Starting phenix.real_space_refine on Fri Mar 22 15:56:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rds_4829/03_2024/6rds_4829_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rds_4829/03_2024/6rds_4829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rds_4829/03_2024/6rds_4829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rds_4829/03_2024/6rds_4829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rds_4829/03_2024/6rds_4829_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rds_4829/03_2024/6rds_4829_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 116 5.16 5 C 21541 2.51 5 N 5795 2.21 5 O 6421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 93": "OD1" <-> "OD2" Residue "P TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q 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 GLU 23": "OE1" <-> "OE2" Residue "R GLU 32": "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 PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 177": "OE1" <-> "OE2" Residue "R GLU 186": "OE1" <-> "OE2" Residue "R GLU 196": "OE1" <-> "OE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 222": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ASP 142": "OD1" <-> "OD2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ASP 172": "OD1" <-> "OD2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 294": "OD1" <-> "OD2" Residue "T TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 325": "OD1" <-> "OD2" Residue "T ASP 326": "OD1" <-> "OD2" Residue "T PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 389": "OD1" <-> "OD2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 429": "NH1" <-> "NH2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 467": "OD1" <-> "OD2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ASP 41": "OD1" <-> "OD2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 107": "OE1" <-> "OE2" Residue "U ASP 112": "OD1" <-> "OD2" Residue "U TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U GLU 221": "OE1" <-> "OE2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ASP 237": "OD1" <-> "OD2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 311": "OE1" <-> "OE2" Residue "U PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U ARG 342": "NH1" <-> "NH2" Residue "U ARG 343": "NH1" <-> "NH2" Residue "U ARG 364": "NH1" <-> "NH2" Residue "U PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 409": "OE1" <-> "OE2" Residue "U GLU 411": "OE1" <-> "OE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U GLU 455": "OE1" <-> "OE2" Residue "U GLU 475": "OE1" <-> "OE2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U GLU 482": "OE1" <-> "OE2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 46": "OD1" <-> "OD2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 142": "OD1" <-> "OD2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V ASP 210": "OD1" <-> "OD2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V ASP 226": "OD1" <-> "OD2" Residue "V ASP 237": "OD1" <-> "OD2" Residue "V ARG 266": "NH1" <-> "NH2" Residue "V PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ARG 335": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "V ARG 347": "NH1" <-> "NH2" Residue "V ARG 360": "NH1" <-> "NH2" Residue "V PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 403": "OD1" <-> "OD2" Residue "V PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 429": "NH1" <-> "NH2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V GLU 455": "OE1" <-> "OE2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 465": "OD1" <-> "OD2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X ASP 36": "OD1" <-> "OD2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 91": "OD1" <-> "OD2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 152": "OE1" <-> "OE2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "X PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 218": "NH1" <-> "NH2" Residue "X GLU 219": "OE1" <-> "OE2" Residue "X ARG 225": "NH1" <-> "NH2" Residue "X GLU 238": "OE1" <-> "OE2" Residue "X ARG 239": "NH1" <-> "NH2" Residue "X GLU 296": "OE1" <-> "OE2" Residue "X TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 401": "NH1" <-> "NH2" Residue "X ASP 409": "OD1" <-> "OD2" Residue "X ASP 462": "OD1" <-> "OD2" Residue "X ASP 480": "OD1" <-> "OD2" Residue "X GLU 494": "OE1" <-> "OE2" Residue "X ASP 500": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X GLU 511": "OE1" <-> "OE2" Residue "X ASP 513": "OD1" <-> "OD2" Residue "X GLU 519": "OE1" <-> "OE2" Residue "X GLU 520": "OE1" <-> "OE2" Residue "X GLU 536": "OE1" <-> "OE2" Residue "X GLU 563": "OE1" <-> "OE2" Residue "Y PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 64": "OE1" <-> "OE2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y ASP 82": "OD1" <-> "OD2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ASP 104": "OD1" <-> "OD2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y ARG 145": "NH1" <-> "NH2" Residue "Y GLU 149": "OE1" <-> "OE2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 215": "OE1" <-> "OE2" Residue "Y GLU 238": "OE1" <-> "OE2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y GLU 270": "OE1" <-> "OE2" Residue "Y GLU 296": "OE1" <-> "OE2" Residue "Y TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 345": "OD1" <-> "OD2" Residue "Y ARG 366": "NH1" <-> "NH2" Residue "Y ASP 378": "OD1" <-> "OD2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y ASP 423": "OD1" <-> "OD2" Residue "Y PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 511": "OE1" <-> "OE2" Residue "Y ASP 513": "OD1" <-> "OD2" Residue "Y GLU 519": "OE1" <-> "OE2" Residue "Y ASP 523": "OD1" <-> "OD2" Residue "Y ASP 528": "OD1" <-> "OD2" Residue "Y GLU 533": "OE1" <-> "OE2" Residue "Y GLU 541": "OE1" <-> "OE2" Residue "Y GLU 547": "OE1" <-> "OE2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 49": "OD1" <-> "OD2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "Z ARG 98": "NH1" <-> "NH2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z ASP 136": "OD1" <-> "OD2" Residue "Z GLU 156": "OE1" <-> "OE2" Residue "Z PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 216": "NH1" <-> "NH2" Residue "Z ARG 258": "NH1" <-> "NH2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 289": "NH1" <-> "NH2" Residue "Z GLU 323": "OE1" <-> "OE2" Residue "Z ASP 348": "OD1" <-> "OD2" Residue "Z PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 415": "OD1" <-> "OD2" Residue "Z ASP 423": "OD1" <-> "OD2" Residue "Z GLU 424": "OE1" <-> "OE2" Residue "Z GLU 428": "OE1" <-> "OE2" Residue "Z ARG 435": "NH1" <-> "NH2" Residue "Z ARG 437": "NH1" <-> "NH2" Residue "Z PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 465": "OD1" <-> "OD2" Residue "Z ASP 505": "OD1" <-> "OD2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z GLU 520": "OE1" <-> "OE2" Residue "Z GLU 536": "OE1" <-> "OE2" Residue "Z GLU 541": "OE1" <-> "OE2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 552": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33891 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "P" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 895 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3609 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 456} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.93, per 1000 atoms: 0.53 Number of scatterers: 33891 At special positions: 0 Unit cell: (161.109, 133.731, 206.388, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 13 15.00 Mg 5 11.99 O 6421 8.00 N 5795 7.00 C 21541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.37 Conformation dependent library (CDL) restraints added in 6.8 seconds 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 165 helices and 27 sheets defined 46.2% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.78 Creating SS restraints... Processing helix chain 'A' and resid 55 through 71 removed outlier: 3.863A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 91 removed outlier: 3.735A pdb=" N GLY A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 98 through 125 removed outlier: 3.708A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.777A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 126 removed outlier: 3.619A pdb=" N ALA B 96 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LYS B 97 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 99 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL B 100 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU B 104 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA B 108 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 115 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU B 125 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B 126 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 89 removed outlier: 4.197A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 98 through 126 removed outlier: 3.892A pdb=" N LEU C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 91 removed outlier: 3.972A pdb=" N LYS D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 126 removed outlier: 3.901A pdb=" N VAL D 100 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 115 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU D 119 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE D 124 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE D 126 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 89 removed outlier: 3.635A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 99 through 126 removed outlier: 3.809A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 91 removed outlier: 3.992A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 126 removed outlier: 4.848A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU F 125 " --> pdb=" O VAL F 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 91 removed outlier: 3.900A pdb=" N LYS G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 121 removed outlier: 5.128A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU G 99 " --> pdb=" O ALA G 96 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER G 112 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU G 118 " --> pdb=" O LEU G 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 91 removed outlier: 4.082A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA H 70 " --> pdb=" O CYS H 66 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LEU H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA H 72 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 125 removed outlier: 3.641A pdb=" N ALA H 96 " --> pdb=" O PRO H 93 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU H 119 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL H 120 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL H 121 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE H 124 " --> pdb=" O VAL H 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 91 removed outlier: 3.583A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR I 68 " --> pdb=" O ALA I 64 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA I 70 " --> pdb=" O CYS I 66 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA I 72 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 126 removed outlier: 3.584A pdb=" N ALA I 96 " --> pdb=" O PRO I 93 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LYS I 97 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU I 99 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL I 100 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA I 108 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU I 111 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER I 112 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE I 113 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL I 121 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE I 124 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE I 126 " --> pdb=" O LEU I 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 65 removed outlier: 3.865A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 89 removed outlier: 3.866A pdb=" N GLY J 73 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL J 74 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU J 78 " --> pdb=" O GLY J 75 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET J 81 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE J 82 " --> pdb=" O GLY J 79 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU J 85 " --> pdb=" O PHE J 82 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY J 88 " --> pdb=" O LEU J 85 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA J 89 " --> pdb=" O ILE J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 125 removed outlier: 3.595A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR J 110 " --> pdb=" O GLY J 106 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 64 removed outlier: 3.680A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 83 removed outlier: 3.812A pdb=" N PHE P 77 " --> pdb=" O GLU P 73 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU P 79 " --> pdb=" O TYR P 75 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE P 81 " --> pdb=" O PHE P 77 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS P 82 " --> pdb=" O ILE P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 92 removed outlier: 4.103A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 108 removed outlier: 3.879A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER P 106 " --> pdb=" O THR P 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 118 through 121 No H-bonds generated for 'chain 'P' and resid 118 through 121' Processing helix chain 'P' and resid 124 through 127 No H-bonds generated for 'chain 'P' and resid 124 through 127' Processing helix chain 'P' and resid 130 through 149 removed outlier: 4.105A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU P 142 " --> pdb=" O VAL P 139 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU P 143 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET P 145 " --> pdb=" O GLU P 142 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS P 149 " --> pdb=" O LEU P 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 11 No H-bonds generated for 'chain 'Q' and resid 8 through 11' Processing helix chain 'Q' and resid 16 through 30 removed outlier: 3.993A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 36 No H-bonds generated for 'chain 'Q' and resid 33 through 36' Processing helix chain 'Q' and resid 38 through 41 No H-bonds generated for 'chain 'Q' and resid 38 through 41' Processing helix chain 'R' and resid 30 through 40 removed outlier: 3.649A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 167 Processing helix chain 'R' and resid 175 through 196 Processing helix chain 'S' and resid 41 through 70 removed outlier: 3.959A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 78 removed outlier: 4.479A pdb=" N GLU S 76 " --> pdb=" O GLN S 72 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLN S 77 " --> pdb=" O ILE S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 89 Processing helix chain 'S' and resid 116 through 128 removed outlier: 3.663A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 147 No H-bonds generated for 'chain 'S' and resid 144 through 147' Processing helix chain 'S' and resid 150 through 153 No H-bonds generated for 'chain 'S' and resid 150 through 153' Processing helix chain 'S' and resid 172 through 183 Processing helix chain 'S' and resid 217 through 220 No H-bonds generated for 'chain 'S' and resid 217 through 220' Processing helix chain 'S' and resid 239 through 312 removed outlier: 4.043A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP S 245 " --> pdb=" O ASP S 241 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN S 276 " --> pdb=" O SER S 272 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS S 279 " --> pdb=" O GLU S 275 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE S 307 " --> pdb=" O GLU S 303 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 137 No H-bonds generated for 'chain 'T' and resid 135 through 137' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 207 through 210 No H-bonds generated for 'chain 'T' and resid 207 through 210' Processing helix chain 'T' and resid 231 through 246 removed outlier: 3.853A pdb=" N ALA T 238 " --> pdb=" O VAL T 234 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN T 244 " --> pdb=" O ILE T 240 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN T 246 " --> pdb=" O GLN T 242 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 279 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 296 through 299 No H-bonds generated for 'chain 'T' and resid 296 through 299' Processing helix chain 'T' and resid 302 through 315 removed outlier: 3.615A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 338 removed outlier: 4.011A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET T 337 " --> pdb=" O ALA T 333 " (cutoff:3.500A) Processing helix chain 'T' and resid 352 through 364 removed outlier: 3.942A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER T 359 " --> pdb=" O TYR T 356 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG T 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU T 362 " --> pdb=" O SER T 359 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU T 363 " --> pdb=" O ARG T 360 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 401 removed outlier: 3.552A pdb=" N ASN T 397 " --> pdb=" O TYR T 393 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL T 398 " --> pdb=" O ILE T 394 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER T 400 " --> pdb=" O THR T 396 " (cutoff:3.500A) 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 removed outlier: 4.033A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL T 442 " --> pdb=" O GLY T 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 437 through 442' Processing helix chain 'T' and resid 446 through 457 removed outlier: 3.524A pdb=" N ARG T 454 " --> pdb=" O LEU T 450 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) Processing helix chain 'T' and resid 460 through 462 No H-bonds generated for 'chain 'T' and resid 460 through 462' Processing helix chain 'T' and resid 470 through 481 Processing helix chain 'T' and resid 495 through 505 removed outlier: 3.777A pdb=" N VAL T 499 " --> pdb=" O GLU T 495 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 526 removed outlier: 4.965A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA T 523 " --> pdb=" O ALA T 519 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL T 524 " --> pdb=" O ALA T 520 " (cutoff:3.500A) Processing helix chain 'T' and resid 531 through 538 removed outlier: 3.826A pdb=" N ILE T 535 " --> pdb=" O ALA T 531 " (cutoff:3.500A) Processing helix chain 'T' and resid 544 through 553 removed outlier: 4.537A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 48 removed outlier: 4.892A pdb=" N GLU U 47 " --> pdb=" O LYS U 43 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU U 48 " --> pdb=" O ALA U 44 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 63 Processing helix chain 'U' and resid 66 through 72 Processing helix chain 'U' and resid 135 through 137 No H-bonds generated for 'chain 'U' and resid 135 through 137' Processing helix chain 'U' and resid 207 through 212 Processing helix chain 'U' and resid 231 through 248 removed outlier: 3.912A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLN U 248 " --> pdb=" O ASN U 244 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 279 Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 296 through 315 Proline residue: U 303 - end of helix removed outlier: 3.655A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 341 removed outlier: 3.694A pdb=" N LEU U 341 " --> pdb=" O MET U 337 " (cutoff:3.500A) Processing helix chain 'U' and resid 354 through 364 removed outlier: 4.858A pdb=" N ARG U 364 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 394 through 399 Processing helix chain 'U' and resid 410 through 414 Processing helix chain 'U' and resid 437 through 459 removed outlier: 4.417A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 484 removed outlier: 3.757A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 495 through 505 removed outlier: 3.816A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 515 through 527 removed outlier: 3.774A pdb=" N VAL U 518 " --> pdb=" O GLN U 515 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLU U 521 " --> pdb=" O VAL U 518 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU U 522 " --> pdb=" O ALA U 519 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN U 527 " --> pdb=" O VAL U 524 " (cutoff:3.500A) Processing helix chain 'U' and resid 531 through 539 Processing helix chain 'U' and resid 544 through 555 removed outlier: 4.282A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU U 554 " --> pdb=" O LEU U 550 " (cutoff:3.500A) removed outlier: 4.163A 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 56 through 69 removed outlier: 4.696A pdb=" N ILE V 59 " --> pdb=" O LYS V 56 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN V 60 " --> pdb=" O TYR V 57 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER V 63 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE V 67 " --> pdb=" O GLN V 64 " (cutoff:3.500A) Proline residue: V 68 - end of helix Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 212 Processing helix chain 'V' and resid 231 through 248 removed outlier: 4.305A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLN V 248 " --> pdb=" O ASN V 244 " (cutoff:3.500A) Processing helix chain 'V' and resid 251 through 253 No H-bonds generated for 'chain 'V' and resid 251 through 253' Processing helix chain 'V' and resid 266 through 279 Processing helix chain 'V' and resid 281 through 283 No H-bonds generated for 'chain 'V' and resid 281 through 283' Processing helix chain 'V' and resid 296 through 314 Proline residue: V 303 - end of helix removed outlier: 3.826A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 341 Processing helix chain 'V' and resid 352 through 364 removed outlier: 4.124A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU V 363 " --> pdb=" O ARG V 360 " (cutoff:3.500A) Processing helix chain 'V' and resid 393 through 401 Processing helix chain 'V' and resid 431 through 434 removed outlier: 3.981A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 431 through 434' Processing helix chain 'V' and resid 440 through 456 removed outlier: 3.979A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 481 Processing helix chain 'V' and resid 494 through 506 Processing helix chain 'V' and resid 514 through 520 removed outlier: 4.180A pdb=" N ILE V 517 " --> pdb=" O VAL V 514 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N VAL V 518 " --> pdb=" O GLN V 515 " (cutoff:3.500A) Processing helix chain 'V' and resid 522 through 525 No H-bonds generated for 'chain 'V' and resid 522 through 525' Processing helix chain 'V' and resid 530 through 539 removed outlier: 3.509A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) Processing helix chain 'V' and resid 544 through 555 removed outlier: 4.488A pdb=" N ARG V 555 " --> pdb=" O LYS V 551 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 117 No H-bonds generated for 'chain 'X' and resid 115 through 117' Processing helix chain 'X' and resid 165 through 170 Processing helix chain 'X' and resid 189 through 203 removed outlier: 5.141A pdb=" N LYS X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA X 203 " --> pdb=" O ASN X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 229 removed outlier: 3.731A pdb=" N GLU X 229 " --> pdb=" O ARG X 225 " (cutoff:3.500A) Processing helix chain 'X' and resid 239 through 241 No H-bonds generated for 'chain 'X' and resid 239 through 241' Processing helix chain 'X' and resid 261 through 274 removed outlier: 3.571A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 288 through 298 Processing helix chain 'X' and resid 314 through 322 Processing helix chain 'X' and resid 349 through 357 removed outlier: 4.288A pdb=" N ALA X 356 " --> pdb=" O ALA X 352 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N HIS X 357 " --> pdb=" O THR X 353 " (cutoff:3.500A) Processing helix chain 'X' and resid 367 through 370 No H-bonds generated for 'chain 'X' and resid 367 through 370' Processing helix chain 'X' and resid 394 through 419 removed outlier: 4.999A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) Processing helix chain 'X' and resid 427 through 442 Processing helix chain 'X' and resid 450 through 452 No H-bonds generated for 'chain 'X' and resid 450 through 452' Processing helix chain 'X' and resid 463 through 475 Processing helix chain 'X' and resid 484 through 486 No H-bonds generated for 'chain 'X' and resid 484 through 486' Processing helix chain 'X' and resid 492 through 506 removed outlier: 3.595A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE X 506 " --> pdb=" O MET X 502 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 531 Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 165 through 170 Processing helix chain 'Y' and resid 189 through 200 Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 4.561A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 258 No H-bonds generated for 'chain 'Y' and resid 255 through 258' Processing helix chain 'Y' and resid 261 through 274 Processing helix chain 'Y' and resid 287 through 297 removed outlier: 3.581A pdb=" N GLU Y 296 " --> pdb=" O ALA Y 293 " (cutoff:3.500A) Processing helix chain 'Y' and resid 314 through 324 removed outlier: 4.677A pdb=" N ARG Y 324 " --> pdb=" O GLY Y 320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 349 through 357 removed outlier: 3.892A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N HIS Y 357 " --> pdb=" O THR Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 370 Processing helix chain 'Y' and resid 389 through 392 No H-bonds generated for 'chain 'Y' and resid 389 through 392' Processing helix chain 'Y' and resid 394 through 415 removed outlier: 3.611A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) Processing helix chain 'Y' and resid 429 through 442 Processing helix chain 'Y' and resid 450 through 452 No H-bonds generated for 'chain 'Y' and resid 450 through 452' Processing helix chain 'Y' and resid 463 through 474 Processing helix chain 'Y' and resid 483 through 486 removed outlier: 3.861A pdb=" N PHE Y 486 " --> pdb=" O GLU Y 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 483 through 486' Processing helix chain 'Y' and resid 492 through 507 removed outlier: 3.892A pdb=" N ASP Y 500 " --> pdb=" O LYS Y 496 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS Y 501 " --> pdb=" O GLU Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 527 through 531 Processing helix chain 'Y' and resid 545 through 554 removed outlier: 3.901A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 117 No H-bonds generated for 'chain 'Z' and resid 115 through 117' Processing helix chain 'Z' and resid 165 through 169 Processing helix chain 'Z' and resid 189 through 203 Processing helix chain 'Z' and resid 217 through 229 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 4.318A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN Z 241 " --> pdb=" O GLU Z 238 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 258 No H-bonds generated for 'chain 'Z' and resid 255 through 258' Processing helix chain 'Z' and resid 261 through 274 Processing helix chain 'Z' and resid 287 through 300 Processing helix chain 'Z' and resid 314 through 322 removed outlier: 4.227A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 349 through 354 Processing helix chain 'Z' and resid 367 through 370 No H-bonds generated for 'chain 'Z' and resid 367 through 370' Processing helix chain 'Z' and resid 394 through 412 removed outlier: 3.613A pdb=" N ASN Z 412 " --> pdb=" O GLN Z 408 " (cutoff:3.500A) Processing helix chain 'Z' and resid 416 through 419 No H-bonds generated for 'chain 'Z' and resid 416 through 419' Processing helix chain 'Z' and resid 422 through 424 No H-bonds generated for 'chain 'Z' and resid 422 through 424' Processing helix chain 'Z' and resid 427 through 439 removed outlier: 3.788A pdb=" N LEU Z 431 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR Z 432 " --> pdb=" O GLU Z 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 448 through 454 removed outlier: 3.605A pdb=" N GLU Z 451 " --> pdb=" O GLN Z 448 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL Z 452 " --> pdb=" O VAL Z 449 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR Z 454 " --> pdb=" O GLU Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 463 through 475 removed outlier: 3.875A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 492 through 509 removed outlier: 3.736A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA Z 503 " --> pdb=" O ALA Z 499 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER Z 508 " --> pdb=" O LYS Z 504 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG Z 509 " --> pdb=" O ASP Z 505 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 531 Processing sheet with id= A, first strand: chain 'Q' and resid 45 through 49 removed outlier: 3.571A pdb=" N PHE Q 47 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'R' and resid 72 through 75 removed outlier: 6.515A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.372A 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: 6.832A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 158 through 162 removed outlier: 7.992A pdb=" N VAL S 139 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA S 161 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N SER S 141 " --> pdb=" O ALA S 161 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER S 189 " --> pdb=" O VAL S 101 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL S 103 " --> pdb=" O SER S 189 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN S 191 " --> pdb=" O VAL S 103 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL S 105 " --> pdb=" O GLN S 191 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU S 193 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS S 204 " --> pdb=" O LYS S 196 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'T' and resid 144 through 146 removed outlier: 3.766A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY T 128 " --> pdb=" O LEU T 120 " (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 223 through 225 Processing sheet with id= H, first strand: chain 'T' and resid 376 through 379 removed outlier: 6.360A pdb=" N ILE T 286 " --> pdb=" O TYR T 259 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ALA T 261 " --> pdb=" O ILE T 286 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL T 288 " --> pdb=" O ALA T 261 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLY T 263 " --> pdb=" O VAL T 288 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ALA T 290 " --> pdb=" O GLY T 263 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'T' and resid 86 through 91 removed outlier: 6.556A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.728A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU U 107 " --> pdb=" O ALA U 119 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= L, first strand: chain 'U' and resid 405 through 408 removed outlier: 6.718A pdb=" N LEU U 222 " --> pdb=" O ILE U 406 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU U 408 " --> pdb=" O LEU U 222 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE U 224 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'U' and resid 319 through 325 removed outlier: 3.538A pdb=" N LEU U 321 " --> pdb=" O TYR U 256 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'V' and resid 84 through 86 removed outlier: 7.127A pdb=" N LEU V 108 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLY V 128 " --> pdb=" O LEU V 120 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU V 122 " --> pdb=" O HIS V 126 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N HIS V 126 " --> pdb=" O LEU V 122 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= P, first strand: chain 'V' and resid 223 through 226 Processing sheet with id= Q, first strand: chain 'V' and resid 286 through 290 removed outlier: 6.702A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'X' and resid 39 through 44 removed outlier: 6.653A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'X' and resid 110 through 113 Processing sheet with id= T, first strand: chain 'X' and resid 360 through 363 removed outlier: 7.258A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N GLY X 183 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL X 339 " --> pdb=" O GLY X 183 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= V, first strand: chain 'Y' and resid 38 through 44 removed outlier: 6.291A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Y' and resid 361 through 363 removed outlier: 7.930A pdb=" N THR Y 362 " --> pdb=" O LYS Y 178 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY Y 180 " --> pdb=" O THR Y 362 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE Y 207 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N PHE Y 283 " --> pdb=" O PHE Y 207 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.104A 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: 6.573A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN Z 78 " --> pdb=" O ARG Z 86 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU Z 64 " --> pdb=" O VAL Z 103 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Z' and resid 110 through 113 removed outlier: 3.595A 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: 8.192A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL Z 284 " --> pdb=" O VAL Z 336 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA Z 338 " --> pdb=" O VAL Z 284 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Z' and resid 559 through 561 1381 hydrogen bonds defined for protein. 3597 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.95 Time building geometry restraints manager: 14.48 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: 11168 1.34 - 1.46: 6738 1.46 - 1.58: 16285 1.58 - 1.70: 21 1.70 - 1.82: 200 Bond restraints: 34412 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 5.86e+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 5.86e+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 5.65e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.95e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.19e+01 ... (remaining 34407 not shown) Histogram of bond angle deviations from ideal: 98.51 - 106.02: 790 106.02 - 113.53: 19601 113.53 - 121.04: 17138 121.04 - 128.54: 8981 128.54 - 136.05: 128 Bond angle restraints: 46638 Sorted by residual: angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 116.67 23.20 1.00e+00 1.00e+00 5.38e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 117.27 22.60 1.00e+00 1.00e+00 5.11e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 119.00 20.87 1.00e+00 1.00e+00 4.35e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 117.89 18.94 1.00e+00 1.00e+00 3.59e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 119.79 17.04 1.00e+00 1.00e+00 2.90e+02 ... (remaining 46633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.61: 19799 26.61 - 53.21: 907 53.21 - 79.82: 91 79.82 - 106.42: 23 106.42 - 133.03: 3 Dihedral angle restraints: 20823 sinusoidal: 8066 harmonic: 12757 Sorted by residual: dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual 180.00 -120.85 -59.15 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -123.59 -56.41 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual -180.00 -123.81 -56.19 0 5.00e+00 4.00e-02 1.26e+02 ... (remaining 20820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3873 0.055 - 0.109: 1332 0.109 - 0.164: 280 0.164 - 0.219: 28 0.219 - 0.274: 6 Chirality restraints: 5519 Sorted by residual: chirality pdb=" CB VAL U 137 " pdb=" CA VAL U 137 " pdb=" CG1 VAL U 137 " pdb=" CG2 VAL U 137 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB VAL V 456 " pdb=" CA VAL V 456 " pdb=" CG1 VAL V 456 " pdb=" CG2 VAL V 456 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE V 138 " pdb=" CA ILE V 138 " pdb=" CG1 ILE V 138 " pdb=" CG2 ILE V 138 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 5516 not shown) Planarity restraints: 5997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.030 2.00e-02 2.50e+03 5.89e-02 3.47e+01 pdb=" C ALA Z 503 " -0.102 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA X 307 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.85e+00 pdb=" C ALA X 307 " -0.051 2.00e-02 2.50e+03 pdb=" O ALA X 307 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL X 308 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA Y 350 " 0.046 5.00e-02 4.00e+02 7.00e-02 7.83e+00 pdb=" N PRO Y 351 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO Y 351 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO Y 351 " 0.040 5.00e-02 4.00e+02 ... (remaining 5994 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 259 2.51 - 3.10: 23636 3.10 - 3.70: 54512 3.70 - 4.30: 78204 4.30 - 4.90: 127447 Nonbonded interactions: 284058 Sorted by model distance: nonbonded pdb=" CZ PHE I 107 " pdb=" OE2 GLU I 111 " model vdw 1.908 3.340 nonbonded pdb=" OG1 THR X 190 " pdb="MG MG X 602 " model vdw 2.068 2.170 nonbonded pdb=" O2B ADP X 601 " pdb="MG MG X 602 " model vdw 2.117 2.170 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.174 2.170 nonbonded pdb=" OE2 GLU X 215 " pdb="MG MG X 602 " model vdw 2.179 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 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.300 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: 0.040 Extract box with map and model: 24.780 Check model and map are aligned: 0.500 Set scattering table: 0.320 Process input model: 90.740 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 : 0.007 0.109 34412 Z= 0.455 Angle : 0.981 23.196 46638 Z= 0.578 Chirality : 0.056 0.274 5519 Planarity : 0.007 0.070 5997 Dihedral : 15.275 133.031 12663 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.31 % Favored : 94.49 % Rotamer: Outliers : 0.51 % Allowed : 10.07 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.14 % 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: -4.24 (0.10), residues: 4461 helix: -3.18 (0.08), residues: 2120 sheet: -2.07 (0.20), residues: 570 loop : -2.31 (0.13), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP Z 141 HIS 0.010 0.002 HIS U 549 PHE 0.038 0.002 PHE X 355 TYR 0.019 0.002 TYR T 414 ARG 0.007 0.001 ARG U 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 699 time to evaluate : 3.718 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: symmetry clash REVERT: C 56 LEU cc_start: 0.5848 (mp) cc_final: 0.5451 (tp) REVERT: F 102 TYR cc_start: 0.3045 (m-10) cc_final: 0.2816 (m-80) REVERT: F 112 SER cc_start: 0.6866 (p) cc_final: 0.5347 (p) REVERT: G 71 LEU cc_start: 0.4517 (mt) cc_final: 0.4258 (mt) REVERT: H 91 ARG cc_start: 0.4782 (mtt-85) cc_final: 0.4504 (mtm-85) REVERT: P 56 LEU cc_start: 0.8990 (tp) cc_final: 0.8733 (tp) REVERT: P 83 GLN cc_start: 0.7307 (mt0) cc_final: 0.5989 (mt0) REVERT: P 143 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7519 (tm-30) REVERT: R 62 GLU cc_start: 0.4689 (mm-30) cc_final: 0.4269 (mp0) REVERT: R 125 GLU cc_start: 0.4306 (pm20) cc_final: 0.2918 (mt-10) REVERT: S 63 VAL cc_start: 0.7695 (t) cc_final: 0.7366 (t) REVERT: S 141 SER cc_start: 0.5093 (p) cc_final: 0.4851 (p) REVERT: S 193 LEU cc_start: 0.6116 (mm) cc_final: 0.5835 (mm) REVERT: T 311 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7487 (mt-10) REVERT: U 49 ARG cc_start: 0.8014 (ttp-110) cc_final: 0.7596 (tpp-160) REVERT: U 326 ASP cc_start: 0.7125 (m-30) cc_final: 0.6867 (m-30) REVERT: U 489 PHE cc_start: 0.7248 (m-10) cc_final: 0.6964 (m-10) REVERT: V 61 HIS cc_start: 0.7331 (t70) cc_final: 0.7071 (t70) REVERT: V 73 TRP cc_start: 0.7528 (m-10) cc_final: 0.7304 (m-10) REVERT: V 222 LEU cc_start: 0.9240 (tp) cc_final: 0.9037 (tt) REVERT: X 266 LEU cc_start: 0.9130 (tp) cc_final: 0.8710 (tp) REVERT: X 359 ASP cc_start: 0.8040 (t0) cc_final: 0.7792 (t0) REVERT: X 431 LEU cc_start: 0.7395 (tt) cc_final: 0.6848 (mt) REVERT: Y 82 ASP cc_start: 0.7664 (p0) cc_final: 0.7441 (p0) REVERT: Y 317 ASP cc_start: 0.6857 (t0) cc_final: 0.6597 (t0) REVERT: Y 347 THR cc_start: 0.8106 (m) cc_final: 0.7854 (m) REVERT: Y 386 MET cc_start: 0.8353 (mmm) cc_final: 0.8108 (tpp) REVERT: Z 405 LYS cc_start: 0.7602 (tppt) cc_final: 0.7191 (tptp) REVERT: Z 488 MET cc_start: 0.6088 (mmt) cc_final: 0.5608 (mmp) outliers start: 18 outliers final: 7 residues processed: 715 average time/residue: 0.4932 time to fit residues: 553.9540 Evaluate side-chains 400 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 393 time to evaluate : 3.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain X residue 538 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 0.7980 chunk 335 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 225 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 346 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 257 optimal weight: 0.8980 chunk 401 optimal weight: 3.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 94 ASN B 94 ASN C 98 GLN F 87 ASN F 98 GLN G 87 ASN G 94 ASN H 87 ASN I 94 ASN J 98 GLN P 52 GLN P 65 ASN P 140 ASN Q 21 ASN Q 40 GLN Q 43 GLN Q 46 HIS R 38 ASN R 53 ASN R 171 GLN ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN S 219 GLN S 293 ASN ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN T 271 GLN U 123 GLN U 140 GLN U 179 ASN U 248 GLN U 319 HIS U 358 HIS U 471 GLN U 549 HIS V 61 HIS V 64 GLN V 104 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 GLN V 241 HIS V 242 GLN V 278 GLN V 358 HIS V 486 GLN V 497 GLN ** V 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 199 ASN X 278 GLN X 337 GLN X 388 ASN X 448 GLN Y 68 HIS Y 83 ASN Y 153 GLN Y 204 HIS Y 278 GLN Z 144 HIS Z 199 ASN Z 241 ASN Z 250 GLN Z 278 GLN Z 294 ASN Z 404 GLN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 34412 Z= 0.189 Angle : 0.615 10.474 46638 Z= 0.316 Chirality : 0.044 0.385 5519 Planarity : 0.005 0.068 5997 Dihedral : 7.249 110.231 4926 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.17 % Favored : 95.63 % Rotamer: Outliers : 2.64 % Allowed : 16.98 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.11), residues: 4461 helix: -1.66 (0.10), residues: 2098 sheet: -1.63 (0.22), residues: 529 loop : -1.89 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Z 141 HIS 0.013 0.001 HIS R 78 PHE 0.019 0.001 PHE X 355 TYR 0.017 0.001 TYR V 502 ARG 0.013 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 463 time to evaluate : 4.466 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: B 95 ILE cc_start: 0.4959 (OUTLIER) cc_final: 0.4722 (tp) REVERT: B 98 GLN cc_start: 0.4746 (OUTLIER) cc_final: 0.4090 (pp30) REVERT: B 105 LEU cc_start: 0.3714 (tt) cc_final: 0.2624 (mp) REVERT: D 61 MET cc_start: 0.3564 (OUTLIER) cc_final: 0.3320 (mmm) REVERT: E 56 LEU cc_start: 0.5207 (OUTLIER) cc_final: 0.4340 (pt) REVERT: F 112 SER cc_start: 0.6589 (p) cc_final: 0.5409 (p) REVERT: H 91 ARG cc_start: 0.4828 (mtt-85) cc_final: 0.4452 (mtm-85) REVERT: I 61 MET cc_start: 0.3103 (mmt) cc_final: 0.2492 (mmm) REVERT: P 52 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7488 (mm-40) REVERT: P 77 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8424 (t80) REVERT: P 93 ASP cc_start: 0.9034 (t0) cc_final: 0.8734 (t0) REVERT: P 128 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6863 (mt-10) REVERT: R 125 GLU cc_start: 0.3894 (pm20) cc_final: 0.2373 (mt-10) REVERT: S 193 LEU cc_start: 0.6310 (mm) cc_final: 0.5960 (mm) REVERT: T 311 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7403 (mt-10) REVERT: U 49 ARG cc_start: 0.7843 (ttp-110) cc_final: 0.7575 (tpp-160) REVERT: U 364 ARG cc_start: 0.7682 (mtp85) cc_final: 0.7418 (mtt-85) REVERT: V 73 TRP cc_start: 0.7648 (m-10) cc_final: 0.7291 (m-10) REVERT: V 449 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: X 478 TYR cc_start: 0.7700 (m-80) cc_final: 0.7073 (m-80) REVERT: Y 195 GLU cc_start: 0.5741 (tm-30) cc_final: 0.5496 (tm-30) REVERT: Y 347 THR cc_start: 0.8216 (m) cc_final: 0.7940 (m) REVERT: Y 380 LEU cc_start: 0.8571 (mm) cc_final: 0.8046 (pp) REVERT: Y 409 ASP cc_start: 0.8034 (m-30) cc_final: 0.7589 (m-30) REVERT: Y 463 LEU cc_start: 0.6728 (tp) cc_final: 0.6298 (mp) REVERT: Z 282 LEU cc_start: 0.8872 (tp) cc_final: 0.8594 (tt) REVERT: Z 405 LYS cc_start: 0.7619 (tppt) cc_final: 0.7192 (tptp) REVERT: Z 484 MET cc_start: 0.7986 (mmm) cc_final: 0.7302 (mpp) outliers start: 94 outliers final: 46 residues processed: 527 average time/residue: 0.4462 time to fit residues: 389.4696 Evaluate side-chains 443 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 390 time to evaluate : 3.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain T residue 134 ASN Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 402 THR Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 494 ILE Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 524 VAL Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain V residue 384 GLU Chi-restraints excluded: chain V residue 449 GLU Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 363 VAL Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 345 ASP Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 223 optimal weight: 7.9990 chunk 124 optimal weight: 0.0770 chunk 334 optimal weight: 6.9990 chunk 273 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 402 optimal weight: 8.9990 chunk 434 optimal weight: 0.7980 chunk 358 optimal weight: 1.9990 chunk 398 optimal weight: 0.0970 chunk 137 optimal weight: 7.9990 chunk 322 optimal weight: 4.9990 overall best weight: 1.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 GLN F 87 ASN F 98 GLN J 98 GLN ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN U 549 HIS ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 448 GLN Z 241 ASN ** Z 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 34412 Z= 0.224 Angle : 0.610 9.593 46638 Z= 0.310 Chirality : 0.043 0.256 5519 Planarity : 0.004 0.058 5997 Dihedral : 6.915 110.425 4920 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.13 % Favored : 94.66 % Rotamer: Outliers : 3.20 % Allowed : 18.88 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.12), residues: 4461 helix: -1.19 (0.11), residues: 2121 sheet: -1.37 (0.22), residues: 548 loop : -1.68 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Z 141 HIS 0.007 0.001 HIS S 250 PHE 0.032 0.001 PHE X 355 TYR 0.022 0.002 TYR R 75 ARG 0.007 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 415 time to evaluate : 3.750 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: A 123 LEU cc_start: 0.4308 (tt) cc_final: 0.4065 (tp) REVERT: B 105 LEU cc_start: 0.4003 (tt) cc_final: 0.2671 (mt) REVERT: D 61 MET cc_start: 0.3703 (OUTLIER) cc_final: 0.3400 (mmm) REVERT: E 56 LEU cc_start: 0.5086 (OUTLIER) cc_final: 0.4373 (pt) REVERT: F 112 SER cc_start: 0.6403 (p) cc_final: 0.5586 (p) REVERT: H 91 ARG cc_start: 0.4715 (mtt-85) cc_final: 0.4425 (mtm-85) REVERT: I 124 ILE cc_start: 0.6478 (mm) cc_final: 0.6062 (tt) REVERT: P 77 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8400 (t80) REVERT: P 93 ASP cc_start: 0.8991 (t0) cc_final: 0.8630 (t0) REVERT: P 128 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7035 (mt-10) REVERT: R 117 GLU cc_start: 0.4888 (mp0) cc_final: 0.3141 (mp0) REVERT: S 193 LEU cc_start: 0.6491 (mm) cc_final: 0.6240 (mm) REVERT: S 291 ASP cc_start: 0.8301 (t70) cc_final: 0.8039 (t0) REVERT: T 311 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7494 (mt-10) REVERT: T 521 GLU cc_start: 0.7430 (mt-10) cc_final: 0.6799 (mt-10) REVERT: U 311 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7930 (mm-30) REVERT: U 364 ARG cc_start: 0.7862 (mtp85) cc_final: 0.7472 (mtt180) REVERT: V 73 TRP cc_start: 0.7700 (m-10) cc_final: 0.7258 (m-10) REVERT: V 488 GLN cc_start: 0.6532 (OUTLIER) cc_final: 0.5375 (tp40) REVERT: X 415 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7782 (t0) REVERT: X 509 ARG cc_start: 0.3613 (OUTLIER) cc_final: 0.0775 (ttt90) REVERT: Y 195 GLU cc_start: 0.5808 (tm-30) cc_final: 0.5549 (tm-30) REVERT: Y 204 HIS cc_start: 0.6867 (OUTLIER) cc_final: 0.6251 (p90) REVERT: Y 347 THR cc_start: 0.8329 (m) cc_final: 0.8013 (m) REVERT: Y 380 LEU cc_start: 0.8587 (mm) cc_final: 0.7983 (pp) REVERT: Y 409 ASP cc_start: 0.7995 (m-30) cc_final: 0.7713 (m-30) REVERT: Y 463 LEU cc_start: 0.6689 (tp) cc_final: 0.6385 (mp) REVERT: Z 282 LEU cc_start: 0.8950 (tp) cc_final: 0.8676 (tt) REVERT: Z 386 MET cc_start: 0.7334 (mmm) cc_final: 0.6793 (tpp) REVERT: Z 405 LYS cc_start: 0.7564 (tppt) cc_final: 0.7259 (tptp) outliers start: 114 outliers final: 69 residues processed: 490 average time/residue: 0.4293 time to fit residues: 350.8505 Evaluate side-chains 457 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 381 time to evaluate : 3.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 396 THR Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 494 ILE Chi-restraints excluded: chain T residue 498 THR Chi-restraints excluded: chain T residue 524 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 277 THR Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 549 HIS Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 384 GLU Chi-restraints excluded: chain V residue 403 ASP Chi-restraints excluded: chain V residue 488 GLN Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 363 VAL Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 462 ASP Chi-restraints excluded: chain X residue 509 ARG Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 162 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 345 ASP Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 397 optimal weight: 7.9990 chunk 302 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 191 optimal weight: 0.4980 chunk 270 optimal weight: 7.9990 chunk 403 optimal weight: 9.9990 chunk 427 optimal weight: 8.9990 chunk 210 optimal weight: 1.9990 chunk 382 optimal weight: 7.9990 chunk 115 optimal weight: 0.0570 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 87 ASN I 98 GLN ** P 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN ** Z 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34412 Z= 0.174 Angle : 0.579 9.812 46638 Z= 0.291 Chirality : 0.042 0.221 5519 Planarity : 0.004 0.058 5997 Dihedral : 6.541 105.018 4919 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.28 % Favored : 95.52 % Rotamer: Outliers : 3.17 % Allowed : 19.98 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.12), residues: 4461 helix: -0.86 (0.11), residues: 2125 sheet: -1.23 (0.22), residues: 541 loop : -1.54 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Y 141 HIS 0.021 0.001 HIS U 549 PHE 0.026 0.001 PHE X 355 TYR 0.044 0.001 TYR R 75 ARG 0.008 0.000 ARG U 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 420 time to evaluate : 3.960 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: A 86 ILE cc_start: 0.4177 (OUTLIER) cc_final: 0.3894 (mt) REVERT: D 61 MET cc_start: 0.3608 (OUTLIER) cc_final: 0.3359 (mmm) REVERT: E 56 LEU cc_start: 0.5097 (OUTLIER) cc_final: 0.4425 (pt) REVERT: E 104 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.5875 (mm) REVERT: F 61 MET cc_start: 0.3601 (ptp) cc_final: 0.3063 (ptp) REVERT: F 112 SER cc_start: 0.6493 (p) cc_final: 0.5596 (p) REVERT: H 91 ARG cc_start: 0.4927 (mtt-85) cc_final: 0.4455 (mtm-85) REVERT: I 61 MET cc_start: 0.2785 (mmt) cc_final: 0.2200 (mmm) REVERT: I 124 ILE cc_start: 0.6467 (mm) cc_final: 0.5976 (tt) REVERT: P 52 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7362 (mm-40) REVERT: P 77 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8162 (t80) REVERT: P 93 ASP cc_start: 0.8990 (t0) cc_final: 0.8635 (t0) REVERT: P 128 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6732 (mt-10) REVERT: R 117 GLU cc_start: 0.4826 (mp0) cc_final: 0.3303 (mp0) REVERT: S 193 LEU cc_start: 0.6625 (mm) cc_final: 0.6160 (mm) REVERT: S 291 ASP cc_start: 0.8303 (t70) cc_final: 0.8060 (t0) REVERT: U 311 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8019 (mm-30) REVERT: U 364 ARG cc_start: 0.7815 (mtp85) cc_final: 0.7529 (mtt180) REVERT: U 489 PHE cc_start: 0.7136 (m-10) cc_final: 0.6880 (m-10) REVERT: V 73 TRP cc_start: 0.7659 (m-10) cc_final: 0.7406 (m-10) REVERT: V 311 GLU cc_start: 0.6694 (mt-10) cc_final: 0.6376 (mt-10) REVERT: X 182 PHE cc_start: 0.8571 (m-80) cc_final: 0.8098 (m-10) REVERT: X 355 PHE cc_start: 0.7383 (m-80) cc_final: 0.7170 (m-80) REVERT: X 509 ARG cc_start: 0.3737 (OUTLIER) cc_final: 0.0683 (ttt90) REVERT: Y 195 GLU cc_start: 0.5770 (tm-30) cc_final: 0.5496 (tm-30) REVERT: Y 347 THR cc_start: 0.8187 (m) cc_final: 0.7901 (m) REVERT: Y 409 ASP cc_start: 0.7966 (m-30) cc_final: 0.7757 (m-30) REVERT: Y 463 LEU cc_start: 0.6647 (tp) cc_final: 0.6439 (mp) REVERT: Z 282 LEU cc_start: 0.8899 (tp) cc_final: 0.8618 (tt) REVERT: Z 386 MET cc_start: 0.7182 (mmm) cc_final: 0.6878 (tpp) REVERT: Z 405 LYS cc_start: 0.7729 (tppt) cc_final: 0.7407 (tptp) outliers start: 113 outliers final: 70 residues processed: 496 average time/residue: 0.4256 time to fit residues: 353.2687 Evaluate side-chains 456 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 380 time to evaluate : 4.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 260 VAL Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 494 ILE Chi-restraints excluded: chain T residue 524 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 277 THR Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 423 VAL Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain U residue 549 HIS Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 403 ASP Chi-restraints excluded: chain V residue 481 THR Chi-restraints excluded: chain V residue 488 GLN Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 363 VAL Chi-restraints excluded: chain X residue 462 ASP Chi-restraints excluded: chain X residue 509 ARG Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 527 LEU Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 162 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 274 ASP Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 345 ASP Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 355 optimal weight: 6.9990 chunk 242 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 318 optimal weight: 6.9990 chunk 176 optimal weight: 0.9980 chunk 364 optimal weight: 3.9990 chunk 295 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 218 optimal weight: 0.2980 chunk 383 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN S 174 GLN ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 435 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 286 ASN ** Z 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 34412 Z= 0.163 Angle : 0.570 11.182 46638 Z= 0.284 Chirality : 0.042 0.199 5519 Planarity : 0.004 0.050 5997 Dihedral : 6.245 101.239 4919 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.35 % Favored : 95.49 % Rotamer: Outliers : 3.34 % Allowed : 20.65 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.12), residues: 4461 helix: -0.62 (0.11), residues: 2105 sheet: -1.07 (0.23), residues: 525 loop : -1.40 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Y 141 HIS 0.005 0.001 HIS S 250 PHE 0.018 0.001 PHE C 116 TYR 0.033 0.001 TYR R 75 ARG 0.005 0.000 ARG Z 437 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 416 time to evaluate : 4.118 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 86 ILE cc_start: 0.4139 (OUTLIER) cc_final: 0.3784 (mt) REVERT: D 61 MET cc_start: 0.3312 (OUTLIER) cc_final: 0.3010 (mmm) REVERT: E 56 LEU cc_start: 0.5247 (OUTLIER) cc_final: 0.4644 (pt) REVERT: F 61 MET cc_start: 0.3398 (ptp) cc_final: 0.3122 (ptp) REVERT: F 112 SER cc_start: 0.6365 (p) cc_final: 0.5420 (p) REVERT: H 71 LEU cc_start: 0.5016 (mp) cc_final: 0.4098 (mt) REVERT: H 91 ARG cc_start: 0.4930 (mtt-85) cc_final: 0.4431 (mtm-85) REVERT: I 61 MET cc_start: 0.2933 (mmt) cc_final: 0.2399 (mmm) REVERT: P 77 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8187 (t80) REVERT: P 93 ASP cc_start: 0.8996 (t0) cc_final: 0.8641 (t0) REVERT: P 128 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6855 (mt-10) REVERT: S 193 LEU cc_start: 0.6500 (mm) cc_final: 0.6093 (mm) REVERT: S 259 MET cc_start: 0.6601 (mtm) cc_final: 0.6263 (mtp) REVERT: T 245 CYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7468 (m) REVERT: T 311 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7511 (tt0) REVERT: T 521 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7248 (mm-30) REVERT: U 364 ARG cc_start: 0.7795 (mtp85) cc_final: 0.7538 (mtt180) REVERT: U 407 PHE cc_start: 0.6990 (m-80) cc_final: 0.6733 (t80) REVERT: U 489 PHE cc_start: 0.6997 (m-10) cc_final: 0.6782 (m-10) REVERT: V 73 TRP cc_start: 0.7651 (m-10) cc_final: 0.7438 (m-10) REVERT: V 403 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: X 194 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8034 (mmm) REVERT: X 509 ARG cc_start: 0.3728 (OUTLIER) cc_final: 0.0646 (ttt180) REVERT: X 528 ASP cc_start: 0.7545 (t0) cc_final: 0.7340 (m-30) REVERT: Y 49 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7715 (t0) REVERT: Y 195 GLU cc_start: 0.5743 (tm-30) cc_final: 0.5531 (tm-30) REVERT: Y 250 GLN cc_start: 0.6831 (mm-40) cc_final: 0.6597 (mm-40) REVERT: Y 347 THR cc_start: 0.8205 (m) cc_final: 0.7916 (m) REVERT: Y 383 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8212 (p) REVERT: Y 502 MET cc_start: 0.8007 (tmm) cc_final: 0.6322 (ptt) REVERT: Z 282 LEU cc_start: 0.8868 (tp) cc_final: 0.8572 (tt) REVERT: Z 386 MET cc_start: 0.7086 (mmm) cc_final: 0.6761 (tpp) REVERT: Z 405 LYS cc_start: 0.7732 (tppt) cc_final: 0.7395 (tptp) REVERT: Z 484 MET cc_start: 0.7672 (mmp) cc_final: 0.7086 (mmp) outliers start: 119 outliers final: 80 residues processed: 498 average time/residue: 0.4205 time to fit residues: 351.3963 Evaluate side-chains 466 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 376 time to evaluate : 3.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 253 VAL Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 134 ASN Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 245 CYS Chi-restraints excluded: chain T residue 260 VAL Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 494 ILE Chi-restraints excluded: chain T residue 498 THR Chi-restraints excluded: chain T residue 524 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 277 THR Chi-restraints excluded: chain U residue 423 VAL Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain U residue 549 HIS Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 384 GLU Chi-restraints excluded: chain V residue 402 THR Chi-restraints excluded: chain V residue 403 ASP Chi-restraints excluded: chain V residue 481 THR Chi-restraints excluded: chain V residue 488 GLN Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 363 VAL Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 462 ASP Chi-restraints excluded: chain X residue 509 ARG Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 162 THR Chi-restraints excluded: chain Y residue 169 LEU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 274 ASP Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 345 ASP Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 143 optimal weight: 0.9990 chunk 384 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 250 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 427 optimal weight: 0.9980 chunk 355 optimal weight: 0.7980 chunk 198 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 141 optimal weight: 0.9990 chunk 224 optimal weight: 0.0370 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN G 87 ASN ** P 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN S 174 GLN ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 515 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 286 ASN Z 440 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 34412 Z= 0.166 Angle : 0.582 12.452 46638 Z= 0.287 Chirality : 0.043 0.397 5519 Planarity : 0.004 0.048 5997 Dihedral : 6.072 99.225 4919 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.19 % Favored : 95.65 % Rotamer: Outliers : 3.31 % Allowed : 21.49 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.13), residues: 4461 helix: -0.51 (0.11), residues: 2107 sheet: -0.95 (0.23), residues: 534 loop : -1.29 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Y 141 HIS 0.004 0.001 HIS S 250 PHE 0.035 0.001 PHE X 355 TYR 0.028 0.001 TYR R 75 ARG 0.005 0.000 ARG U 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 410 time to evaluate : 3.894 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: D 61 MET cc_start: 0.2960 (OUTLIER) cc_final: 0.2740 (mmm) REVERT: E 56 LEU cc_start: 0.5119 (OUTLIER) cc_final: 0.4598 (pt) REVERT: F 61 MET cc_start: 0.3434 (ptp) cc_final: 0.2322 (mtm) REVERT: H 71 LEU cc_start: 0.5443 (mp) cc_final: 0.4453 (mt) REVERT: H 81 MET cc_start: 0.5846 (mmm) cc_final: 0.5615 (mmm) REVERT: H 91 ARG cc_start: 0.4950 (mtt-85) cc_final: 0.4461 (mtm-85) REVERT: I 61 MET cc_start: 0.2923 (mmt) cc_final: 0.2420 (mmm) REVERT: I 81 MET cc_start: 0.6808 (tmm) cc_final: 0.6474 (tmm) REVERT: J 104 LEU cc_start: 0.3718 (OUTLIER) cc_final: 0.3340 (pt) REVERT: P 77 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8155 (t80) REVERT: P 93 ASP cc_start: 0.9018 (t0) cc_final: 0.8703 (t0) REVERT: P 128 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6815 (mt-10) REVERT: S 193 LEU cc_start: 0.6503 (mm) cc_final: 0.6113 (mm) REVERT: T 311 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7520 (tt0) REVERT: T 471 GLN cc_start: 0.7611 (mp10) cc_final: 0.7088 (pm20) REVERT: T 515 GLN cc_start: 0.7803 (mm110) cc_final: 0.7579 (mm-40) REVERT: T 521 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7403 (mm-30) REVERT: U 407 PHE cc_start: 0.6955 (m-80) cc_final: 0.6697 (t80) REVERT: U 489 PHE cc_start: 0.6920 (m-10) cc_final: 0.6689 (m-10) REVERT: U 549 HIS cc_start: 0.6828 (OUTLIER) cc_final: 0.6415 (t-90) REVERT: V 403 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7403 (m-30) REVERT: X 270 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7378 (mt-10) REVERT: X 509 ARG cc_start: 0.3699 (OUTLIER) cc_final: 0.0634 (ttt180) REVERT: X 528 ASP cc_start: 0.7509 (t0) cc_final: 0.7249 (m-30) REVERT: Y 195 GLU cc_start: 0.5667 (tm-30) cc_final: 0.5440 (tm-30) REVERT: Y 347 THR cc_start: 0.8205 (m) cc_final: 0.7900 (m) REVERT: Y 383 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8129 (p) REVERT: Y 502 MET cc_start: 0.7849 (tmm) cc_final: 0.6166 (ptt) REVERT: Z 282 LEU cc_start: 0.8853 (tp) cc_final: 0.8556 (tt) REVERT: Z 386 MET cc_start: 0.6927 (mmm) cc_final: 0.6592 (tpp) REVERT: Z 405 LYS cc_start: 0.7698 (tppt) cc_final: 0.7347 (tptp) REVERT: Z 484 MET cc_start: 0.7632 (mmp) cc_final: 0.7389 (mmp) outliers start: 118 outliers final: 75 residues processed: 488 average time/residue: 0.4330 time to fit residues: 352.0627 Evaluate side-chains 457 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 373 time to evaluate : 3.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 134 ASN Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 212 LEU Chi-restraints excluded: chain T residue 260 VAL Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 494 ILE Chi-restraints excluded: chain T residue 498 THR Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 524 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 277 THR Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain U residue 549 HIS Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 384 GLU Chi-restraints excluded: chain V residue 402 THR Chi-restraints excluded: chain V residue 403 ASP Chi-restraints excluded: chain V residue 481 THR Chi-restraints excluded: chain V residue 488 GLN Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 270 GLU Chi-restraints excluded: chain X residue 363 VAL Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 462 ASP Chi-restraints excluded: chain X residue 509 ARG Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 527 LEU Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 162 THR Chi-restraints excluded: chain Y residue 169 LEU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 274 ASP Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 345 ASP Chi-restraints excluded: chain Z residue 521 LEU Chi-restraints excluded: chain Z residue 537 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 412 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 chunk 243 optimal weight: 4.9990 chunk 312 optimal weight: 2.9990 chunk 241 optimal weight: 0.7980 chunk 359 optimal weight: 0.7980 chunk 238 optimal weight: 3.9990 chunk 426 optimal weight: 3.9990 chunk 266 optimal weight: 0.7980 chunk 259 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 87 ASN G 87 ASN ** P 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34412 Z= 0.166 Angle : 0.575 10.014 46638 Z= 0.284 Chirality : 0.042 0.207 5519 Planarity : 0.004 0.065 5997 Dihedral : 5.903 97.227 4919 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.46 % Favored : 95.43 % Rotamer: Outliers : 3.31 % Allowed : 22.25 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.13), residues: 4461 helix: -0.37 (0.11), residues: 2103 sheet: -0.89 (0.23), residues: 535 loop : -1.17 (0.15), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP V 73 HIS 0.005 0.001 HIS U 241 PHE 0.028 0.001 PHE X 355 TYR 0.025 0.001 TYR R 75 ARG 0.004 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 403 time to evaluate : 3.621 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: D 92 ASN cc_start: 0.4588 (p0) cc_final: 0.4268 (p0) REVERT: E 56 LEU cc_start: 0.5141 (OUTLIER) cc_final: 0.4600 (pt) REVERT: F 61 MET cc_start: 0.3443 (ptp) cc_final: 0.2467 (mtm) REVERT: H 71 LEU cc_start: 0.5471 (mp) cc_final: 0.4540 (mt) REVERT: H 91 ARG cc_start: 0.4965 (mtt-85) cc_final: 0.4485 (mtm-85) REVERT: I 61 MET cc_start: 0.2920 (mmt) cc_final: 0.2421 (mmm) REVERT: J 104 LEU cc_start: 0.3636 (OUTLIER) cc_final: 0.3318 (pt) REVERT: P 52 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7597 (mm-40) REVERT: P 77 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8110 (t80) REVERT: P 93 ASP cc_start: 0.9011 (t0) cc_final: 0.8706 (t0) REVERT: P 128 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6811 (mt-10) REVERT: R 117 GLU cc_start: 0.4843 (mp0) cc_final: 0.3379 (mp0) REVERT: S 193 LEU cc_start: 0.6631 (mm) cc_final: 0.6282 (mm) REVERT: T 108 LEU cc_start: 0.8670 (tp) cc_final: 0.8350 (tp) REVERT: T 311 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7528 (tt0) REVERT: T 521 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7034 (mm-30) REVERT: U 49 ARG cc_start: 0.7507 (tpm170) cc_final: 0.6911 (tpp-160) REVERT: U 284 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.7281 (m-80) REVERT: U 407 PHE cc_start: 0.6961 (m-80) cc_final: 0.6690 (t80) REVERT: U 549 HIS cc_start: 0.6814 (OUTLIER) cc_final: 0.6477 (t-90) REVERT: X 60 LEU cc_start: 0.8504 (mt) cc_final: 0.8259 (mp) REVERT: X 182 PHE cc_start: 0.8280 (m-80) cc_final: 0.7885 (m-80) REVERT: X 194 MET cc_start: 0.8453 (mmm) cc_final: 0.8146 (mmm) REVERT: X 270 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7430 (mt-10) REVERT: X 509 ARG cc_start: 0.3687 (OUTLIER) cc_final: 0.0656 (ttt180) REVERT: X 528 ASP cc_start: 0.7452 (t0) cc_final: 0.7196 (m-30) REVERT: Y 195 GLU cc_start: 0.5524 (tm-30) cc_final: 0.5302 (tm-30) REVERT: Y 347 THR cc_start: 0.8255 (m) cc_final: 0.7914 (m) REVERT: Z 282 LEU cc_start: 0.8832 (tp) cc_final: 0.8530 (tt) REVERT: Z 386 MET cc_start: 0.6928 (mmm) cc_final: 0.6717 (tpp) REVERT: Z 405 LYS cc_start: 0.7701 (tppt) cc_final: 0.7366 (tptp) REVERT: Z 484 MET cc_start: 0.7668 (mmp) cc_final: 0.7131 (mmp) outliers start: 118 outliers final: 81 residues processed: 481 average time/residue: 0.4126 time to fit residues: 332.7858 Evaluate side-chains 466 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 378 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain P residue 127 ASP Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 253 VAL Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 134 ASN Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 212 LEU Chi-restraints excluded: chain T residue 260 VAL Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 494 ILE Chi-restraints excluded: chain T residue 498 THR Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 524 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 277 THR Chi-restraints excluded: chain U residue 284 TYR Chi-restraints excluded: chain U residue 423 VAL Chi-restraints excluded: chain U residue 440 LYS Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain U residue 549 HIS Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 402 THR Chi-restraints excluded: chain V residue 488 GLN Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 251 MET Chi-restraints excluded: chain X residue 270 GLU Chi-restraints excluded: chain X residue 363 VAL Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 462 ASP Chi-restraints excluded: chain X residue 509 ARG Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 527 LEU Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 162 THR Chi-restraints excluded: chain Y residue 169 LEU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 274 ASP Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 345 ASP Chi-restraints excluded: chain Z residue 521 LEU Chi-restraints excluded: chain Z residue 537 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 263 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 254 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 270 optimal weight: 4.9990 chunk 290 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 334 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 34412 Z= 0.188 Angle : 0.595 11.207 46638 Z= 0.292 Chirality : 0.043 0.304 5519 Planarity : 0.004 0.055 5997 Dihedral : 5.875 97.078 4919 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.71 % Favored : 95.18 % Rotamer: Outliers : 2.89 % Allowed : 23.01 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.13), residues: 4461 helix: -0.31 (0.11), residues: 2109 sheet: -0.89 (0.23), residues: 554 loop : -1.15 (0.15), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 73 HIS 0.007 0.001 HIS U 241 PHE 0.025 0.001 PHE X 355 TYR 0.025 0.001 TYR R 75 ARG 0.005 0.000 ARG V 555 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 386 time to evaluate : 3.685 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: A 82 PHE cc_start: 0.4387 (m-80) cc_final: 0.3980 (m-80) REVERT: D 92 ASN cc_start: 0.4624 (p0) cc_final: 0.4266 (p0) REVERT: E 56 LEU cc_start: 0.4997 (OUTLIER) cc_final: 0.4557 (pt) REVERT: F 61 MET cc_start: 0.2955 (ptp) cc_final: 0.2192 (mtm) REVERT: H 71 LEU cc_start: 0.5452 (mp) cc_final: 0.4613 (mt) REVERT: H 81 MET cc_start: 0.5792 (mmm) cc_final: 0.5573 (mmm) REVERT: H 91 ARG cc_start: 0.4958 (mtt-85) cc_final: 0.4467 (mtm-85) REVERT: I 61 MET cc_start: 0.2723 (mmt) cc_final: 0.2234 (mmm) REVERT: I 85 LEU cc_start: 0.4628 (OUTLIER) cc_final: 0.4321 (mm) REVERT: J 104 LEU cc_start: 0.3670 (OUTLIER) cc_final: 0.3231 (pt) REVERT: P 52 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7602 (mm-40) REVERT: P 77 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8175 (t80) REVERT: P 93 ASP cc_start: 0.9004 (t0) cc_final: 0.8711 (t0) REVERT: P 111 ASP cc_start: 0.5849 (OUTLIER) cc_final: 0.4937 (t0) REVERT: P 128 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6846 (mt-10) REVERT: R 117 GLU cc_start: 0.4932 (mp0) cc_final: 0.3394 (mp0) REVERT: S 193 LEU cc_start: 0.6667 (mm) cc_final: 0.6325 (mm) REVERT: T 108 LEU cc_start: 0.8693 (tp) cc_final: 0.8373 (tp) REVERT: T 311 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7518 (tt0) REVERT: U 49 ARG cc_start: 0.7516 (tpm170) cc_final: 0.6923 (tpp-160) REVERT: U 284 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7353 (m-80) REVERT: U 407 PHE cc_start: 0.6956 (m-80) cc_final: 0.6687 (t80) REVERT: U 549 HIS cc_start: 0.6814 (OUTLIER) cc_final: 0.6509 (t-90) REVERT: X 60 LEU cc_start: 0.8473 (mt) cc_final: 0.8270 (mp) REVERT: X 182 PHE cc_start: 0.8179 (m-80) cc_final: 0.7767 (m-80) REVERT: X 270 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: X 509 ARG cc_start: 0.3800 (OUTLIER) cc_final: 0.0760 (ttt180) REVERT: X 528 ASP cc_start: 0.7463 (t0) cc_final: 0.7210 (m-30) REVERT: Y 102 VAL cc_start: 0.9369 (OUTLIER) cc_final: 0.9140 (p) REVERT: Y 195 GLU cc_start: 0.5442 (tm-30) cc_final: 0.5211 (tm-30) REVERT: Y 250 GLN cc_start: 0.6570 (mm-40) cc_final: 0.6120 (mm-40) REVERT: Y 347 THR cc_start: 0.8258 (m) cc_final: 0.7969 (m) REVERT: Y 502 MET cc_start: 0.7510 (tmm) cc_final: 0.6204 (ptm) REVERT: Z 281 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8523 (tt) REVERT: Z 282 LEU cc_start: 0.8855 (tp) cc_final: 0.8510 (tt) REVERT: Z 405 LYS cc_start: 0.7742 (tppt) cc_final: 0.7421 (tptp) REVERT: Z 484 MET cc_start: 0.7648 (mmp) cc_final: 0.7046 (mmp) outliers start: 103 outliers final: 83 residues processed: 454 average time/residue: 0.4524 time to fit residues: 345.4065 Evaluate side-chains 458 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 364 time to evaluate : 3.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain S residue 62 MET Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 253 VAL Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 134 ASN Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 212 LEU Chi-restraints excluded: chain T residue 260 VAL Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 494 ILE Chi-restraints excluded: chain T residue 498 THR Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 524 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 277 THR Chi-restraints excluded: chain U residue 284 TYR Chi-restraints excluded: chain U residue 423 VAL Chi-restraints excluded: chain U residue 440 LYS Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain U residue 549 HIS Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 226 ASP Chi-restraints excluded: chain V residue 402 THR Chi-restraints excluded: chain V residue 488 GLN Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 251 MET Chi-restraints excluded: chain X residue 270 GLU Chi-restraints excluded: chain X residue 363 VAL Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 462 ASP Chi-restraints excluded: chain X residue 509 ARG Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 527 LEU Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 162 THR Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 169 LEU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 274 ASP Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 328 THR Chi-restraints excluded: chain Z residue 345 ASP Chi-restraints excluded: chain Z residue 521 LEU Chi-restraints excluded: chain Z residue 537 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 387 optimal weight: 5.9990 chunk 408 optimal weight: 0.8980 chunk 372 optimal weight: 5.9990 chunk 396 optimal weight: 0.6980 chunk 238 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 311 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 358 optimal weight: 0.9990 chunk 375 optimal weight: 8.9990 chunk 395 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 34412 Z= 0.189 Angle : 0.600 11.184 46638 Z= 0.295 Chirality : 0.043 0.214 5519 Planarity : 0.004 0.052 5997 Dihedral : 5.864 95.653 4919 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.57 % Favored : 95.31 % Rotamer: Outliers : 2.95 % Allowed : 23.32 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.13), residues: 4461 helix: -0.25 (0.11), residues: 2109 sheet: -0.84 (0.23), residues: 552 loop : -1.12 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 73 HIS 0.004 0.001 HIS U 241 PHE 0.015 0.001 PHE X 355 TYR 0.033 0.001 TYR Q 16 ARG 0.006 0.000 ARG T 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 390 time to evaluate : 3.749 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: D 92 ASN cc_start: 0.4663 (p0) cc_final: 0.4294 (p0) REVERT: E 56 LEU cc_start: 0.5038 (OUTLIER) cc_final: 0.4568 (pt) REVERT: F 61 MET cc_start: 0.3051 (ptp) cc_final: 0.2338 (mtm) REVERT: H 71 LEU cc_start: 0.5516 (mp) cc_final: 0.4689 (mt) REVERT: H 81 MET cc_start: 0.5829 (mmm) cc_final: 0.5510 (mmm) REVERT: H 91 ARG cc_start: 0.4883 (mtt-85) cc_final: 0.4458 (mtm-85) REVERT: I 61 MET cc_start: 0.2711 (mmt) cc_final: 0.2214 (mmm) REVERT: J 104 LEU cc_start: 0.3670 (OUTLIER) cc_final: 0.3228 (pt) REVERT: P 77 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8150 (t80) REVERT: P 93 ASP cc_start: 0.8973 (t0) cc_final: 0.8710 (t0) REVERT: P 111 ASP cc_start: 0.5984 (OUTLIER) cc_final: 0.5149 (t0) REVERT: P 128 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6979 (mt-10) REVERT: R 117 GLU cc_start: 0.4947 (mp0) cc_final: 0.3333 (mp0) REVERT: S 193 LEU cc_start: 0.6681 (mm) cc_final: 0.6325 (mm) REVERT: T 108 LEU cc_start: 0.8716 (tp) cc_final: 0.8415 (tp) REVERT: T 311 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7516 (tt0) REVERT: U 49 ARG cc_start: 0.7555 (tpm170) cc_final: 0.6961 (tpp-160) REVERT: U 284 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.7353 (m-80) REVERT: U 407 PHE cc_start: 0.6956 (m-80) cc_final: 0.6688 (t80) REVERT: U 549 HIS cc_start: 0.6781 (OUTLIER) cc_final: 0.6499 (t-90) REVERT: X 182 PHE cc_start: 0.8119 (m-80) cc_final: 0.7858 (m-80) REVERT: X 270 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: X 509 ARG cc_start: 0.3819 (OUTLIER) cc_final: 0.0800 (ttt180) REVERT: X 528 ASP cc_start: 0.7458 (t0) cc_final: 0.7206 (m-30) REVERT: Y 102 VAL cc_start: 0.9354 (OUTLIER) cc_final: 0.9126 (p) REVERT: Y 347 THR cc_start: 0.8252 (m) cc_final: 0.7960 (m) REVERT: Y 502 MET cc_start: 0.7264 (tmm) cc_final: 0.6115 (ptm) REVERT: Z 281 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8500 (tt) REVERT: Z 282 LEU cc_start: 0.8853 (tp) cc_final: 0.8530 (tt) REVERT: Z 405 LYS cc_start: 0.7713 (tppt) cc_final: 0.7404 (tptp) REVERT: Z 484 MET cc_start: 0.7673 (mmp) cc_final: 0.7033 (mmp) outliers start: 105 outliers final: 83 residues processed: 458 average time/residue: 0.4382 time to fit residues: 336.2521 Evaluate side-chains 464 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 371 time to evaluate : 3.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain S residue 62 MET Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 253 VAL Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 134 ASN Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 212 LEU Chi-restraints excluded: chain T residue 260 VAL Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 494 ILE Chi-restraints excluded: chain T residue 498 THR Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 277 THR Chi-restraints excluded: chain U residue 284 TYR Chi-restraints excluded: chain U residue 423 VAL Chi-restraints excluded: chain U residue 440 LYS Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain U residue 549 HIS Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 402 THR Chi-restraints excluded: chain V residue 488 GLN Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 251 MET Chi-restraints excluded: chain X residue 270 GLU Chi-restraints excluded: chain X residue 363 VAL Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 462 ASP Chi-restraints excluded: chain X residue 509 ARG Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 527 LEU Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 162 THR Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 169 LEU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 374 TYR Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 274 ASP Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 328 THR Chi-restraints excluded: chain Z residue 345 ASP Chi-restraints excluded: chain Z residue 521 LEU Chi-restraints excluded: chain Z residue 537 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 260 optimal weight: 2.9990 chunk 419 optimal weight: 0.0010 chunk 256 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 291 optimal weight: 3.9990 chunk 440 optimal weight: 7.9990 chunk 405 optimal weight: 0.8980 chunk 350 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 270 optimal weight: 5.9990 chunk 215 optimal weight: 0.4980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 64 GLN ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 405 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 153 GLN ** Z 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 34412 Z= 0.164 Angle : 0.601 14.598 46638 Z= 0.294 Chirality : 0.042 0.219 5519 Planarity : 0.004 0.050 5997 Dihedral : 5.754 95.628 4919 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 2.61 % Allowed : 24.02 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 4461 helix: -0.15 (0.12), residues: 2106 sheet: -0.75 (0.23), residues: 547 loop : -1.04 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 73 HIS 0.011 0.001 HIS P 84 PHE 0.016 0.001 PHE S 203 TYR 0.027 0.001 TYR Q 16 ARG 0.006 0.000 ARG U 476 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 408 time to evaluate : 3.824 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: A 61 MET cc_start: 0.3379 (ptt) cc_final: 0.3087 (ptt) REVERT: D 92 ASN cc_start: 0.4626 (p0) cc_final: 0.4270 (p0) REVERT: E 56 LEU cc_start: 0.5195 (OUTLIER) cc_final: 0.4685 (pp) REVERT: F 61 MET cc_start: 0.3006 (ptp) cc_final: 0.2289 (mtm) REVERT: H 71 LEU cc_start: 0.5310 (mp) cc_final: 0.4622 (mt) REVERT: H 81 MET cc_start: 0.5807 (mmm) cc_final: 0.5350 (mmm) REVERT: H 91 ARG cc_start: 0.4859 (mtt-85) cc_final: 0.4445 (mtm-85) REVERT: I 61 MET cc_start: 0.2679 (mmt) cc_final: 0.2180 (mmm) REVERT: J 104 LEU cc_start: 0.4057 (OUTLIER) cc_final: 0.3640 (pt) REVERT: P 52 GLN cc_start: 0.7885 (mm110) cc_final: 0.7651 (mm-40) REVERT: P 77 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.8013 (t80) REVERT: P 93 ASP cc_start: 0.8960 (t0) cc_final: 0.8744 (t0) REVERT: P 111 ASP cc_start: 0.5963 (OUTLIER) cc_final: 0.5166 (t0) REVERT: P 128 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6909 (mt-10) REVERT: R 117 GLU cc_start: 0.4768 (mp0) cc_final: 0.3239 (mp0) REVERT: S 193 LEU cc_start: 0.6608 (mm) cc_final: 0.6253 (mm) REVERT: T 108 LEU cc_start: 0.8704 (tp) cc_final: 0.8417 (tp) REVERT: T 311 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7521 (tt0) REVERT: U 49 ARG cc_start: 0.7540 (tpm170) cc_final: 0.6952 (tpp-160) REVERT: U 284 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.7389 (m-80) REVERT: U 407 PHE cc_start: 0.6935 (m-80) cc_final: 0.6674 (t80) REVERT: U 423 VAL cc_start: 0.7221 (OUTLIER) cc_final: 0.6974 (t) REVERT: U 549 HIS cc_start: 0.6803 (OUTLIER) cc_final: 0.6575 (t-90) REVERT: V 488 GLN cc_start: 0.5034 (OUTLIER) cc_final: 0.4255 (tp40) REVERT: X 182 PHE cc_start: 0.8028 (m-80) cc_final: 0.7798 (m-80) REVERT: X 326 THR cc_start: 0.7993 (t) cc_final: 0.7770 (p) REVERT: X 509 ARG cc_start: 0.3752 (OUTLIER) cc_final: 0.0765 (ttt180) REVERT: X 527 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6146 (pp) REVERT: X 528 ASP cc_start: 0.7467 (t0) cc_final: 0.7219 (m-30) REVERT: Y 102 VAL cc_start: 0.9310 (OUTLIER) cc_final: 0.9068 (p) REVERT: Y 347 THR cc_start: 0.8177 (m) cc_final: 0.7892 (m) REVERT: Y 501 LYS cc_start: 0.7621 (tttp) cc_final: 0.6914 (mttm) REVERT: Y 502 MET cc_start: 0.7126 (tmm) cc_final: 0.5941 (ptm) REVERT: Z 281 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8467 (tt) REVERT: Z 282 LEU cc_start: 0.8802 (tp) cc_final: 0.8477 (tt) REVERT: Z 405 LYS cc_start: 0.7685 (tppt) cc_final: 0.7374 (tptp) REVERT: Z 484 MET cc_start: 0.7688 (mmp) cc_final: 0.7009 (mmp) outliers start: 93 outliers final: 73 residues processed: 467 average time/residue: 0.4376 time to fit residues: 339.9284 Evaluate side-chains 460 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 375 time to evaluate : 4.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain S residue 62 MET Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 253 VAL Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 134 ASN Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 212 LEU Chi-restraints excluded: chain T residue 260 VAL Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 494 ILE Chi-restraints excluded: chain T residue 498 THR Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 277 THR Chi-restraints excluded: chain U residue 284 TYR Chi-restraints excluded: chain U residue 423 VAL Chi-restraints excluded: chain U residue 440 LYS Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain U residue 549 HIS Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 488 GLN Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 251 MET Chi-restraints excluded: chain X residue 363 VAL Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 462 ASP Chi-restraints excluded: chain X residue 509 ARG Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 527 LEU Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 162 THR Chi-restraints excluded: chain Y residue 169 LEU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 374 TYR Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 274 ASP Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 317 ASP Chi-restraints excluded: chain Z residue 328 THR Chi-restraints excluded: chain Z residue 345 ASP Chi-restraints excluded: chain Z residue 521 LEU Chi-restraints excluded: chain Z residue 537 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 278 optimal weight: 6.9990 chunk 373 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 323 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 351 optimal weight: 4.9990 chunk 146 optimal weight: 0.1980 chunk 360 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 ASN ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 64 GLN ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 228 GLN X 414 GLN Y 79 HIS ** Z 132 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 = 0.3963 r_free = 0.3963 target = 0.133840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.112572 restraints weight = 80084.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.111661 restraints weight = 64519.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.112101 restraints weight = 52690.633| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 34412 Z= 0.228 Angle : 0.632 11.539 46638 Z= 0.311 Chirality : 0.044 0.210 5519 Planarity : 0.004 0.058 5997 Dihedral : 5.879 98.125 4919 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.22 % Favored : 94.66 % Rotamer: Outliers : 2.69 % Allowed : 24.35 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.13), residues: 4461 helix: -0.13 (0.12), residues: 2115 sheet: -0.75 (0.23), residues: 554 loop : -1.03 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP V 73 HIS 0.010 0.001 HIS P 84 PHE 0.017 0.001 PHE S 203 TYR 0.026 0.002 TYR R 75 ARG 0.007 0.000 ARG F 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7523.46 seconds wall clock time: 137 minutes 21.42 seconds (8241.42 seconds total)