 0.098 - 0.196: 609 0.196 - 0.294: 39 0.294 - 0.391: 2 0.391 - 0.489: 1 Chirality restraints: 5519 Sorted by residual: chirality pdb=" CB VAL U 81 " pdb=" CA VAL U 81 " pdb=" CG1 VAL U 81 " pdb=" CG2 VAL U 81 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.99e+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 -2.25 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CG LEU U 202 " pdb=" CB LEU U 202 " pdb=" CD1 LEU U 202 " pdb=" CD2 LEU U 202 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 5516 not shown) Planarity restraints: 5997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.030 2.00e-02 2.50e+03 5.88e-02 3.46e+01 pdb=" C ALA Z 503 " -0.102 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA U 296 " 0.058 5.00e-02 4.00e+02 8.68e-02 1.20e+01 pdb=" N PRO U 297 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO U 297 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO U 297 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP X 348 " 0.055 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO X 349 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO X 349 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO X 349 " 0.046 5.00e-02 4.00e+02 ... (remaining 5994 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 372 2.60 - 3.17: 28003 3.17 - 3.75: 55032 3.75 - 4.32: 81202 4.32 - 4.90: 131017 Nonbonded interactions: 295626 Sorted by model distance: nonbonded pdb=" OG1 THR V 232 " pdb="MG MG V1002 " model vdw 2.023 2.170 nonbonded pdb=" O2B ATP U1001 " pdb="MG MG U1002 " model vdw 2.063 2.170 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.104 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.115 2.170 nonbonded pdb=" O3G ATP V1001 " pdb="MG MG V1002 " model vdw 2.120 2.170 ... (remaining 295621 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: 6.320 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: 25.690 Check model and map are aligned: 0.470 Set scattering table: 0.270 Process input model: 90.400 Find NCS groups from input model: 2.440 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 0.122 34412 Z= 0.726 Angle : 1.067 19.079 46638 Z= 0.610 Chirality : 0.064 0.489 5519 Planarity : 0.008 0.087 5997 Dihedral : 14.804 116.422 12663 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.40 % Favored : 94.33 % Rotamer: Outliers : 0.65 % Allowed : 6.93 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.78 (0.10), residues: 4461 helix: -3.04 (0.08), residues: 2160 sheet: -1.26 (0.21), residues: 579 loop : -1.93 (0.13), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP Z 141 HIS 0.013 0.002 HIS S 250 PHE 0.043 0.003 PHE E 122 TYR 0.021 0.003 TYR Q 52 ARG 0.010 0.001 ARG U 217 *********************** 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 626 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 603 time to evaluate : 4.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 61 MET cc_start: 0.4044 (mmp) cc_final: 0.3180 (mmt) REVERT: D 87 ASN cc_start: 0.7387 (m-40) cc_final: 0.7185 (m110) REVERT: D 92 ASN cc_start: 0.6686 (p0) cc_final: 0.6244 (t0) REVERT: E 123 LEU cc_start: 0.6295 (mm) cc_final: 0.5821 (tm) REVERT: H 78 LEU cc_start: 0.6149 (mp) cc_final: 0.5797 (mt) REVERT: P 63 LYS cc_start: 0.7718 (tppt) cc_final: 0.7318 (mtpp) REVERT: P 82 LYS cc_start: 0.8230 (mtpp) cc_final: 0.7938 (mtmt) REVERT: P 88 ARG cc_start: 0.8760 (ptp90) cc_final: 0.8460 (ptp90) REVERT: P 120 LYS cc_start: 0.8070 (mmtt) cc_final: 0.7802 (mmtp) REVERT: P 122 PHE cc_start: 0.7877 (m-10) cc_final: 0.7368 (m-80) REVERT: P 136 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7853 (mt-10) REVERT: P 140 ASN cc_start: 0.8785 (m110) cc_final: 0.8552 (m-40) REVERT: P 146 LEU cc_start: 0.8669 (tt) cc_final: 0.8408 (mt) REVERT: S 58 LYS cc_start: 0.7863 (tttt) cc_final: 0.7637 (tptm) REVERT: S 60 MET cc_start: 0.7308 (mtp) cc_final: 0.7045 (mtm) REVERT: S 144 ASP cc_start: 0.7913 (m-30) cc_final: 0.7695 (m-30) REVERT: S 149 GLN cc_start: 0.7445 (mt0) cc_final: 0.7243 (mt0) REVERT: S 154 GLU cc_start: 0.6565 (mt-10) cc_final: 0.5371 (tp30) REVERT: S 244 ARG cc_start: 0.7347 (tpp-160) cc_final: 0.6948 (tpp80) REVERT: T 471 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7445 (tp-100) REVERT: T 510 ASP cc_start: 0.7309 (m-30) cc_final: 0.6878 (m-30) REVERT: U 47 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6894 (mm-30) REVERT: U 287 MET cc_start: 0.8439 (tpt) cc_final: 0.8015 (tpp) REVERT: U 414 TYR cc_start: 0.7302 (t80) cc_final: 0.6917 (t80) REVERT: V 73 TRP cc_start: 0.8217 (m-10) cc_final: 0.7864 (m-10) REVERT: X 414 GLN cc_start: 0.7559 (mt0) cc_final: 0.7300 (mt0) REVERT: X 429 ASP cc_start: 0.7914 (m-30) cc_final: 0.7553 (m-30) REVERT: X 440 GLN cc_start: 0.8521 (mt0) cc_final: 0.8249 (mt0) REVERT: X 488 MET cc_start: 0.8840 (mmt) cc_final: 0.8629 (mmt) REVERT: X 517 VAL cc_start: 0.5541 (OUTLIER) cc_final: 0.5302 (m) REVERT: Y 371 LEU cc_start: 0.8357 (mp) cc_final: 0.8151 (mt) REVERT: Y 405 LYS cc_start: 0.8192 (tptt) cc_final: 0.7619 (ttpp) REVERT: Y 413 LEU cc_start: 0.7981 (mt) cc_final: 0.7775 (mt) REVERT: Y 437 ARG cc_start: 0.7675 (mtt-85) cc_final: 0.7434 (mtm-85) REVERT: Y 501 LYS cc_start: 0.7406 (tttm) cc_final: 0.6900 (mtpp) REVERT: Z 227 MET cc_start: 0.8876 (mtt) cc_final: 0.8560 (mtt) REVERT: Z 502 MET cc_start: 0.7096 (mtp) cc_final: 0.6670 (mtp) outliers start: 23 outliers final: 10 residues processed: 622 average time/residue: 1.4997 time to fit residues: 1114.9622 Evaluate side-chains 402 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 391 time to evaluate : 3.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain X residue 502 MET Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 504 LYS Chi-restraints excluded: chain Z residue 439 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 1.9990 chunk 335 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 225 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 346 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 210 optimal weight: 0.8980 chunk 257 optimal weight: 0.6980 chunk 401 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN D 94 ASN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN H 98 GLN I 94 ASN R 38 ASN R 73 ASN R 78 HIS R 85 GLN R 110 GLN S 45 GLN S 191 GLN S 293 ASN S 297 GLN T 104 GLN T 134 ASN T 149 GLN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 60 GLN U 104 GLN U 242 GLN U 246 ASN U 248 GLN U 319 HIS U 358 HIS U 386 GLN U 441 GLN U 461 GLN U 497 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 549 HIS V 60 GLN ** V 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN V 139 HIS V 149 GLN V 152 ASN V 196 GLN V 244 ASN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 497 GLN X 199 ASN X 408 GLN ** Y 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 398 ASN Y 440 GLN Z 132 GLN Z 199 ASN Z 278 GLN Z 294 ASN Z 398 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34412 Z= 0.205 Angle : 0.591 12.091 46638 Z= 0.306 Chirality : 0.043 0.224 5519 Planarity : 0.005 0.062 5997 Dihedral : 7.181 93.950 4936 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.88 % Favored : 95.85 % Rotamer: Outliers : 3.20 % Allowed : 12.79 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.17 (0.12), residues: 4461 helix: -1.46 (0.10), residues: 2182 sheet: -0.87 (0.22), residues: 553 loop : -1.36 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 37 HIS 0.005 0.001 HIS S 185 PHE 0.034 0.001 PHE E 122 TYR 0.017 0.001 TYR V 414 ARG 0.006 0.000 ARG T 86 *********************** 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 569 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 455 time to evaluate : 3.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.3504 (OUTLIER) cc_final: 0.2472 (tm) REVERT: A 119 LEU cc_start: 0.5183 (tt) cc_final: 0.4933 (tt) REVERT: D 61 MET cc_start: 0.3993 (mmp) cc_final: 0.3177 (mmt) REVERT: D 98 GLN cc_start: 0.6984 (tp-100) cc_final: 0.6707 (tt0) REVERT: E 123 LEU cc_start: 0.6341 (mm) cc_final: 0.5915 (tm) REVERT: F 81 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6768 (ptm) REVERT: F 84 SER cc_start: 0.7461 (OUTLIER) cc_final: 0.7249 (t) REVERT: H 56 LEU cc_start: 0.3274 (OUTLIER) cc_final: 0.2743 (tm) REVERT: P 49 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.8001 (t) REVERT: P 140 ASN cc_start: 0.8920 (m110) cc_final: 0.8717 (m110) REVERT: S 144 ASP cc_start: 0.7925 (m-30) cc_final: 0.7641 (m-30) REVERT: S 178 ILE cc_start: 0.8864 (mt) cc_final: 0.8561 (mp) REVERT: T 287 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7593 (tpp) REVERT: T 439 MET cc_start: 0.8522 (ttp) cc_final: 0.8286 (tpp) REVERT: T 475 GLU cc_start: 0.7749 (tp30) cc_final: 0.7278 (tp30) REVERT: U 41 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: U 47 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6957 (mm-30) REVERT: U 414 TYR cc_start: 0.7269 (t80) cc_final: 0.6903 (t80) REVERT: U 521 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6571 (pp20) REVERT: V 47 GLU cc_start: 0.7784 (pm20) cc_final: 0.7534 (pm20) REVERT: V 73 TRP cc_start: 0.8083 (m-10) cc_final: 0.7868 (m-10) REVERT: V 101 LYS cc_start: 0.8448 (mmtp) cc_final: 0.8246 (mmtt) REVERT: V 482 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7227 (mm-30) REVERT: X 429 ASP cc_start: 0.7754 (m-30) cc_final: 0.7535 (m-30) REVERT: X 440 GLN cc_start: 0.8365 (mt0) cc_final: 0.7984 (mt0) REVERT: X 471 GLN cc_start: 0.7890 (tt0) cc_final: 0.7552 (tt0) REVERT: X 488 MET cc_start: 0.8880 (mmt) cc_final: 0.8522 (mmt) REVERT: Y 195 GLU cc_start: 0.7467 (tp30) cc_final: 0.6984 (tp30) REVERT: Y 204 HIS cc_start: 0.6767 (OUTLIER) cc_final: 0.6057 (p-80) REVERT: Y 371 LEU cc_start: 0.8304 (mp) cc_final: 0.8038 (mt) REVERT: Y 405 LYS cc_start: 0.8050 (tptt) cc_final: 0.7629 (ttpp) REVERT: Y 501 LYS cc_start: 0.7437 (tttm) cc_final: 0.6864 (mtpp) REVERT: Y 502 MET cc_start: 0.6785 (mtm) cc_final: 0.6585 (mtm) REVERT: Y 529 LYS cc_start: 0.7631 (tttm) cc_final: 0.7410 (tppt) outliers start: 114 outliers final: 26 residues processed: 524 average time/residue: 1.3544 time to fit residues: 855.7776 Evaluate side-chains 404 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 368 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 521 GLU Chi-restraints excluded: chain U residue 526 SER Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 482 GLU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 365 SER Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 178 LYS Chi-restraints excluded: chain Y residue 204 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 223 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 334 optimal weight: 0.8980 chunk 273 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 402 optimal weight: 0.7980 chunk 434 optimal weight: 3.9990 chunk 358 optimal weight: 2.9990 chunk 398 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 322 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN S 118 ASN T 134 ASN T 149 GLN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 196 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 441 GLN ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 549 HIS U 152 ASN U 228 GLN U 244 ASN ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 64 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN V 271 GLN ** V 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 322 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 34412 Z= 0.328 Angle : 0.625 10.184 46638 Z= 0.321 Chirality : 0.046 0.173 5519 Planarity : 0.005 0.061 5997 Dihedral : 7.237 90.493 4927 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.64 % Favored : 95.09 % Rotamer: Outliers : 4.12 % Allowed : 14.73 % Favored : 81.14 % Cbeta Deviations : 0.00 % 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: -1.57 (0.12), residues: 4461 helix: -0.85 (0.11), residues: 2182 sheet: -0.78 (0.22), residues: 557 loop : -1.15 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 37 HIS 0.006 0.001 HIS R 78 PHE 0.028 0.002 PHE E 122 TYR 0.016 0.002 TYR U 502 ARG 0.006 0.000 ARG V 476 *********************** 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 544 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 397 time to evaluate : 4.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.3719 (mm) cc_final: 0.3467 (mt) REVERT: A 119 LEU cc_start: 0.5268 (tt) cc_final: 0.5057 (tt) REVERT: D 61 MET cc_start: 0.4040 (mmp) cc_final: 0.2900 (mpp) REVERT: D 92 ASN cc_start: 0.6309 (p0) cc_final: 0.5996 (t0) REVERT: E 123 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.5939 (tm) REVERT: F 81 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.6696 (ptm) REVERT: F 109 LEU cc_start: 0.8048 (mm) cc_final: 0.7802 (mt) REVERT: H 56 LEU cc_start: 0.3446 (OUTLIER) cc_final: 0.2709 (tm) REVERT: I 61 MET cc_start: 0.4302 (OUTLIER) cc_final: 0.3815 (ttp) REVERT: P 103 LYS cc_start: 0.7986 (tptm) cc_final: 0.7465 (mmtt) REVERT: S 144 ASP cc_start: 0.7926 (m-30) cc_final: 0.7585 (m-30) REVERT: S 244 ARG cc_start: 0.7985 (tpp80) cc_final: 0.7780 (ttt-90) REVERT: T 287 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7676 (tpp) REVERT: T 439 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8345 (tpp) REVERT: T 474 LEU cc_start: 0.8153 (tt) cc_final: 0.7918 (tt) REVERT: T 475 GLU cc_start: 0.7739 (tp30) cc_final: 0.7274 (tp30) REVERT: U 47 GLU cc_start: 0.7277 (mm-30) cc_final: 0.7004 (mm-30) REVERT: U 414 TYR cc_start: 0.7326 (t80) cc_final: 0.6960 (t80) REVERT: U 521 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6530 (pp20) REVERT: V 73 TRP cc_start: 0.8222 (m-10) cc_final: 0.7942 (m-10) REVERT: V 476 ARG cc_start: 0.6821 (tpp80) cc_final: 0.6506 (tpp-160) REVERT: V 482 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7188 (mm-30) REVERT: V 547 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8208 (t70) REVERT: X 429 ASP cc_start: 0.7772 (m-30) cc_final: 0.7532 (m-30) REVERT: X 440 GLN cc_start: 0.8423 (mt0) cc_final: 0.8027 (mt0) REVERT: X 471 GLN cc_start: 0.8078 (tt0) cc_final: 0.7677 (tt0) REVERT: X 488 MET cc_start: 0.8917 (mmt) cc_final: 0.8642 (mmt) REVERT: X 550 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8077 (mttp) REVERT: Y 83 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8138 (t0) REVERT: Y 194 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.5815 (mpp) REVERT: Y 204 HIS cc_start: 0.7109 (OUTLIER) cc_final: 0.6504 (p-80) REVERT: Y 371 LEU cc_start: 0.8312 (mp) cc_final: 0.8090 (mt) REVERT: Y 381 ASP cc_start: 0.7120 (t0) cc_final: 0.6909 (t0) REVERT: Y 405 LYS cc_start: 0.8083 (tptt) cc_final: 0.7488 (ttpp) REVERT: Y 501 LYS cc_start: 0.7401 (tttm) cc_final: 0.6893 (mtpp) REVERT: Y 529 LYS cc_start: 0.7690 (tttm) cc_final: 0.7445 (tppt) REVERT: Z 440 GLN cc_start: 0.8045 (tt0) cc_final: 0.7706 (mt0) outliers start: 147 outliers final: 58 residues processed: 487 average time/residue: 1.3606 time to fit residues: 801.1632 Evaluate side-chains 432 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 361 time to evaluate : 3.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain I residue 61 MET Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 186 ASN Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain T residue 120 LEU Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 269 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 521 GLU Chi-restraints excluded: chain U residue 526 SER Chi-restraints excluded: chain V residue 46 ASP Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 305 SER Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 482 GLU Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain V residue 547 ASP Chi-restraints excluded: chain X residue 117 THR Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 550 LYS Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 178 LYS Chi-restraints excluded: chain Y residue 194 MET Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Z residue 267 THR Chi-restraints excluded: chain Z residue 306 SER Chi-restraints excluded: chain Z residue 321 LEU Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 554 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 397 optimal weight: 4.9990 chunk 302 optimal weight: 0.7980 chunk 208 optimal weight: 0.5980 chunk 44 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 270 optimal weight: 0.0970 chunk 403 optimal weight: 5.9990 chunk 427 optimal weight: 1.9990 chunk 210 optimal weight: 0.1980 chunk 382 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN S 191 GLN T 134 ASN T 149 GLN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 529 ASN U 228 GLN U 441 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 471 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34412 Z= 0.178 Angle : 0.548 9.266 46638 Z= 0.279 Chirality : 0.042 0.147 5519 Planarity : 0.004 0.061 5997 Dihedral : 6.598 82.742 4926 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.06 % Favored : 95.72 % Rotamer: Outliers : 3.79 % Allowed : 16.86 % Favored : 79.35 % Cbeta Deviations : 0.00 % 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: -1.02 (0.13), residues: 4461 helix: -0.35 (0.11), residues: 2167 sheet: -0.68 (0.22), residues: 549 loop : -0.90 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 37 HIS 0.007 0.001 HIS R 78 PHE 0.028 0.001 PHE E 122 TYR 0.018 0.001 TYR T 453 ARG 0.006 0.000 ARG U 454 *********************** 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 554 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 419 time to evaluate : 4.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 61 MET cc_start: 0.4450 (mmp) cc_final: 0.2940 (mpp) REVERT: D 92 ASN cc_start: 0.6413 (p0) cc_final: 0.5929 (t0) REVERT: D 98 GLN cc_start: 0.7088 (tp-100) cc_final: 0.6813 (tt0) REVERT: E 123 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.5940 (tm) REVERT: F 109 LEU cc_start: 0.8048 (mm) cc_final: 0.7813 (mt) REVERT: H 56 LEU cc_start: 0.2832 (OUTLIER) cc_final: 0.2455 (tm) REVERT: H 87 ASN cc_start: 0.7426 (m-40) cc_final: 0.7195 (t0) REVERT: I 61 MET cc_start: 0.4222 (OUTLIER) cc_final: 0.4019 (ttp) REVERT: I 62 VAL cc_start: 0.6157 (OUTLIER) cc_final: 0.5841 (t) REVERT: Q 66 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6624 (mm-30) REVERT: S 144 ASP cc_start: 0.7967 (m-30) cc_final: 0.7642 (m-30) REVERT: T 287 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7447 (tpp) REVERT: T 439 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8283 (tpp) REVERT: T 475 GLU cc_start: 0.7777 (tp30) cc_final: 0.7260 (tp30) REVERT: T 516 ASP cc_start: 0.7172 (p0) cc_final: 0.6790 (p0) REVERT: U 47 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6719 (mm-30) REVERT: U 50 LYS cc_start: 0.7729 (mmtp) cc_final: 0.6588 (ptmm) REVERT: U 414 TYR cc_start: 0.7275 (t80) cc_final: 0.6929 (t80) REVERT: U 521 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6525 (pp20) REVERT: U 546 LEU cc_start: 0.8738 (tp) cc_final: 0.8516 (tm) REVERT: V 73 TRP cc_start: 0.8162 (m-10) cc_final: 0.7946 (m-10) REVERT: V 482 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7429 (tp30) REVERT: X 416 ILE cc_start: 0.8174 (mt) cc_final: 0.7966 (mp) REVERT: X 440 GLN cc_start: 0.8375 (mt0) cc_final: 0.7992 (mt0) REVERT: X 488 MET cc_start: 0.8905 (mmt) cc_final: 0.8558 (mmt) REVERT: X 550 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7902 (mttp) REVERT: Y 55 GLU cc_start: 0.7069 (pt0) cc_final: 0.6590 (pp20) REVERT: Y 83 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8303 (t0) REVERT: Y 178 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8398 (mtmm) REVERT: Y 204 HIS cc_start: 0.6791 (OUTLIER) cc_final: 0.6176 (p-80) REVERT: Y 371 LEU cc_start: 0.8256 (mp) cc_final: 0.8029 (mt) REVERT: Y 388 ASN cc_start: 0.7730 (t0) cc_final: 0.7223 (t0) REVERT: Y 405 LYS cc_start: 0.8044 (tptt) cc_final: 0.7646 (ttpp) REVERT: Y 501 LYS cc_start: 0.7450 (tttm) cc_final: 0.6889 (mtpp) REVERT: Y 529 LYS cc_start: 0.7675 (tttm) cc_final: 0.7399 (tppt) REVERT: Z 428 GLU cc_start: 0.5763 (tp30) cc_final: 0.5560 (tp30) REVERT: Z 440 GLN cc_start: 0.7947 (tt0) cc_final: 0.7692 (mt0) REVERT: Z 441 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7429 (tpp80) REVERT: Z 521 LEU cc_start: 0.5009 (OUTLIER) cc_final: 0.4788 (tt) outliers start: 135 outliers final: 48 residues processed: 515 average time/residue: 1.3164 time to fit residues: 824.1118 Evaluate side-chains 435 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 373 time to evaluate : 3.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 61 MET Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 186 ASN Chi-restraints excluded: chain S residue 191 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 521 GLU Chi-restraints excluded: chain U residue 526 SER Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 482 GLU Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 513 ASP Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 550 LYS Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 154 SER Chi-restraints excluded: chain Y residue 178 LYS Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 468 SER Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 267 THR Chi-restraints excluded: chain Z residue 306 SER Chi-restraints excluded: chain Z residue 321 LEU Chi-restraints excluded: chain Z residue 441 ARG Chi-restraints excluded: chain Z residue 521 LEU Chi-restraints excluded: chain Z residue 554 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 355 optimal weight: 5.9990 chunk 242 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 318 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 364 optimal weight: 0.6980 chunk 295 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 383 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN Q 40 GLN R 85 GLN ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN S 191 GLN T 134 ASN T 149 GLN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 435 GLN U 244 ASN U 441 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 121 ASN V 134 ASN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34412 Z= 0.293 Angle : 0.596 10.515 46638 Z= 0.303 Chirality : 0.045 0.157 5519 Planarity : 0.004 0.061 5997 Dihedral : 6.793 87.011 4924 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.69 % Favored : 95.07 % Rotamer: Outliers : 4.12 % Allowed : 17.59 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.89 (0.13), residues: 4461 helix: -0.23 (0.11), residues: 2179 sheet: -0.72 (0.22), residues: 553 loop : -0.82 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 37 HIS 0.007 0.001 HIS R 78 PHE 0.025 0.001 PHE E 122 TYR 0.013 0.002 TYR U 312 ARG 0.006 0.000 ARG S 198 *********************** 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 535 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 388 time to evaluate : 3.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 85 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7058 (mm) REVERT: D 92 ASN cc_start: 0.6443 (p0) cc_final: 0.5901 (t0) REVERT: D 98 GLN cc_start: 0.7133 (tp-100) cc_final: 0.6780 (tt0) REVERT: F 109 LEU cc_start: 0.8149 (mm) cc_final: 0.7896 (mt) REVERT: H 56 LEU cc_start: 0.2992 (OUTLIER) cc_final: 0.2552 (tm) REVERT: H 92 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7073 (p0) REVERT: I 62 VAL cc_start: 0.5972 (OUTLIER) cc_final: 0.5657 (t) REVERT: P 140 ASN cc_start: 0.9044 (m110) cc_final: 0.8827 (m110) REVERT: Q 40 GLN cc_start: 0.5729 (OUTLIER) cc_final: 0.5480 (tm-30) REVERT: R 148 GLU cc_start: 0.6986 (tp30) cc_final: 0.6617 (tm-30) REVERT: S 82 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7715 (m) REVERT: S 144 ASP cc_start: 0.7891 (m-30) cc_final: 0.7532 (m-30) REVERT: T 287 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7616 (tpp) REVERT: T 439 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8307 (tpp) REVERT: T 475 GLU cc_start: 0.7666 (tp30) cc_final: 0.7173 (tp30) REVERT: T 516 ASP cc_start: 0.7197 (p0) cc_final: 0.6833 (p0) REVERT: U 47 GLU cc_start: 0.7274 (mm-30) cc_final: 0.7031 (mm-30) REVERT: U 414 TYR cc_start: 0.7307 (t80) cc_final: 0.6981 (t80) REVERT: U 521 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6497 (pp20) REVERT: V 73 TRP cc_start: 0.8245 (m-10) cc_final: 0.7893 (m-10) REVERT: V 322 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.8783 (tp) REVERT: V 482 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7465 (tp30) REVERT: V 509 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7474 (mp) REVERT: X 416 ILE cc_start: 0.8207 (mt) cc_final: 0.7978 (mp) REVERT: X 440 GLN cc_start: 0.8403 (mt0) cc_final: 0.8012 (mt0) REVERT: X 488 MET cc_start: 0.8910 (mmt) cc_final: 0.8632 (mmt) REVERT: X 550 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8197 (mttp) REVERT: Y 55 GLU cc_start: 0.7085 (pt0) cc_final: 0.6718 (pp20) REVERT: Y 83 ASN cc_start: 0.8870 (OUTLIER) cc_final: 0.8252 (t0) REVERT: Y 194 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.5871 (mpp) REVERT: Y 204 HIS cc_start: 0.7044 (OUTLIER) cc_final: 0.6474 (p-80) REVERT: Y 371 LEU cc_start: 0.8252 (mp) cc_final: 0.7997 (mt) REVERT: Y 405 LYS cc_start: 0.8109 (tptt) cc_final: 0.7682 (ttpp) REVERT: Y 501 LYS cc_start: 0.7384 (tttm) cc_final: 0.6874 (mtpp) REVERT: Y 529 LYS cc_start: 0.7747 (tttm) cc_final: 0.7410 (tppt) REVERT: Z 440 GLN cc_start: 0.7995 (tt0) cc_final: 0.7695 (mt0) REVERT: Z 441 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7490 (tpp80) REVERT: Z 521 LEU cc_start: 0.5002 (OUTLIER) cc_final: 0.4641 (tt) outliers start: 147 outliers final: 65 residues processed: 484 average time/residue: 1.2644 time to fit residues: 746.4793 Evaluate side-chains 451 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 368 time to evaluate : 3.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain Q residue 40 GLN Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 162 SER Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 186 ASN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 291 ASP Chi-restraints excluded: chain T residue 120 LEU Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 423 VAL Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 521 GLU Chi-restraints excluded: chain U residue 526 SER Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 322 ILE Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 482 GLU Chi-restraints excluded: chain V residue 509 LEU Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain X residue 117 THR Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain X residue 513 ASP Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 550 LYS Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 154 SER Chi-restraints excluded: chain Y residue 178 LYS Chi-restraints excluded: chain Y residue 194 MET Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 321 LEU Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Y residue 468 SER Chi-restraints excluded: chain Z residue 267 THR Chi-restraints excluded: chain Z residue 306 SER Chi-restraints excluded: chain Z residue 321 LEU Chi-restraints excluded: chain Z residue 358 LEU Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 441 ARG Chi-restraints excluded: chain Z residue 521 LEU Chi-restraints excluded: chain Z residue 554 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.4438 > 50: distance: 17 - 23: 3.860 distance: 23 - 24: 6.729 distance: 24 - 25: 10.071 distance: 24 - 27: 5.832 distance: 25 - 26: 16.803 distance: 25 - 32: 20.717 distance: 27 - 28: 9.950 distance: 28 - 29: 17.494 distance: 29 - 30: 15.238 distance: 30 - 31: 10.823 distance: 32 - 33: 27.577 distance: 33 - 34: 11.692 distance: 33 - 36: 26.834 distance: 34 - 35: 13.974 distance: 34 - 41: 4.600 distance: 36 - 37: 10.301 distance: 37 - 38: 7.920 distance: 38 - 39: 6.782 distance: 38 - 40: 9.142 distance: 41 - 42: 11.666 distance: 41 - 47: 6.419 distance: 42 - 43: 11.026 distance: 42 - 45: 9.754 distance: 43 - 44: 9.714 distance: 43 - 48: 6.359 distance: 45 - 46: 6.457 distance: 46 - 47: 14.036 distance: 48 - 49: 6.667 distance: 49 - 50: 7.453 distance: 49 - 52: 5.194 distance: 50 - 51: 4.840 distance: 50 - 59: 10.715 distance: 52 - 53: 9.409 distance: 53 - 54: 7.960 distance: 53 - 55: 6.419 distance: 54 - 56: 5.095 distance: 55 - 57: 3.003 distance: 56 - 58: 5.328 distance: 57 - 58: 8.466 distance: 59 - 60: 5.921 distance: 60 - 61: 15.977 distance: 60 - 63: 6.115 distance: 61 - 62: 21.720 distance: 61 - 68: 16.251 distance: 63 - 64: 4.481 distance: 64 - 65: 7.209 distance: 65 - 66: 4.203 distance: 66 - 67: 12.439 distance: 68 - 69: 12.301 distance: 69 - 70: 24.715 distance: 69 - 72: 24.643 distance: 70 - 71: 17.984 distance: 70 - 73: 14.181 distance: 73 - 74: 5.184 distance: 74 - 75: 9.918 distance: 74 - 77: 5.973 distance: 75 - 76: 7.333 distance: 75 - 82: 9.063 distance: 77 - 78: 13.320 distance: 78 - 79: 15.132 distance: 79 - 80: 7.136 distance: 80 - 81: 18.126 distance: 82 - 83: 15.191 distance: 83 - 84: 13.190 distance: 83 - 86: 5.792 distance: 84 - 85: 7.417 distance: 84 - 87: 9.858 distance: 87 - 88: 16.945 distance: 88 - 89: 12.732 distance: 88 - 91: 5.613 distance: 89 - 90: 9.952 distance: 89 - 96: 10.054 distance: 91 - 92: 12.599 distance: 92 - 93: 10.866 distance: 93 - 94: 27.464 distance: 93 - 95: 35.151 distance: 96 - 97: 12.079 distance: 97 - 98: 8.600 distance: 98 - 99: 17.411 distance: 98 - 101: 18.328