Starting phenix.real_space_refine on Thu Feb 22 10:42:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdv_4832/02_2024/6rdv_4832_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdv_4832/02_2024/6rdv_4832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdv_4832/02_2024/6rdv_4832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdv_4832/02_2024/6rdv_4832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdv_4832/02_2024/6rdv_4832_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdv_4832/02_2024/6rdv_4832_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 116 5.16 5 C 21541 2.51 5 N 5795 2.21 5 O 6421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 111": "OE1" <-> "OE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "I PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 64": "OE1" <-> "OE2" Residue "P ASP 68": "OD1" <-> "OD2" Residue "P ASP 72": "OD1" <-> "OD2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P GLU 142": "OE1" <-> "OE2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 33": "OE1" <-> "OE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 54": "OD1" <-> "OD2" Residue "Q TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 32": "OE1" <-> "OE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 35": "OE1" <-> "OE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 62": "OE1" <-> "OE2" Residue "R PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 87": "OD1" <-> "OD2" Residue "R GLU 148": "OE1" <-> "OE2" Residue "R ASP 153": "OD1" <-> "OD2" Residue "R PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 177": "OE1" <-> "OE2" Residue "R GLU 186": "OE1" <-> "OE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S GLU 131": "OE1" <-> "OE2" Residue "S ASP 136": "OD1" <-> "OD2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 181": "OE1" <-> "OE2" Residue "S ASP 214": "OD1" <-> "OD2" Residue "S ASP 232": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" 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 226": "OD1" <-> "OD2" 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 294": "OD1" <-> "OD2" Residue "T ASP 325": "OD1" <-> "OD2" Residue "T GLU 411": "OE1" <-> "OE2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 429": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 449": "OE1" <-> "OE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T GLU 455": "OE1" <-> "OE2" Residue "T PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 465": "OD1" <-> "OD2" Residue "T GLU 475": "OE1" <-> "OE2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 521": "OE1" <-> "OE2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 112": "OD1" <-> "OD2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 221": "OE1" <-> "OE2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ASP 237": "OD1" <-> "OD2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 311": "OE1" <-> "OE2" Residue "U PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U ARG 342": "NH1" <-> "NH2" Residue "U ARG 343": "NH1" <-> "NH2" Residue "U ARG 364": "NH1" <-> "NH2" Residue "U PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 384": "OE1" <-> "OE2" Residue "U GLU 409": "OE1" <-> "OE2" Residue "U GLU 411": "OE1" <-> "OE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 467": "OD1" <-> "OD2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 510": "OD1" <-> "OD2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V GLU 186": "OE1" <-> "OE2" Residue "V ASP 210": "OD1" <-> "OD2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V ASP 237": "OD1" <-> "OD2" Residue "V TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 266": "NH1" <-> "NH2" Residue "V PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V 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 GLU 409": "OE1" <-> "OE2" Residue "V GLU 411": "OE1" <-> "OE2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 429": "NH1" <-> "NH2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V GLU 455": "OE1" <-> "OE2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 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 PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 510": "OD1" <-> "OD2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V GLU 521": "OE1" <-> "OE2" Residue "V GLU 522": "OE1" <-> "OE2" Residue "V GLU 553": "OE1" <-> "OE2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X ASP 94": "OD1" <-> "OD2" Residue "X GLU 146": "OE1" <-> "OE2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "X GLU 158": "OE1" <-> "OE2" Residue "X PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 215": "OE1" <-> "OE2" Residue "X ARG 218": "NH1" <-> "NH2" Residue "X GLU 219": "OE1" <-> "OE2" Residue "X ASP 222": "OD1" <-> "OD2" Residue "X ARG 225": "NH1" <-> "NH2" Residue "X ARG 239": "NH1" <-> "NH2" Residue "X GLU 253": "OE1" <-> "OE2" Residue "X ASP 285": "OD1" <-> "OD2" Residue "X GLU 296": "OE1" <-> "OE2" Residue "X ASP 359": "OD1" <-> "OD2" 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 TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 401": "NH1" <-> "NH2" Residue "X ASP 409": "OD1" <-> "OD2" Residue "X ASP 423": "OD1" <-> "OD2" Residue "X GLU 427": "OE1" <-> "OE2" Residue "X ASP 462": "OD1" <-> "OD2" Residue "X PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 497": "OE1" <-> "OE2" Residue "X ASP 505": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X GLU 511": "OE1" <-> "OE2" Residue "X GLU 519": "OE1" <-> "OE2" Residue "X GLU 520": "OE1" <-> "OE2" Residue "X GLU 533": "OE1" <-> "OE2" Residue "X GLU 536": "OE1" <-> "OE2" Residue "X GLU 546": "OE1" <-> "OE2" Residue "X ASP 548": "OD1" <-> "OD2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y ASP 82": "OD1" <-> "OD2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ASP 91": "OD1" <-> "OD2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y GLU 131": "OE1" <-> "OE2" Residue "Y ASP 136": "OD1" <-> "OD2" Residue "Y ASP 139": "OD1" <-> "OD2" Residue "Y ARG 145": "NH1" <-> "NH2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 215": "OE1" <-> "OE2" Residue "Y ASP 222": "OD1" <-> "OD2" Residue "Y GLU 226": "OE1" <-> "OE2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y GLU 270": "OE1" <-> "OE2" Residue "Y ASP 285": "OD1" <-> "OD2" Residue "Y TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 344": "OD1" <-> "OD2" Residue "Y ASP 345": "OD1" <-> "OD2" Residue "Y ASP 359": "OD1" <-> "OD2" Residue "Y ARG 366": "NH1" <-> "NH2" Residue "Y TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y ASP 415": "OD1" <-> "OD2" Residue "Y GLU 424": "OE1" <-> "OE2" Residue "Y GLU 427": "OE1" <-> "OE2" Residue "Y PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 533": "OE1" <-> "OE2" Residue "Y GLU 540": "OE1" <-> "OE2" Residue "Y GLU 541": "OE1" <-> "OE2" Residue "Y ASP 548": "OD1" <-> "OD2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 49": "OD1" <-> "OD2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z GLU 75": "OE1" <-> "OE2" Residue "Z ASP 82": "OD1" <-> "OD2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "Z ARG 98": "NH1" <-> "NH2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z ASP 130": "OD1" <-> "OD2" Residue "Z GLU 156": "OE1" <-> "OE2" Residue "Z ASP 168": "OD1" <-> "OD2" Residue "Z PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 216": "NH1" <-> "NH2" Residue "Z ARG 258": "NH1" <-> "NH2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z ARG 289": "NH1" <-> "NH2" Residue "Z ASP 345": "OD1" <-> "OD2" Residue "Z PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 370": "OE1" <-> "OE2" Residue "Z TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z GLU 395": "OE1" <-> "OE2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 423": "OD1" <-> "OD2" Residue "Z GLU 427": "OE1" <-> "OE2" Residue "Z ASP 429": "OD1" <-> "OD2" Residue "Z ARG 435": "NH1" <-> "NH2" Residue "Z ARG 437": "NH1" <-> "NH2" Residue "Z PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 462": "OD1" <-> "OD2" Residue "Z PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 479": "OD1" <-> "OD2" Residue "Z ASP 480": "OD1" <-> "OD2" Residue "Z GLU 497": "OE1" <-> "OE2" Residue "Z ASP 505": "OD1" <-> "OD2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z GLU 519": "OE1" <-> "OE2" Residue "Z GLU 520": "OE1" <-> "OE2" Residue "Z GLU 536": "OE1" <-> "OE2" Residue "Z GLU 541": "OE1" <-> "OE2" Residue "Z ASP 548": "OD1" <-> "OD2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33891 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "P" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 895 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3609 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 456} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.89, per 1000 atoms: 0.53 Number of scatterers: 33891 At special positions: 0 Unit cell: (160.056, 134.784, 209.547, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 13 15.00 Mg 5 11.99 O 6421 8.00 N 5795 7.00 C 21541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.21 Conformation dependent library (CDL) restraints added in 6.8 seconds 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 167 helices and 27 sheets defined 45.6% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.22 Creating SS restraints... Processing helix chain 'A' and resid 56 through 69 removed outlier: 4.350A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 91 removed outlier: 4.074A pdb=" N GLY A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 98 through 125 removed outlier: 4.395A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 4.024A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 99 through 123 removed outlier: 4.418A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 91 removed outlier: 3.782A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 91 " --> pdb=" O ASN C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 99 through 125 removed outlier: 3.867A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU C 125 " --> pdb=" O VAL C 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 91 removed outlier: 3.571A pdb=" N LYS D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 125 removed outlier: 4.127A pdb=" N GLY D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 89 removed outlier: 3.935A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 125 removed outlier: 3.647A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 91 removed outlier: 4.488A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS F 66 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 123 removed outlier: 4.310A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL F 100 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU F 111 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE F 113 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL F 120 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL F 121 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 91 removed outlier: 4.214A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 123 removed outlier: 3.571A pdb=" N ALA G 96 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU G 99 " --> pdb=" O ALA G 96 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL G 100 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU G 104 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER G 112 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL G 121 " --> pdb=" O LEU G 118 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE G 122 " --> pdb=" O LEU G 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 66 Processing helix chain 'H' and resid 71 through 91 removed outlier: 4.012A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 123 removed outlier: 3.652A pdb=" N ALA H 96 " --> pdb=" O PRO H 93 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 117 " --> pdb=" O ALA H 114 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU H 119 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL H 121 " --> pdb=" O LEU H 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 65 removed outlier: 3.665A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 91 removed outlier: 3.985A pdb=" N GLY I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 125 removed outlier: 4.870A pdb=" N LYS I 97 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU I 99 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL I 100 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU I 111 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER I 112 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE I 113 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU I 115 " --> pdb=" O SER I 112 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE I 122 " --> pdb=" O LEU I 119 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE I 124 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU I 125 " --> pdb=" O PHE I 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 88 removed outlier: 4.692A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 124 removed outlier: 3.719A pdb=" N VAL J 100 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 62 Processing helix chain 'P' and resid 67 through 83 removed outlier: 3.622A pdb=" N GLN P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 92 removed outlier: 3.968A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 104 Processing helix chain 'P' and resid 118 through 127 Processing helix chain 'P' and resid 131 through 145 removed outlier: 3.546A pdb=" N LEU P 134 " --> pdb=" O LEU P 131 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU P 136 " --> pdb=" O ALA P 133 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU P 143 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU P 144 " --> pdb=" O TYR P 141 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 11 No H-bonds generated for 'chain 'Q' and resid 8 through 11' Processing helix chain 'Q' and resid 16 through 28 Processing helix chain 'Q' and resid 33 through 39 removed outlier: 4.287A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 43 No H-bonds generated for 'chain 'Q' and resid 41 through 43' Processing helix chain 'R' and resid 32 through 37 Processing helix chain 'R' and resid 51 through 54 removed outlier: 3.597A pdb=" N TYR R 54 " --> pdb=" O PRO R 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 51 through 54' Processing helix chain 'R' and resid 152 through 154 No H-bonds generated for 'chain 'R' and resid 152 through 154' Processing helix chain 'R' and resid 159 through 167 Processing helix chain 'R' and resid 175 through 196 Processing helix chain 'S' and resid 42 through 70 removed outlier: 3.608A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN S 70 " --> pdb=" O SER S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 78 Processing helix chain 'S' and resid 81 through 88 removed outlier: 4.518A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 127 Processing helix chain 'S' and resid 144 through 153 removed outlier: 4.006A pdb=" N SER S 148 " --> pdb=" O ASP S 144 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN S 149 " --> pdb=" O LYS S 145 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR S 151 " --> pdb=" O ARG S 147 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG S 152 " --> pdb=" O SER S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 184 Processing helix chain 'S' and resid 217 through 220 No H-bonds generated for 'chain 'S' and resid 217 through 220' Processing helix chain 'S' and resid 228 through 230 No H-bonds generated for 'chain 'S' and resid 228 through 230' Processing helix chain 'S' and resid 239 through 241 No H-bonds generated for 'chain 'S' and resid 239 through 241' Processing helix chain 'S' and resid 243 through 273 removed outlier: 3.948A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) Processing helix chain 'S' and resid 276 through 312 Processing helix chain 'T' and resid 135 through 137 No H-bonds generated for 'chain 'T' and resid 135 through 137' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 207 through 212 removed outlier: 3.599A pdb=" N ALA T 211 " --> pdb=" O LYS T 207 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 207 through 212' Processing helix chain 'T' and resid 231 through 246 removed outlier: 3.799A pdb=" N ALA T 235 " --> pdb=" O LYS T 231 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN T 244 " --> pdb=" O ILE T 240 " (cutoff:3.500A) Processing helix chain 'T' and resid 270 through 279 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 296 through 299 No H-bonds generated for 'chain 'T' and resid 296 through 299' Processing helix chain 'T' and resid 302 through 315 removed outlier: 4.482A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 340 removed outlier: 3.876A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 352 through 364 removed outlier: 4.349A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU T 357 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER T 359 " --> pdb=" O TYR T 356 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG T 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU T 362 " --> pdb=" O SER T 359 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU T 363 " --> pdb=" O ARG T 360 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 401 Processing helix chain 'T' and resid 410 through 414 removed outlier: 3.501A pdb=" N TYR T 414 " --> pdb=" O THR T 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 410 through 414' Processing helix chain 'T' and resid 437 through 440 No H-bonds generated for 'chain 'T' and resid 437 through 440' Processing helix chain 'T' and resid 446 through 462 removed outlier: 3.986A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA T 458 " --> pdb=" O ARG T 454 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE T 462 " --> pdb=" O ALA T 458 " (cutoff:3.500A) Processing helix chain 'T' and resid 470 through 483 removed outlier: 3.689A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU T 482 " --> pdb=" O ALA T 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 495 through 505 removed outlier: 3.709A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 514 through 516 No H-bonds generated for 'chain 'T' and resid 514 through 516' Processing helix chain 'T' and resid 521 through 526 Processing helix chain 'T' and resid 531 through 539 removed outlier: 3.672A pdb=" N ILE T 535 " --> pdb=" O ALA T 531 " (cutoff:3.500A) Processing helix chain 'T' and resid 544 through 553 removed outlier: 4.123A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS T 551 " --> pdb=" O ASP T 547 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 48 removed outlier: 3.896A pdb=" N GLU U 47 " --> pdb=" O LYS U 43 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU U 48 " --> pdb=" O ALA U 44 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 71 removed outlier: 5.575A 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 207 through 211 Processing helix chain 'U' and resid 231 through 246 removed outlier: 3.805A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 278 Processing helix chain 'U' and resid 281 through 284 Processing helix chain 'U' and resid 296 through 315 Proline residue: U 303 - end of helix removed outlier: 3.892A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 removed outlier: 3.771A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 354 through 362 removed outlier: 3.597A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 393 through 399 Processing helix chain 'U' and resid 410 through 414 Processing helix chain 'U' and resid 437 through 459 removed outlier: 3.862A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) Processing helix chain 'U' and resid 471 through 484 removed outlier: 3.860A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 495 through 505 removed outlier: 3.632A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 517 through 527 removed outlier: 4.121A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 539 removed outlier: 3.725A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) Processing helix chain 'U' and resid 544 through 553 removed outlier: 3.589A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) Processing helix chain 'V' and resid 46 through 48 No H-bonds generated for 'chain 'V' and resid 46 through 48' Processing helix chain 'V' and resid 58 through 69 removed outlier: 3.734A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.631A 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 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 212 Processing helix chain 'V' and resid 231 through 248 removed outlier: 3.905A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN V 248 " --> pdb=" O ASN V 244 " (cutoff:3.500A) Processing helix chain 'V' and resid 266 through 279 Processing helix chain 'V' and resid 281 through 283 No H-bonds generated for 'chain 'V' and resid 281 through 283' Processing helix chain 'V' and resid 296 through 316 Proline residue: V 303 - end of helix removed outlier: 3.736A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 340 Processing helix chain 'V' and resid 352 through 362 removed outlier: 4.452A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER V 359 " --> pdb=" O TYR V 356 " (cutoff:3.500A) Processing helix chain 'V' and resid 393 through 401 Processing helix chain 'V' and resid 410 through 414 removed outlier: 3.824A pdb=" N TYR V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 410 through 414' Processing helix chain 'V' and resid 431 through 434 removed outlier: 3.681A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 431 through 434' Processing helix chain 'V' and resid 440 through 456 removed outlier: 3.674A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU V 448 " --> pdb=" O GLY V 444 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 484 removed outlier: 3.629A pdb=" N GLU V 482 " --> pdb=" O ALA V 478 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU V 484 " --> pdb=" O LEU V 480 " (cutoff:3.500A) Processing helix chain 'V' and resid 494 through 506 Processing helix chain 'V' and resid 514 through 520 removed outlier: 4.179A pdb=" N ILE V 517 " --> pdb=" O VAL V 514 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL V 518 " --> pdb=" O GLN V 515 " (cutoff:3.500A) Processing helix chain 'V' and resid 522 through 525 No H-bonds generated for 'chain 'V' and resid 522 through 525' Processing helix chain 'V' and resid 531 through 539 removed outlier: 4.046A pdb=" N ILE V 535 " --> pdb=" O ALA V 531 " (cutoff:3.500A) Processing helix chain 'V' and resid 544 through 554 removed outlier: 4.068A pdb=" N LYS V 551 " --> pdb=" O ASP V 547 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 117 No H-bonds generated for 'chain 'X' and resid 115 through 117' Processing helix chain 'X' and resid 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 removed outlier: 4.763A pdb=" N LYS X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA X 203 " --> pdb=" O ASN X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 228 Processing helix chain 'X' and resid 236 through 241 removed outlier: 4.730A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN X 241 " --> pdb=" O GLU X 238 " (cutoff:3.500A) Processing helix chain 'X' and resid 255 through 259 Processing helix chain 'X' and resid 261 through 274 removed outlier: 3.746A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 288 through 298 Processing helix chain 'X' and resid 314 through 324 removed outlier: 4.296A pdb=" N ARG X 324 " --> pdb=" O GLY X 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 349 through 352 No H-bonds generated for 'chain 'X' and resid 349 through 352' Processing helix chain 'X' and resid 355 through 357 No H-bonds generated for 'chain 'X' and resid 355 through 357' Processing helix chain 'X' and resid 366 through 371 removed outlier: 3.740A pdb=" N LEU X 371 " --> pdb=" O SER X 367 " (cutoff:3.500A) Processing helix chain 'X' and resid 394 through 419 removed outlier: 4.715A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) Processing helix chain 'X' and resid 422 through 424 No H-bonds generated for 'chain 'X' and resid 422 through 424' Processing helix chain 'X' and resid 427 through 442 Processing helix chain 'X' and resid 451 through 454 No H-bonds generated for 'chain 'X' and resid 451 through 454' Processing helix chain 'X' and resid 463 through 475 Processing helix chain 'X' and resid 492 through 506 removed outlier: 3.870A pdb=" N ILE X 506 " --> pdb=" O MET X 502 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 532 removed outlier: 3.887A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 165 through 170 Processing helix chain 'Y' and resid 189 through 200 Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 4.733A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 258 No H-bonds generated for 'chain 'Y' and resid 255 through 258' Processing helix chain 'Y' and resid 261 through 274 Processing helix chain 'Y' and resid 288 through 298 removed outlier: 3.790A pdb=" N VAL Y 297 " --> pdb=" O ALA Y 293 " (cutoff:3.500A) Processing helix chain 'Y' and resid 314 through 322 Processing helix chain 'Y' and resid 349 through 357 removed outlier: 3.623A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N HIS Y 357 " --> pdb=" O THR Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 371 removed outlier: 3.997A pdb=" N LEU Y 371 " --> pdb=" O SER Y 367 " (cutoff:3.500A) Processing helix chain 'Y' and resid 394 through 420 removed outlier: 3.878A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA Y 418 " --> pdb=" O GLN Y 414 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 429 through 443 Processing helix chain 'Y' and resid 463 through 474 Processing helix chain 'Y' and resid 483 through 485 No H-bonds generated for 'chain 'Y' and resid 483 through 485' Processing helix chain 'Y' and resid 492 through 507 Processing helix chain 'Y' and resid 527 through 532 Processing helix chain 'Y' and resid 545 through 554 removed outlier: 3.881A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 117 No H-bonds generated for 'chain 'Z' and resid 115 through 117' Processing helix chain 'Z' and resid 165 through 169 Processing helix chain 'Z' and resid 189 through 203 Processing helix chain 'Z' and resid 217 through 228 Processing helix chain 'Z' and resid 237 through 241 removed outlier: 4.486A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 259 Processing helix chain 'Z' and resid 261 through 274 removed outlier: 3.548A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 300 Processing helix chain 'Z' and resid 314 through 322 removed outlier: 3.930A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 349 through 357 removed outlier: 4.158A pdb=" N ALA Z 356 " --> pdb=" O ALA Z 352 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N HIS Z 357 " --> pdb=" O THR Z 353 " (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 410 Processing helix chain 'Z' and resid 422 through 424 No H-bonds generated for 'chain 'Z' and resid 422 through 424' Processing helix chain 'Z' and resid 427 through 439 removed outlier: 3.711A pdb=" N THR Z 432 " --> pdb=" O GLU Z 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 451 through 454 No H-bonds generated for 'chain 'Z' and resid 451 through 454' Processing helix chain 'Z' and resid 463 through 475 removed outlier: 3.746A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 483 through 485 No H-bonds generated for 'chain 'Z' and resid 483 through 485' Processing helix chain 'Z' and resid 492 through 504 removed outlier: 3.652A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 532 Processing sheet with id= A, first strand: chain 'Q' and resid 45 through 50 Processing sheet with id= B, first strand: chain 'R' and resid 72 through 75 removed outlier: 6.950A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE R 144 " --> pdb=" O TYR R 75 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'R' and resid 97 through 100 removed outlier: 3.538A pdb=" N VAL R 89 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU R 125 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 203 through 211 removed outlier: 5.545A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.543A 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: 6.659A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN T 121 " --> pdb=" O GLY T 128 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'T' and resid 152 through 155 Processing sheet with id= G, first strand: chain 'T' and resid 404 through 408 removed outlier: 3.721A pdb=" N LEU T 222 " --> pdb=" O GLY T 404 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'T' and resid 286 through 290 removed outlier: 6.669A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER T 376 " --> pdb=" O GLY T 320 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE T 322 " --> pdb=" O SER T 376 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.648A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'U' and resid 109 through 111 Processing sheet with id= K, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= L, first strand: chain 'U' and resid 404 through 408 Processing sheet with id= M, first strand: chain 'U' and resid 285 through 290 removed outlier: 8.857A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE U 380 " --> pdb=" O TYR U 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'V' and resid 84 through 86 removed outlier: 3.868A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLY V 128 " --> pdb=" O LEU V 120 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU V 122 " --> pdb=" O HIS V 126 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N HIS V 126 " --> pdb=" O LEU V 122 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N TYR V 98 " --> pdb=" O VAL V 87 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL V 87 " --> pdb=" O TYR V 98 " (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: 4.008A pdb=" N LEU V 222 " --> pdb=" O GLY V 404 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'V' and resid 285 through 290 removed outlier: 9.013A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE V 380 " --> pdb=" O TYR V 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'X' and resid 37 through 39 removed outlier: 6.579A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ARG X 51 " --> pdb=" O VAL X 40 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL X 40 " --> pdb=" O ARG X 51 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'X' and resid 110 through 113 Processing sheet with id= T, first strand: chain 'X' and resid 360 through 363 removed outlier: 7.765A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N GLY X 183 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL X 339 " --> pdb=" O GLY X 183 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE X 207 " --> pdb=" O LEU X 281 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE X 283 " --> pdb=" O PHE X 207 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL X 209 " --> pdb=" O PHE X 283 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ASP X 285 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA X 211 " --> 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 39 through 44 removed outlier: 6.510A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Y' and resid 360 through 363 removed outlier: 7.471A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLY Y 183 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL Y 339 " --> pdb=" O GLY Y 183 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE Y 207 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N PHE Y 283 " --> pdb=" O PHE Y 207 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ALA Y 211 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Z' and resid 38 through 44 removed outlier: 6.399A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Z' and resid 110 through 113 removed outlier: 3.540A pdb=" N ASP Z 139 " --> pdb=" O VAL Z 113 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Z' and resid 244 through 250 removed outlier: 6.926A pdb=" N SER Z 208 " --> pdb=" O THR Z 245 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N VAL Z 247 " --> pdb=" O SER Z 208 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE Z 210 " --> pdb=" O VAL Z 247 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLY Z 249 " --> pdb=" O PHE Z 210 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLY Z 212 " --> pdb=" O GLY Z 249 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL Z 209 " --> pdb=" O ASP Z 279 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU Z 281 " --> pdb=" O VAL Z 209 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA Z 211 " --> pdb=" O LEU Z 281 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE Z 283 " --> pdb=" O ALA Z 211 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL Z 213 " --> pdb=" O PHE Z 283 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASP Z 285 " --> pdb=" O VAL Z 213 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLU Z 215 " --> pdb=" O ASP Z 285 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N SER Z 332 " --> pdb=" O VAL Z 280 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU Z 282 " --> pdb=" O SER Z 332 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N THR Z 334 " --> pdb=" O LEU Z 282 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL Z 284 " --> pdb=" O THR Z 334 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL Z 336 " --> pdb=" O VAL Z 284 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLY Z 180 " --> pdb=" O ASP Z 359 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N THR Z 361 " --> pdb=" O GLY Z 180 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Z' and resid 559 through 561 1362 hydrogen bonds defined for protein. 3732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.60 Time building geometry restraints manager: 15.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9790 1.33 - 1.45: 5809 1.45 - 1.57: 18592 1.57 - 1.69: 21 1.69 - 1.82: 200 Bond restraints: 34412 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.41e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.16e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.96e+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 4.28e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.64e+01 ... (remaining 34407 not shown) Histogram of bond angle deviations from ideal: 97.66 - 105.35: 671 105.35 - 113.03: 18862 113.03 - 120.71: 16317 120.71 - 128.39: 10631 128.39 - 136.07: 157 Bond angle restraints: 46638 Sorted by residual: angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 120.16 19.71 1.00e+00 1.00e+00 3.88e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 120.26 19.61 1.00e+00 1.00e+00 3.84e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 122.05 17.82 1.00e+00 1.00e+00 3.18e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 123.74 13.09 1.00e+00 1.00e+00 1.71e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 123.80 13.03 1.00e+00 1.00e+00 1.70e+02 ... (remaining 46633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.26: 20241 33.26 - 66.53: 527 66.53 - 99.79: 53 99.79 - 133.06: 1 133.06 - 166.32: 1 Dihedral angle restraints: 20823 sinusoidal: 8066 harmonic: 12757 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 -120.54 -59.46 0 5.00e+00 4.00e-02 1.41e+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 -122.18 -57.82 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual 180.00 -125.88 -54.12 0 5.00e+00 4.00e-02 1.17e+02 ... (remaining 20820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4268 0.072 - 0.144: 1105 0.144 - 0.216: 123 0.216 - 0.288: 16 0.288 - 0.360: 7 Chirality restraints: 5519 Sorted by residual: chirality pdb=" CB VAL U 198 " pdb=" CA VAL U 198 " pdb=" CG1 VAL U 198 " pdb=" CG2 VAL U 198 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CB VAL U 180 " pdb=" CA VAL U 180 " pdb=" CG1 VAL U 180 " pdb=" CG2 VAL U 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB VAL Y 124 " pdb=" CA VAL Y 124 " pdb=" CG1 VAL Y 124 " pdb=" CG2 VAL Y 124 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 5516 not shown) Planarity restraints: 5997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.030 2.00e-02 2.50e+03 5.77e-02 3.33e+01 pdb=" C ALA Z 503 " -0.100 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.037 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 307 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.33e+00 pdb=" C ALA Z 307 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA Z 307 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL Z 308 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU Q 33 " -0.049 5.00e-02 4.00e+02 7.35e-02 8.65e+00 pdb=" N PRO Q 34 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO Q 34 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO Q 34 " -0.041 5.00e-02 4.00e+02 ... (remaining 5994 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 468 2.63 - 3.20: 29424 3.20 - 3.76: 54717 3.76 - 4.33: 79149 4.33 - 4.90: 128803 Nonbonded interactions: 292561 Sorted by model distance: nonbonded pdb=" OG1 THR V 232 " pdb="MG MG V1002 " model vdw 2.059 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.134 2.170 nonbonded pdb=" O2B ATP U1001 " pdb="MG MG U1002 " model vdw 2.151 2.170 nonbonded pdb=" O ALA X 503 " pdb=" CG1 ILE X 506 " model vdw 2.218 3.440 nonbonded pdb=" O GLY X 45 " pdb=" OG1 THR X 93 " model vdw 2.232 2.440 ... (remaining 292556 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.730 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: 0.020 Extract box with map and model: 25.010 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 92.240 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.220 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: 0.020 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.124 34412 Z= 0.705 Angle : 1.065 19.707 46638 Z= 0.605 Chirality : 0.063 0.360 5519 Planarity : 0.008 0.074 5997 Dihedral : 15.426 166.320 12663 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.76 % Favored : 93.93 % Rotamer: Outliers : 0.67 % Allowed : 11.39 % Favored : 87.93 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.10), residues: 4461 helix: -3.14 (0.08), residues: 2150 sheet: -1.46 (0.22), residues: 528 loop : -2.07 (0.13), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP Z 141 HIS 0.007 0.002 HIS U 139 PHE 0.032 0.003 PHE Z 486 TYR 0.025 0.003 TYR P 75 ARG 0.011 0.001 ARG V 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 582 time to evaluate : 3.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 61 MET cc_start: 0.5243 (ttm) cc_final: 0.5014 (ttm) REVERT: E 87 ASN cc_start: 0.6826 (m-40) cc_final: 0.6588 (t0) REVERT: J 109 LEU cc_start: 0.7198 (mm) cc_final: 0.6811 (mt) REVERT: P 64 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8375 (mm-30) REVERT: P 119 LYS cc_start: 0.7805 (mtpt) cc_final: 0.7534 (mttt) REVERT: P 128 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7376 (mp0) REVERT: P 135 LEU cc_start: 0.8632 (mt) cc_final: 0.8342 (mt) REVERT: P 136 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7927 (mm-30) REVERT: P 140 ASN cc_start: 0.8798 (m-40) cc_final: 0.8490 (m110) REVERT: P 150 LYS cc_start: 0.6573 (mttp) cc_final: 0.6314 (mmmt) REVERT: S 76 GLU cc_start: 0.5875 (tp30) cc_final: 0.5611 (tp30) REVERT: S 271 MET cc_start: 0.7530 (ttp) cc_final: 0.7092 (tmm) REVERT: T 389 ASP cc_start: 0.8002 (t0) cc_final: 0.7552 (p0) REVERT: T 447 LYS cc_start: 0.8266 (ptpt) cc_final: 0.7485 (tttt) REVERT: T 483 MET cc_start: 0.7064 (ttp) cc_final: 0.6745 (ptp) REVERT: T 488 GLN cc_start: 0.7823 (tp40) cc_final: 0.7498 (tp40) REVERT: T 516 ASP cc_start: 0.7793 (t70) cc_final: 0.7078 (t0) REVERT: T 518 VAL cc_start: 0.8421 (m) cc_final: 0.7789 (t) REVERT: T 534 LYS cc_start: 0.7745 (mttp) cc_final: 0.7323 (mmtt) REVERT: U 118 MET cc_start: 0.8549 (ttt) cc_final: 0.8147 (tmm) REVERT: U 439 MET cc_start: 0.8798 (tpp) cc_final: 0.8369 (tpt) REVERT: U 449 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6815 (mt-10) REVERT: U 502 TYR cc_start: 0.8178 (t80) cc_final: 0.7771 (t80) REVERT: U 535 ILE cc_start: 0.8712 (mt) cc_final: 0.8462 (mm) REVERT: V 61 HIS cc_start: 0.7921 (t70) cc_final: 0.7335 (m90) REVERT: V 409 GLU cc_start: 0.6842 (tp30) cc_final: 0.6596 (tp30) REVERT: V 508 PHE cc_start: 0.8364 (m-80) cc_final: 0.7957 (m-80) REVERT: V 527 GLN cc_start: 0.8267 (mm110) cc_final: 0.7860 (mt0) REVERT: V 555 ARG cc_start: 0.6135 (mtt-85) cc_final: 0.5788 (mmt180) REVERT: X 195 GLU cc_start: 0.7803 (tp30) cc_final: 0.7417 (tp30) REVERT: X 557 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6439 (mm-30) REVERT: Y 385 ARG cc_start: 0.7749 (mmt90) cc_final: 0.7503 (mmt-90) REVERT: Y 405 LYS cc_start: 0.7814 (tptt) cc_final: 0.7261 (tttt) REVERT: Y 409 ASP cc_start: 0.7246 (m-30) cc_final: 0.6497 (m-30) REVERT: Y 413 LEU cc_start: 0.7874 (mt) cc_final: 0.7532 (mt) REVERT: Y 414 GLN cc_start: 0.7473 (mt0) cc_final: 0.7069 (mt0) REVERT: Y 430 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7827 (mttm) REVERT: Y 437 ARG cc_start: 0.7411 (mtt-85) cc_final: 0.7001 (mtt90) outliers start: 24 outliers final: 17 residues processed: 602 average time/residue: 0.5058 time to fit residues: 471.9623 Evaluate side-chains 428 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 411 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 332 VAL Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 502 MET Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 326 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 0.9990 chunk 335 optimal weight: 4.9990 chunk 185 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 225 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 346 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 210 optimal weight: 0.7980 chunk 257 optimal weight: 0.6980 chunk 401 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 98 GLN F 94 ASN J 98 GLN P 65 ASN ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 46 HIS Q 74 ASN R 181 ASN S 174 GLN S 185 HIS S 262 ASN S 276 ASN S 297 GLN T 134 ASN T 196 GLN T 386 GLN ** T 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 461 GLN T 497 GLN ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 ASN U 248 GLN U 386 GLN U 441 GLN U 471 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 64 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 GLN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 242 GLN V 264 GLN V 271 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 497 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 199 ASN X 278 GLN X 398 ASN X 408 GLN X 412 ASN X 414 GLN X 471 GLN Y 83 ASN Y 174 GLN Y 414 GLN Z 42 GLN Z 78 GLN Z 198 ASN Z 199 ASN Z 241 ASN Z 250 GLN Z 278 GLN Z 388 ASN Z 398 ASN Z 404 GLN Z 440 GLN Z 448 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34412 Z= 0.172 Angle : 0.565 10.219 46638 Z= 0.293 Chirality : 0.042 0.182 5519 Planarity : 0.005 0.050 5997 Dihedral : 7.248 122.168 4940 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.38 % Favored : 96.35 % Rotamer: Outliers : 1.63 % Allowed : 15.35 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.12), residues: 4461 helix: -1.51 (0.10), residues: 2169 sheet: -1.14 (0.22), residues: 536 loop : -1.50 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 37 HIS 0.003 0.001 HIS Q 46 PHE 0.022 0.001 PHE A 116 TYR 0.021 0.001 TYR S 256 ARG 0.007 0.000 ARG T 496 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 497 time to evaluate : 3.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6512 (mtp) REVERT: D 56 LEU cc_start: 0.5299 (mt) cc_final: 0.5088 (mt) REVERT: E 81 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.6284 (ppp) REVERT: E 87 ASN cc_start: 0.6816 (m-40) cc_final: 0.6540 (t0) REVERT: G 61 MET cc_start: 0.5543 (ttp) cc_final: 0.5208 (tpp) REVERT: I 95 ILE cc_start: 0.5404 (OUTLIER) cc_final: 0.4772 (mm) REVERT: J 109 LEU cc_start: 0.7162 (mm) cc_final: 0.6758 (mt) REVERT: P 79 GLU cc_start: 0.7851 (tp30) cc_final: 0.7519 (tp30) REVERT: P 103 LYS cc_start: 0.8091 (mttp) cc_final: 0.7826 (mmtm) REVERT: P 128 GLU cc_start: 0.7591 (mm-30) cc_final: 0.6960 (mp0) REVERT: Q 40 GLN cc_start: 0.5685 (tp-100) cc_final: 0.5284 (mp10) REVERT: R 137 HIS cc_start: 0.4717 (m-70) cc_final: 0.4349 (m-70) REVERT: R 177 GLU cc_start: 0.5933 (mp0) cc_final: 0.5416 (tp30) REVERT: S 76 GLU cc_start: 0.6067 (tp30) cc_final: 0.5863 (tp30) REVERT: S 88 LEU cc_start: 0.8436 (tp) cc_final: 0.8025 (mm) REVERT: S 271 MET cc_start: 0.7429 (ttp) cc_final: 0.7085 (tmm) REVERT: T 447 LYS cc_start: 0.7901 (ptpt) cc_final: 0.7205 (tttt) REVERT: T 479 ARG cc_start: 0.7771 (mmt180) cc_final: 0.7489 (mmt-90) REVERT: U 118 MET cc_start: 0.8541 (ttt) cc_final: 0.8048 (tmm) REVERT: U 502 TYR cc_start: 0.8081 (t80) cc_final: 0.7745 (t80) REVERT: V 409 GLU cc_start: 0.6708 (tp30) cc_final: 0.6445 (tp30) REVERT: V 489 PHE cc_start: 0.6184 (m-80) cc_final: 0.5850 (m-10) REVERT: V 508 PHE cc_start: 0.8394 (m-80) cc_final: 0.7995 (m-80) REVERT: V 527 GLN cc_start: 0.8103 (mm110) cc_final: 0.7819 (mt0) REVERT: X 178 LYS cc_start: 0.8475 (mtmt) cc_final: 0.8229 (mtmm) REVERT: X 386 MET cc_start: 0.8482 (mmm) cc_final: 0.8247 (mmm) REVERT: X 390 ASN cc_start: 0.8172 (m110) cc_final: 0.7934 (m110) REVERT: Y 405 LYS cc_start: 0.7691 (tptt) cc_final: 0.6996 (ttmt) REVERT: Y 409 ASP cc_start: 0.7222 (m-30) cc_final: 0.6642 (m-30) REVERT: Y 411 LYS cc_start: 0.8297 (mtmt) cc_final: 0.8032 (mtmt) REVERT: Y 414 GLN cc_start: 0.7287 (mt0) cc_final: 0.6970 (mt0) REVERT: Y 430 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7835 (mttm) REVERT: Y 437 ARG cc_start: 0.7555 (mtt-85) cc_final: 0.7181 (mtt90) REVERT: Y 502 MET cc_start: 0.6182 (mtp) cc_final: 0.5966 (mtm) REVERT: Z 441 ARG cc_start: 0.7857 (mmt-90) cc_final: 0.7640 (mmt-90) outliers start: 58 outliers final: 34 residues processed: 533 average time/residue: 0.5081 time to fit residues: 429.7232 Evaluate side-chains 451 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 414 time to evaluate : 3.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain T residue 326 ASP Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 515 GLN Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 466 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Z residue 326 THR Chi-restraints excluded: chain Z residue 456 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 223 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 334 optimal weight: 0.9980 chunk 273 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 402 optimal weight: 3.9990 chunk 434 optimal weight: 6.9990 chunk 358 optimal weight: 0.8980 chunk 398 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 322 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN C 87 ASN F 98 GLN J 98 GLN ** P 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN P 140 ASN Q 74 ASN ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 149 GLN S 174 GLN S 186 ASN S 293 ASN T 196 GLN ** T 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 358 HIS ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 GLN V 152 ASN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 174 GLN X 198 ASN X 390 ASN X 408 GLN X 412 ASN X 414 GLN Y 68 HIS Z 42 GLN ** Z 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 278 GLN ** Z 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 34412 Z= 0.367 Angle : 0.645 10.227 46638 Z= 0.330 Chirality : 0.046 0.223 5519 Planarity : 0.005 0.054 5997 Dihedral : 7.515 115.960 4932 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.16 % Favored : 94.55 % Rotamer: Outliers : 3.11 % Allowed : 17.31 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.12), residues: 4461 helix: -1.03 (0.11), residues: 2149 sheet: -0.96 (0.22), residues: 526 loop : -1.32 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP V 73 HIS 0.005 0.001 HIS U 139 PHE 0.018 0.002 PHE A 116 TYR 0.025 0.002 TYR S 256 ARG 0.006 0.001 ARG Q 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 427 time to evaluate : 3.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 VAL cc_start: 0.6342 (OUTLIER) cc_final: 0.6127 (t) REVERT: B 123 LEU cc_start: 0.5706 (OUTLIER) cc_final: 0.5239 (tt) REVERT: C 81 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.7022 (ttp) REVERT: G 61 MET cc_start: 0.4944 (OUTLIER) cc_final: 0.4511 (mmm) REVERT: I 95 ILE cc_start: 0.5415 (OUTLIER) cc_final: 0.4802 (mm) REVERT: J 109 LEU cc_start: 0.7181 (mm) cc_final: 0.6732 (mt) REVERT: P 49 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7960 (t) REVERT: P 64 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8016 (mm-30) REVERT: R 177 GLU cc_start: 0.5852 (mp0) cc_final: 0.5288 (tp30) REVERT: T 121 ASN cc_start: 0.8592 (p0) cc_final: 0.8385 (p0) REVERT: T 447 LYS cc_start: 0.8175 (ptpt) cc_final: 0.7468 (tttt) REVERT: T 516 ASP cc_start: 0.7960 (t70) cc_final: 0.7104 (t0) REVERT: T 539 ASN cc_start: 0.8109 (t0) cc_final: 0.7340 (m110) REVERT: U 118 MET cc_start: 0.8644 (ttt) cc_final: 0.8010 (tmm) REVERT: U 199 ARG cc_start: 0.7509 (mmt-90) cc_final: 0.7224 (mmt180) REVERT: U 449 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6743 (mt-10) REVERT: U 455 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7178 (tm-30) REVERT: V 61 HIS cc_start: 0.7743 (t70) cc_final: 0.7288 (m90) REVERT: V 409 GLU cc_start: 0.6776 (tp30) cc_final: 0.6494 (tp30) REVERT: V 489 PHE cc_start: 0.6571 (m-80) cc_final: 0.6124 (m-10) REVERT: V 508 PHE cc_start: 0.8477 (m-80) cc_final: 0.8212 (m-80) REVERT: V 527 GLN cc_start: 0.8179 (mm110) cc_final: 0.7783 (mt0) REVERT: X 49 ASP cc_start: 0.7423 (m-30) cc_final: 0.7130 (m-30) REVERT: X 178 LYS cc_start: 0.8648 (mtmt) cc_final: 0.8357 (mttm) REVERT: X 325 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8450 (mt) REVERT: X 386 MET cc_start: 0.8719 (mmm) cc_final: 0.8508 (mmm) REVERT: Y 83 ASN cc_start: 0.8089 (OUTLIER) cc_final: 0.7838 (t0) REVERT: Y 405 LYS cc_start: 0.7772 (tptt) cc_final: 0.7150 (tttt) REVERT: Y 409 ASP cc_start: 0.7279 (m-30) cc_final: 0.6652 (m-30) REVERT: Y 411 LYS cc_start: 0.8218 (mtmt) cc_final: 0.7984 (mtmt) REVERT: Y 414 GLN cc_start: 0.7272 (mt0) cc_final: 0.6936 (mt0) REVERT: Y 430 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7920 (mttm) REVERT: Z 441 ARG cc_start: 0.7837 (mmt-90) cc_final: 0.7614 (mmt-90) outliers start: 111 outliers final: 64 residues processed: 510 average time/residue: 0.4666 time to fit residues: 384.3645 Evaluate side-chains 462 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 390 time to evaluate : 4.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 247 THR Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 535 ILE Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 136 SER Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 332 VAL Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 466 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 159 ILE Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 42 GLN Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 359 ASP Chi-restraints excluded: chain Z residue 456 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 397 optimal weight: 4.9990 chunk 302 optimal weight: 1.9990 chunk 208 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 270 optimal weight: 0.0980 chunk 403 optimal weight: 6.9990 chunk 427 optimal weight: 7.9990 chunk 210 optimal weight: 0.9990 chunk 382 optimal weight: 0.2980 chunk 115 optimal weight: 5.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 71 GLN P 76 GLN R 85 GLN R 119 HIS ** T 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 549 HIS ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 278 GLN X 408 GLN X 412 ASN Y 250 GLN Z 294 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34412 Z= 0.154 Angle : 0.538 9.936 46638 Z= 0.272 Chirality : 0.042 0.179 5519 Planarity : 0.004 0.046 5997 Dihedral : 6.807 103.685 4931 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.50 % Favored : 96.30 % Rotamer: Outliers : 2.64 % Allowed : 18.24 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.13), residues: 4461 helix: -0.52 (0.11), residues: 2162 sheet: -0.74 (0.23), residues: 519 loop : -1.10 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 73 HIS 0.003 0.000 HIS S 185 PHE 0.015 0.001 PHE A 116 TYR 0.017 0.001 TYR X 487 ARG 0.008 0.000 ARG S 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 455 time to evaluate : 3.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6830 (ttp) REVERT: E 60 LYS cc_start: 0.5423 (mtpp) cc_final: 0.5017 (mttp) REVERT: E 61 MET cc_start: 0.4498 (mtp) cc_final: 0.4175 (mtp) REVERT: E 105 LEU cc_start: 0.4669 (tt) cc_final: 0.4328 (pp) REVERT: G 61 MET cc_start: 0.5217 (OUTLIER) cc_final: 0.4379 (tpp) REVERT: G 122 PHE cc_start: 0.3264 (OUTLIER) cc_final: 0.2767 (m-80) REVERT: I 95 ILE cc_start: 0.5564 (OUTLIER) cc_final: 0.4930 (mm) REVERT: J 109 LEU cc_start: 0.7043 (mm) cc_final: 0.6593 (mt) REVERT: P 49 THR cc_start: 0.7895 (OUTLIER) cc_final: 0.7334 (m) REVERT: P 103 LYS cc_start: 0.8190 (mtpp) cc_final: 0.7912 (mmtm) REVERT: R 177 GLU cc_start: 0.6113 (mp0) cc_final: 0.5554 (tp30) REVERT: T 300 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8909 (t80) REVERT: T 439 MET cc_start: 0.8676 (tpp) cc_final: 0.8464 (tpp) REVERT: T 447 LYS cc_start: 0.8075 (ptpt) cc_final: 0.7393 (tttt) REVERT: T 479 ARG cc_start: 0.8105 (mmt-90) cc_final: 0.7692 (mmt-90) REVERT: T 516 ASP cc_start: 0.7802 (t70) cc_final: 0.7027 (t0) REVERT: U 118 MET cc_start: 0.8560 (ttt) cc_final: 0.8336 (ttm) REVERT: U 439 MET cc_start: 0.8682 (tpp) cc_final: 0.8349 (tpt) REVERT: U 449 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6679 (mt-10) REVERT: U 509 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7817 (mp) REVERT: V 409 GLU cc_start: 0.6604 (tp30) cc_final: 0.6359 (tp30) REVERT: V 489 PHE cc_start: 0.6253 (m-80) cc_final: 0.5862 (m-10) REVERT: V 555 ARG cc_start: 0.6649 (mtt180) cc_final: 0.5991 (mmt180) REVERT: X 178 LYS cc_start: 0.8476 (mtmt) cc_final: 0.8218 (mtmm) REVERT: X 195 GLU cc_start: 0.7988 (tp30) cc_final: 0.7574 (tp30) REVERT: X 325 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8628 (mt) REVERT: X 388 ASN cc_start: 0.8296 (t0) cc_final: 0.7993 (t0) REVERT: X 390 ASN cc_start: 0.8094 (m-40) cc_final: 0.7839 (m110) REVERT: Y 405 LYS cc_start: 0.7610 (tptt) cc_final: 0.6914 (ttmt) REVERT: Y 409 ASP cc_start: 0.7278 (m-30) cc_final: 0.6641 (m-30) REVERT: Y 414 GLN cc_start: 0.7091 (mt0) cc_final: 0.6742 (mt0) REVERT: Y 430 LYS cc_start: 0.8236 (mtpt) cc_final: 0.7941 (mttm) REVERT: Z 471 GLN cc_start: 0.8115 (tp40) cc_final: 0.7698 (tt0) outliers start: 94 outliers final: 52 residues processed: 518 average time/residue: 0.4822 time to fit residues: 400.7053 Evaluate side-chains 467 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 407 time to evaluate : 3.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 PHE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 71 GLN Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 326 ASP Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 466 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 359 ASP Chi-restraints excluded: chain Z residue 456 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 355 optimal weight: 0.9990 chunk 242 optimal weight: 0.6980 chunk 6 optimal weight: 8.9990 chunk 318 optimal weight: 4.9990 chunk 176 optimal weight: 0.6980 chunk 364 optimal weight: 0.3980 chunk 295 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 218 optimal weight: 0.6980 chunk 383 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN P 76 GLN R 119 HIS T 441 GLN T 515 GLN T 549 HIS ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 527 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 78 GLN X 408 GLN X 412 ASN Y 83 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34412 Z= 0.147 Angle : 0.524 9.300 46638 Z= 0.264 Chirality : 0.041 0.168 5519 Planarity : 0.003 0.049 5997 Dihedral : 6.403 97.130 4930 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.77 % Favored : 96.03 % Rotamer: Outliers : 2.92 % Allowed : 19.02 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.13), residues: 4461 helix: -0.15 (0.12), residues: 2143 sheet: -0.60 (0.23), residues: 534 loop : -0.89 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 73 HIS 0.002 0.001 HIS S 185 PHE 0.020 0.001 PHE A 116 TYR 0.022 0.001 TYR S 256 ARG 0.008 0.000 ARG T 496 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 468 time to evaluate : 3.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6870 (ttp) REVERT: E 105 LEU cc_start: 0.4815 (tt) cc_final: 0.3722 (mm) REVERT: G 105 LEU cc_start: 0.5521 (OUTLIER) cc_final: 0.4561 (mp) REVERT: G 122 PHE cc_start: 0.3563 (OUTLIER) cc_final: 0.3039 (m-80) REVERT: I 95 ILE cc_start: 0.5496 (OUTLIER) cc_final: 0.5180 (mp) REVERT: J 109 LEU cc_start: 0.7060 (mm) cc_final: 0.6624 (mt) REVERT: P 49 THR cc_start: 0.7819 (OUTLIER) cc_final: 0.7241 (m) REVERT: P 64 GLU cc_start: 0.8261 (mm-30) cc_final: 0.8009 (mm-30) REVERT: P 71 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: P 103 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7928 (mmtm) REVERT: P 136 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8119 (mm-30) REVERT: Q 14 MET cc_start: 0.6397 (tmm) cc_final: 0.5499 (tmm) REVERT: R 177 GLU cc_start: 0.5847 (mp0) cc_final: 0.5387 (tp30) REVERT: S 255 LEU cc_start: 0.8391 (tp) cc_final: 0.8176 (tp) REVERT: S 271 MET cc_start: 0.7607 (tmm) cc_final: 0.7260 (tmm) REVERT: T 300 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8941 (t80) REVERT: T 335 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8388 (ttt180) REVERT: T 439 MET cc_start: 0.8661 (tpp) cc_final: 0.8460 (tpp) REVERT: T 447 LYS cc_start: 0.8035 (ptpt) cc_final: 0.7416 (tttm) REVERT: T 516 ASP cc_start: 0.7667 (t70) cc_final: 0.6930 (t0) REVERT: T 541 LYS cc_start: 0.7175 (tptt) cc_final: 0.6814 (tptt) REVERT: U 60 GLN cc_start: 0.7422 (mt0) cc_final: 0.7005 (tt0) REVERT: U 118 MET cc_start: 0.8552 (ttt) cc_final: 0.8304 (ttm) REVERT: U 439 MET cc_start: 0.8735 (tpp) cc_final: 0.8429 (tpt) REVERT: U 449 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6673 (mt-10) REVERT: U 509 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7827 (mp) REVERT: V 409 GLU cc_start: 0.6597 (tp30) cc_final: 0.6348 (tp30) REVERT: V 489 PHE cc_start: 0.6333 (m-80) cc_final: 0.5935 (m-10) REVERT: V 555 ARG cc_start: 0.6711 (mtt180) cc_final: 0.6127 (mmt180) REVERT: X 178 LYS cc_start: 0.8469 (mtmt) cc_final: 0.8207 (mtmm) REVERT: X 195 GLU cc_start: 0.8021 (tp30) cc_final: 0.7612 (tp30) REVERT: X 325 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8678 (mt) REVERT: X 388 ASN cc_start: 0.8287 (t0) cc_final: 0.7970 (t0) REVERT: X 390 ASN cc_start: 0.7902 (m-40) cc_final: 0.7695 (m110) REVERT: Y 139 ASP cc_start: 0.7318 (t0) cc_final: 0.7079 (t0) REVERT: Y 405 LYS cc_start: 0.7622 (tptt) cc_final: 0.6894 (ttmt) REVERT: Y 409 ASP cc_start: 0.7335 (m-30) cc_final: 0.6747 (m-30) REVERT: Y 411 LYS cc_start: 0.8114 (mtmt) cc_final: 0.7878 (mtmt) REVERT: Y 414 GLN cc_start: 0.7040 (mt0) cc_final: 0.6728 (mt0) REVERT: Y 430 LYS cc_start: 0.8343 (mtpt) cc_final: 0.8078 (mttm) REVERT: Z 365 SER cc_start: 0.8709 (t) cc_final: 0.8213 (m) REVERT: Z 471 GLN cc_start: 0.8088 (tp40) cc_final: 0.7751 (tt0) outliers start: 104 outliers final: 70 residues processed: 543 average time/residue: 0.4702 time to fit residues: 414.7399 Evaluate side-chains 502 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 422 time to evaluate : 3.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 PHE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 71 GLN Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 202 SER Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 326 ASP Chi-restraints excluded: chain T residue 335 ARG Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 210 ASP Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 136 SER Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 466 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 198 ASN Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 314 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 359 ASP Chi-restraints excluded: chain Z residue 456 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 143 optimal weight: 2.9990 chunk 384 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 250 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 427 optimal weight: 6.9990 chunk 355 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN P 140 ASN T 549 HIS ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 152 ASN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 250 GLN Z 42 GLN ** Z 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 34412 Z= 0.293 Angle : 0.588 9.490 46638 Z= 0.298 Chirality : 0.045 0.208 5519 Planarity : 0.004 0.057 5997 Dihedral : 6.705 93.411 4930 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.69 % Favored : 95.09 % Rotamer: Outliers : 3.11 % Allowed : 19.44 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.13), residues: 4461 helix: -0.18 (0.12), residues: 2141 sheet: -0.60 (0.23), residues: 530 loop : -0.87 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP V 73 HIS 0.004 0.001 HIS S 185 PHE 0.020 0.002 PHE U 300 TYR 0.026 0.002 TYR X 487 ARG 0.007 0.000 ARG T 496 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 426 time to evaluate : 4.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.7078 (ttp) REVERT: D 81 MET cc_start: 0.7189 (mmm) cc_final: 0.6947 (mmt) REVERT: E 105 LEU cc_start: 0.4873 (tt) cc_final: 0.3832 (mm) REVERT: G 105 LEU cc_start: 0.5539 (OUTLIER) cc_final: 0.4710 (mt) REVERT: G 122 PHE cc_start: 0.3624 (OUTLIER) cc_final: 0.3129 (m-80) REVERT: I 95 ILE cc_start: 0.5554 (OUTLIER) cc_final: 0.4890 (mm) REVERT: J 109 LEU cc_start: 0.7023 (mm) cc_final: 0.6546 (mt) REVERT: P 49 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.6899 (p) REVERT: P 52 GLN cc_start: 0.8681 (mt0) cc_final: 0.8176 (mt0) REVERT: P 64 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8003 (mm-30) REVERT: P 73 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7704 (mt-10) REVERT: P 103 LYS cc_start: 0.8149 (mtpp) cc_final: 0.7926 (mtpp) REVERT: R 177 GLU cc_start: 0.5837 (mp0) cc_final: 0.5269 (tp30) REVERT: S 271 MET cc_start: 0.7695 (tmm) cc_final: 0.7410 (tmm) REVERT: T 300 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.8815 (t80) REVERT: T 335 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8731 (ttp-170) REVERT: T 447 LYS cc_start: 0.8149 (ptpt) cc_final: 0.7392 (tttt) REVERT: T 449 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6584 (tp30) REVERT: T 479 ARG cc_start: 0.8083 (mmt-90) cc_final: 0.7803 (mmt-90) REVERT: T 488 GLN cc_start: 0.7842 (tp40) cc_final: 0.7575 (tp40) REVERT: T 516 ASP cc_start: 0.8035 (t70) cc_final: 0.7210 (t0) REVERT: T 539 ASN cc_start: 0.8151 (t0) cc_final: 0.7608 (m110) REVERT: T 541 LYS cc_start: 0.7286 (tptt) cc_final: 0.6787 (pttm) REVERT: U 60 GLN cc_start: 0.7421 (mt0) cc_final: 0.7030 (tt0) REVERT: U 118 MET cc_start: 0.8636 (ttt) cc_final: 0.8384 (ttm) REVERT: U 322 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8711 (tp) REVERT: U 509 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8035 (mp) REVERT: U 529 ASN cc_start: 0.7710 (t0) cc_final: 0.7390 (t0) REVERT: V 61 HIS cc_start: 0.7698 (t70) cc_final: 0.7278 (m90) REVERT: V 409 GLU cc_start: 0.6713 (tp30) cc_final: 0.6504 (tp30) REVERT: V 476 ARG cc_start: 0.7247 (tpp80) cc_final: 0.6762 (tpp80) REVERT: V 555 ARG cc_start: 0.6729 (mtt180) cc_final: 0.6091 (mmt180) REVERT: X 49 ASP cc_start: 0.7391 (m-30) cc_final: 0.7114 (m-30) REVERT: X 178 LYS cc_start: 0.8590 (mtmt) cc_final: 0.8334 (mttm) REVERT: X 195 GLU cc_start: 0.8005 (tp30) cc_final: 0.7662 (tp30) REVERT: X 325 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8481 (mt) REVERT: X 390 ASN cc_start: 0.8028 (m-40) cc_final: 0.7706 (m110) REVERT: Y 405 LYS cc_start: 0.7688 (tptt) cc_final: 0.7090 (ttmt) REVERT: Y 409 ASP cc_start: 0.7347 (m-30) cc_final: 0.6643 (m-30) REVERT: Y 411 LYS cc_start: 0.8164 (mtmt) cc_final: 0.7899 (mtmt) REVERT: Y 414 GLN cc_start: 0.7106 (mt0) cc_final: 0.6805 (mt0) REVERT: Y 430 LYS cc_start: 0.8251 (mtpt) cc_final: 0.7915 (mttm) REVERT: Y 448 GLN cc_start: 0.7397 (mt0) cc_final: 0.7101 (mt0) REVERT: Z 365 SER cc_start: 0.8682 (t) cc_final: 0.8203 (m) REVERT: Z 471 GLN cc_start: 0.8089 (tp40) cc_final: 0.7782 (tt0) REVERT: Z 484 MET cc_start: 0.8087 (mmm) cc_final: 0.7877 (tpt) outliers start: 111 outliers final: 81 residues processed: 512 average time/residue: 0.4914 time to fit residues: 402.4074 Evaluate side-chains 491 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 399 time to evaluate : 4.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 PHE Chi-restraints excluded: chain H residue 61 MET Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 35 GLU Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 202 SER Chi-restraints excluded: chain S residue 247 THR Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 335 ARG Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 449 GLU Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 210 ASP Chi-restraints excluded: chain U residue 322 ILE Chi-restraints excluded: chain U residue 423 VAL Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 136 SER Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 466 LEU Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 198 ASN Chi-restraints excluded: chain X residue 279 ASP Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 159 ILE Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 42 GLN Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 292 GLN Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 412 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 312 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 359 optimal weight: 0.3980 chunk 238 optimal weight: 3.9990 chunk 426 optimal weight: 0.9980 chunk 266 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN R 119 HIS ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 42 GLN ** Z 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 398 ASN ** Z 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 34412 Z= 0.230 Angle : 0.559 9.365 46638 Z= 0.283 Chirality : 0.043 0.261 5519 Planarity : 0.004 0.047 5997 Dihedral : 6.532 86.529 4930 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.24 % Favored : 95.54 % Rotamer: Outliers : 3.28 % Allowed : 19.70 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 4461 helix: -0.04 (0.12), residues: 2142 sheet: -0.57 (0.22), residues: 540 loop : -0.87 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 37 HIS 0.003 0.001 HIS S 185 PHE 0.019 0.001 PHE U 300 TYR 0.023 0.001 TYR X 487 ARG 0.006 0.000 ARG T 496 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 428 time to evaluate : 3.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 98 GLN cc_start: 0.6749 (pt0) cc_final: 0.6532 (pt0) REVERT: C 81 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6997 (ttp) REVERT: E 105 LEU cc_start: 0.4779 (tt) cc_final: 0.3805 (mm) REVERT: G 61 MET cc_start: 0.4609 (ttp) cc_final: 0.3762 (tpp) REVERT: G 105 LEU cc_start: 0.5379 (OUTLIER) cc_final: 0.4600 (mt) REVERT: G 122 PHE cc_start: 0.3860 (OUTLIER) cc_final: 0.3139 (m-80) REVERT: I 95 ILE cc_start: 0.5589 (OUTLIER) cc_final: 0.5268 (mp) REVERT: J 109 LEU cc_start: 0.7023 (mm) cc_final: 0.6541 (mt) REVERT: P 49 THR cc_start: 0.7915 (OUTLIER) cc_final: 0.6928 (m) REVERT: P 52 GLN cc_start: 0.8674 (mt0) cc_final: 0.8165 (mt0) REVERT: P 103 LYS cc_start: 0.8115 (mtpp) cc_final: 0.7770 (mmtt) REVERT: R 177 GLU cc_start: 0.5895 (mp0) cc_final: 0.5382 (tp30) REVERT: S 271 MET cc_start: 0.7710 (tmm) cc_final: 0.7406 (tmm) REVERT: T 300 PHE cc_start: 0.9245 (OUTLIER) cc_final: 0.8850 (t80) REVERT: T 335 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8529 (ttp-170) REVERT: T 447 LYS cc_start: 0.8135 (ptpt) cc_final: 0.7488 (tttm) REVERT: T 449 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6554 (tp30) REVERT: T 479 ARG cc_start: 0.8051 (mmt-90) cc_final: 0.7771 (mmt-90) REVERT: T 488 GLN cc_start: 0.7748 (tp40) cc_final: 0.7533 (tp40) REVERT: T 516 ASP cc_start: 0.8055 (t70) cc_final: 0.7188 (t0) REVERT: T 541 LYS cc_start: 0.7233 (tptt) cc_final: 0.6960 (tptt) REVERT: U 60 GLN cc_start: 0.7421 (mt0) cc_final: 0.7028 (tt0) REVERT: U 118 MET cc_start: 0.8616 (ttt) cc_final: 0.8392 (ttm) REVERT: U 449 GLU cc_start: 0.6771 (mt-10) cc_final: 0.6441 (mt-10) REVERT: U 509 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8000 (mp) REVERT: U 529 ASN cc_start: 0.7772 (t0) cc_final: 0.7436 (t0) REVERT: V 61 HIS cc_start: 0.7676 (t70) cc_final: 0.7273 (m90) REVERT: V 409 GLU cc_start: 0.6699 (tp30) cc_final: 0.6490 (tp30) REVERT: V 476 ARG cc_start: 0.7228 (tpp80) cc_final: 0.6749 (tpp80) REVERT: V 489 PHE cc_start: 0.6314 (m-80) cc_final: 0.5976 (m-80) REVERT: V 555 ARG cc_start: 0.6713 (mtt180) cc_final: 0.6095 (mmt180) REVERT: X 178 LYS cc_start: 0.8541 (mtmt) cc_final: 0.8304 (mttm) REVERT: X 195 GLU cc_start: 0.8027 (tp30) cc_final: 0.7653 (tp30) REVERT: X 325 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8360 (mt) REVERT: X 390 ASN cc_start: 0.8015 (m-40) cc_final: 0.7700 (m110) REVERT: Y 405 LYS cc_start: 0.7632 (tptt) cc_final: 0.6873 (ttmt) REVERT: Y 409 ASP cc_start: 0.7344 (m-30) cc_final: 0.6638 (m-30) REVERT: Y 414 GLN cc_start: 0.6929 (mt0) cc_final: 0.6638 (mt0) REVERT: Y 430 LYS cc_start: 0.8314 (mtpt) cc_final: 0.8022 (mttm) REVERT: Z 365 SER cc_start: 0.8694 (t) cc_final: 0.8212 (m) REVERT: Z 471 GLN cc_start: 0.8046 (tp40) cc_final: 0.7786 (tt0) outliers start: 117 outliers final: 92 residues processed: 517 average time/residue: 0.5313 time to fit residues: 445.0706 Evaluate side-chains 509 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 407 time to evaluate : 3.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 PHE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 202 SER Chi-restraints excluded: chain S residue 247 THR Chi-restraints excluded: chain S residue 284 MET Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 335 ARG Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 449 GLU Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 210 ASP Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 136 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 466 LEU Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 198 ASN Chi-restraints excluded: chain X residue 279 ASP Chi-restraints excluded: chain X residue 291 THR Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 159 ILE Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 217 THR Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 452 VAL Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 42 GLN Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 292 GLN Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 263 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 254 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 270 optimal weight: 0.0070 chunk 290 optimal weight: 4.9990 chunk 210 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 334 optimal weight: 2.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 94 ASN ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 34412 Z= 0.247 Angle : 0.571 9.530 46638 Z= 0.289 Chirality : 0.044 0.190 5519 Planarity : 0.004 0.048 5997 Dihedral : 6.439 88.377 4929 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.66 % Favored : 95.11 % Rotamer: Outliers : 3.25 % Allowed : 19.95 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.13), residues: 4461 helix: 0.05 (0.12), residues: 2123 sheet: -0.55 (0.22), residues: 540 loop : -0.85 (0.15), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 37 HIS 0.004 0.001 HIS S 185 PHE 0.019 0.001 PHE A 116 TYR 0.023 0.001 TYR X 487 ARG 0.004 0.000 ARG V 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 417 time to evaluate : 3.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.4129 (OUTLIER) cc_final: 0.3814 (mmm) REVERT: B 98 GLN cc_start: 0.6859 (pt0) cc_final: 0.6641 (pt0) REVERT: C 81 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.7069 (ttp) REVERT: G 61 MET cc_start: 0.4446 (ttp) cc_final: 0.2924 (tpp) REVERT: G 105 LEU cc_start: 0.5195 (OUTLIER) cc_final: 0.4422 (mt) REVERT: G 122 PHE cc_start: 0.3391 (OUTLIER) cc_final: 0.2879 (m-80) REVERT: I 95 ILE cc_start: 0.5615 (OUTLIER) cc_final: 0.5312 (mp) REVERT: J 109 LEU cc_start: 0.7027 (mm) cc_final: 0.6537 (mt) REVERT: P 49 THR cc_start: 0.7885 (OUTLIER) cc_final: 0.6899 (m) REVERT: P 52 GLN cc_start: 0.8716 (mt0) cc_final: 0.8176 (mt0) REVERT: P 64 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7983 (mm-30) REVERT: P 73 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7756 (mt-10) REVERT: P 103 LYS cc_start: 0.8106 (mtpp) cc_final: 0.7767 (mmtt) REVERT: P 136 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7925 (mm-30) REVERT: P 145 MET cc_start: 0.8040 (mmm) cc_final: 0.7704 (mmm) REVERT: R 177 GLU cc_start: 0.6072 (mp0) cc_final: 0.5438 (tp30) REVERT: S 271 MET cc_start: 0.7722 (tmm) cc_final: 0.7418 (tmm) REVERT: T 300 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8860 (t80) REVERT: T 335 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8574 (ttp-170) REVERT: T 447 LYS cc_start: 0.8146 (ptpt) cc_final: 0.7505 (tttm) REVERT: T 449 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6560 (tp30) REVERT: T 479 ARG cc_start: 0.8040 (mmt-90) cc_final: 0.7740 (mmt-90) REVERT: T 516 ASP cc_start: 0.8079 (t70) cc_final: 0.7191 (t0) REVERT: T 541 LYS cc_start: 0.7277 (tptt) cc_final: 0.6988 (tptt) REVERT: U 60 GLN cc_start: 0.7410 (mt0) cc_final: 0.7059 (tt0) REVERT: U 118 MET cc_start: 0.8605 (ttt) cc_final: 0.8382 (ttm) REVERT: U 449 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6409 (mt-10) REVERT: U 509 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8012 (mp) REVERT: U 529 ASN cc_start: 0.7743 (t0) cc_final: 0.7343 (t0) REVERT: V 61 HIS cc_start: 0.7690 (t70) cc_final: 0.7275 (m90) REVERT: V 409 GLU cc_start: 0.6725 (tp30) cc_final: 0.6495 (tp30) REVERT: V 418 ARG cc_start: 0.7157 (mtt180) cc_final: 0.6904 (mtt-85) REVERT: V 476 ARG cc_start: 0.7246 (tpp80) cc_final: 0.6783 (tpp80) REVERT: V 555 ARG cc_start: 0.6705 (mtt180) cc_final: 0.6089 (mmt180) REVERT: X 178 LYS cc_start: 0.8566 (mtmt) cc_final: 0.8328 (mttm) REVERT: X 195 GLU cc_start: 0.8024 (tp30) cc_final: 0.7675 (tp30) REVERT: X 390 ASN cc_start: 0.8004 (m-40) cc_final: 0.7678 (m110) REVERT: Y 405 LYS cc_start: 0.7634 (tptt) cc_final: 0.7020 (ttmt) REVERT: Y 409 ASP cc_start: 0.7334 (m-30) cc_final: 0.6650 (m-30) REVERT: Y 430 LYS cc_start: 0.8315 (mtpt) cc_final: 0.8014 (mttm) REVERT: Z 365 SER cc_start: 0.8710 (t) cc_final: 0.8225 (m) REVERT: Z 471 GLN cc_start: 0.8039 (tp40) cc_final: 0.7792 (tt0) outliers start: 116 outliers final: 96 residues processed: 502 average time/residue: 0.4702 time to fit residues: 380.6002 Evaluate side-chains 509 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 403 time to evaluate : 3.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 PHE Chi-restraints excluded: chain H residue 61 MET Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 35 GLU Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 202 SER Chi-restraints excluded: chain S residue 247 THR Chi-restraints excluded: chain S residue 284 MET Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 335 ARG Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 449 GLU Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 210 ASP Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 136 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 466 LEU Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 198 ASN Chi-restraints excluded: chain X residue 279 ASP Chi-restraints excluded: chain X residue 291 THR Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 159 ILE Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 217 THR Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 452 VAL Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Z residue 42 GLN Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 292 GLN Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 387 optimal weight: 2.9990 chunk 408 optimal weight: 0.6980 chunk 372 optimal weight: 3.9990 chunk 396 optimal weight: 0.9980 chunk 238 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 311 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 chunk 358 optimal weight: 0.7980 chunk 375 optimal weight: 4.9990 chunk 395 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 76 GLN R 119 HIS ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 264 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 42 GLN ** Z 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34412 Z= 0.168 Angle : 0.548 14.793 46638 Z= 0.274 Chirality : 0.042 0.159 5519 Planarity : 0.003 0.047 5997 Dihedral : 6.139 87.759 4929 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.97 % Favored : 95.83 % Rotamer: Outliers : 3.03 % Allowed : 20.23 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.13), residues: 4461 helix: 0.16 (0.12), residues: 2146 sheet: -0.39 (0.23), residues: 530 loop : -0.80 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP R 37 HIS 0.003 0.001 HIS X 396 PHE 0.019 0.001 PHE Q 8 TYR 0.021 0.001 TYR X 487 ARG 0.009 0.000 ARG U 227 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 442 time to evaluate : 3.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.4011 (OUTLIER) cc_final: 0.3709 (mmm) REVERT: C 81 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.7056 (ttp) REVERT: G 61 MET cc_start: 0.4588 (ttp) cc_final: 0.3119 (tpp) REVERT: G 105 LEU cc_start: 0.4920 (OUTLIER) cc_final: 0.4131 (mt) REVERT: G 122 PHE cc_start: 0.3222 (OUTLIER) cc_final: 0.2613 (m-80) REVERT: I 95 ILE cc_start: 0.5917 (OUTLIER) cc_final: 0.5670 (mp) REVERT: J 109 LEU cc_start: 0.6989 (mm) cc_final: 0.6537 (mt) REVERT: P 49 THR cc_start: 0.7779 (OUTLIER) cc_final: 0.6779 (m) REVERT: P 52 GLN cc_start: 0.8681 (mt0) cc_final: 0.8154 (mt0) REVERT: P 64 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7927 (mm-30) REVERT: P 76 GLN cc_start: 0.8074 (mt0) cc_final: 0.7765 (mt0) REVERT: P 103 LYS cc_start: 0.8061 (mtpp) cc_final: 0.7824 (mmtm) REVERT: S 271 MET cc_start: 0.7745 (tmm) cc_final: 0.7435 (tmm) REVERT: T 335 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8316 (ttt180) REVERT: T 447 LYS cc_start: 0.8104 (ptpt) cc_final: 0.7481 (tttm) REVERT: T 449 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6510 (tp30) REVERT: T 516 ASP cc_start: 0.7994 (t70) cc_final: 0.7176 (t0) REVERT: T 541 LYS cc_start: 0.7199 (tptt) cc_final: 0.6910 (tptt) REVERT: U 60 GLN cc_start: 0.7381 (mt0) cc_final: 0.7002 (tt0) REVERT: U 449 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6484 (mt-10) REVERT: U 509 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7950 (mp) REVERT: U 529 ASN cc_start: 0.7657 (t0) cc_final: 0.7299 (t0) REVERT: V 61 HIS cc_start: 0.7624 (t70) cc_final: 0.7255 (m90) REVERT: V 409 GLU cc_start: 0.6662 (tp30) cc_final: 0.6442 (tp30) REVERT: V 489 PHE cc_start: 0.6206 (m-80) cc_final: 0.5911 (m-80) REVERT: V 551 LYS cc_start: 0.7979 (ttmt) cc_final: 0.7646 (ttpp) REVERT: V 555 ARG cc_start: 0.6656 (mtt180) cc_final: 0.6088 (mmt180) REVERT: X 178 LYS cc_start: 0.8478 (mtmt) cc_final: 0.8260 (mttm) REVERT: X 195 GLU cc_start: 0.8075 (tp30) cc_final: 0.7699 (tp30) REVERT: X 390 ASN cc_start: 0.7873 (m-40) cc_final: 0.7572 (m110) REVERT: Y 405 LYS cc_start: 0.7626 (tptt) cc_final: 0.6916 (ttmt) REVERT: Y 409 ASP cc_start: 0.7314 (m-30) cc_final: 0.6726 (m-30) REVERT: Y 430 LYS cc_start: 0.8318 (mtpt) cc_final: 0.8037 (mttm) REVERT: Z 365 SER cc_start: 0.8759 (t) cc_final: 0.8293 (m) REVERT: Z 471 GLN cc_start: 0.8052 (tp40) cc_final: 0.7824 (tt0) outliers start: 108 outliers final: 84 residues processed: 521 average time/residue: 0.4732 time to fit residues: 393.6087 Evaluate side-chains 506 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 413 time to evaluate : 3.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 PHE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 35 GLU Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 202 SER Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 335 ARG Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 449 GLU Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 210 ASP Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 136 SER Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 466 LEU Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 198 ASN Chi-restraints excluded: chain X residue 279 ASP Chi-restraints excluded: chain X residue 291 THR Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 452 VAL Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 151 THR Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 260 optimal weight: 0.8980 chunk 419 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 chunk 291 optimal weight: 0.8980 chunk 440 optimal weight: 6.9990 chunk 405 optimal weight: 0.7980 chunk 350 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 270 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN P 71 GLN R 119 HIS ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 264 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 414 GLN Z 42 GLN ** Z 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34412 Z= 0.178 Angle : 0.555 12.772 46638 Z= 0.278 Chirality : 0.043 0.281 5519 Planarity : 0.003 0.047 5997 Dihedral : 6.067 85.936 4929 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.48 % Favored : 95.29 % Rotamer: Outliers : 2.89 % Allowed : 20.51 % Favored : 76.60 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 4461 helix: 0.25 (0.12), residues: 2145 sheet: -0.33 (0.23), residues: 530 loop : -0.74 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 37 HIS 0.003 0.001 HIS X 396 PHE 0.021 0.001 PHE G 107 TYR 0.021 0.001 TYR X 487 ARG 0.009 0.000 ARG T 496 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 415 time to evaluate : 5.528 Fit side-chains revert: symmetry clash REVERT: C 81 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.7119 (ttp) REVERT: G 61 MET cc_start: 0.4591 (ttp) cc_final: 0.3141 (tpp) REVERT: G 105 LEU cc_start: 0.4856 (OUTLIER) cc_final: 0.4109 (mt) REVERT: G 122 PHE cc_start: 0.3287 (OUTLIER) cc_final: 0.2752 (m-80) REVERT: H 81 MET cc_start: 0.6311 (ptt) cc_final: 0.5658 (ttp) REVERT: I 95 ILE cc_start: 0.5961 (OUTLIER) cc_final: 0.5744 (mp) REVERT: J 109 LEU cc_start: 0.6942 (mm) cc_final: 0.6525 (mt) REVERT: P 49 THR cc_start: 0.7742 (OUTLIER) cc_final: 0.6775 (m) REVERT: P 52 GLN cc_start: 0.8681 (mt0) cc_final: 0.8160 (mt0) REVERT: P 64 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7924 (mm-30) REVERT: P 103 LYS cc_start: 0.8094 (mtpp) cc_final: 0.7813 (mmtm) REVERT: S 156 GLN cc_start: 0.6358 (tm-30) cc_final: 0.6130 (tm-30) REVERT: S 271 MET cc_start: 0.7739 (tmm) cc_final: 0.7405 (tmm) REVERT: T 335 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8365 (ttt180) REVERT: T 447 LYS cc_start: 0.8085 (ptpt) cc_final: 0.7494 (tttm) REVERT: T 449 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6510 (tp30) REVERT: T 516 ASP cc_start: 0.7963 (t70) cc_final: 0.7144 (t0) REVERT: T 541 LYS cc_start: 0.7194 (tptt) cc_final: 0.6892 (tptt) REVERT: U 60 GLN cc_start: 0.7233 (mt0) cc_final: 0.6902 (tt0) REVERT: U 449 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6559 (mt-10) REVERT: U 502 TYR cc_start: 0.8308 (t80) cc_final: 0.7901 (t80) REVERT: U 509 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7955 (mp) REVERT: V 61 HIS cc_start: 0.7638 (t70) cc_final: 0.7252 (m90) REVERT: V 409 GLU cc_start: 0.6612 (tp30) cc_final: 0.6407 (tp30) REVERT: V 489 PHE cc_start: 0.6164 (m-80) cc_final: 0.5870 (m-80) REVERT: V 551 LYS cc_start: 0.7966 (ttmt) cc_final: 0.7580 (ttpp) REVERT: V 555 ARG cc_start: 0.6647 (mtt180) cc_final: 0.6087 (mmt180) REVERT: X 178 LYS cc_start: 0.8497 (mtmt) cc_final: 0.8274 (mttm) REVERT: X 195 GLU cc_start: 0.8066 (tp30) cc_final: 0.7760 (tp30) REVERT: X 390 ASN cc_start: 0.7801 (m-40) cc_final: 0.7507 (m110) REVERT: Y 139 ASP cc_start: 0.7282 (t0) cc_final: 0.7039 (t0) REVERT: Y 405 LYS cc_start: 0.7634 (tptt) cc_final: 0.6932 (ttmt) REVERT: Y 409 ASP cc_start: 0.7290 (m-30) cc_final: 0.6724 (m-30) REVERT: Y 430 LYS cc_start: 0.8162 (mtpt) cc_final: 0.7853 (mttm) REVERT: Z 365 SER cc_start: 0.8726 (t) cc_final: 0.8270 (m) REVERT: Z 471 GLN cc_start: 0.8052 (tp40) cc_final: 0.7825 (tt0) outliers start: 103 outliers final: 84 residues processed: 491 average time/residue: 0.4652 time to fit residues: 370.5100 Evaluate side-chains 489 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 397 time to evaluate : 4.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 PHE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 35 GLU Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 202 SER Chi-restraints excluded: chain S residue 247 THR Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 335 ARG Chi-restraints excluded: chain T residue 449 GLU Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 210 ASP Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 136 SER Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 466 LEU Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 198 ASN Chi-restraints excluded: chain X residue 279 ASP Chi-restraints excluded: chain X residue 291 THR Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 452 VAL Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Z residue 42 GLN Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 151 THR Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 292 GLN Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 278 optimal weight: 0.0870 chunk 373 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 323 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 351 optimal weight: 1.9990 chunk 146 optimal weight: 0.0670 chunk 360 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 76 GLN R 119 HIS ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 42 GLN ** Z 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.163285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.128799 restraints weight = 48490.989| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.76 r_work: 0.3342 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34412 Z= 0.155 Angle : 0.549 12.612 46638 Z= 0.273 Chirality : 0.042 0.211 5519 Planarity : 0.004 0.048 5997 Dihedral : 5.960 83.714 4929 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.95 % Favored : 95.85 % Rotamer: Outliers : 2.64 % Allowed : 21.13 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.13), residues: 4461 helix: 0.34 (0.12), residues: 2146 sheet: -0.31 (0.23), residues: 538 loop : -0.66 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 37 HIS 0.003 0.001 HIS X 396 PHE 0.020 0.001 PHE S 194 TYR 0.020 0.001 TYR X 487 ARG 0.011 0.000 ARG V 418 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9081.01 seconds wall clock time: 164 minutes 51.57 seconds (9891.57 seconds total)