Starting phenix.real_space_refine on Thu Feb 22 09:12:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rea_4847/02_2024/6rea_4847_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rea_4847/02_2024/6rea_4847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rea_4847/02_2024/6rea_4847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rea_4847/02_2024/6rea_4847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rea_4847/02_2024/6rea_4847_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rea_4847/02_2024/6rea_4847_updated.pdb" } resolution = 3.6 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 21526 2.51 5 N 5790 2.21 5 O 6413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 111": "OE1" <-> "OE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "J PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 64": "OE1" <-> "OE2" Residue "P GLU 79": "OE1" <-> "OE2" Residue "P ASP 93": "OD1" <-> "OD2" Residue "P GLU 116": "OE1" <-> "OE2" Residue "P PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 25": "OD1" <-> "OD2" Residue "Q GLU 33": "OE1" <-> "OE2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 54": "OD1" <-> "OD2" Residue "Q TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 66": "OE1" <-> "OE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 35": "OE1" <-> "OE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 62": "OE1" <-> "OE2" Residue "R PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "R GLU 148": "OE1" <-> "OE2" Residue "R ASP 156": "OD1" <-> "OD2" Residue "R PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S GLU 154": "OE1" <-> "OE2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 181": "OE1" <-> "OE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 214": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S ASP 245": "OD1" <-> "OD2" Residue "S GLU 275": "OE1" <-> "OE2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 303": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ASP 112": "OD1" <-> "OD2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 226": "OD1" <-> "OD2" Residue "T ASP 237": "OD1" <-> "OD2" Residue "T TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 325": "OD1" <-> "OD2" Residue "T ASP 353": "OD1" <-> "OD2" Residue "T GLU 371": "OE1" <-> "OE2" Residue "T GLU 384": "OE1" <-> "OE2" Residue "T ASP 389": "OD1" <-> "OD2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 418": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 449": "OE1" <-> "OE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T GLU 455": "OE1" <-> "OE2" Residue "T PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 467": "OD1" <-> "OD2" Residue "T GLU 475": "OE1" <-> "OE2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 522": "OE1" <-> "OE2" Residue "T ASP 547": "OD1" <-> "OD2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ASP 41": "OD1" <-> "OD2" Residue "U ASP 46": "OD1" <-> "OD2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 92": "OD1" <-> "OD2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 112": "OD1" <-> "OD2" Residue "U ASP 142": "OD1" <-> "OD2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U GLU 200": "OE1" <-> "OE2" Residue "U PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U ASP 326": "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 411": "OE1" <-> "OE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 467": "OD1" <-> "OD2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 510": "OD1" <-> "OD2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U 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 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 142": "OD1" <-> "OD2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V GLU 186": "OE1" <-> "OE2" Residue "V ASP 210": "OD1" <-> "OD2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V ASP 226": "OD1" <-> "OD2" Residue "V TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 266": "NH1" <-> "NH2" Residue "V PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ARG 335": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "V ARG 347": "NH1" <-> "NH2" Residue "V ARG 360": "NH1" <-> "NH2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 429": "NH1" <-> "NH2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V GLU 482": "OE1" <-> "OE2" Residue "V PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X ASP 53": "OD1" <-> "OD2" Residue "X ARG 71": "NH1" <-> "NH2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X ASP 104": "OD1" <-> "OD2" Residue "X ARG 120": "NH1" <-> "NH2" Residue "X GLU 195": "OE1" <-> "OE2" Residue "X PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "X GLU 219": "OE1" <-> "OE2" Residue "X ASP 222": "OD1" <-> "OD2" Residue "X GLU 238": "OE1" <-> "OE2" Residue "X ARG 258": "NH1" <-> "NH2" Residue "X ASP 285": "OD1" <-> "OD2" Residue "X ASP 317": "OD1" <-> "OD2" Residue "X ASP 345": "OD1" <-> "OD2" Residue "X ASP 348": "OD1" <-> "OD2" Residue "X PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 370": "OE1" <-> "OE2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X ARG 401": "NH1" <-> "NH2" Residue "X ASP 409": "OD1" <-> "OD2" Residue "X TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 435": "NH1" <-> "NH2" Residue "X ARG 437": "NH1" <-> "NH2" Residue "X PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 500": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X GLU 511": "OE1" <-> "OE2" Residue "X GLU 519": "OE1" <-> "OE2" Residue "X GLU 520": "OE1" <-> "OE2" Residue "X PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 552": "OE1" <-> "OE2" Residue "X GLU 557": "OE1" <-> "OE2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y ASP 82": "OD1" <-> "OD2" Residue "Y ASP 94": "OD1" <-> "OD2" Residue "Y ASP 104": "OD1" <-> "OD2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 168": "OD1" <-> "OD2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 218": "NH1" <-> "NH2" Residue "Y ARG 225": "NH1" <-> "NH2" Residue "Y ARG 239": "NH1" <-> "NH2" Residue "Y TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 296": "OE1" <-> "OE2" Residue "Y TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 401": "NH1" <-> "NH2" Residue "Y ASP 429": "OD1" <-> "OD2" Residue "Y PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 479": "OD1" <-> "OD2" Residue "Y GLU 494": "OE1" <-> "OE2" Residue "Y ARG 509": "NH1" <-> "NH2" Residue "Y GLU 540": "OE1" <-> "OE2" Residue "Y GLU 541": "OE1" <-> "OE2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 552": "OE1" <-> "OE2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z ASP 82": "OD1" <-> "OD2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "Z ARG 115": "NH1" <-> "NH2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z ASP 136": "OD1" <-> "OD2" Residue "Z ARG 145": "NH1" <-> "NH2" Residue "Z PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 152": "OE1" <-> "OE2" Residue "Z TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 195": "OE1" <-> "OE2" Residue "Z PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 258": "NH1" <-> "NH2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z ASP 279": "OD1" <-> "OD2" Residue "Z GLU 296": "OE1" <-> "OE2" Residue "Z TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 317": "OD1" <-> "OD2" Residue "Z GLU 323": "OE1" <-> "OE2" Residue "Z ASP 344": "OD1" <-> "OD2" Residue "Z ARG 366": "NH1" <-> "NH2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z ASP 415": "OD1" <-> "OD2" Residue "Z GLU 427": "OE1" <-> "OE2" Residue "Z ASP 429": "OD1" <-> "OD2" Residue "Z PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 513": "OD1" <-> "OD2" Residue "Z GLU 520": "OE1" <-> "OE2" Residue "Z ASP 523": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33863 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: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 3961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3961 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "Y" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3952 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 497} Chain: "Z" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.59, per 1000 atoms: 0.55 Number of scatterers: 33863 At special positions: 0 Unit cell: (167.427, 135.837, 210.6, 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 6413 8.00 N 5790 7.00 C 21526 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: 13.36 Conformation dependent library (CDL) restraints added in 6.2 seconds 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8150 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 163 helices and 27 sheets defined 47.0% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.42 Creating SS restraints... Processing helix chain 'A' and resid 55 through 91 removed outlier: 3.580A pdb=" N ALA A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 126 removed outlier: 3.729A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 66 Processing helix chain 'B' and resid 68 through 91 removed outlier: 3.557A pdb=" N VAL B 74 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE B 82 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 85 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 125 removed outlier: 3.752A pdb=" N SER B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 91 removed outlier: 3.966A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 125 removed outlier: 4.937A pdb=" N LYS C 97 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER C 112 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU C 119 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 124 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU C 125 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 91 removed outlier: 3.998A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 126 removed outlier: 3.571A pdb=" N ALA D 96 " --> pdb=" O PRO D 93 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LYS D 97 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL D 100 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 104 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR D 110 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER D 117 " --> pdb=" O ALA D 114 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 119 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE D 126 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 91 removed outlier: 3.964A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 126 removed outlier: 5.321A pdb=" N LYS E 97 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU E 99 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL E 100 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU E 119 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE E 122 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE E 124 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU E 125 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE E 126 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 91 removed outlier: 3.644A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 95 No H-bonds generated for 'chain 'F' and resid 93 through 95' Processing helix chain 'F' and resid 98 through 126 removed outlier: 4.147A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 89 removed outlier: 4.944A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 125 removed outlier: 3.539A pdb=" N ALA G 96 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL G 100 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU G 104 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR G 110 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER G 112 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE G 122 " --> pdb=" O LEU G 119 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU G 125 " --> pdb=" O PHE G 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 65 removed outlier: 3.898A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY H 65 " --> pdb=" O MET H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 91 removed outlier: 3.672A pdb=" N GLY H 73 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA H 89 " --> pdb=" O ILE H 86 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG H 91 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 126 removed outlier: 4.699A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL H 100 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR H 110 " --> pdb=" O PHE H 107 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU H 125 " --> pdb=" O PHE H 122 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE H 126 " --> pdb=" O LEU H 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 91 removed outlier: 3.693A pdb=" N VAL I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ALA I 70 " --> pdb=" O CYS I 66 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LEU I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA I 72 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 126 removed outlier: 5.173A pdb=" N LYS I 97 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL I 100 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER I 112 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER I 117 " --> pdb=" O ALA I 114 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU I 119 " --> pdb=" O PHE I 116 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU I 125 " --> pdb=" O PHE I 122 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE I 126 " --> pdb=" O LEU I 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 91 removed outlier: 3.588A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY J 75 " --> pdb=" O LEU J 71 " (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 125 removed outlier: 4.119A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 63 Processing helix chain 'P' and resid 69 through 83 Processing helix chain 'P' and resid 85 through 92 removed outlier: 4.054A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 108 Processing helix chain 'P' and resid 116 through 127 Processing helix chain 'P' and resid 130 through 148 removed outlier: 4.100A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU P 136 " --> pdb=" O ALA P 133 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 12 No H-bonds generated for 'chain 'Q' and resid 10 through 12' Processing helix chain 'Q' and resid 16 through 30 removed outlier: 3.624A pdb=" N ASN Q 29 " --> pdb=" O ASP Q 25 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 43 removed outlier: 3.815A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG Q 42 " --> pdb=" O LYS Q 38 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN Q 43 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 38 removed outlier: 3.818A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 169 removed outlier: 3.762A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 194 removed outlier: 3.772A pdb=" N ALA R 190 " --> pdb=" O GLU R 186 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER R 193 " --> pdb=" O SER R 189 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 78 removed outlier: 3.633A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN S 77 " --> pdb=" O ILE S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 88 Processing helix chain 'S' and resid 116 through 130 removed outlier: 3.511A pdb=" N THR S 120 " --> pdb=" O ASN S 116 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 150 Processing helix chain 'S' and resid 172 through 183 Processing helix chain 'S' and resid 213 through 220 removed outlier: 5.713A pdb=" N LYS S 218 " --> pdb=" O ASP S 214 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLN S 219 " --> pdb=" O LEU S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 239 through 312 removed outlier: 3.520A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN S 276 " --> pdb=" O SER S 272 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR S 278 " --> pdb=" O MET S 274 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS S 279 " --> pdb=" O GLU S 275 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (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 207 through 212 Processing helix chain 'T' and resid 231 through 246 Processing helix chain 'T' and resid 266 through 278 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 296 through 315 Proline residue: T 303 - end of helix removed outlier: 4.264A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 341 Processing helix chain 'T' and resid 347 through 349 No H-bonds generated for 'chain 'T' and resid 347 through 349' Processing helix chain 'T' and resid 354 through 364 removed outlier: 3.538A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU T 363 " --> pdb=" O SER T 359 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ARG T 364 " --> 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 413 No H-bonds generated for 'chain 'T' and resid 410 through 413' Processing helix chain 'T' and resid 431 through 434 Processing helix chain 'T' and resid 437 through 442 Processing helix chain 'T' and resid 444 through 457 Processing helix chain 'T' and resid 470 through 483 Processing helix chain 'T' and resid 494 through 505 removed outlier: 3.664A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 527 removed outlier: 4.170A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 539 Processing helix chain 'T' and resid 544 through 555 removed outlier: 3.787A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA T 552 " --> pdb=" O ALA T 548 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 48 No H-bonds generated for 'chain 'U' and resid 46 through 48' Processing helix chain 'U' and resid 62 through 71 removed outlier: 4.927A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix Processing helix chain 'U' and resid 157 through 159 No H-bonds generated for 'chain 'U' and resid 157 through 159' Processing helix chain 'U' and resid 207 through 211 Processing helix chain 'U' and resid 231 through 247 removed outlier: 3.660A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 279 Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 296 through 316 Proline residue: U 303 - end of helix removed outlier: 4.096A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG U 314 " --> pdb=" O ALA U 310 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR U 316 " --> pdb=" O TYR U 312 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 Processing helix chain 'U' and resid 347 through 349 No H-bonds generated for 'chain 'U' and resid 347 through 349' Processing helix chain 'U' and resid 354 through 364 removed outlier: 4.555A pdb=" N ARG U 364 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 393 through 401 Processing helix chain 'U' and resid 411 through 414 No H-bonds generated for 'chain 'U' and resid 411 through 414' Processing helix chain 'U' and resid 437 through 459 removed outlier: 4.543A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR U 453 " --> pdb=" O GLU U 449 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU U 455 " --> pdb=" O ALA U 451 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL U 456 " --> pdb=" O GLN U 452 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ALA U 458 " --> pdb=" O ARG U 454 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE U 459 " --> pdb=" O GLU U 455 " (cutoff:3.500A) Processing helix chain 'U' and resid 468 through 484 removed outlier: 3.695A pdb=" N TYR U 472 " --> pdb=" O ALA U 468 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL U 473 " --> pdb=" O ALA U 469 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET U 483 " --> pdb=" O ARG U 479 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 505 removed outlier: 3.897A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 517 through 527 removed outlier: 3.708A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 531 through 539 removed outlier: 3.966A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 544 through 555 removed outlier: 3.711A pdb=" N ARG U 555 " --> pdb=" O LYS U 551 " (cutoff:3.500A) Processing helix chain 'V' and resid 46 through 48 No H-bonds generated for 'chain 'V' and resid 46 through 48' Processing helix chain 'V' and resid 58 through 66 removed outlier: 3.876A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 210 No H-bonds generated for 'chain 'V' and resid 207 through 210' Processing helix chain 'V' and resid 231 through 246 removed outlier: 3.894A pdb=" N GLN V 242 " --> pdb=" O ALA V 238 " (cutoff:3.500A) Processing helix chain 'V' and resid 251 through 253 No H-bonds generated for 'chain 'V' and resid 251 through 253' Processing helix chain 'V' and resid 266 through 279 Processing helix chain 'V' and resid 281 through 284 Processing helix chain 'V' and resid 296 through 314 Proline residue: V 303 - end of helix removed outlier: 3.907A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG V 314 " --> pdb=" O ALA V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 341 removed outlier: 3.568A pdb=" N LEU V 341 " --> pdb=" O MET V 337 " (cutoff:3.500A) Processing helix chain 'V' and resid 347 through 349 No H-bonds generated for 'chain 'V' and resid 347 through 349' Processing helix chain 'V' and resid 352 through 364 removed outlier: 3.981A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU V 363 " --> pdb=" O ARG V 360 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG V 364 " --> pdb=" O LEU V 361 " (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 431 through 433 No H-bonds generated for 'chain 'V' and resid 431 through 433' Processing helix chain 'V' and resid 439 through 455 removed outlier: 4.146A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 483 removed outlier: 3.507A pdb=" N ALA V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) Processing helix chain 'V' and resid 494 through 505 removed outlier: 3.529A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) Processing helix chain 'V' and resid 517 through 527 removed outlier: 4.265A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 530 through 539 removed outlier: 3.812A pdb=" N ALA V 538 " --> pdb=" O LYS V 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 549 through 553 Processing helix chain 'X' and resid 150 through 152 No H-bonds generated for 'chain 'X' and resid 150 through 152' Processing helix chain 'X' and resid 166 through 169 No H-bonds generated for 'chain 'X' and resid 166 through 169' Processing helix chain 'X' and resid 189 through 203 Processing helix chain 'X' and resid 217 through 230 Processing helix chain 'X' and resid 236 through 241 removed outlier: 4.567A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 255 through 258 No H-bonds generated for 'chain 'X' and resid 255 through 258' Processing helix chain 'X' and resid 261 through 274 removed outlier: 3.914A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 300 Processing helix chain 'X' and resid 315 through 322 Processing helix chain 'X' and resid 342 through 344 No H-bonds generated for 'chain 'X' and resid 342 through 344' Processing helix chain 'X' and resid 349 through 354 Processing helix chain 'X' and resid 366 through 370 Processing helix chain 'X' and resid 389 through 392 No H-bonds generated for 'chain 'X' and resid 389 through 392' Processing helix chain 'X' and resid 394 through 412 removed outlier: 3.883A pdb=" N VAL X 399 " --> pdb=" O GLU X 395 " (cutoff:3.500A) Processing helix chain 'X' and resid 414 through 420 removed outlier: 3.939A pdb=" N ALA X 418 " --> pdb=" O GLN X 414 " (cutoff:3.500A) Processing helix chain 'X' and resid 427 through 442 removed outlier: 3.556A pdb=" N LEU X 431 " --> pdb=" O GLU X 427 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG X 441 " --> pdb=" O ARG X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 463 through 475 removed outlier: 3.741A pdb=" N SER X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) Processing helix chain 'X' and resid 492 through 508 removed outlier: 4.269A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP X 505 " --> pdb=" O LYS X 501 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE X 506 " --> pdb=" O MET X 502 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA X 507 " --> pdb=" O ALA X 503 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 533 removed outlier: 3.615A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 165 through 170 Processing helix chain 'Y' and resid 189 through 200 Processing helix chain 'Y' and resid 217 through 230 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 3.833A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 258 No H-bonds generated for 'chain 'Y' and resid 255 through 258' Processing helix chain 'Y' and resid 261 through 274 removed outlier: 3.610A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 288 through 297 Processing helix chain 'Y' and resid 314 through 322 Processing helix chain 'Y' and resid 349 through 357 removed outlier: 3.759A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N HIS Y 357 " --> pdb=" O THR Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 371 removed outlier: 3.931A pdb=" N LEU Y 371 " --> pdb=" O SER Y 367 " (cutoff:3.500A) Processing helix chain 'Y' and resid 394 through 419 removed outlier: 3.804A pdb=" N LEU Y 413 " --> pdb=" O ASP Y 409 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN Y 414 " --> pdb=" O TYR Y 410 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) Processing helix chain 'Y' and resid 422 through 424 No H-bonds generated for 'chain 'Y' and resid 422 through 424' Processing helix chain 'Y' and resid 427 through 443 removed outlier: 3.872A pdb=" N ALA Y 434 " --> pdb=" O LYS Y 430 " (cutoff:3.500A) Processing helix chain 'Y' and resid 450 through 454 removed outlier: 3.870A pdb=" N THR Y 454 " --> pdb=" O GLU Y 451 " (cutoff:3.500A) Processing helix chain 'Y' and resid 463 through 475 Processing helix chain 'Y' and resid 483 through 485 No H-bonds generated for 'chain 'Y' and resid 483 through 485' Processing helix chain 'Y' and resid 492 through 504 removed outlier: 4.020A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) Processing helix chain 'Y' and resid 512 through 514 No H-bonds generated for 'chain 'Y' and resid 512 through 514' Processing helix chain 'Y' and resid 527 through 532 Processing helix chain 'Y' and resid 542 through 544 No H-bonds generated for 'chain 'Y' and resid 542 through 544' Processing helix chain 'Z' and resid 115 through 117 No H-bonds generated for 'chain 'Z' and resid 115 through 117' Processing helix chain 'Z' and resid 165 through 170 Processing helix chain 'Z' and resid 189 through 197 Processing helix chain 'Z' and resid 217 through 229 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 3.929A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 274 removed outlier: 5.008A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 297 removed outlier: 3.610A pdb=" N GLU Z 296 " --> pdb=" O ALA Z 293 " (cutoff:3.500A) Processing helix chain 'Z' and resid 315 through 324 removed outlier: 4.847A pdb=" N ARG Z 324 " --> pdb=" O GLY Z 320 " (cutoff:3.500A) Processing helix chain 'Z' and resid 342 through 344 No H-bonds generated for 'chain 'Z' and resid 342 through 344' Processing helix chain 'Z' and resid 349 through 355 removed outlier: 3.795A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE Z 355 " --> pdb=" O PRO Z 351 " (cutoff:3.500A) Processing helix chain 'Z' and resid 366 through 370 Processing helix chain 'Z' and resid 385 through 387 No H-bonds generated for 'chain 'Z' and resid 385 through 387' Processing helix chain 'Z' and resid 389 through 392 No H-bonds generated for 'chain 'Z' and resid 389 through 392' Processing helix chain 'Z' and resid 394 through 417 removed outlier: 4.353A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) Processing helix chain 'Z' and resid 430 through 442 Processing helix chain 'Z' and resid 449 through 451 No H-bonds generated for 'chain 'Z' and resid 449 through 451' Processing helix chain 'Z' and resid 463 through 475 Processing helix chain 'Z' and resid 484 through 486 No H-bonds generated for 'chain 'Z' and resid 484 through 486' Processing helix chain 'Z' and resid 492 through 506 removed outlier: 3.942A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS Z 501 " --> pdb=" O GLU Z 497 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 533 removed outlier: 4.221A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'Q' and resid 45 through 49 Processing sheet with id= B, first strand: chain 'R' and resid 72 through 75 removed outlier: 6.781A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE R 144 " --> pdb=" O TYR R 75 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'R' and resid 96 through 100 removed outlier: 4.393A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 203 through 211 removed outlier: 3.585A pdb=" N VAL S 101 " --> pdb=" O SER S 189 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ALA S 161 " --> pdb=" O SER S 141 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'T' and resid 87 through 90 removed outlier: 6.686A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'T' and resid 152 through 155 Processing sheet with id= G, first strand: chain 'T' and resid 382 through 384 removed outlier: 6.731A pdb=" N ILE T 223 " --> pdb=" O ILE T 383 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ILE T 406 " --> pdb=" O ILE T 224 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'T' and resid 285 through 290 removed outlier: 9.028A pdb=" N ILE T 286 " --> pdb=" O VAL T 255 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N CYS T 257 " --> pdb=" O ILE T 286 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N VAL T 288 " --> pdb=" O CYS T 257 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR T 259 " --> pdb=" O VAL T 288 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA T 290 " --> pdb=" O TYR T 259 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA T 261 " --> pdb=" O ALA T 290 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) removed outlier: 6.515A 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: 6.724A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (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 223 through 225 Processing sheet with id= L, first strand: chain 'U' and resid 286 through 290 removed outlier: 7.101A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE U 380 " --> pdb=" O TYR U 324 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'V' and resid 85 through 91 removed outlier: 6.620A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL V 90 " --> pdb=" O ILE V 94 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE V 94 " --> pdb=" O VAL V 90 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLN V 149 " --> pdb=" O LEU V 108 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N CYS V 110 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR V 147 " --> pdb=" O CYS V 110 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= O, first strand: chain 'V' and resid 404 through 408 removed outlier: 3.739A pdb=" N LEU V 222 " --> pdb=" O GLY V 404 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE V 383 " --> pdb=" O ILE V 223 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'V' and resid 285 through 290 removed outlier: 8.856A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'X' and resid 38 through 44 removed outlier: 6.387A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (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: 8.309A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL X 284 " --> pdb=" O VAL X 336 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL X 213 " --> pdb=" O ASP X 285 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N THR X 245 " --> pdb=" O PHE X 210 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLY X 212 " --> pdb=" O THR X 245 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL X 247 " --> pdb=" O GLY X 212 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLY X 214 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLY X 249 " --> pdb=" O GLY X 214 " (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 37 through 39 removed outlier: 6.648A pdb=" N ARG Y 86 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N HIS Y 79 " --> pdb=" O THR Y 84 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR Y 84 " --> pdb=" O HIS Y 79 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ARG Y 51 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL Y 40 " --> pdb=" O ARG Y 51 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'Y' and resid 110 through 113 Processing sheet with id= W, first strand: chain 'Y' and resid 360 through 363 removed outlier: 7.548A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL Y 280 " --> pdb=" O THR Y 334 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N VAL Y 336 " --> pdb=" O VAL Y 280 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU Y 282 " --> pdb=" O VAL Y 336 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA Y 338 " --> pdb=" O LEU Y 282 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL Y 284 " --> pdb=" O ALA Y 338 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA Y 211 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Z' and resid 39 through 44 removed outlier: 6.529A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Z' and resid 110 through 113 removed outlier: 3.517A pdb=" N ASP Z 139 " --> pdb=" O VAL Z 113 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Z' and resid 360 through 363 removed outlier: 6.393A pdb=" N THR Z 245 " --> pdb=" O PHE Z 210 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLY Z 212 " --> pdb=" O THR Z 245 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL Z 247 " --> pdb=" O GLY Z 212 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Z' and resid 559 through 561 1434 hydrogen bonds defined for protein. 3633 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.00 Time building geometry restraints manager: 14.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10625 1.34 - 1.46: 4831 1.46 - 1.57: 18707 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34384 Sorted by residual: bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.88e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.87e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.66e+01 bond pdb=" C5 ATP T1001 " pdb=" C6 ATP T1001 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.43e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.31e+01 ... (remaining 34379 not shown) Histogram of bond angle deviations from ideal: 96.88 - 104.70: 581 104.70 - 112.53: 17799 112.53 - 120.35: 15227 120.35 - 128.17: 12849 128.17 - 136.00: 142 Bond angle restraints: 46598 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 118.84 21.03 1.00e+00 1.00e+00 4.42e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 119.87 20.00 1.00e+00 1.00e+00 4.00e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 117.79 19.04 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 119.15 17.68 1.00e+00 1.00e+00 3.13e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 124.42 15.45 1.00e+00 1.00e+00 2.39e+02 ... (remaining 46593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.61: 19451 22.61 - 45.22: 1173 45.22 - 67.83: 138 67.83 - 90.44: 39 90.44 - 113.05: 2 Dihedral angle restraints: 20803 sinusoidal: 8060 harmonic: 12743 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 -127.03 -52.97 0 5.00e+00 4.00e-02 1.12e+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 -131.21 -48.79 0 5.00e+00 4.00e-02 9.52e+01 dihedral pdb=" CA PRO U 250 " pdb=" C PRO U 250 " pdb=" N LYS U 251 " pdb=" CA LYS U 251 " ideal model delta harmonic sigma weight residual 180.00 150.48 29.52 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 20800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4115 0.058 - 0.116: 1164 0.116 - 0.174: 212 0.174 - 0.231: 14 0.231 - 0.289: 8 Chirality restraints: 5513 Sorted by residual: chirality pdb=" CB ILE Z 524 " pdb=" CA ILE Z 524 " pdb=" CG1 ILE Z 524 " pdb=" CG2 ILE Z 524 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB ILE B 95 " pdb=" CA ILE B 95 " pdb=" CG1 ILE B 95 " pdb=" CG2 ILE B 95 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CB VAL Z 129 " pdb=" CA VAL Z 129 " pdb=" CG1 VAL Z 129 " pdb=" CG2 VAL Z 129 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 5510 not shown) Planarity restraints: 5991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Y 503 " 0.031 2.00e-02 2.50e+03 6.10e-02 3.72e+01 pdb=" C ALA Y 503 " -0.106 2.00e-02 2.50e+03 pdb=" O ALA Y 503 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS Y 504 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 6.02e-02 3.63e+01 pdb=" C ALA Z 503 " -0.104 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU Q 33 " -0.051 5.00e-02 4.00e+02 7.62e-02 9.30e+00 pdb=" N PRO Q 34 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO Q 34 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO Q 34 " -0.043 5.00e-02 4.00e+02 ... (remaining 5988 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 341 2.57 - 3.15: 26361 3.15 - 3.73: 54255 3.73 - 4.32: 76757 4.32 - 4.90: 126344 Nonbonded interactions: 284058 Sorted by model distance: nonbonded pdb=" O ASN Z 514 " pdb=" CG2 VAL Z 517 " model vdw 1.985 3.460 nonbonded pdb=" O2B ATP V1001 " pdb="MG MG V1002 " model vdw 2.055 2.170 nonbonded pdb=" O1B ATP U1001 " pdb="MG MG U1002 " model vdw 2.059 2.170 nonbonded pdb=" OG1 THR Y 190 " pdb="MG MG Y 602 " model vdw 2.067 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.090 2.170 ... (remaining 284053 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 562 or resid 1001 through 1002)) selection = (chain 'V' and (resid 85 through 562 or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 552) selection = (chain 'Y' and resid 37 through 552) selection = (chain 'Z' and resid 37 through 552) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.460 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: 26.260 Check model and map are aligned: 0.500 Set scattering table: 0.260 Process input model: 90.490 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 34384 Z= 0.390 Angle : 0.895 21.028 46598 Z= 0.534 Chirality : 0.054 0.289 5513 Planarity : 0.007 0.076 5991 Dihedral : 14.715 113.051 12653 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.17 % Favored : 95.62 % Rotamer: Outliers : 0.20 % Allowed : 8.82 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.10), residues: 4457 helix: -2.91 (0.08), residues: 2101 sheet: -2.33 (0.21), residues: 501 loop : -2.42 (0.12), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP X 141 HIS 0.010 0.002 HIS R 66 PHE 0.019 0.002 PHE R 70 TYR 0.018 0.002 TYR V 356 ARG 0.006 0.001 ARG T 555 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 794 time to evaluate : 3.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.7097 (tp) cc_final: 0.6819 (mt) REVERT: F 110 THR cc_start: 0.7753 (t) cc_final: 0.7499 (m) REVERT: G 86 ILE cc_start: 0.7333 (mt) cc_final: 0.7042 (mt) REVERT: G 99 LEU cc_start: 0.7267 (mt) cc_final: 0.6712 (mp) REVERT: G 107 PHE cc_start: 0.7284 (t80) cc_final: 0.6948 (t80) REVERT: J 94 ASN cc_start: 0.7659 (t0) cc_final: 0.7419 (t0) REVERT: S 60 MET cc_start: 0.7636 (ttm) cc_final: 0.7087 (mtp) REVERT: S 68 MET cc_start: 0.7229 (ttp) cc_final: 0.6906 (ttt) REVERT: U 58 LEU cc_start: 0.7374 (mt) cc_final: 0.7152 (tp) REVERT: U 151 VAL cc_start: 0.8526 (t) cc_final: 0.8286 (t) REVERT: U 236 ILE cc_start: 0.9170 (mm) cc_final: 0.8894 (mt) REVERT: U 309 MET cc_start: 0.9057 (mtt) cc_final: 0.8856 (mtp) REVERT: U 448 LEU cc_start: 0.8627 (mt) cc_final: 0.8187 (mp) REVERT: U 495 GLU cc_start: 0.7644 (pm20) cc_final: 0.7367 (pm20) REVERT: U 558 LYS cc_start: 0.6019 (tmtt) cc_final: 0.5590 (mmmt) REVERT: V 210 ASP cc_start: 0.7752 (m-30) cc_final: 0.7479 (m-30) REVERT: V 479 ARG cc_start: 0.7973 (mmt-90) cc_final: 0.7678 (tpp-160) REVERT: V 522 GLU cc_start: 0.7287 (tp30) cc_final: 0.7047 (tp30) REVERT: X 198 ASN cc_start: 0.7776 (t0) cc_final: 0.7443 (m-40) REVERT: X 497 GLU cc_start: 0.7490 (pp20) cc_final: 0.7120 (pp20) REVERT: Y 221 ASN cc_start: 0.8710 (t0) cc_final: 0.8456 (t0) REVERT: Y 439 ILE cc_start: 0.8187 (pt) cc_final: 0.7891 (mt) REVERT: Z 225 ARG cc_start: 0.7110 (mmt180) cc_final: 0.6668 (mmm-85) REVERT: Z 401 ARG cc_start: 0.7101 (tpt-90) cc_final: 0.6438 (ptp-170) REVERT: Z 502 MET cc_start: 0.7225 (mtp) cc_final: 0.6744 (mtm) REVERT: Z 535 LYS cc_start: 0.7116 (pttp) cc_final: 0.6859 (mmmt) outliers start: 7 outliers final: 3 residues processed: 799 average time/residue: 0.5093 time to fit residues: 652.9017 Evaluate side-chains 487 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 484 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain Y residue 166 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 372 optimal weight: 3.9990 chunk 334 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 345 optimal weight: 0.0030 chunk 133 optimal weight: 4.9990 chunk 210 optimal weight: 0.8980 chunk 257 optimal weight: 0.8980 chunk 400 optimal weight: 6.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 ASN A 98 GLN C 87 ASN C 98 GLN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN I 87 ASN P 140 ASN P 148 HIS ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN R 85 GLN S 40 ASN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN S 174 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN T 435 GLN ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 104 GLN U 123 GLN ** U 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 241 HIS U 248 GLN U 264 GLN ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 319 HIS ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 527 GLN ** U 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 GLN V 139 HIS V 149 GLN V 152 ASN V 242 GLN V 244 ASN V 264 GLN V 271 GLN V 278 GLN ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 386 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 549 HIS X 78 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 144 HIS X 157 GLN X 199 ASN X 278 GLN X 294 ASN X 337 GLN X 404 GLN X 414 GLN Y 174 GLN Y 199 ASN Y 252 ASN ** Y 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 174 GLN Z 562 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 34384 Z= 0.179 Angle : 0.567 10.430 46598 Z= 0.294 Chirality : 0.042 0.199 5513 Planarity : 0.005 0.059 5991 Dihedral : 6.492 84.675 4916 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.32 % Favored : 96.54 % Rotamer: Outliers : 2.44 % Allowed : 14.80 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.11), residues: 4457 helix: -1.27 (0.10), residues: 2142 sheet: -1.93 (0.21), residues: 526 loop : -1.79 (0.13), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 141 HIS 0.005 0.001 HIS Y 204 PHE 0.024 0.001 PHE B 107 TYR 0.022 0.001 TYR C 102 ARG 0.007 0.000 ARG T 342 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 599 time to evaluate : 3.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6516 (ppp) cc_final: 0.5941 (ptt) REVERT: A 123 LEU cc_start: 0.7025 (tp) cc_final: 0.6591 (mt) REVERT: C 66 CYS cc_start: 0.6983 (m) cc_final: 0.6692 (t) REVERT: E 61 MET cc_start: 0.4369 (mtp) cc_final: 0.4126 (mtm) REVERT: F 110 THR cc_start: 0.7800 (t) cc_final: 0.7382 (m) REVERT: G 81 MET cc_start: 0.7507 (tmm) cc_final: 0.7260 (tmm) REVERT: G 107 PHE cc_start: 0.7508 (t80) cc_final: 0.7271 (t80) REVERT: H 95 ILE cc_start: 0.7162 (mm) cc_final: 0.6741 (mm) REVERT: P 146 LEU cc_start: 0.8356 (mp) cc_final: 0.8121 (mt) REVERT: S 45 GLN cc_start: 0.6985 (mm-40) cc_final: 0.6620 (mm-40) REVERT: S 60 MET cc_start: 0.7640 (ttm) cc_final: 0.7032 (mtp) REVERT: S 68 MET cc_start: 0.7237 (ttp) cc_final: 0.6844 (ttt) REVERT: S 147 ARG cc_start: 0.6745 (pmt-80) cc_final: 0.6516 (pmt-80) REVERT: S 216 LEU cc_start: 0.7766 (mt) cc_final: 0.7366 (mt) REVERT: T 213 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8164 (m) REVERT: T 439 MET cc_start: 0.8151 (tpp) cc_final: 0.7803 (mmm) REVERT: T 441 GLN cc_start: 0.6573 (pp30) cc_final: 0.6278 (tm-30) REVERT: T 508 PHE cc_start: 0.7187 (m-80) cc_final: 0.6980 (m-80) REVERT: U 418 ARG cc_start: 0.8156 (mtt180) cc_final: 0.7831 (mtt180) REVERT: U 558 LYS cc_start: 0.5967 (tmtt) cc_final: 0.5580 (mmmt) REVERT: V 439 MET cc_start: 0.8684 (tpp) cc_final: 0.8179 (tpp) REVERT: V 479 ARG cc_start: 0.8038 (mmt-90) cc_final: 0.7772 (tpp-160) REVERT: V 522 GLU cc_start: 0.7323 (tp30) cc_final: 0.7113 (tp30) REVERT: X 82 ASP cc_start: 0.6735 (t70) cc_final: 0.6462 (t70) REVERT: X 198 ASN cc_start: 0.7830 (t0) cc_final: 0.7507 (m-40) REVERT: X 215 GLU cc_start: 0.6533 (tp30) cc_final: 0.6288 (tp30) REVERT: Y 221 ASN cc_start: 0.8697 (t0) cc_final: 0.8300 (t0) REVERT: Y 266 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8494 (mm) REVERT: Y 439 ILE cc_start: 0.8304 (pt) cc_final: 0.8085 (mt) REVERT: Z 195 GLU cc_start: 0.6514 (tp30) cc_final: 0.6259 (tp30) REVERT: Z 227 MET cc_start: 0.8367 (mtp) cc_final: 0.8165 (mtp) REVERT: Z 502 MET cc_start: 0.7235 (mtp) cc_final: 0.6749 (mtm) REVERT: Z 535 LYS cc_start: 0.7144 (pttp) cc_final: 0.6919 (mmmt) REVERT: Z 562 ASN cc_start: 0.7464 (OUTLIER) cc_final: 0.6884 (m110) outliers start: 87 outliers final: 45 residues processed: 651 average time/residue: 0.4543 time to fit residues: 482.9128 Evaluate side-chains 532 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 484 time to evaluate : 3.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 222 ASP Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain T residue 125 ASP Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain U residue 255 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 169 LEU Chi-restraints excluded: chain X residue 294 ASN Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 562 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 222 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 333 optimal weight: 9.9990 chunk 272 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 401 optimal weight: 3.9990 chunk 433 optimal weight: 4.9990 chunk 357 optimal weight: 0.7980 chunk 397 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 321 optimal weight: 7.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN C 98 GLN D 87 ASN E 98 GLN H 98 GLN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 ASN S 116 ASN S 174 GLN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 297 GLN ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 264 GLN ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 336 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 294 ASN X 414 GLN X 448 GLN ** X 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 252 ASN ** Y 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 357 HIS ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 68 HIS ** Z 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 34384 Z= 0.377 Angle : 0.659 11.593 46598 Z= 0.339 Chirality : 0.046 0.293 5513 Planarity : 0.005 0.054 5991 Dihedral : 6.651 81.192 4912 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.05 % Favored : 94.79 % Rotamer: Outliers : 4.21 % Allowed : 17.52 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.12), residues: 4457 helix: -0.88 (0.11), residues: 2155 sheet: -1.67 (0.22), residues: 532 loop : -1.62 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 73 HIS 0.010 0.001 HIS T 241 PHE 0.025 0.002 PHE B 107 TYR 0.022 0.002 TYR Q 16 ARG 0.006 0.001 ARG Y 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 493 time to evaluate : 3.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.4757 (OUTLIER) cc_final: 0.4269 (tp) REVERT: A 123 LEU cc_start: 0.7152 (tp) cc_final: 0.6553 (mt) REVERT: B 81 MET cc_start: 0.7444 (tpt) cc_final: 0.6781 (tpp) REVERT: B 98 GLN cc_start: 0.8173 (tp40) cc_final: 0.7640 (mp10) REVERT: D 116 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7615 (m-10) REVERT: E 71 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7172 (tp) REVERT: E 104 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6843 (mm) REVERT: F 110 THR cc_start: 0.7661 (t) cc_final: 0.7238 (m) REVERT: G 81 MET cc_start: 0.7577 (tmm) cc_final: 0.7264 (tmm) REVERT: G 107 PHE cc_start: 0.7586 (t80) cc_final: 0.7283 (t80) REVERT: H 94 ASN cc_start: 0.8239 (m110) cc_final: 0.8019 (m-40) REVERT: J 61 MET cc_start: 0.4411 (mpp) cc_final: 0.3847 (mpp) REVERT: S 45 GLN cc_start: 0.7255 (mm-40) cc_final: 0.6882 (mm-40) REVERT: S 60 MET cc_start: 0.7728 (ttm) cc_final: 0.7108 (mtp) REVERT: S 68 MET cc_start: 0.7545 (ttp) cc_final: 0.7085 (ttt) REVERT: S 147 ARG cc_start: 0.6839 (pmt-80) cc_final: 0.6482 (pmt-80) REVERT: S 216 LEU cc_start: 0.7647 (mt) cc_final: 0.7407 (mt) REVERT: U 213 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8198 (m) REVERT: U 309 MET cc_start: 0.9099 (mtt) cc_final: 0.8860 (mtp) REVERT: U 558 LYS cc_start: 0.6087 (tmtt) cc_final: 0.5794 (mmmt) REVERT: V 43 LYS cc_start: 0.6673 (tppt) cc_final: 0.5939 (mtpt) REVERT: X 82 ASP cc_start: 0.6733 (t70) cc_final: 0.6458 (t70) REVERT: X 198 ASN cc_start: 0.7848 (t0) cc_final: 0.7434 (m-40) REVERT: Z 195 GLU cc_start: 0.6787 (tp30) cc_final: 0.6399 (tp30) REVERT: Z 502 MET cc_start: 0.7468 (mtp) cc_final: 0.6976 (mtm) REVERT: Z 535 LYS cc_start: 0.7192 (pttp) cc_final: 0.6906 (mmmt) outliers start: 150 outliers final: 105 residues processed: 591 average time/residue: 0.4434 time to fit residues: 437.8256 Evaluate side-chains 548 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 438 time to evaluate : 3.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 116 PHE Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 222 ASP Chi-restraints excluded: chain S residue 228 LEU Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain T residue 125 ASP Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 369 SER Chi-restraints excluded: chain T residue 501 VAL Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 229 THR Chi-restraints excluded: chain V residue 326 ASP Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 543 THR Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 127 GLU Chi-restraints excluded: chain X residue 136 ASP Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 169 LEU Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 252 ASN Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 326 THR Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 414 GLN Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 548 ASP Chi-restraints excluded: chain Y residue 60 LEU Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 97 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 347 THR Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 170 LEU Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 368 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 396 optimal weight: 0.9980 chunk 301 optimal weight: 0.9980 chunk 208 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 269 optimal weight: 10.0000 chunk 402 optimal weight: 5.9990 chunk 426 optimal weight: 8.9990 chunk 210 optimal weight: 0.6980 chunk 381 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN S 174 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 GLN V 241 HIS ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 144 HIS ** Y 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34384 Z= 0.167 Angle : 0.545 11.450 46598 Z= 0.276 Chirality : 0.042 0.196 5513 Planarity : 0.004 0.045 5991 Dihedral : 6.017 88.148 4912 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.39 % Favored : 96.48 % Rotamer: Outliers : 2.98 % Allowed : 19.63 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.12), residues: 4457 helix: -0.37 (0.11), residues: 2135 sheet: -1.43 (0.22), residues: 510 loop : -1.29 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 141 HIS 0.005 0.001 HIS R 66 PHE 0.025 0.001 PHE D 107 TYR 0.017 0.001 TYR U 414 ARG 0.004 0.000 ARG T 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 500 time to evaluate : 3.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.4621 (OUTLIER) cc_final: 0.4255 (tp) REVERT: A 123 LEU cc_start: 0.7126 (tp) cc_final: 0.6424 (mt) REVERT: B 98 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7687 (mp10) REVERT: E 71 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6997 (tp) REVERT: E 104 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6712 (mm) REVERT: F 110 THR cc_start: 0.7739 (t) cc_final: 0.7338 (m) REVERT: G 107 PHE cc_start: 0.7544 (t80) cc_final: 0.7343 (t80) REVERT: H 94 ASN cc_start: 0.8134 (m110) cc_final: 0.7904 (m-40) REVERT: P 106 SER cc_start: 0.6593 (p) cc_final: 0.6321 (t) REVERT: P 144 LEU cc_start: 0.9014 (mt) cc_final: 0.8775 (mt) REVERT: S 45 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6970 (mm-40) REVERT: S 60 MET cc_start: 0.7542 (ttm) cc_final: 0.6913 (mtp) REVERT: S 68 MET cc_start: 0.7282 (ttp) cc_final: 0.6863 (ttt) REVERT: S 147 ARG cc_start: 0.6720 (pmt-80) cc_final: 0.6513 (pmt-80) REVERT: S 216 LEU cc_start: 0.7604 (mt) cc_final: 0.7353 (mt) REVERT: T 213 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8156 (m) REVERT: T 284 TYR cc_start: 0.8275 (m-80) cc_final: 0.7982 (m-80) REVERT: T 439 MET cc_start: 0.8149 (tpp) cc_final: 0.7799 (mmm) REVERT: U 213 VAL cc_start: 0.8315 (OUTLIER) cc_final: 0.8107 (m) REVERT: U 236 ILE cc_start: 0.9222 (mm) cc_final: 0.8888 (mt) REVERT: U 558 LYS cc_start: 0.5889 (tmtt) cc_final: 0.5683 (mmmt) REVERT: U 559 LEU cc_start: 0.6899 (mp) cc_final: 0.6378 (tp) REVERT: V 43 LYS cc_start: 0.6607 (tppt) cc_final: 0.5821 (mtpt) REVERT: X 82 ASP cc_start: 0.6788 (t70) cc_final: 0.6447 (t70) REVERT: X 198 ASN cc_start: 0.7771 (t0) cc_final: 0.7416 (m-40) REVERT: X 558 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8352 (p) REVERT: Y 221 ASN cc_start: 0.8672 (t0) cc_final: 0.8301 (t0) REVERT: Z 195 GLU cc_start: 0.6703 (tp30) cc_final: 0.6338 (tp30) REVERT: Z 502 MET cc_start: 0.7377 (mtp) cc_final: 0.6903 (mtm) REVERT: Z 535 LYS cc_start: 0.7175 (pttp) cc_final: 0.6879 (mmmt) outliers start: 106 outliers final: 65 residues processed: 566 average time/residue: 0.4325 time to fit residues: 407.1997 Evaluate side-chains 509 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 437 time to evaluate : 4.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 122 PHE Chi-restraints excluded: chain J residue 116 PHE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain T residue 125 ASP Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 229 THR Chi-restraints excluded: chain V residue 326 ASP Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 117 THR Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 169 LEU Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 558 THR Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 135 ILE Chi-restraints excluded: chain Z residue 228 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 355 optimal weight: 5.9990 chunk 241 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 317 optimal weight: 8.9990 chunk 175 optimal weight: 0.5980 chunk 363 optimal weight: 0.7980 chunk 294 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 217 optimal weight: 8.9990 chunk 382 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 ASN H 98 GLN Q 29 ASN ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN S 174 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 195 ASN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 152 ASN ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 336 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 34384 Z= 0.351 Angle : 0.632 11.290 46598 Z= 0.323 Chirality : 0.045 0.209 5513 Planarity : 0.004 0.051 5991 Dihedral : 6.347 87.258 4912 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.27 % Favored : 94.59 % Rotamer: Outliers : 4.30 % Allowed : 20.08 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.12), residues: 4457 helix: -0.32 (0.11), residues: 2125 sheet: -1.40 (0.22), residues: 541 loop : -1.29 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 73 HIS 0.009 0.001 HIS T 241 PHE 0.026 0.002 PHE B 107 TYR 0.020 0.002 TYR U 414 ARG 0.004 0.000 ARG V 476 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 443 time to evaluate : 4.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7667 (mp10) REVERT: E 104 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6893 (mm) REVERT: G 107 PHE cc_start: 0.7765 (t80) cc_final: 0.7511 (t80) REVERT: H 94 ASN cc_start: 0.8218 (m110) cc_final: 0.7957 (m-40) REVERT: I 99 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6922 (mp) REVERT: P 106 SER cc_start: 0.6771 (p) cc_final: 0.6421 (t) REVERT: Q 35 PHE cc_start: 0.6711 (m-80) cc_final: 0.6464 (m-10) REVERT: S 60 MET cc_start: 0.7693 (ttm) cc_final: 0.7060 (mtp) REVERT: S 68 MET cc_start: 0.7546 (ttp) cc_final: 0.7076 (ttt) REVERT: S 133 GLU cc_start: 0.4992 (OUTLIER) cc_final: 0.3607 (pp20) REVERT: S 147 ARG cc_start: 0.6932 (pmt-80) cc_final: 0.6618 (pmt-80) REVERT: S 216 LEU cc_start: 0.7651 (mt) cc_final: 0.7348 (mt) REVERT: T 284 TYR cc_start: 0.8398 (m-80) cc_final: 0.8119 (m-80) REVERT: T 323 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8638 (mp) REVERT: U 53 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.7053 (p90) REVERT: U 213 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8177 (m) REVERT: U 236 ILE cc_start: 0.9305 (mm) cc_final: 0.8969 (mt) REVERT: U 558 LYS cc_start: 0.6004 (tmtt) cc_final: 0.5753 (mmmt) REVERT: V 43 LYS cc_start: 0.6715 (tppt) cc_final: 0.5889 (mtpt) REVERT: V 450 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7116 (mm) REVERT: X 198 ASN cc_start: 0.7890 (t0) cc_final: 0.7564 (m-40) REVERT: X 558 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8380 (p) REVERT: Y 513 ASP cc_start: 0.1716 (OUTLIER) cc_final: 0.0932 (m-30) REVERT: Z 386 MET cc_start: 0.7533 (mmm) cc_final: 0.6420 (mmm) REVERT: Z 502 MET cc_start: 0.7467 (mtp) cc_final: 0.6979 (mtm) REVERT: Z 535 LYS cc_start: 0.7192 (pttp) cc_final: 0.6951 (mmmt) outliers start: 153 outliers final: 109 residues processed: 556 average time/residue: 0.4120 time to fit residues: 386.0134 Evaluate side-chains 532 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 413 time to evaluate : 3.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 122 PHE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 116 PHE Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 228 LEU Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain T residue 125 ASP Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 323 ILE Chi-restraints excluded: chain T residue 369 SER Chi-restraints excluded: chain T residue 501 VAL Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 229 THR Chi-restraints excluded: chain V residue 326 ASP Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 421 LEU Chi-restraints excluded: chain V residue 450 LEU Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 543 THR Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 117 THR Chi-restraints excluded: chain X residue 127 GLU Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 169 LEU Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 252 ASN Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 326 THR Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 407 LEU Chi-restraints excluded: chain X residue 422 MET Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 548 ASP Chi-restraints excluded: chain X residue 558 THR Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 97 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 513 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 135 ILE Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 452 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 143 optimal weight: 3.9990 chunk 383 optimal weight: 0.0060 chunk 84 optimal weight: 3.9990 chunk 250 optimal weight: 0.8980 chunk 105 optimal weight: 0.0040 chunk 426 optimal weight: 5.9990 chunk 354 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 224 optimal weight: 0.0870 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 ASN P 66 GLN Q 29 ASN ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN S 174 GLN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 152 ASN ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 144 HIS Y 357 HIS ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 157 GLN ** Z 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 34384 Z= 0.150 Angle : 0.540 11.022 46598 Z= 0.272 Chirality : 0.042 0.224 5513 Planarity : 0.004 0.043 5991 Dihedral : 5.686 83.237 4912 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.01 % Favored : 96.86 % Rotamer: Outliers : 3.12 % Allowed : 21.51 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.13), residues: 4457 helix: 0.11 (0.12), residues: 2112 sheet: -1.15 (0.23), residues: 522 loop : -1.05 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Z 141 HIS 0.008 0.001 HIS V 241 PHE 0.028 0.001 PHE B 107 TYR 0.027 0.001 TYR Q 16 ARG 0.005 0.000 ARG V 347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 509 time to evaluate : 4.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.7357 (tp) cc_final: 0.7107 (tp) REVERT: F 110 THR cc_start: 0.7408 (t) cc_final: 0.6949 (m) REVERT: H 94 ASN cc_start: 0.8118 (m110) cc_final: 0.7896 (m-40) REVERT: P 106 SER cc_start: 0.6734 (p) cc_final: 0.6443 (t) REVERT: S 60 MET cc_start: 0.7533 (ttm) cc_final: 0.6880 (mtp) REVERT: S 62 MET cc_start: 0.7589 (mmm) cc_final: 0.7349 (mmm) REVERT: S 68 MET cc_start: 0.7281 (ttp) cc_final: 0.6895 (ttt) REVERT: T 213 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8296 (m) REVERT: U 213 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8091 (m) REVERT: U 236 ILE cc_start: 0.9215 (mm) cc_final: 0.8889 (mt) REVERT: U 558 LYS cc_start: 0.5837 (tmtt) cc_final: 0.5552 (mmmt) REVERT: U 559 LEU cc_start: 0.6870 (mp) cc_final: 0.6559 (tp) REVERT: V 43 LYS cc_start: 0.6599 (tppt) cc_final: 0.5790 (mtpt) REVERT: X 198 ASN cc_start: 0.7826 (t0) cc_final: 0.7523 (m-40) REVERT: Y 266 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8180 (mm) REVERT: Z 502 MET cc_start: 0.7345 (mtp) cc_final: 0.6869 (mtm) outliers start: 111 outliers final: 81 residues processed: 586 average time/residue: 0.4195 time to fit residues: 414.7999 Evaluate side-chains 530 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 446 time to evaluate : 4.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 122 PHE Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 116 PHE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 166 TYR Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain T residue 125 ASP Chi-restraints excluded: chain T residue 139 HIS Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 152 ASN Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 125 ASP Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 229 THR Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 543 THR Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 117 THR Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 169 LEU Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 407 LEU Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 347 THR Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 495 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 411 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 243 optimal weight: 0.0770 chunk 311 optimal weight: 4.9990 chunk 241 optimal weight: 0.5980 chunk 359 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 425 optimal weight: 2.9990 chunk 266 optimal weight: 0.0670 chunk 259 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN C 94 ASN D 87 ASN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 GLN S 77 GLN S 116 ASN S 174 GLN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 297 GLN ** T 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 152 ASN U 264 GLN ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 246 ASN V 336 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 34384 Z= 0.148 Angle : 0.537 10.087 46598 Z= 0.271 Chirality : 0.042 0.183 5513 Planarity : 0.004 0.039 5991 Dihedral : 5.422 76.973 4912 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.52 % Favored : 96.32 % Rotamer: Outliers : 3.06 % Allowed : 22.35 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 4457 helix: 0.27 (0.12), residues: 2130 sheet: -1.03 (0.23), residues: 544 loop : -0.91 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 141 HIS 0.010 0.001 HIS V 241 PHE 0.027 0.001 PHE B 107 TYR 0.022 0.001 TYR Q 16 ARG 0.004 0.000 ARG V 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 504 time to evaluate : 3.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.4574 (OUTLIER) cc_final: 0.4220 (tp) REVERT: A 123 LEU cc_start: 0.6980 (tp) cc_final: 0.6236 (mt) REVERT: B 98 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7507 (mp10) REVERT: F 110 THR cc_start: 0.7240 (t) cc_final: 0.6617 (m) REVERT: H 94 ASN cc_start: 0.8159 (m110) cc_final: 0.7944 (m-40) REVERT: J 61 MET cc_start: 0.4052 (mpp) cc_final: 0.3832 (mpp) REVERT: P 144 LEU cc_start: 0.8971 (mt) cc_final: 0.8759 (mt) REVERT: Q 35 PHE cc_start: 0.6115 (m-10) cc_final: 0.5872 (m-10) REVERT: R 176 PHE cc_start: 0.4849 (t80) cc_final: 0.4548 (t80) REVERT: S 60 MET cc_start: 0.7524 (ttm) cc_final: 0.6868 (mtp) REVERT: S 62 MET cc_start: 0.7576 (mmm) cc_final: 0.7327 (mmm) REVERT: S 67 LYS cc_start: 0.7998 (mtpt) cc_final: 0.7750 (mttt) REVERT: S 68 MET cc_start: 0.7342 (ttp) cc_final: 0.6959 (ttt) REVERT: S 133 GLU cc_start: 0.4941 (OUTLIER) cc_final: 0.3485 (pp20) REVERT: T 213 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8207 (m) REVERT: T 309 MET cc_start: 0.7984 (mtt) cc_final: 0.7638 (mtt) REVERT: U 213 VAL cc_start: 0.8309 (OUTLIER) cc_final: 0.7991 (m) REVERT: U 304 TYR cc_start: 0.8822 (m-80) cc_final: 0.8422 (m-10) REVERT: U 558 LYS cc_start: 0.5756 (tmtt) cc_final: 0.5494 (mmmt) REVERT: U 559 LEU cc_start: 0.6842 (mp) cc_final: 0.6551 (tp) REVERT: V 450 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.6978 (mm) REVERT: V 539 ASN cc_start: 0.6258 (p0) cc_final: 0.5870 (p0) REVERT: X 82 ASP cc_start: 0.6728 (t70) cc_final: 0.6417 (t70) REVERT: X 198 ASN cc_start: 0.7847 (t0) cc_final: 0.7525 (m-40) REVERT: X 454 THR cc_start: 0.7325 (OUTLIER) cc_final: 0.7009 (p) REVERT: Y 266 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8133 (mm) REVERT: Y 484 MET cc_start: 0.7716 (mmm) cc_final: 0.7456 (mmt) REVERT: Z 502 MET cc_start: 0.7290 (mtp) cc_final: 0.6822 (mtm) outliers start: 109 outliers final: 79 residues processed: 581 average time/residue: 0.4232 time to fit residues: 412.7818 Evaluate side-chains 547 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 460 time to evaluate : 3.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain C residue 66 CYS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 122 PHE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain T residue 125 ASP Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 125 ASP Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 229 THR Chi-restraints excluded: chain V residue 450 LEU Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 127 GLU Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain X residue 294 ASN Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 407 LEU Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 347 THR Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 495 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 262 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 253 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 270 optimal weight: 7.9990 chunk 289 optimal weight: 0.8980 chunk 210 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 334 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN S 174 GLN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 144 HIS ** Z 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 34384 Z= 0.165 Angle : 0.551 9.845 46598 Z= 0.276 Chirality : 0.042 0.190 5513 Planarity : 0.004 0.042 5991 Dihedral : 5.361 73.983 4912 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.39 % Favored : 96.48 % Rotamer: Outliers : 3.00 % Allowed : 23.00 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.13), residues: 4457 helix: 0.33 (0.12), residues: 2132 sheet: -0.91 (0.23), residues: 533 loop : -0.86 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Z 141 HIS 0.010 0.001 HIS V 241 PHE 0.028 0.001 PHE C 107 TYR 0.023 0.001 TYR Q 16 ARG 0.004 0.000 ARG Y 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 472 time to evaluate : 3.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.4347 (OUTLIER) cc_final: 0.3954 (tp) REVERT: A 123 LEU cc_start: 0.6902 (tp) cc_final: 0.6155 (mt) REVERT: B 98 GLN cc_start: 0.8254 (tp40) cc_final: 0.7332 (mp10) REVERT: F 110 THR cc_start: 0.7108 (t) cc_final: 0.6499 (m) REVERT: H 94 ASN cc_start: 0.8124 (m110) cc_final: 0.7881 (m-40) REVERT: Q 35 PHE cc_start: 0.6095 (m-10) cc_final: 0.5846 (m-10) REVERT: S 60 MET cc_start: 0.7504 (ttm) cc_final: 0.6895 (mtp) REVERT: S 62 MET cc_start: 0.7571 (mmm) cc_final: 0.7322 (mmm) REVERT: S 67 LYS cc_start: 0.7999 (mtpt) cc_final: 0.7756 (mttt) REVERT: S 68 MET cc_start: 0.7357 (ttp) cc_final: 0.6958 (ttt) REVERT: S 133 GLU cc_start: 0.4902 (OUTLIER) cc_final: 0.3441 (pp20) REVERT: T 213 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8239 (m) REVERT: T 508 PHE cc_start: 0.7314 (m-80) cc_final: 0.6913 (m-80) REVERT: U 213 VAL cc_start: 0.8271 (OUTLIER) cc_final: 0.8059 (m) REVERT: U 558 LYS cc_start: 0.5762 (tmtt) cc_final: 0.5500 (mmmt) REVERT: U 559 LEU cc_start: 0.6862 (mp) cc_final: 0.6585 (tp) REVERT: V 450 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7007 (mm) REVERT: V 558 LYS cc_start: 0.7091 (tptt) cc_final: 0.6597 (pttt) REVERT: X 82 ASP cc_start: 0.6709 (t70) cc_final: 0.6418 (t70) REVERT: X 198 ASN cc_start: 0.7874 (t0) cc_final: 0.7543 (m-40) REVERT: X 454 THR cc_start: 0.7279 (OUTLIER) cc_final: 0.6962 (p) REVERT: Y 221 ASN cc_start: 0.8668 (t0) cc_final: 0.8190 (t0) REVERT: Y 266 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8308 (mm) REVERT: Z 194 MET cc_start: 0.7503 (mmt) cc_final: 0.7154 (mmt) REVERT: Z 502 MET cc_start: 0.7268 (mtp) cc_final: 0.6800 (mtm) outliers start: 107 outliers final: 84 residues processed: 551 average time/residue: 0.4152 time to fit residues: 383.1514 Evaluate side-chains 552 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 461 time to evaluate : 3.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 122 PHE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 166 TYR Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain T residue 125 ASP Chi-restraints excluded: chain T residue 139 HIS Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 125 ASP Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 229 THR Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 450 LEU Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 543 THR Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 127 GLU Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain X residue 294 ASN Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 407 LEU Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 548 ASP Chi-restraints excluded: chain Y residue 97 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 347 THR Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 452 VAL Chi-restraints excluded: chain Z residue 491 ASP Chi-restraints excluded: chain Z residue 495 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 386 optimal weight: 0.9990 chunk 407 optimal weight: 0.0070 chunk 371 optimal weight: 7.9990 chunk 396 optimal weight: 4.9990 chunk 238 optimal weight: 6.9990 chunk 172 optimal weight: 0.6980 chunk 311 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 357 optimal weight: 0.9990 chunk 374 optimal weight: 0.9990 chunk 394 optimal weight: 0.0870 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 34384 Z= 0.151 Angle : 0.552 10.324 46598 Z= 0.276 Chirality : 0.042 0.252 5513 Planarity : 0.003 0.042 5991 Dihedral : 5.255 74.183 4912 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.39 % Favored : 96.48 % Rotamer: Outliers : 2.81 % Allowed : 23.84 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.13), residues: 4457 helix: 0.45 (0.12), residues: 2101 sheet: -0.81 (0.23), residues: 514 loop : -0.79 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Z 141 HIS 0.004 0.001 HIS R 66 PHE 0.030 0.001 PHE C 116 TYR 0.034 0.001 TYR B 102 ARG 0.004 0.000 ARG J 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 486 time to evaluate : 3.958 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: A 119 LEU cc_start: 0.4300 (OUTLIER) cc_final: 0.4001 (tp) REVERT: A 123 LEU cc_start: 0.6802 (tp) cc_final: 0.6079 (mt) REVERT: D 80 VAL cc_start: 0.8472 (p) cc_final: 0.8173 (m) REVERT: F 110 THR cc_start: 0.7057 (t) cc_final: 0.6417 (m) REVERT: G 104 LEU cc_start: 0.5836 (mt) cc_final: 0.5632 (mp) REVERT: H 94 ASN cc_start: 0.8126 (m110) cc_final: 0.7905 (m-40) REVERT: Q 35 PHE cc_start: 0.6046 (m-10) cc_final: 0.5782 (m-10) REVERT: S 60 MET cc_start: 0.7493 (ttm) cc_final: 0.6873 (mtp) REVERT: S 62 MET cc_start: 0.7557 (mmm) cc_final: 0.7324 (mmm) REVERT: S 67 LYS cc_start: 0.7994 (mtpt) cc_final: 0.7748 (mttt) REVERT: S 68 MET cc_start: 0.7372 (ttp) cc_final: 0.6966 (ttt) REVERT: S 133 GLU cc_start: 0.4891 (OUTLIER) cc_final: 0.3423 (pp20) REVERT: T 213 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8164 (m) REVERT: T 309 MET cc_start: 0.7905 (mtt) cc_final: 0.7595 (mtt) REVERT: T 508 PHE cc_start: 0.7296 (m-80) cc_final: 0.6876 (m-80) REVERT: U 558 LYS cc_start: 0.5730 (tmtt) cc_final: 0.5466 (mmmt) REVERT: U 559 LEU cc_start: 0.6816 (mp) cc_final: 0.6561 (tp) REVERT: V 439 MET cc_start: 0.8472 (tpp) cc_final: 0.8134 (tpp) REVERT: V 450 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.6937 (mm) REVERT: V 539 ASN cc_start: 0.6386 (p0) cc_final: 0.5760 (p0) REVERT: V 558 LYS cc_start: 0.6953 (tptt) cc_final: 0.6499 (pttt) REVERT: X 82 ASP cc_start: 0.6713 (t70) cc_final: 0.6436 (t70) REVERT: X 194 MET cc_start: 0.7136 (mtm) cc_final: 0.6758 (mtp) REVERT: X 198 ASN cc_start: 0.7867 (t0) cc_final: 0.7514 (m-40) REVERT: X 471 GLN cc_start: 0.7198 (tp40) cc_final: 0.6991 (tm-30) REVERT: Y 221 ASN cc_start: 0.8648 (t0) cc_final: 0.8172 (t160) REVERT: Y 266 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8142 (mm) REVERT: Z 386 MET cc_start: 0.6972 (mmm) cc_final: 0.6749 (mtt) REVERT: Z 502 MET cc_start: 0.7210 (mtp) cc_final: 0.6731 (mtm) outliers start: 100 outliers final: 83 residues processed: 559 average time/residue: 0.4439 time to fit residues: 414.6061 Evaluate side-chains 546 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 458 time to evaluate : 4.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 122 PHE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 228 LEU Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain T residue 125 ASP Chi-restraints excluded: chain T residue 139 HIS Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 125 ASP Chi-restraints excluded: chain V residue 165 ASP Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 229 THR Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 450 LEU Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 252 ASN Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain X residue 294 ASN Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 407 LEU Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 548 ASP Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 325 ILE Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 347 THR Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 452 VAL Chi-restraints excluded: chain Z residue 491 ASP Chi-restraints excluded: chain Z residue 495 VAL Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 260 optimal weight: 0.8980 chunk 418 optimal weight: 0.4980 chunk 255 optimal weight: 7.9990 chunk 198 optimal weight: 1.9990 chunk 291 optimal weight: 10.0000 chunk 439 optimal weight: 7.9990 chunk 404 optimal weight: 7.9990 chunk 349 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 270 optimal weight: 0.6980 chunk 214 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 94 ASN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 34384 Z= 0.177 Angle : 0.577 12.870 46598 Z= 0.287 Chirality : 0.043 0.334 5513 Planarity : 0.004 0.042 5991 Dihedral : 5.290 74.687 4912 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.70 % Favored : 96.14 % Rotamer: Outliers : 2.61 % Allowed : 24.26 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.13), residues: 4457 helix: 0.39 (0.12), residues: 2110 sheet: -0.83 (0.23), residues: 536 loop : -0.78 (0.15), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Z 141 HIS 0.004 0.001 HIS T 241 PHE 0.040 0.001 PHE C 116 TYR 0.028 0.001 TYR Q 16 ARG 0.004 0.000 ARG E 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 472 time to evaluate : 3.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.4136 (OUTLIER) cc_final: 0.3809 (tp) REVERT: A 123 LEU cc_start: 0.6841 (tp) cc_final: 0.6349 (mt) REVERT: B 98 GLN cc_start: 0.8290 (tp40) cc_final: 0.7896 (tm-30) REVERT: B 102 TYR cc_start: 0.5762 (m-80) cc_final: 0.5352 (m-80) REVERT: D 80 VAL cc_start: 0.8482 (p) cc_final: 0.8156 (m) REVERT: F 110 THR cc_start: 0.6817 (t) cc_final: 0.6209 (m) REVERT: H 94 ASN cc_start: 0.8108 (m110) cc_final: 0.7858 (m-40) REVERT: Q 35 PHE cc_start: 0.6082 (m-10) cc_final: 0.5814 (m-10) REVERT: S 60 MET cc_start: 0.7504 (ttm) cc_final: 0.6915 (mtp) REVERT: S 62 MET cc_start: 0.7572 (mmm) cc_final: 0.7323 (mmm) REVERT: S 67 LYS cc_start: 0.8050 (mtpt) cc_final: 0.7798 (mttt) REVERT: S 68 MET cc_start: 0.7408 (ttp) cc_final: 0.6982 (ttt) REVERT: S 133 GLU cc_start: 0.4824 (OUTLIER) cc_final: 0.3406 (pp20) REVERT: S 203 PHE cc_start: 0.7273 (m-10) cc_final: 0.7009 (m-80) REVERT: T 213 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.8239 (m) REVERT: T 309 MET cc_start: 0.7937 (mtt) cc_final: 0.7630 (mtt) REVERT: T 508 PHE cc_start: 0.7395 (m-80) cc_final: 0.6975 (m-80) REVERT: U 558 LYS cc_start: 0.5715 (tmtt) cc_final: 0.5449 (mmmt) REVERT: U 559 LEU cc_start: 0.6858 (mp) cc_final: 0.6542 (tp) REVERT: V 439 MET cc_start: 0.8500 (tpp) cc_final: 0.8158 (tpp) REVERT: V 450 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.6984 (mm) REVERT: V 539 ASN cc_start: 0.6468 (p0) cc_final: 0.5842 (p0) REVERT: V 558 LYS cc_start: 0.6928 (tptt) cc_final: 0.6503 (pttt) REVERT: X 82 ASP cc_start: 0.6696 (t70) cc_final: 0.6467 (t70) REVERT: X 198 ASN cc_start: 0.7896 (t0) cc_final: 0.7610 (m-40) REVERT: Y 221 ASN cc_start: 0.8759 (t0) cc_final: 0.8334 (t160) REVERT: Y 266 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8181 (mm) REVERT: Z 386 MET cc_start: 0.6979 (mmm) cc_final: 0.6643 (mtt) REVERT: Z 502 MET cc_start: 0.7229 (mtp) cc_final: 0.6780 (mtm) outliers start: 93 outliers final: 84 residues processed: 541 average time/residue: 0.4317 time to fit residues: 392.6834 Evaluate side-chains 544 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 455 time to evaluate : 3.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 122 PHE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 228 LEU Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain T residue 125 ASP Chi-restraints excluded: chain T residue 139 HIS Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 125 ASP Chi-restraints excluded: chain V residue 165 ASP Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 229 THR Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 450 LEU Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 127 GLU Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 252 ASN Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain X residue 294 ASN Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 407 LEU Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 548 ASP Chi-restraints excluded: chain Y residue 97 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 347 THR Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 452 VAL Chi-restraints excluded: chain Z residue 491 ASP Chi-restraints excluded: chain Z residue 495 VAL Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 277 optimal weight: 1.9990 chunk 372 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 322 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 350 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 359 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 ASN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN S 174 GLN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 414 GLN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 204 HIS ** Z 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.137149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.115721 restraints weight = 61849.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.115450 restraints weight = 41531.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115990 restraints weight = 31741.711| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 34384 Z= 0.305 Angle : 0.638 10.272 46598 Z= 0.323 Chirality : 0.045 0.224 5513 Planarity : 0.004 0.043 5991 Dihedral : 5.743 78.326 4912 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.85 % Favored : 95.00 % Rotamer: Outliers : 2.92 % Allowed : 24.23 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.13), residues: 4457 helix: 0.23 (0.12), residues: 2093 sheet: -1.03 (0.22), residues: 571 loop : -0.93 (0.15), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 73 HIS 0.008 0.001 HIS T 241 PHE 0.031 0.002 PHE B 107 TYR 0.028 0.002 TYR Q 16 ARG 0.004 0.000 ARG E 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8098.25 seconds wall clock time: 147 minutes 43.83 seconds (8863.83 seconds total)