Starting phenix.real_space_refine on Fri Mar 22 15:40:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re1_4838/03_2024/6re1_4838_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re1_4838/03_2024/6re1_4838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re1_4838/03_2024/6re1_4838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re1_4838/03_2024/6re1_4838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re1_4838/03_2024/6re1_4838_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re1_4838/03_2024/6re1_4838_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 116 5.16 5 C 21526 2.51 5 N 5790 2.21 5 O 6413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 111": "OE1" <-> "OE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "E PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 64": "OE1" <-> "OE2" Residue "P ASP 72": "OD1" <-> "OD2" Residue "P GLU 86": "OE1" <-> "OE2" Residue "P PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 127": "OD1" <-> "OD2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P GLU 143": "OE1" <-> "OE2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 25": "OD1" <-> "OD2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "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 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 62": "OE1" <-> "OE2" Residue "R GLU 117": "OE1" <-> "OE2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "R GLU 148": "OE1" <-> "OE2" Residue "R ASP 156": "OD1" <-> "OD2" Residue "R ASP 174": "OD1" <-> "OD2" Residue "R GLU 175": "OE1" <-> "OE2" Residue "R PHE 176": "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 ASP 91": "OD1" <-> "OD2" Residue "S ASP 136": "OD1" <-> "OD2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S ASP 164": "OD1" <-> "OD2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 217": "OE1" <-> "OE2" Residue "S ASP 222": "OD1" <-> "OD2" Residue "S GLU 234": "OE1" <-> "OE2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 303": "OE1" <-> "OE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ASP 125": "OD1" <-> "OD2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ASP 172": "OD1" <-> "OD2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 237": "OD1" <-> "OD2" Residue "T TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 325": "OD1" <-> "OD2" Residue "T ASP 353": "OD1" <-> "OD2" Residue "T GLU 371": "OE1" <-> "OE2" Residue "T ASP 389": "OD1" <-> "OD2" Residue "T GLU 409": "OE1" <-> "OE2" Residue "T GLU 411": "OE1" <-> "OE2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 418": "NH1" <-> "NH2" Residue "T ARG 429": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 449": "OE1" <-> "OE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 475": "OE1" <-> "OE2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 516": "OD1" <-> "OD2" Residue "T GLU 521": "OE1" <-> "OE2" Residue "T GLU 522": "OE1" <-> "OE2" Residue "T ASP 547": "OD1" <-> "OD2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ASP 46": "OD1" <-> "OD2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U ASP 92": "OD1" <-> "OD2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 112": "OD1" <-> "OD2" Residue "U TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 311": "OE1" <-> "OE2" Residue "U PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U ARG 342": "NH1" <-> "NH2" Residue "U ARG 343": "NH1" <-> "NH2" Residue "U ARG 364": "NH1" <-> "NH2" Residue "U GLU 371": "OE1" <-> "OE2" Residue "U PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 465": "OD1" <-> "OD2" Residue "U GLU 475": "OE1" <-> "OE2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 510": "OD1" <-> "OD2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U GLU 521": "OE1" <-> "OE2" Residue "U GLU 522": "OE1" <-> "OE2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 72": "OE1" <-> "OE2" Residue "V PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 142": "OD1" <-> "OD2" Residue "V TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 237": "OD1" <-> "OD2" Residue "V TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 266": "NH1" <-> "NH2" Residue "V PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ASP 326": "OD1" <-> "OD2" Residue "V ARG 335": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "V ARG 347": "NH1" <-> "NH2" Residue "V ARG 360": "NH1" <-> "NH2" Residue "V ASP 403": "OD1" <-> "OD2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 429": "NH1" <-> "NH2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V ASP 467": "OD1" <-> "OD2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V GLU 553": "OE1" <-> "OE2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 49": "OD1" <-> "OD2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X GLU 55": "OE1" <-> "OE2" Residue "X ARG 71": "NH1" <-> "NH2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X ASP 94": "OD1" <-> "OD2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X ASP 104": "OD1" <-> "OD2" Residue "X ARG 120": "NH1" <-> "NH2" Residue "X ASP 130": "OD1" <-> "OD2" Residue "X GLU 131": "OE1" <-> "OE2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "X PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "X ASP 222": "OD1" <-> "OD2" Residue "X GLU 229": "OE1" <-> "OE2" Residue "X ARG 258": "NH1" <-> "NH2" Residue "X GLU 270": "OE1" <-> "OE2" Residue "X PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 378": "OD1" <-> "OD2" Residue "X ASP 381": "OD1" <-> "OD2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X ARG 401": "NH1" <-> "NH2" Residue "X TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 427": "OE1" <-> "OE2" Residue "X ARG 435": "NH1" <-> "NH2" Residue "X ARG 437": "NH1" <-> "NH2" Residue "X PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 480": "OD1" <-> "OD2" Residue "X PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 523": "OD1" <-> "OD2" Residue "X GLU 547": "OE1" <-> "OE2" Residue "X PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y ASP 53": "OD1" <-> "OD2" Residue "Y ASP 94": "OD1" <-> "OD2" Residue "Y ASP 104": "OD1" <-> "OD2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 158": "OE1" <-> "OE2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 218": "NH1" <-> "NH2" Residue "Y ARG 225": "NH1" <-> "NH2" Residue "Y GLU 229": "OE1" <-> "OE2" Residue "Y GLU 238": "OE1" <-> "OE2" Residue "Y ARG 239": "NH1" <-> "NH2" Residue "Y TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 296": "OE1" <-> "OE2" Residue "Y ASP 359": "OD1" <-> "OD2" Residue "Y TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 401": "NH1" <-> "NH2" Residue "Y ASP 415": "OD1" <-> "OD2" Residue "Y ASP 429": "OD1" <-> "OD2" Residue "Y PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 494": "OE1" <-> "OE2" Residue "Y ASP 505": "OD1" <-> "OD2" Residue "Y ARG 509": "NH1" <-> "NH2" Residue "Y GLU 520": "OE1" <-> "OE2" Residue "Y GLU 533": "OE1" <-> "OE2" Residue "Y GLU 540": "OE1" <-> "OE2" Residue "Y GLU 541": "OE1" <-> "OE2" Residue "Y ASP 542": "OD1" <-> "OD2" Residue "Y ASP 543": "OD1" <-> "OD2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 66": "OE1" <-> "OE2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "Z ARG 115": "NH1" <-> "NH2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z ASP 136": "OD1" <-> "OD2" Residue "Z ARG 145": "NH1" <-> "NH2" Residue "Z PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 229": "OE1" <-> "OE2" Residue "Z ARG 258": "NH1" <-> "NH2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z GLU 296": "OE1" <-> "OE2" Residue "Z TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 344": "OD1" <-> "OD2" Residue "Z ASP 345": "OD1" <-> "OD2" Residue "Z ARG 366": "NH1" <-> "NH2" Residue "Z TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z GLU 424": "OE1" <-> "OE2" Residue "Z GLU 428": "OE1" <-> "OE2" Residue "Z ASP 429": "OD1" <-> "OD2" Residue "Z PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 462": "OD1" <-> "OD2" Residue "Z PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 480": "OD1" <-> "OD2" Residue "Z TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 500": "OD1" <-> "OD2" Residue "Z ASP 528": "OD1" <-> "OD2" Residue "Z GLU 541": "OE1" <-> "OE2" Residue "Z ASP 543": "OD1" <-> "OD2" Residue "Z GLU 547": "OE1" <-> "OE2" Residue "Z ASP 548": "OD1" <-> "OD2" Residue "Z GLU 564": "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: 33863 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "P" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 895 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3609 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 456} Chain: "U" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 3961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3961 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "Y" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3952 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 497} Chain: "Z" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.18, per 1000 atoms: 0.51 Number of scatterers: 33863 At special positions: 0 Unit cell: (165.321, 127.413, 208.494, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 13 15.00 Mg 5 11.99 O 6413 8.00 N 5790 7.00 C 21526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.14 Conformation dependent library (CDL) restraints added in 6.2 seconds 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8150 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 160 helices and 28 sheets defined 46.4% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.85 Creating SS restraints... Processing helix chain 'A' and resid 55 through 68 removed outlier: 3.513A pdb=" N CYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 91 Processing helix chain 'A' and resid 93 through 125 removed outlier: 3.740A pdb=" N ALA A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LYS A 97 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL A 100 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 104 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 105 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A 111 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 112 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 113 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 118 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 119 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE A 124 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU A 125 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 removed outlier: 4.156A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 91 removed outlier: 4.138A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 125 removed outlier: 3.610A pdb=" N SER B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 91 removed outlier: 4.331A pdb=" N LYS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 125 removed outlier: 3.557A pdb=" N ALA C 96 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LYS C 97 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU C 104 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER C 112 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE C 113 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 119 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE C 122 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU C 125 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 91 removed outlier: 4.041A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 125 removed outlier: 3.733A pdb=" N LEU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER D 112 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 3.697A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 91 removed outlier: 3.525A pdb=" N VAL E 80 " --> pdb=" O ALA E 76 " (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: 4.286A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 90 removed outlier: 3.998A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 95 No H-bonds generated for 'chain 'F' and resid 93 through 95' Processing helix chain 'F' and resid 98 through 125 removed outlier: 3.769A pdb=" N LEU F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 89 removed outlier: 3.970A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 126 removed outlier: 3.528A pdb=" N GLY G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR G 102 " --> pdb=" O GLN G 98 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 67 removed outlier: 3.918A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLY H 65 " --> pdb=" O MET H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 89 removed outlier: 3.866A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 125 removed outlier: 5.102A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL H 100 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU H 104 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N PHE H 107 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR H 110 " --> pdb=" O PHE H 107 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU H 125 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 91 removed outlier: 4.348A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ALA I 70 " --> pdb=" O CYS I 66 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA I 72 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 126 removed outlier: 5.589A pdb=" N LYS I 97 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL I 100 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU I 111 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER I 112 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU I 125 " --> pdb=" O PHE I 122 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE I 126 " --> pdb=" O LEU I 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 91 removed outlier: 4.113A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ALA J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 126 removed outlier: 3.787A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER J 112 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 62 Processing helix chain 'P' and resid 67 through 83 removed outlier: 3.564A pdb=" N GLU P 79 " --> pdb=" O TYR P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 92 No H-bonds generated for 'chain 'P' and resid 89 through 92' Processing helix chain 'P' and resid 98 through 108 removed outlier: 3.980A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER P 106 " --> pdb=" O THR P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 126 removed outlier: 3.733A pdb=" N ALA P 124 " --> pdb=" O LYS P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 137 removed outlier: 3.927A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU P 136 " --> pdb=" O ALA P 133 " (cutoff:3.500A) Processing helix chain 'P' and resid 139 through 148 removed outlier: 4.014A pdb=" N ALA P 147 " --> pdb=" O GLU P 143 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N HIS P 148 " --> pdb=" O LEU P 144 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 30 removed outlier: 4.443A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 43 removed outlier: 3.622A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG Q 42 " --> pdb=" O LYS Q 38 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN Q 43 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 38 removed outlier: 3.684A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 54 Processing helix chain 'R' and resid 162 through 169 removed outlier: 3.958A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 196 removed outlier: 3.508A pdb=" N LEU R 187 " --> pdb=" O ALA R 183 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA R 190 " --> pdb=" O GLU R 186 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER R 193 " --> pdb=" O SER R 189 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL R 195 " --> pdb=" O LEU R 191 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU R 196 " --> pdb=" O GLU R 192 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 78 removed outlier: 3.836A pdb=" N LYS S 44 " --> pdb=" O ASN S 40 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS S 55 " --> pdb=" O LYS S 51 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN S 70 " --> pdb=" O SER S 66 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU S 76 " --> pdb=" O GLN S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 86 Proline residue: S 84 - end of helix Processing helix chain 'S' and resid 116 through 129 removed outlier: 3.507A pdb=" N LEU S 127 " --> pdb=" O THR S 123 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 150 removed outlier: 3.616A pdb=" N SER S 148 " --> pdb=" O ASP S 144 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN S 149 " --> pdb=" O LYS S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 183 Processing helix chain 'S' and resid 213 through 216 No H-bonds generated for 'chain 'S' and resid 213 through 216' Processing helix chain 'S' and resid 219 through 221 No H-bonds generated for 'chain 'S' and resid 219 through 221' Processing helix chain 'S' and resid 239 through 312 removed outlier: 3.759A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR S 278 " --> pdb=" O MET S 274 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 137 No H-bonds generated for 'chain 'T' and resid 135 through 137' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 207 through 211 Processing helix chain 'T' and resid 231 through 248 removed outlier: 3.828A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN T 248 " --> pdb=" O ASN T 244 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 278 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 296 through 315 Proline residue: T 303 - end of helix removed outlier: 4.175A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 340 Processing helix chain 'T' and resid 347 through 349 No H-bonds generated for 'chain 'T' and resid 347 through 349' Processing helix chain 'T' and resid 352 through 364 removed outlier: 4.362A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU T 357 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG T 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU T 362 " --> pdb=" O SER T 359 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU T 363 " --> pdb=" O ARG T 360 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 399 Processing helix chain 'T' and resid 410 through 415 Processing helix chain 'T' and resid 432 through 434 No H-bonds generated for 'chain 'T' and resid 432 through 434' Processing helix chain 'T' and resid 437 through 459 removed outlier: 3.561A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY T 444 " --> pdb=" O LYS T 440 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N THR T 445 " --> pdb=" O GLN T 441 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU T 446 " --> pdb=" O VAL T 442 " (cutoff:3.500A) Processing helix chain 'T' and resid 470 through 483 removed outlier: 3.790A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU T 482 " --> pdb=" O ALA T 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 505 removed outlier: 3.572A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 527 removed outlier: 4.519A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 539 Processing helix chain 'T' and resid 546 through 555 removed outlier: 4.120A pdb=" N ALA T 552 " --> pdb=" O ALA T 548 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 48 No H-bonds generated for 'chain 'U' and resid 46 through 48' Processing helix chain 'U' and resid 59 through 71 removed outlier: 4.427A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix Processing helix chain 'U' and resid 135 through 137 No H-bonds generated for 'chain 'U' and resid 135 through 137' Processing helix chain 'U' and resid 207 through 211 Processing helix chain 'U' and resid 231 through 246 Processing helix chain 'U' and resid 266 through 278 Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 296 through 315 Proline residue: U 303 - end of helix removed outlier: 3.870A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG U 314 " --> pdb=" O ALA U 310 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 removed outlier: 4.021A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 347 through 349 No H-bonds generated for 'chain 'U' and resid 347 through 349' Processing helix chain 'U' and resid 352 through 364 removed outlier: 4.310A pdb=" N PHE U 355 " --> pdb=" O GLY U 352 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR U 356 " --> pdb=" O ASP U 353 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU U 357 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG U 360 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU U 363 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 370 through 372 No H-bonds generated for 'chain 'U' and resid 370 through 372' Processing helix chain 'U' and resid 393 through 401 Processing helix chain 'U' and resid 410 through 414 removed outlier: 3.591A pdb=" N TYR U 414 " --> pdb=" O THR U 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 410 through 414' Processing helix chain 'U' and resid 437 through 457 removed outlier: 4.288A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR U 453 " --> pdb=" O GLU U 449 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU U 455 " --> pdb=" O ALA U 451 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL U 456 " --> pdb=" O GLN U 452 " (cutoff:3.500A) Processing helix chain 'U' and resid 468 through 483 removed outlier: 3.853A pdb=" N TYR U 472 " --> pdb=" O ALA U 468 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL U 473 " --> pdb=" O ALA U 469 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 498 through 505 Processing helix chain 'U' and resid 517 through 527 removed outlier: 3.914A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 531 through 539 removed outlier: 3.601A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 544 through 553 Processing helix chain 'V' and resid 46 through 48 No H-bonds generated for 'chain 'V' and resid 46 through 48' Processing helix chain 'V' and resid 59 through 69 removed outlier: 3.926A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Proline residue: V 68 - end of helix Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 210 No H-bonds generated for 'chain 'V' and resid 207 through 210' Processing helix chain 'V' and resid 231 through 247 removed outlier: 4.058A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 266 through 278 Processing helix chain 'V' and resid 281 through 284 Processing helix chain 'V' and resid 296 through 315 Proline residue: V 303 - end of helix removed outlier: 3.616A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 339 Processing helix chain 'V' and resid 347 through 349 No H-bonds generated for 'chain 'V' and resid 347 through 349' Processing helix chain 'V' and resid 352 through 364 removed outlier: 4.063A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU V 363 " --> pdb=" O ARG V 360 " (cutoff:3.500A) Processing helix chain 'V' and resid 370 through 372 No H-bonds generated for 'chain 'V' and resid 370 through 372' Processing helix chain 'V' and resid 393 through 401 Processing helix chain 'V' and resid 410 through 413 No H-bonds generated for 'chain 'V' and resid 410 through 413' Processing helix chain 'V' and resid 440 through 456 removed outlier: 3.861A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) Processing helix chain 'V' and resid 471 through 483 removed outlier: 3.574A pdb=" N ALA V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) Processing helix chain 'V' and resid 494 through 505 removed outlier: 3.805A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) Processing helix chain 'V' and resid 517 through 527 removed outlier: 3.989A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 532 through 539 Processing helix chain 'V' and resid 544 through 553 removed outlier: 4.087A pdb=" N ALA V 548 " --> pdb=" O PRO V 544 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) Processing helix chain 'X' and resid 150 through 152 No H-bonds generated for 'chain 'X' and resid 150 through 152' Processing helix chain 'X' and resid 165 through 170 Processing helix chain 'X' and resid 189 through 203 Processing helix chain 'X' and resid 217 through 230 Processing helix chain 'X' and resid 236 through 241 removed outlier: 3.680A pdb=" N ARG X 239 " --> pdb=" O GLY X 236 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 255 through 259 Processing helix chain 'X' and resid 261 through 274 removed outlier: 3.756A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 299 Processing helix chain 'X' and resid 314 through 324 removed outlier: 4.739A pdb=" N ARG X 324 " --> pdb=" O GLY X 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 342 through 344 No H-bonds generated for 'chain 'X' and resid 342 through 344' Processing helix chain 'X' and resid 349 through 354 Processing helix chain 'X' and resid 366 through 370 Processing helix chain 'X' and resid 394 through 419 removed outlier: 3.620A pdb=" N LEU X 413 " --> pdb=" O ASP X 409 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA X 418 " --> pdb=" O GLN X 414 " (cutoff:3.500A) Processing helix chain 'X' and resid 427 through 442 removed outlier: 3.697A pdb=" N ARG X 441 " --> pdb=" O ARG X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 463 through 474 Processing helix chain 'X' and resid 483 through 485 No H-bonds generated for 'chain 'X' and resid 483 through 485' Processing helix chain 'X' and resid 492 through 502 removed outlier: 4.033A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 533 Processing helix chain 'Y' and resid 165 through 170 Processing helix chain 'Y' and resid 191 through 200 Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 3.571A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 274 removed outlier: 3.762A pdb=" N ARG Y 260 " --> pdb=" O GLY Y 256 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR Y 264 " --> pdb=" O ARG Y 260 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 288 through 298 Processing helix chain 'Y' and resid 314 through 324 removed outlier: 4.467A pdb=" N ARG Y 324 " --> pdb=" O GLY Y 320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 342 through 344 No H-bonds generated for 'chain 'Y' and resid 342 through 344' Processing helix chain 'Y' and resid 349 through 357 removed outlier: 3.668A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) removed outlier: 4.289A 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 394 through 420 removed outlier: 3.672A pdb=" N LEU Y 413 " --> pdb=" O ASP Y 409 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN Y 414 " --> pdb=" O TYR Y 410 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) Processing helix chain 'Y' and resid 422 through 424 No H-bonds generated for 'chain 'Y' and resid 422 through 424' Processing helix chain 'Y' and resid 427 through 443 removed outlier: 3.535A pdb=" N THR Y 432 " --> pdb=" O GLU Y 428 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA Y 434 " --> pdb=" O LYS Y 430 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU Y 443 " --> pdb=" O ILE Y 439 " (cutoff:3.500A) Processing helix chain 'Y' and resid 451 through 454 No H-bonds generated for 'chain 'Y' and resid 451 through 454' Processing helix chain 'Y' and resid 463 through 475 Processing helix chain 'Y' and resid 492 through 504 removed outlier: 3.786A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) Processing helix chain 'Y' and resid 527 through 533 Processing helix chain 'Y' and resid 542 through 549 removed outlier: 4.533A pdb=" N LEU Y 545 " --> pdb=" O ASP Y 542 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLU Y 546 " --> pdb=" O ASP Y 543 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU Y 547 " --> pdb=" O GLY Y 544 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP Y 548 " --> pdb=" O LEU Y 545 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE Y 549 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 542 through 549' 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 200 Processing helix chain 'Z' and resid 217 through 229 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 3.672A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 274 removed outlier: 3.633A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 298 removed outlier: 3.552A pdb=" N GLN Z 292 " --> pdb=" O ARG Z 289 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER Z 298 " --> pdb=" O SER Z 295 " (cutoff:3.500A) Processing helix chain 'Z' and resid 314 through 324 removed outlier: 4.647A pdb=" N ARG Z 324 " --> pdb=" O GLY Z 320 " (cutoff:3.500A) Processing helix chain 'Z' and resid 342 through 344 No H-bonds generated for 'chain 'Z' and resid 342 through 344' Processing helix chain 'Z' and resid 349 through 355 removed outlier: 4.201A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE Z 355 " --> pdb=" O PRO Z 351 " (cutoff:3.500A) Processing helix chain 'Z' and resid 366 through 370 Processing helix chain 'Z' and resid 389 through 392 No H-bonds generated for 'chain 'Z' and resid 389 through 392' Processing helix chain 'Z' and resid 394 through 417 removed outlier: 4.654A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) Processing helix chain 'Z' and resid 430 through 443 removed outlier: 4.110A pdb=" N LYS Z 438 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG Z 441 " --> pdb=" O ARG Z 437 " (cutoff:3.500A) Processing helix chain 'Z' and resid 463 through 475 removed outlier: 3.687A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 492 through 505 removed outlier: 3.672A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 533 removed outlier: 4.011A pdb=" N VAL Z 531 " --> pdb=" O LEU Z 527 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'Q' and resid 45 through 49 removed outlier: 3.659A pdb=" N PHE Q 47 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN Q 49 " --> pdb=" O LYS Q 61 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'R' and resid 72 through 75 removed outlier: 6.731A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE R 144 " --> pdb=" O TYR R 75 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'R' and resid 97 through 100 removed outlier: 4.176A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 203 through 211 removed outlier: 3.710A pdb=" N SER S 189 " --> pdb=" O LYS S 99 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA S 161 " --> pdb=" O SER S 141 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'T' and resid 86 through 91 removed outlier: 6.572A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'T' and resid 152 through 155 Processing sheet with id= G, first strand: chain 'T' and resid 382 through 384 removed outlier: 6.514A pdb=" N ILE T 223 " --> pdb=" O ILE T 383 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE T 406 " --> pdb=" O ILE T 224 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'T' and resid 376 through 379 Processing sheet with id= I, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.658A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= K, first strand: chain 'U' and resid 405 through 408 removed outlier: 7.105A pdb=" N LEU U 222 " --> pdb=" O ILE U 406 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU U 408 " --> pdb=" O LEU U 222 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE U 224 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'U' and resid 286 through 290 removed outlier: 6.690A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'U' and resid 107 through 111 removed outlier: 4.829A pdb=" N GLN U 149 " --> pdb=" O LEU U 108 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N CYS U 110 " --> pdb=" O THR U 147 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR U 147 " --> pdb=" O CYS U 110 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'V' and resid 143 through 145 removed outlier: 6.587A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL V 90 " --> pdb=" O ILE V 94 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE V 94 " --> pdb=" O VAL V 90 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLN V 149 " --> pdb=" O LEU V 108 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N CYS V 110 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR V 147 " --> pdb=" O CYS V 110 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= P, first strand: chain 'V' and resid 404 through 408 removed outlier: 3.876A pdb=" N LEU V 222 " --> pdb=" O GLY V 404 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'V' and resid 286 through 290 removed outlier: 6.770A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'X' and resid 38 through 44 removed outlier: 6.557A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 5.534A 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 removed outlier: 3.552A pdb=" N ASP X 139 " --> pdb=" O VAL X 113 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'X' and resid 360 through 363 removed outlier: 8.505A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL X 213 " --> pdb=" O ASP X 285 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= V, first strand: chain 'Y' and resid 37 through 39 removed outlier: 6.536A pdb=" N ARG Y 86 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N HIS Y 79 " --> pdb=" O THR Y 84 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR Y 84 " --> pdb=" O HIS Y 79 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ARG Y 51 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL Y 40 " --> pdb=" O ARG Y 51 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Y' and resid 110 through 113 Processing sheet with id= X, first strand: chain 'Y' and resid 360 through 363 removed outlier: 7.671A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N GLY Y 183 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL Y 339 " --> pdb=" O GLY Y 183 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE Y 207 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N PHE Y 283 " --> pdb=" O PHE Y 207 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ALA Y 211 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Z' and resid 38 through 44 removed outlier: 6.536A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Z' and resid 110 through 113 removed outlier: 3.593A pdb=" N ASP Z 139 " --> pdb=" O VAL Z 113 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Z' and resid 360 through 363 removed outlier: 6.253A pdb=" N THR Z 245 " --> pdb=" O PHE Z 210 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLY Z 212 " --> pdb=" O THR Z 245 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL Z 247 " --> pdb=" O GLY Z 212 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Z' and resid 559 through 561 1424 hydrogen bonds defined for protein. 3870 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: 11.89 Time building geometry restraints manager: 14.23 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: 10562 1.34 - 1.46: 5559 1.46 - 1.57: 18042 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34384 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.46e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.44e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.26e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.22e+01 bond pdb=" C5 ATP T1001 " pdb=" C6 ATP T1001 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.63e+01 ... (remaining 34379 not shown) Histogram of bond angle deviations from ideal: 96.92 - 104.84: 604 104.84 - 112.75: 18323 112.75 - 120.67: 16614 120.67 - 128.59: 10918 128.59 - 136.50: 139 Bond angle restraints: 46598 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 119.42 20.45 1.00e+00 1.00e+00 4.18e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 120.65 19.22 1.00e+00 1.00e+00 3.69e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 121.46 18.41 1.00e+00 1.00e+00 3.39e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 120.06 16.77 1.00e+00 1.00e+00 2.81e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 123.63 13.20 1.00e+00 1.00e+00 1.74e+02 ... (remaining 46593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 20320 35.22 - 70.44: 442 70.44 - 105.66: 39 105.66 - 140.89: 1 140.89 - 176.11: 1 Dihedral angle restraints: 20803 sinusoidal: 8060 harmonic: 12743 Sorted by residual: dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -127.71 -52.29 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -130.85 -49.15 0 5.00e+00 4.00e-02 9.66e+01 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 -144.46 -35.54 0 5.00e+00 4.00e-02 5.05e+01 ... (remaining 20800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4484 0.076 - 0.151: 942 0.151 - 0.227: 72 0.227 - 0.303: 14 0.303 - 0.379: 1 Chirality restraints: 5513 Sorted by residual: chirality pdb=" CB ILE C 95 " pdb=" CA ILE C 95 " pdb=" CG1 ILE C 95 " pdb=" CG2 ILE C 95 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CB VAL V 209 " pdb=" CA VAL V 209 " pdb=" CG1 VAL V 209 " pdb=" CG2 VAL V 209 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB ILE B 95 " pdb=" CA ILE B 95 " pdb=" CG1 ILE B 95 " pdb=" CG2 ILE B 95 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 5510 not shown) Planarity restraints: 5991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.032 2.00e-02 2.50e+03 6.24e-02 3.89e+01 pdb=" C ALA Z 503 " -0.108 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.040 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Y 503 " 0.031 2.00e-02 2.50e+03 6.12e-02 3.74e+01 pdb=" C ALA Y 503 " -0.106 2.00e-02 2.50e+03 pdb=" O ALA Y 503 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS Y 504 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA T 296 " -0.053 5.00e-02 4.00e+02 7.90e-02 9.99e+00 pdb=" N PRO T 297 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO T 297 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO T 297 " -0.045 5.00e-02 4.00e+02 ... (remaining 5988 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 268 2.52 - 3.11: 24014 3.11 - 3.71: 54124 3.71 - 4.30: 80352 4.30 - 4.90: 132174 Nonbonded interactions: 290932 Sorted by model distance: nonbonded pdb=" CZ PHE G 107 " pdb=" OE1 GLU G 111 " model vdw 1.921 3.340 nonbonded pdb=" O ALA X 499 " pdb=" CB ALA X 503 " model vdw 2.003 3.460 nonbonded pdb=" O3B ADP Y 601 " pdb="MG MG Y 602 " model vdw 2.237 2.170 nonbonded pdb=" OG1 THR Z 190 " pdb="MG MG Z 602 " model vdw 2.240 2.170 nonbonded pdb=" OH TYR U 259 " pdb=" OD2 ASP U 325 " model vdw 2.255 2.440 ... (remaining 290927 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 85 through 562 or resid 1001 through 1002)) selection = (chain 'V' and (resid 85 through 562 or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 552) selection = (chain 'Y' and resid 37 through 552) selection = (chain 'Z' and resid 37 through 552) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.900 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: 0.000 Extract box with map and model: 24.980 Check model and map are aligned: 0.520 Set scattering table: 0.280 Process input model: 88.280 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 : 0.009 0.093 34384 Z= 0.591 Angle : 1.000 20.447 46598 Z= 0.576 Chirality : 0.059 0.379 5513 Planarity : 0.007 0.079 5991 Dihedral : 15.257 176.107 12653 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.27 % Favored : 94.48 % Rotamer: Outliers : 0.45 % Allowed : 10.22 % Favored : 89.33 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.15 (0.10), residues: 4457 helix: -3.11 (0.08), residues: 2129 sheet: -1.87 (0.20), residues: 531 loop : -2.33 (0.12), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP Y 141 HIS 0.014 0.002 HIS S 250 PHE 0.028 0.003 PHE S 249 TYR 0.027 0.003 TYR V 393 ARG 0.010 0.001 ARG U 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 567 time to evaluate : 3.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 105 LEU cc_start: 0.1913 (tt) cc_final: 0.1708 (mp) REVERT: J 119 LEU cc_start: 0.5770 (tt) cc_final: 0.5339 (pp) REVERT: P 39 LEU cc_start: 0.8034 (mp) cc_final: 0.7791 (mt) REVERT: R 111 LEU cc_start: 0.7224 (mp) cc_final: 0.7010 (mp) REVERT: S 234 GLU cc_start: 0.6702 (tm-30) cc_final: 0.6406 (tm-30) REVERT: T 282 MET cc_start: 0.8534 (tpp) cc_final: 0.8154 (tpt) REVERT: T 325 ASP cc_start: 0.8197 (t70) cc_final: 0.7852 (t0) REVERT: T 558 LYS cc_start: 0.7859 (mppt) cc_final: 0.7612 (mmmm) REVERT: V 61 HIS cc_start: 0.7422 (t70) cc_final: 0.7094 (t-90) REVERT: V 112 ASP cc_start: 0.8265 (p0) cc_final: 0.8012 (p0) REVERT: V 325 ASP cc_start: 0.8133 (t0) cc_final: 0.7860 (t0) REVERT: V 506 LYS cc_start: 0.6958 (mmtm) cc_final: 0.6491 (mmmt) REVERT: X 488 MET cc_start: 0.7718 (mmt) cc_final: 0.7325 (mmm) REVERT: Y 195 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6390 (tm-30) REVERT: Y 317 ASP cc_start: 0.8003 (m-30) cc_final: 0.7752 (m-30) REVERT: Z 90 MET cc_start: 0.8663 (mmt) cc_final: 0.8433 (mmt) REVERT: Z 195 GLU cc_start: 0.6991 (tp30) cc_final: 0.6638 (tp30) REVERT: Z 385 ARG cc_start: 0.7207 (mmt180) cc_final: 0.7006 (mpt-90) REVERT: Z 448 GLN cc_start: 0.6405 (tm-30) cc_final: 0.5893 (mt0) REVERT: Z 488 MET cc_start: 0.7789 (mmt) cc_final: 0.7580 (mmt) outliers start: 16 outliers final: 5 residues processed: 580 average time/residue: 0.5102 time to fit residues: 458.2067 Evaluate side-chains 408 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 403 time to evaluate : 3.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain X residue 502 MET Chi-restraints excluded: chain Z residue 314 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 372 optimal weight: 0.9990 chunk 334 optimal weight: 7.9990 chunk 185 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 225 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 345 optimal weight: 0.0370 chunk 133 optimal weight: 1.9990 chunk 210 optimal weight: 0.7980 chunk 257 optimal weight: 0.9980 chunk 400 optimal weight: 4.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN B 98 GLN D 92 ASN E 98 GLN ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN I 94 ASN J 98 GLN P 66 GLN P 71 GLN Q 29 ASN Q 46 HIS R 66 HIS R 104 HIS R 137 HIS R 181 ASN S 156 GLN S 186 ASN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 195 ASN S 267 HIS T 104 GLN T 134 ASN T 241 HIS T 386 GLN T 452 GLN U 104 GLN U 140 GLN U 196 GLN U 246 ASN U 264 GLN U 441 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 123 GLN ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS V 242 GLN V 244 ASN V 264 GLN V 278 GLN V 386 GLN V 486 GLN ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 497 GLN X 144 HIS X 174 GLN X 199 ASN X 294 ASN ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 414 GLN Y 199 ASN Y 278 GLN ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 83 ASN Z 174 GLN Z 294 ASN Z 412 ASN Z 440 GLN Z 574 ASN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34384 Z= 0.189 Angle : 0.557 8.689 46598 Z= 0.288 Chirality : 0.042 0.169 5513 Planarity : 0.005 0.057 5991 Dihedral : 7.136 176.692 4921 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.32 % Favored : 96.50 % Rotamer: Outliers : 1.91 % Allowed : 14.86 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.12), residues: 4457 helix: -1.45 (0.10), residues: 2126 sheet: -1.47 (0.21), residues: 573 loop : -1.69 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 73 HIS 0.004 0.001 HIS U 61 PHE 0.023 0.001 PHE A 107 TYR 0.026 0.001 TYR P 75 ARG 0.005 0.000 ARG S 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 502 time to evaluate : 3.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 PHE cc_start: 0.4630 (m-10) cc_final: 0.4243 (m-10) REVERT: J 123 LEU cc_start: 0.2706 (tp) cc_final: 0.2464 (mt) REVERT: P 39 LEU cc_start: 0.7771 (mp) cc_final: 0.7486 (mt) REVERT: R 98 PHE cc_start: 0.6313 (p90) cc_final: 0.5941 (p90) REVERT: R 119 HIS cc_start: 0.3880 (m-70) cc_final: 0.3180 (m90) REVERT: S 234 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6290 (tm-30) REVERT: T 282 MET cc_start: 0.8426 (tpp) cc_final: 0.7663 (tpt) REVERT: T 407 PHE cc_start: 0.7581 (t80) cc_final: 0.7339 (t80) REVERT: T 481 THR cc_start: 0.8545 (m) cc_final: 0.8325 (p) REVERT: T 495 GLU cc_start: 0.7164 (pm20) cc_final: 0.6951 (pm20) REVERT: U 282 MET cc_start: 0.8689 (mmt) cc_final: 0.8392 (mmt) REVERT: V 45 LEU cc_start: 0.7782 (tp) cc_final: 0.7477 (tp) REVERT: V 112 ASP cc_start: 0.8025 (p0) cc_final: 0.7564 (p0) REVERT: V 445 THR cc_start: 0.7083 (OUTLIER) cc_final: 0.6776 (t) REVERT: V 506 LYS cc_start: 0.7055 (mmtm) cc_final: 0.6601 (mmmt) REVERT: X 488 MET cc_start: 0.7720 (mmt) cc_final: 0.7390 (mmm) REVERT: Y 195 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6466 (tm-30) REVERT: Y 317 ASP cc_start: 0.7661 (m-30) cc_final: 0.7408 (m-30) REVERT: Z 385 ARG cc_start: 0.7126 (mmt180) cc_final: 0.6919 (mpt-90) REVERT: Z 448 GLN cc_start: 0.6410 (tm-30) cc_final: 0.5899 (mt0) REVERT: Z 488 MET cc_start: 0.7793 (mmt) cc_final: 0.7574 (mmt) outliers start: 68 outliers final: 38 residues processed: 550 average time/residue: 0.4661 time to fit residues: 415.9801 Evaluate side-chains 449 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 410 time to evaluate : 3.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 430 VAL Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 510 ASP Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 178 THR Chi-restraints excluded: chain U residue 196 GLN Chi-restraints excluded: chain U residue 236 ILE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 532 VAL Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain Z residue 160 LEU Chi-restraints excluded: chain Z residue 314 LEU Chi-restraints excluded: chain Z residue 326 THR Chi-restraints excluded: chain Z residue 344 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 222 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 333 optimal weight: 8.9990 chunk 272 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 401 optimal weight: 2.9990 chunk 433 optimal weight: 9.9990 chunk 357 optimal weight: 0.9980 chunk 397 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 321 optimal weight: 0.2980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 ASN ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 GLN P 83 GLN ** R 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 ASN T 152 ASN T 358 HIS T 452 GLN ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 488 GLN X 322 GLN X 337 GLN ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 408 GLN Z 412 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 34384 Z= 0.210 Angle : 0.553 7.514 46598 Z= 0.284 Chirality : 0.043 0.184 5513 Planarity : 0.004 0.048 5991 Dihedral : 6.685 166.935 4917 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.90 % Favored : 95.96 % Rotamer: Outliers : 2.39 % Allowed : 17.05 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.12), residues: 4457 helix: -0.81 (0.11), residues: 2153 sheet: -1.21 (0.21), residues: 593 loop : -1.41 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 73 HIS 0.004 0.001 HIS R 137 PHE 0.022 0.001 PHE G 107 TYR 0.021 0.001 TYR P 75 ARG 0.007 0.000 ARG U 496 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 432 time to evaluate : 3.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 95 ILE cc_start: 0.1124 (OUTLIER) cc_final: 0.0689 (tt) REVERT: J 119 LEU cc_start: 0.5870 (tt) cc_final: 0.5320 (pp) REVERT: J 123 LEU cc_start: 0.2867 (tp) cc_final: 0.2578 (mt) REVERT: P 49 THR cc_start: 0.7657 (OUTLIER) cc_final: 0.7151 (m) REVERT: R 98 PHE cc_start: 0.6338 (p90) cc_final: 0.6012 (p90) REVERT: S 234 GLU cc_start: 0.6842 (tm-30) cc_final: 0.6249 (tm-30) REVERT: S 274 MET cc_start: 0.8223 (mmp) cc_final: 0.7758 (mmt) REVERT: T 227 ARG cc_start: 0.7866 (ttp80) cc_final: 0.7646 (ttp-110) REVERT: T 282 MET cc_start: 0.8455 (tpp) cc_final: 0.7743 (tpt) REVERT: T 421 LEU cc_start: 0.8731 (tp) cc_final: 0.8514 (tp) REVERT: T 495 GLU cc_start: 0.7204 (pm20) cc_final: 0.6932 (pm20) REVERT: U 49 ARG cc_start: 0.7086 (mtm-85) cc_final: 0.6777 (mtm-85) REVERT: V 45 LEU cc_start: 0.7829 (tp) cc_final: 0.7504 (tp) REVERT: V 112 ASP cc_start: 0.8053 (p0) cc_final: 0.7680 (p0) REVERT: V 445 THR cc_start: 0.7130 (p) cc_final: 0.6771 (t) REVERT: V 506 LYS cc_start: 0.7050 (mmtm) cc_final: 0.6669 (mmmt) REVERT: X 488 MET cc_start: 0.7659 (mmt) cc_final: 0.7349 (mmm) REVERT: X 541 GLU cc_start: 0.4267 (OUTLIER) cc_final: 0.3974 (tp30) REVERT: Y 195 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6447 (tm-30) REVERT: Y 317 ASP cc_start: 0.7660 (m-30) cc_final: 0.7437 (m-30) REVERT: Y 538 VAL cc_start: 0.7399 (OUTLIER) cc_final: 0.7165 (t) REVERT: Z 448 GLN cc_start: 0.6387 (tm-30) cc_final: 0.5946 (mt0) REVERT: Z 488 MET cc_start: 0.7704 (mmt) cc_final: 0.7363 (mmt) outliers start: 85 outliers final: 51 residues processed: 491 average time/residue: 0.4610 time to fit residues: 366.0736 Evaluate side-chains 451 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 396 time to evaluate : 3.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 118 THR Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 158 TYR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 510 ASP Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 178 THR Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 532 VAL Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 417 ILE Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 541 GLU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain Z residue 160 LEU Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 314 LEU Chi-restraints excluded: chain Z residue 326 THR Chi-restraints excluded: chain Z residue 344 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 396 optimal weight: 3.9990 chunk 301 optimal weight: 0.9980 chunk 208 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 191 optimal weight: 0.2980 chunk 269 optimal weight: 7.9990 chunk 402 optimal weight: 0.9980 chunk 426 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 381 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 ASN ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN P 76 GLN P 83 GLN ** R 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 452 GLN T 461 GLN U 196 GLN V 64 GLN ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 221 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34384 Z= 0.231 Angle : 0.555 7.464 46598 Z= 0.283 Chirality : 0.043 0.166 5513 Planarity : 0.004 0.045 5991 Dihedral : 6.495 155.376 4917 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.90 % Favored : 95.94 % Rotamer: Outliers : 3.00 % Allowed : 18.03 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.13), residues: 4457 helix: -0.48 (0.11), residues: 2151 sheet: -1.08 (0.21), residues: 595 loop : -1.20 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 73 HIS 0.004 0.001 HIS U 61 PHE 0.022 0.001 PHE B 82 TYR 0.021 0.001 TYR X 410 ARG 0.004 0.000 ARG U 496 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 419 time to evaluate : 3.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 LEU cc_start: 0.5481 (OUTLIER) cc_final: 0.5199 (mp) REVERT: I 81 MET cc_start: 0.6035 (tpp) cc_final: 0.5224 (tpp) REVERT: J 119 LEU cc_start: 0.5370 (tt) cc_final: 0.4987 (pt) REVERT: P 49 THR cc_start: 0.7677 (OUTLIER) cc_final: 0.7144 (m) REVERT: R 98 PHE cc_start: 0.6411 (p90) cc_final: 0.6169 (p90) REVERT: S 193 LEU cc_start: 0.6607 (mt) cc_final: 0.6363 (mt) REVERT: T 112 ASP cc_start: 0.7722 (p0) cc_final: 0.7465 (p0) REVERT: T 227 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7667 (ttp-110) REVERT: T 282 MET cc_start: 0.8441 (tpp) cc_final: 0.7759 (tpt) REVERT: T 357 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8796 (tp) REVERT: U 282 MET cc_start: 0.8785 (mmt) cc_final: 0.8448 (mmt) REVERT: V 45 LEU cc_start: 0.7845 (tp) cc_final: 0.7535 (tp) REVERT: V 112 ASP cc_start: 0.8075 (p0) cc_final: 0.7718 (p0) REVERT: V 445 THR cc_start: 0.7142 (OUTLIER) cc_final: 0.6832 (t) REVERT: X 488 MET cc_start: 0.7648 (mmt) cc_final: 0.7352 (mmm) REVERT: X 541 GLU cc_start: 0.4263 (OUTLIER) cc_final: 0.3923 (tp30) REVERT: Y 195 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6500 (tm-30) REVERT: Y 317 ASP cc_start: 0.7693 (m-30) cc_final: 0.7479 (m-30) REVERT: Y 538 VAL cc_start: 0.7309 (OUTLIER) cc_final: 0.7069 (t) REVERT: Z 429 ASP cc_start: 0.6637 (OUTLIER) cc_final: 0.6312 (t70) REVERT: Z 448 GLN cc_start: 0.6419 (tm-30) cc_final: 0.5837 (mt0) REVERT: Z 488 MET cc_start: 0.7703 (mmt) cc_final: 0.7388 (mmt) outliers start: 107 outliers final: 68 residues processed: 499 average time/residue: 0.4588 time to fit residues: 373.1603 Evaluate side-chains 456 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 381 time to evaluate : 3.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 158 TYR Chi-restraints excluded: chain S residue 182 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 481 THR Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 178 THR Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 517 ILE Chi-restraints excluded: chain V residue 532 VAL Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 417 ILE Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 506 ILE Chi-restraints excluded: chain X residue 541 GLU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 495 VAL Chi-restraints excluded: chain Y residue 506 ILE Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain Z residue 160 LEU Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 314 LEU Chi-restraints excluded: chain Z residue 326 THR Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 429 ASP Chi-restraints excluded: chain Z residue 466 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 355 optimal weight: 1.9990 chunk 241 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 317 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 363 optimal weight: 2.9990 chunk 294 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 217 optimal weight: 4.9990 chunk 382 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 ASN ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 452 GLN T 488 GLN U 196 GLN V 64 GLN ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 398 ASN ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 34384 Z= 0.260 Angle : 0.573 9.267 46598 Z= 0.291 Chirality : 0.044 0.167 5513 Planarity : 0.004 0.042 5991 Dihedral : 6.430 146.396 4917 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.22 % Favored : 95.62 % Rotamer: Outliers : 3.59 % Allowed : 18.56 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.13), residues: 4457 helix: -0.41 (0.12), residues: 2092 sheet: -1.02 (0.22), residues: 593 loop : -1.04 (0.15), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP U 73 HIS 0.004 0.001 HIS U 61 PHE 0.033 0.002 PHE J 126 TYR 0.021 0.002 TYR Z 248 ARG 0.004 0.000 ARG X 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 390 time to evaluate : 3.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 60 LYS cc_start: 0.6566 (mtpt) cc_final: 0.6273 (tptt) REVERT: I 85 LEU cc_start: 0.6531 (mt) cc_final: 0.6255 (mt) REVERT: Q 70 PRO cc_start: 0.3657 (Cg_endo) cc_final: 0.3147 (Cg_exo) REVERT: T 227 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7707 (ttp-110) REVERT: T 282 MET cc_start: 0.8449 (tpp) cc_final: 0.7780 (tpt) REVERT: T 357 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8795 (tp) REVERT: V 45 LEU cc_start: 0.7817 (tp) cc_final: 0.7535 (tp) REVERT: V 112 ASP cc_start: 0.8122 (p0) cc_final: 0.7774 (p0) REVERT: V 445 THR cc_start: 0.7137 (OUTLIER) cc_final: 0.6803 (t) REVERT: X 488 MET cc_start: 0.7656 (mmt) cc_final: 0.7366 (mmm) REVERT: X 541 GLU cc_start: 0.4116 (OUTLIER) cc_final: 0.3775 (tp30) REVERT: Y 193 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8743 (tt) REVERT: Y 195 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6614 (tm-30) REVERT: Y 317 ASP cc_start: 0.7784 (m-30) cc_final: 0.7584 (m-30) REVERT: Y 538 VAL cc_start: 0.7320 (OUTLIER) cc_final: 0.7081 (t) REVERT: Z 429 ASP cc_start: 0.6679 (OUTLIER) cc_final: 0.6301 (t70) REVERT: Z 448 GLN cc_start: 0.6418 (tm-30) cc_final: 0.5935 (mt0) REVERT: Z 488 MET cc_start: 0.7713 (mmt) cc_final: 0.7363 (mmt) outliers start: 128 outliers final: 90 residues processed: 483 average time/residue: 0.4565 time to fit residues: 359.4882 Evaluate side-chains 465 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 369 time to evaluate : 3.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 54 TYR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 158 TYR Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 421 LEU Chi-restraints excluded: chain T residue 430 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 481 THR Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 178 THR Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 517 ILE Chi-restraints excluded: chain V residue 532 VAL Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 417 ILE Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 506 ILE Chi-restraints excluded: chain X residue 541 GLU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 415 ASP Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 495 VAL Chi-restraints excluded: chain Y residue 506 ILE Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain Z residue 160 LEU Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 314 LEU Chi-restraints excluded: chain Z residue 326 THR Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 429 ASP Chi-restraints excluded: chain Z residue 466 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 143 optimal weight: 6.9990 chunk 383 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 250 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 426 optimal weight: 0.8980 chunk 354 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 224 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 ASN ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN R 181 ASN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 ASN T 452 GLN U 64 GLN U 196 GLN U 549 HIS ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 144 HIS Z 198 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34384 Z= 0.153 Angle : 0.526 10.227 46598 Z= 0.264 Chirality : 0.042 0.162 5513 Planarity : 0.003 0.040 5991 Dihedral : 6.023 139.205 4917 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.59 % Favored : 96.28 % Rotamer: Outliers : 2.75 % Allowed : 19.94 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.13), residues: 4457 helix: -0.12 (0.12), residues: 2106 sheet: -0.86 (0.22), residues: 599 loop : -0.88 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 73 HIS 0.004 0.001 HIS V 549 PHE 0.027 0.001 PHE J 126 TYR 0.018 0.001 TYR Z 248 ARG 0.004 0.000 ARG X 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 417 time to evaluate : 3.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 ILE cc_start: 0.6768 (tp) cc_final: 0.6109 (tp) REVERT: U 282 MET cc_start: 0.8827 (mmt) cc_final: 0.8493 (mmt) REVERT: V 45 LEU cc_start: 0.7800 (tp) cc_final: 0.7536 (tp) REVERT: V 112 ASP cc_start: 0.8006 (p0) cc_final: 0.7662 (p0) REVERT: V 445 THR cc_start: 0.7102 (OUTLIER) cc_final: 0.6793 (t) REVERT: X 541 GLU cc_start: 0.4045 (OUTLIER) cc_final: 0.3676 (tp30) REVERT: Y 193 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8633 (tt) REVERT: Y 538 VAL cc_start: 0.7232 (OUTLIER) cc_final: 0.7009 (t) REVERT: Z 429 ASP cc_start: 0.6548 (OUTLIER) cc_final: 0.6311 (t70) REVERT: Z 448 GLN cc_start: 0.6264 (tm-30) cc_final: 0.5896 (mt0) REVERT: Z 488 MET cc_start: 0.7623 (mmt) cc_final: 0.7245 (mmt) outliers start: 98 outliers final: 72 residues processed: 493 average time/residue: 0.4489 time to fit residues: 360.3238 Evaluate side-chains 445 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 368 time to evaluate : 3.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 122 PHE Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 148 HIS Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 54 TYR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 158 TYR Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 421 LEU Chi-restraints excluded: chain T residue 430 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 178 THR Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 405 GLN Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 459 PHE Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 378 THR Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 517 ILE Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 541 GLU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 495 VAL Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 160 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 198 ASN Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 314 LEU Chi-restraints excluded: chain Z residue 326 THR Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 429 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 411 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 311 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 chunk 359 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 chunk 425 optimal weight: 3.9990 chunk 266 optimal weight: 0.8980 chunk 259 optimal weight: 1.9990 chunk 196 optimal weight: 0.2980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 ASN ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 452 GLN U 196 GLN ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 488 GLN ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34384 Z= 0.186 Angle : 0.538 10.795 46598 Z= 0.271 Chirality : 0.042 0.188 5513 Planarity : 0.003 0.036 5991 Dihedral : 5.945 129.623 4917 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.84 % Favored : 96.03 % Rotamer: Outliers : 2.92 % Allowed : 20.30 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.13), residues: 4457 helix: 0.04 (0.12), residues: 2077 sheet: -0.88 (0.22), residues: 600 loop : -0.80 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 73 HIS 0.003 0.001 HIS U 61 PHE 0.024 0.001 PHE B 82 TYR 0.014 0.001 TYR Z 248 ARG 0.010 0.000 ARG S 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 391 time to evaluate : 3.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 ILE cc_start: 0.6819 (tp) cc_final: 0.6228 (tp) REVERT: H 81 MET cc_start: 0.5308 (tpp) cc_final: 0.4925 (tpp) REVERT: I 85 LEU cc_start: 0.6396 (mt) cc_final: 0.6189 (mt) REVERT: J 61 MET cc_start: 0.1370 (mmm) cc_final: 0.1120 (mmm) REVERT: P 59 GLN cc_start: 0.7592 (tt0) cc_final: 0.7323 (tt0) REVERT: T 537 LYS cc_start: 0.7914 (tptt) cc_final: 0.7636 (tppt) REVERT: U 282 MET cc_start: 0.8837 (mmt) cc_final: 0.8495 (mmt) REVERT: V 45 LEU cc_start: 0.7837 (tp) cc_final: 0.7541 (tp) REVERT: V 445 THR cc_start: 0.7138 (OUTLIER) cc_final: 0.6846 (t) REVERT: X 541 GLU cc_start: 0.4320 (OUTLIER) cc_final: 0.3848 (tp30) REVERT: Y 193 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8654 (tt) REVERT: Y 538 VAL cc_start: 0.7443 (OUTLIER) cc_final: 0.7236 (t) REVERT: Z 429 ASP cc_start: 0.6625 (OUTLIER) cc_final: 0.6296 (t70) REVERT: Z 448 GLN cc_start: 0.6230 (tm-30) cc_final: 0.5814 (mt0) REVERT: Z 488 MET cc_start: 0.7665 (mmt) cc_final: 0.7274 (mmt) outliers start: 104 outliers final: 83 residues processed: 473 average time/residue: 0.4566 time to fit residues: 354.9608 Evaluate side-chains 464 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 376 time to evaluate : 3.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 122 PHE Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 148 HIS Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 54 TYR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 158 TYR Chi-restraints excluded: chain S residue 177 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 246 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 421 LEU Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 510 ASP Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 178 THR Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 399 ILE Chi-restraints excluded: chain U residue 405 GLN Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 378 THR Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 505 THR Chi-restraints excluded: chain V residue 517 ILE Chi-restraints excluded: chain V residue 535 ILE Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 306 SER Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 541 GLU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 495 VAL Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 160 LEU Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 198 ASN Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 314 LEU Chi-restraints excluded: chain Z residue 326 THR Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 429 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 262 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 chunk 253 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 270 optimal weight: 6.9990 chunk 289 optimal weight: 3.9990 chunk 210 optimal weight: 0.0170 chunk 39 optimal weight: 20.0000 chunk 334 optimal weight: 4.9990 overall best weight: 2.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 ASN F 92 ASN H 87 ASN I 87 ASN ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN S 185 HIS ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 452 GLN U 64 GLN ** V 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 422 ASN V 488 GLN ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 198 ASN Z 278 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 34384 Z= 0.336 Angle : 0.619 11.118 46598 Z= 0.313 Chirality : 0.045 0.195 5513 Planarity : 0.004 0.043 5991 Dihedral : 6.384 122.104 4917 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.73 % Favored : 95.13 % Rotamer: Outliers : 3.29 % Allowed : 20.70 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.13), residues: 4457 helix: -0.13 (0.12), residues: 2080 sheet: -0.97 (0.22), residues: 608 loop : -0.83 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP U 73 HIS 0.005 0.001 HIS U 61 PHE 0.035 0.002 PHE P 122 TYR 0.017 0.002 TYR U 304 ARG 0.007 0.000 ARG U 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 381 time to evaluate : 4.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 81 MET cc_start: 0.6548 (tpp) cc_final: 0.6224 (tpp) REVERT: Q 71 LYS cc_start: 0.5642 (mttp) cc_final: 0.5004 (ttpt) REVERT: U 217 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7776 (mmt-90) REVERT: V 112 ASP cc_start: 0.8190 (p0) cc_final: 0.7848 (p0) REVERT: V 445 THR cc_start: 0.7172 (OUTLIER) cc_final: 0.6844 (t) REVERT: V 456 VAL cc_start: 0.6440 (OUTLIER) cc_final: 0.5990 (m) REVERT: X 541 GLU cc_start: 0.4588 (OUTLIER) cc_final: 0.4080 (tp30) REVERT: Y 193 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8751 (tt) REVERT: Y 538 VAL cc_start: 0.7341 (OUTLIER) cc_final: 0.7087 (t) REVERT: Z 429 ASP cc_start: 0.6514 (OUTLIER) cc_final: 0.6218 (t70) REVERT: Z 448 GLN cc_start: 0.6431 (tm-30) cc_final: 0.5829 (mt0) outliers start: 117 outliers final: 89 residues processed: 468 average time/residue: 0.4485 time to fit residues: 343.4357 Evaluate side-chains 462 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 366 time to evaluate : 3.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 87 ASN Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 122 PHE Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 148 HIS Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 54 TYR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 158 TYR Chi-restraints excluded: chain S residue 177 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 421 LEU Chi-restraints excluded: chain T residue 430 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 178 THR Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 217 ARG Chi-restraints excluded: chain U residue 278 GLN Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 399 ILE Chi-restraints excluded: chain U residue 405 GLN Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 378 THR Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 505 THR Chi-restraints excluded: chain V residue 517 ILE Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 306 SER Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 417 ILE Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 541 GLU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 325 ILE Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 415 ASP Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 495 VAL Chi-restraints excluded: chain Y residue 506 ILE Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 160 LEU Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 198 ASN Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 314 LEU Chi-restraints excluded: chain Z residue 326 THR Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 429 ASP Chi-restraints excluded: chain Z residue 480 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 386 optimal weight: 10.0000 chunk 407 optimal weight: 0.9980 chunk 371 optimal weight: 4.9990 chunk 396 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 311 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 357 optimal weight: 0.0980 chunk 374 optimal weight: 0.9990 chunk 394 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 ASN I 87 ASN S 185 HIS ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 452 GLN V 64 GLN ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 34384 Z= 0.194 Angle : 0.553 10.405 46598 Z= 0.279 Chirality : 0.043 0.180 5513 Planarity : 0.004 0.041 5991 Dihedral : 6.056 117.433 4917 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.93 % Favored : 95.94 % Rotamer: Outliers : 2.72 % Allowed : 21.43 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.63 (0.13), residues: 4457 helix: 0.09 (0.12), residues: 2062 sheet: -0.82 (0.22), residues: 595 loop : -0.69 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP U 73 HIS 0.005 0.001 HIS S 185 PHE 0.026 0.001 PHE P 122 TYR 0.014 0.001 TYR Z 248 ARG 0.006 0.000 ARG U 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 382 time to evaluate : 3.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 69 ILE cc_start: 0.6827 (tp) cc_final: 0.6260 (tp) REVERT: Q 71 LYS cc_start: 0.5640 (mttp) cc_final: 0.5019 (ttpt) REVERT: U 282 MET cc_start: 0.8855 (mmt) cc_final: 0.8470 (mmt) REVERT: V 112 ASP cc_start: 0.8086 (p0) cc_final: 0.7585 (p0) REVERT: V 445 THR cc_start: 0.7095 (OUTLIER) cc_final: 0.6769 (t) REVERT: X 541 GLU cc_start: 0.4506 (OUTLIER) cc_final: 0.4037 (tp30) REVERT: Y 193 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8665 (tt) REVERT: Y 538 VAL cc_start: 0.7310 (OUTLIER) cc_final: 0.7093 (t) REVERT: Z 448 GLN cc_start: 0.6262 (tm-30) cc_final: 0.5856 (mt0) REVERT: Z 488 MET cc_start: 0.7587 (mmt) cc_final: 0.7215 (mmt) outliers start: 97 outliers final: 84 residues processed: 452 average time/residue: 0.4525 time to fit residues: 337.3144 Evaluate side-chains 458 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 370 time to evaluate : 3.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 122 PHE Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 148 HIS Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 54 TYR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 158 TYR Chi-restraints excluded: chain S residue 177 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 271 MET Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 421 LEU Chi-restraints excluded: chain T residue 430 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 178 THR Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 405 GLN Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 378 THR Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 505 THR Chi-restraints excluded: chain V residue 517 ILE Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 306 SER Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 541 GLU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 325 ILE Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 415 ASP Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 495 VAL Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 160 LEU Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 208 SER Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 314 LEU Chi-restraints excluded: chain Z residue 326 THR Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 480 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 260 optimal weight: 1.9990 chunk 418 optimal weight: 1.9990 chunk 255 optimal weight: 6.9990 chunk 198 optimal weight: 0.8980 chunk 291 optimal weight: 0.4980 chunk 439 optimal weight: 7.9990 chunk 404 optimal weight: 4.9990 chunk 349 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 270 optimal weight: 7.9990 chunk 214 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 185 HIS T 452 GLN ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 34384 Z= 0.193 Angle : 0.553 10.738 46598 Z= 0.278 Chirality : 0.043 0.181 5513 Planarity : 0.003 0.038 5991 Dihedral : 5.848 101.773 4917 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.88 % Favored : 95.98 % Rotamer: Outliers : 2.58 % Allowed : 21.57 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.13), residues: 4457 helix: 0.17 (0.12), residues: 2058 sheet: -0.82 (0.22), residues: 604 loop : -0.61 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 73 HIS 0.006 0.001 HIS S 185 PHE 0.024 0.001 PHE E 107 TYR 0.014 0.001 TYR Z 248 ARG 0.007 0.000 ARG Q 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 386 time to evaluate : 3.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.5282 (mmm) cc_final: 0.4902 (mmt) REVERT: D 69 ILE cc_start: 0.6628 (tp) cc_final: 0.6181 (tp) REVERT: Q 71 LYS cc_start: 0.5564 (mttp) cc_final: 0.5001 (ttpt) REVERT: T 272 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8903 (tp) REVERT: U 282 MET cc_start: 0.8851 (mmt) cc_final: 0.8458 (mmt) REVERT: V 112 ASP cc_start: 0.8069 (p0) cc_final: 0.7833 (p0) REVERT: X 541 GLU cc_start: 0.4528 (OUTLIER) cc_final: 0.4049 (tp30) REVERT: Y 193 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8650 (tt) REVERT: Y 538 VAL cc_start: 0.7384 (OUTLIER) cc_final: 0.7175 (t) REVERT: Z 448 GLN cc_start: 0.6260 (tm-30) cc_final: 0.5846 (mt0) outliers start: 92 outliers final: 83 residues processed: 454 average time/residue: 0.4508 time to fit residues: 339.0527 Evaluate side-chains 464 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 377 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 122 PHE Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 148 HIS Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 54 TYR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 158 TYR Chi-restraints excluded: chain S residue 177 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 271 MET Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 421 LEU Chi-restraints excluded: chain T residue 430 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 178 THR Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 405 GLN Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 378 THR Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 505 THR Chi-restraints excluded: chain V residue 517 ILE Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 306 SER Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 541 GLU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 325 ILE Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 415 ASP Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 495 VAL Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 160 LEU Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 208 SER Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 314 LEU Chi-restraints excluded: chain Z residue 326 THR Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 480 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 277 optimal weight: 0.0000 chunk 372 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 322 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 350 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 359 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 GLN S 185 HIS T 452 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 488 GLN ** Y 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.163253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.129206 restraints weight = 50553.117| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.63 r_work: 0.3366 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34384 Z= 0.166 Angle : 0.535 10.270 46598 Z= 0.268 Chirality : 0.042 0.178 5513 Planarity : 0.003 0.036 5991 Dihedral : 5.535 81.192 4917 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.59 % Favored : 96.28 % Rotamer: Outliers : 2.50 % Allowed : 21.65 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.37 (0.13), residues: 4457 helix: 0.30 (0.12), residues: 2063 sheet: -0.73 (0.22), residues: 610 loop : -0.54 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 73 HIS 0.005 0.001 HIS S 185 PHE 0.025 0.001 PHE E 107 TYR 0.019 0.001 TYR Z 397 ARG 0.006 0.000 ARG Q 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8424.47 seconds wall clock time: 152 minutes 42.97 seconds (9162.97 seconds total)