Starting phenix.real_space_refine on Thu Feb 22 10:34:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdy_4835/02_2024/6rdy_4835_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdy_4835/02_2024/6rdy_4835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdy_4835/02_2024/6rdy_4835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdy_4835/02_2024/6rdy_4835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdy_4835/02_2024/6rdy_4835_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdy_4835/02_2024/6rdy_4835_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "H 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 86": "OE1" <-> "OE2" Residue "P PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 127": "OD1" <-> "OD2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 25": "OD1" <-> "OD2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q GLU 64": "OE1" <-> "OE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 95": "OD1" <-> "OD2" Residue "R GLU 117": "OE1" <-> "OE2" Residue "R ASP 143": "OD1" <-> "OD2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 180": "OE1" <-> "OE2" Residue "S GLU 181": "OE1" <-> "OE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 222": "OD1" <-> "OD2" Residue "S TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 241": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S GLU 248": "OE1" <-> "OE2" Residue "S GLU 283": "OE1" <-> "OE2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ASP 92": "OD1" <-> "OD2" Residue "T ASP 125": "OD1" <-> "OD2" Residue "T ASP 135": "OD1" <-> "OD2" Residue "T ASP 142": "OD1" <-> "OD2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ASP 172": "OD1" <-> "OD2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 294": "OD1" <-> "OD2" Residue "T TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 403": "OD1" <-> "OD2" Residue "T PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 429": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T GLU 475": "OE1" <-> "OE2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 516": "OD1" <-> "OD2" Residue "T GLU 521": "OE1" <-> "OE2" Residue "T ASP 547": "OD1" <-> "OD2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ASP 41": "OD1" <-> "OD2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 92": "OD1" <-> "OD2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 125": "OD1" <-> "OD2" Residue "U TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ASP 165": "OD1" <-> "OD2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U ASP 210": "OD1" <-> "OD2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ASP 237": "OD1" <-> "OD2" Residue "U ARG 254": "NH1" <-> "NH2" 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 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 ASP 389": "OD1" <-> "OD2" Residue "U PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 449": "OE1" <-> "OE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U GLU 455": "OE1" <-> "OE2" Residue "U PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 475": "OE1" <-> "OE2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U ASP 516": "OD1" <-> "OD2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 547": "OD1" <-> "OD2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 74": "OE1" <-> "OE2" Residue "V PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 135": "OD1" <-> "OD2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V GLU 247": "OE1" <-> "OE2" Residue "V TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 266": "NH1" <-> "NH2" Residue "V TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ARG 335": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "V ARG 347": "NH1" <-> "NH2" Residue "V ARG 360": "NH1" <-> "NH2" Residue "V GLU 384": "OE1" <-> "OE2" Residue "V PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 409": "OE1" <-> "OE2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 429": "NH1" <-> "NH2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V GLU 521": "OE1" <-> "OE2" Residue "V GLU 522": "OE1" <-> "OE2" Residue "V GLU 553": "OE1" <-> "OE2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 75": "OE1" <-> "OE2" Residue "X ASP 82": "OD1" <-> "OD2" Residue "X GLU 146": "OE1" <-> "OE2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "X GLU 158": "OE1" <-> "OE2" Residue "X ASP 168": "OD1" <-> "OD2" 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 ARG 218": "NH1" <-> "NH2" Residue "X ARG 225": "NH1" <-> "NH2" Residue "X ARG 239": "NH1" <-> "NH2" Residue "X TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 253": "OE1" <-> "OE2" Residue "X ASP 274": "OD1" <-> "OD2" Residue "X GLU 296": "OE1" <-> "OE2" Residue "X ASP 317": "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 GLU 424": "OE1" <-> "OE2" Residue "X GLU 427": "OE1" <-> "OE2" Residue "X ASP 465": "OD1" <-> "OD2" Residue "X ASP 479": "OD1" <-> "OD2" Residue "X ASP 480": "OD1" <-> "OD2" Residue "X GLU 483": "OE1" <-> "OE2" Residue "X PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 494": "OE1" <-> "OE2" Residue "X GLU 497": "OE1" <-> "OE2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X GLU 511": "OE1" <-> "OE2" Residue "X ASP 543": "OD1" <-> "OD2" Residue "X ASP 548": "OD1" <-> "OD2" Residue "X GLU 552": "OE1" <-> "OE2" Residue "Y ASP 36": "OD1" <-> "OD2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y GLU 75": "OE1" <-> "OE2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ASP 91": "OD1" <-> "OD2" Residue "Y ASP 94": "OD1" <-> "OD2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y ASP 139": "OD1" <-> "OD2" Residue "Y ARG 145": "NH1" <-> "NH2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 195": "OE1" <-> "OE2" Residue "Y PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 215": "OE1" <-> "OE2" Residue "Y ASP 222": "OD1" <-> "OD2" 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 ARG 366": "NH1" <-> "NH2" Residue "Y ASP 381": "OD1" <-> "OD2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y ASP 409": "OD1" <-> "OD2" Residue "Y ASP 415": "OD1" <-> "OD2" Residue "Y PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 497": "OE1" <-> "OE2" Residue "Y GLU 511": "OE1" <-> "OE2" Residue "Y GLU 519": "OE1" <-> "OE2" Residue "Y GLU 520": "OE1" <-> "OE2" Residue "Y GLU 540": "OE1" <-> "OE2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 49": "OD1" <-> "OD2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z GLU 75": "OE1" <-> "OE2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "Z ASP 94": "OD1" <-> "OD2" Residue "Z ARG 98": "NH1" <-> "NH2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z GLU 156": "OE1" <-> "OE2" Residue "Z PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 215": "OE1" <-> "OE2" Residue "Z ARG 216": "NH1" <-> "NH2" Residue "Z GLU 238": "OE1" <-> "OE2" Residue "Z ARG 258": "NH1" <-> "NH2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z ASP 285": "OD1" <-> "OD2" Residue "Z ARG 289": "NH1" <-> "NH2" Residue "Z GLU 296": "OE1" <-> "OE2" Residue "Z ASP 317": "OD1" <-> "OD2" Residue "Z GLU 323": "OE1" <-> "OE2" Residue "Z ASP 344": "OD1" <-> "OD2" Residue "Z ASP 345": "OD1" <-> "OD2" Residue "Z ASP 348": "OD1" <-> "OD2" Residue "Z PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 370": "OE1" <-> "OE2" Residue "Z ASP 378": "OD1" <-> "OD2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z GLU 395": "OE1" <-> "OE2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z ASP 409": "OD1" <-> "OD2" Residue "Z TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 424": "OE1" <-> "OE2" 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 ASP 505": "OD1" <-> "OD2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z ASP 513": "OD1" <-> "OD2" Residue "Z GLU 519": "OE1" <-> "OE2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 563": "OE1" <-> "OE2" Residue "Z GLU 564": "OE1" <-> "OE2" 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: 18.91, per 1000 atoms: 0.56 Number of scatterers: 33891 At special positions: 0 Unit cell: (163.215, 134.784, 208.494, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 13 15.00 Mg 5 11.99 O 6421 8.00 N 5795 7.00 C 21541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.14 Conformation dependent library (CDL) restraints added in 6.2 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: 172 helices and 28 sheets defined 45.8% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.94 Creating SS restraints... Processing helix chain 'A' and resid 56 through 91 removed outlier: 4.500A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.610A 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 110 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.633A pdb=" N PHE A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 67 removed outlier: 3.767A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 91 removed outlier: 3.558A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 126 removed outlier: 4.086A pdb=" N GLY B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE B 126 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 89 removed outlier: 4.097A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 125 removed outlier: 4.861A pdb=" N LYS C 97 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 99 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU C 104 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER C 112 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE C 113 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C 124 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 125 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 65 removed outlier: 3.532A pdb=" N SER D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 91 removed outlier: 3.811A pdb=" N GLY D 79 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU D 85 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG D 91 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 126 removed outlier: 3.558A pdb=" N ALA D 96 " --> pdb=" O PRO D 93 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LYS D 97 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL D 100 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU D 104 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU D 119 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE D 126 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 65 removed outlier: 3.742A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 89 removed outlier: 3.539A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 98 through 125 removed outlier: 4.249A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 67 removed outlier: 3.972A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 91 Processing helix chain 'F' and resid 93 through 126 removed outlier: 4.909A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL F 100 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU F 104 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA F 108 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU F 111 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU F 119 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL F 121 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU F 123 " --> pdb=" O VAL F 120 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE F 124 " --> pdb=" O VAL F 121 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE F 126 " --> pdb=" O LEU F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 91 removed outlier: 4.178A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 125 removed outlier: 4.868A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU G 104 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU G 109 " --> pdb=" O GLY G 106 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER G 112 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE G 124 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU G 125 " --> pdb=" O PHE G 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 91 removed outlier: 4.029A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ALA H 70 " --> pdb=" O CYS H 66 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA H 72 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 125 removed outlier: 5.528A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL H 100 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA H 108 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR H 110 " --> pdb=" O PHE H 107 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL H 120 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL H 121 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU H 125 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 91 removed outlier: 3.974A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR I 68 " --> pdb=" O ALA I 64 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ALA I 70 " --> pdb=" O CYS I 66 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LEU I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA I 72 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 95 No H-bonds generated for 'chain 'I' and resid 93 through 95' Processing helix chain 'I' and resid 98 through 125 removed outlier: 3.677A pdb=" N SER I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 89 removed outlier: 4.366A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 126 removed outlier: 4.940A pdb=" N LYS J 97 " --> pdb=" O ASN J 94 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU J 99 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU J 104 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR J 110 " --> pdb=" O PHE J 107 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU J 111 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER J 112 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE J 113 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU J 115 " --> pdb=" O SER J 112 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU J 118 " --> pdb=" O LEU J 115 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU J 125 " --> pdb=" O PHE J 122 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE J 126 " --> pdb=" O LEU J 123 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 64 removed outlier: 3.721A pdb=" N LEU P 56 " --> pdb=" O GLN P 52 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 83 removed outlier: 3.691A pdb=" N GLN P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN P 76 " --> pdb=" O ASP P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 92 removed outlier: 4.059A pdb=" N THR P 92 " --> pdb=" O ARG P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 101 No H-bonds generated for 'chain 'P' and resid 98 through 101' Processing helix chain 'P' and resid 105 through 108 No H-bonds generated for 'chain 'P' and resid 105 through 108' Processing helix chain 'P' and resid 118 through 128 removed outlier: 3.645A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA P 126 " --> pdb=" O PHE P 122 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP P 127 " --> pdb=" O GLU P 123 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU P 128 " --> pdb=" O ALA P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 145 removed outlier: 3.529A pdb=" N LEU P 134 " --> pdb=" O LEU P 131 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU P 136 " --> pdb=" O ALA P 133 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU P 143 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 3.963A 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 30 removed outlier: 3.995A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 39 removed outlier: 3.868A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 40 removed outlier: 3.631A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 54 removed outlier: 3.782A pdb=" N TYR R 54 " --> pdb=" O PRO R 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 51 through 54' Processing helix chain 'R' and resid 152 through 154 No H-bonds generated for 'chain 'R' and resid 152 through 154' Processing helix chain 'R' and resid 159 through 167 removed outlier: 3.983A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 196 Processing helix chain 'S' and resid 42 through 69 removed outlier: 3.620A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 88 removed outlier: 3.595A pdb=" N VAL S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 116 through 127 Processing helix chain 'S' and resid 144 through 150 removed outlier: 3.817A pdb=" N SER S 148 " --> pdb=" O ASP S 144 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLN S 149 " --> pdb=" O LYS S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 182 Processing helix chain 'S' and resid 213 through 221 removed outlier: 6.304A pdb=" N LYS S 218 " --> pdb=" O ASP S 214 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLN S 219 " --> pdb=" O LEU S 215 " (cutoff:3.500A) 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 311 removed outlier: 4.128A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR S 278 " --> pdb=" O MET S 274 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE S 307 " --> pdb=" O GLU S 303 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 137 No H-bonds generated for 'chain 'T' and resid 135 through 137' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 207 through 210 No H-bonds generated for 'chain 'T' and resid 207 through 210' Processing helix chain 'T' and resid 231 through 246 removed outlier: 3.809A pdb=" N GLN T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN T 244 " --> pdb=" O ILE T 240 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 279 removed outlier: 3.550A pdb=" N GLN T 278 " --> pdb=" O LYS T 274 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 284 Processing helix chain 'T' and resid 296 through 300 Processing helix chain 'T' and resid 302 through 310 Processing helix chain 'T' and resid 312 through 315 No H-bonds generated for 'chain 'T' and resid 312 through 315' Processing helix chain 'T' and resid 327 through 340 removed outlier: 3.701A pdb=" N ALA T 333 " --> pdb=" O LYS T 329 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET T 337 " --> pdb=" O ALA T 333 " (cutoff:3.500A) Processing helix chain 'T' and resid 352 through 364 removed outlier: 4.166A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER T 359 " --> pdb=" O TYR T 356 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG T 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU T 361 " --> pdb=" O HIS T 358 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU T 362 " --> pdb=" O SER T 359 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU T 363 " --> pdb=" O ARG T 360 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 399 removed outlier: 3.513A pdb=" N ASN T 397 " --> pdb=" O TYR T 393 " (cutoff:3.500A) Processing helix chain 'T' and resid 410 through 414 removed outlier: 3.868A pdb=" N TYR T 414 " --> pdb=" O THR T 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 410 through 414' Processing helix chain 'T' and resid 431 through 434 removed outlier: 3.645A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 431 through 434' 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 444 through 449 removed outlier: 3.963A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) Processing helix chain 'T' and resid 451 through 459 removed outlier: 4.185A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA T 458 " --> pdb=" O ARG T 454 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 470 through 483 removed outlier: 3.742A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR T 481 " --> pdb=" O GLY T 477 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU T 482 " --> pdb=" O ALA T 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 495 through 498 No H-bonds generated for 'chain 'T' and resid 495 through 498' Processing helix chain 'T' and resid 502 through 505 No H-bonds generated for 'chain 'T' and resid 502 through 505' Processing helix chain 'T' and resid 518 through 526 removed outlier: 4.451A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA T 523 " --> pdb=" O ALA T 519 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL T 524 " --> pdb=" O ALA T 520 " (cutoff:3.500A) Processing helix chain 'T' and resid 531 through 539 removed outlier: 3.533A pdb=" N ILE T 535 " --> pdb=" O ALA T 531 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA T 538 " --> pdb=" O LYS T 534 " (cutoff:3.500A) Processing helix chain 'T' and resid 544 through 551 removed outlier: 4.360A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 49 removed outlier: 3.801A pdb=" N GLU U 47 " --> pdb=" O LYS U 43 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU U 48 " --> pdb=" O ALA U 44 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG U 49 " --> pdb=" O LEU U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 70 removed outlier: 5.375A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix Processing helix chain 'U' and resid 135 through 137 No H-bonds generated for 'chain 'U' and resid 135 through 137' Processing helix chain 'U' and resid 157 through 159 No H-bonds generated for 'chain 'U' and resid 157 through 159' Processing helix chain 'U' and resid 207 through 212 Processing helix chain 'U' and resid 231 through 248 removed outlier: 3.799A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN U 248 " --> pdb=" O ASN U 244 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 278 Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 296 through 314 Proline residue: U 303 - end of helix removed outlier: 3.999A 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 341 removed outlier: 3.975A pdb=" N LEU U 341 " --> pdb=" O MET U 337 " (cutoff:3.500A) Processing helix chain 'U' and resid 354 through 364 removed outlier: 3.537A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ARG U 364 " --> pdb=" O ARG U 360 " (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: 4.056A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) Processing helix chain 'U' and resid 471 through 484 removed outlier: 4.262A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 496 No H-bonds generated for 'chain 'U' and resid 494 through 496' Processing helix chain 'U' and resid 498 through 505 removed outlier: 4.234A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 515 through 527 removed outlier: 4.196A pdb=" N VAL U 518 " --> pdb=" O GLN U 515 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU U 522 " --> pdb=" O ALA U 519 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 539 removed outlier: 3.929A pdb=" N LYS U 534 " --> pdb=" O ALA U 531 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU U 536 " --> pdb=" O PHE U 533 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASN U 539 " --> pdb=" O LEU U 536 " (cutoff:3.500A) Processing helix chain 'U' and resid 544 through 553 Processing helix chain 'V' and resid 46 through 48 No H-bonds generated for 'chain 'V' and resid 46 through 48' Processing helix chain 'V' and resid 59 through 66 removed outlier: 4.214A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 207 through 212 Processing helix chain 'V' and resid 231 through 248 removed outlier: 3.816A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLN V 248 " --> pdb=" O ASN V 244 " (cutoff:3.500A) Processing helix chain 'V' and resid 251 through 253 No H-bonds generated for 'chain 'V' and resid 251 through 253' Processing helix chain 'V' and resid 266 through 278 Processing helix chain 'V' and resid 282 through 284 No H-bonds generated for 'chain 'V' and resid 282 through 284' Processing helix chain 'V' and resid 296 through 315 Proline residue: V 303 - end of helix removed outlier: 3.703A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 341 Processing helix chain 'V' and resid 352 through 364 removed outlier: 3.972A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER V 359 " --> pdb=" O TYR V 356 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU V 363 " --> pdb=" O ARG V 360 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG V 364 " --> pdb=" O LEU V 361 " (cutoff:3.500A) Processing helix chain 'V' and resid 370 through 372 No H-bonds generated for 'chain 'V' and resid 370 through 372' Processing helix chain 'V' and resid 393 through 401 Processing helix chain 'V' and resid 431 through 434 removed outlier: 4.080A 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 439 through 455 removed outlier: 4.276A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU V 448 " --> pdb=" O GLY V 444 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 481 Processing helix chain 'V' and resid 494 through 505 Processing helix chain 'V' and resid 514 through 516 No H-bonds generated for 'chain 'V' and resid 514 through 516' 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: 3.563A pdb=" N ILE V 535 " --> pdb=" O ALA V 531 " (cutoff:3.500A) Processing helix chain 'V' and resid 544 through 553 removed outlier: 4.027A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (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: 4.839A pdb=" N LYS X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA X 203 " --> pdb=" O ASN X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 229 removed outlier: 3.625A pdb=" N GLU X 229 " --> pdb=" O ARG X 225 " (cutoff:3.500A) Processing helix chain 'X' and resid 239 through 241 No H-bonds generated for 'chain 'X' and resid 239 through 241' Processing helix chain 'X' and resid 255 through 259 removed outlier: 3.779A pdb=" N ALA X 259 " --> pdb=" O PRO X 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 255 through 259' Processing helix chain 'X' and resid 261 through 274 removed outlier: 3.786A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 288 through 299 removed outlier: 3.897A pdb=" N ALA X 299 " --> pdb=" O SER X 295 " (cutoff:3.500A) Processing helix chain 'X' and resid 314 through 324 removed outlier: 4.502A 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 366 through 371 removed outlier: 3.840A pdb=" N LEU X 371 " --> pdb=" O SER X 367 " (cutoff:3.500A) Processing helix chain 'X' and resid 389 through 420 removed outlier: 7.662A pdb=" N ALA X 394 " --> pdb=" O ASN X 390 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N GLU X 395 " --> pdb=" O VAL X 391 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS X 396 " --> pdb=" O ILE X 392 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.155A 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 441 removed outlier: 3.543A pdb=" N THR X 432 " --> pdb=" O GLU X 428 " (cutoff:3.500A) 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 484 through 486 No H-bonds generated for 'chain 'X' and resid 484 through 486' Processing helix chain 'X' and resid 492 through 506 removed outlier: 3.847A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP X 505 " --> pdb=" O LYS X 501 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 533 removed outlier: 3.870A pdb=" N VAL X 531 " --> pdb=" O LEU X 527 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU X 533 " --> pdb=" O LYS X 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 527 through 533' 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: 4.530A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 274 removed outlier: 3.556A pdb=" N ALA Y 259 " --> pdb=" O PRO Y 255 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG Y 260 " --> pdb=" O GLY Y 256 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL Y 261 " --> pdb=" O ALA Y 257 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR Y 264 " --> pdb=" O ARG Y 260 " (cutoff:3.500A) Processing helix chain 'Y' and resid 288 through 296 Processing helix chain 'Y' and resid 314 through 324 removed outlier: 4.883A pdb=" N ARG Y 324 " --> pdb=" O GLY Y 320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 349 through 352 No H-bonds generated for 'chain 'Y' and resid 349 through 352' Processing helix chain 'Y' and resid 355 through 357 No H-bonds generated for 'chain 'Y' and resid 355 through 357' Processing helix chain 'Y' and resid 367 through 370 No H-bonds generated for 'chain 'Y' and resid 367 through 370' Processing helix chain 'Y' and resid 394 through 420 removed outlier: 3.726A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA Y 418 " --> pdb=" O GLN Y 414 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 429 through 442 Processing helix chain 'Y' and resid 449 through 451 No H-bonds generated for 'chain 'Y' and resid 449 through 451' Processing helix chain 'Y' and resid 463 through 475 removed outlier: 3.600A pdb=" N GLY Y 472 " --> pdb=" O SER Y 468 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR Y 475 " --> pdb=" O GLN Y 471 " (cutoff:3.500A) Processing helix chain 'Y' and resid 492 through 508 removed outlier: 3.708A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS Y 501 " --> pdb=" O GLU Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 527 through 531 Processing helix chain 'Y' and resid 545 through 554 removed outlier: 4.221A 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 236 through 241 removed outlier: 3.798A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 258 No H-bonds generated for 'chain 'Z' and resid 255 through 258' Processing helix chain 'Z' and resid 261 through 274 Processing helix chain 'Z' and resid 287 through 300 Processing helix chain 'Z' and resid 314 through 322 removed outlier: 4.418A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 349 through 354 Processing helix chain 'Z' and resid 368 through 371 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 413 removed outlier: 4.202A pdb=" N LEU Z 413 " --> pdb=" O ASP Z 409 " (cutoff:3.500A) Processing helix chain 'Z' and resid 427 through 440 removed outlier: 3.576A pdb=" N LEU Z 431 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) removed outlier: 4.179A 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: 3.907A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) removed outlier: 3.732A 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 501 removed outlier: 3.736A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 531 Processing sheet with id= A, first strand: chain 'Q' and resid 45 through 48 Processing sheet with id= B, first strand: chain 'R' and resid 72 through 76 removed outlier: 6.582A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ILE R 144 " --> pdb=" O TYR R 75 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY R 132 " --> pdb=" O LEU R 111 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'R' and resid 96 through 100 removed outlier: 6.751A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) removed outlier: 3.516A 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: 3.509A pdb=" N SER S 189 " --> pdb=" O LYS S 99 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.480A 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: 6.716A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN T 121 " --> pdb=" O GLY T 128 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'T' and resid 109 through 111 Processing sheet with id= G, first strand: chain 'T' and resid 152 through 155 Processing sheet with id= H, first strand: chain 'T' and resid 404 through 407 removed outlier: 3.859A pdb=" N LEU T 222 " --> pdb=" O GLY T 404 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'T' and resid 286 through 290 removed outlier: 6.867A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER T 376 " --> pdb=" O GLY T 320 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE T 322 " --> pdb=" O SER T 376 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.628A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= L, first strand: chain 'U' and resid 404 through 408 removed outlier: 3.720A pdb=" N LEU U 222 " --> pdb=" O GLY U 404 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'U' and resid 319 through 325 Processing sheet with id= N, first strand: chain 'V' and resid 84 through 86 removed outlier: 3.815A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY V 128 " --> pdb=" O LEU V 120 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU V 122 " --> pdb=" O HIS V 126 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N HIS V 126 " --> pdb=" O LEU V 122 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= P, first strand: chain 'V' and resid 382 through 384 removed outlier: 6.451A pdb=" N ILE V 223 " --> pdb=" O ILE V 383 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE V 406 " --> pdb=" O ILE V 224 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'V' and resid 286 through 290 removed outlier: 6.615A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE V 380 " --> pdb=" O TYR V 324 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'X' and resid 37 through 39 removed outlier: 4.732A pdb=" N LEU X 72 " --> pdb=" O VAL X 65 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ARG X 51 " --> pdb=" O VAL X 40 " (cutoff:3.500A) removed outlier: 5.421A 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: 7.607A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N GLY X 183 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL X 339 " --> pdb=" O GLY X 183 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'X' and resid 208 through 212 Processing sheet with id= V, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= W, first strand: chain 'Y' and resid 39 through 44 removed outlier: 6.569A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Y' and resid 360 through 362 removed outlier: 3.826A pdb=" N ALA Y 360 " --> pdb=" O LYS Y 178 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N GLY Y 183 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL Y 339 " --> pdb=" O GLY Y 183 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE Y 207 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N PHE Y 283 " --> pdb=" O PHE Y 207 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ALA Y 211 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N THR Y 245 " --> pdb=" O PHE Y 210 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLY Y 212 " --> pdb=" O THR Y 245 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL Y 247 " --> pdb=" O GLY Y 212 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Z' and resid 39 through 44 removed outlier: 6.589A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU Z 72 " --> pdb=" O VAL Z 65 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id= AA, first strand: chain 'Z' and resid 178 through 181 removed outlier: 8.516A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL Z 284 " --> pdb=" O VAL Z 336 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Z' and resid 559 through 561 1336 hydrogen bonds defined for protein. 3426 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: 13.35 Time building geometry restraints manager: 14.15 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: 9257 1.33 - 1.45: 5662 1.45 - 1.57: 19272 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34412 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.02e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.90e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.37e+01 bond pdb=" C4 ATP T1001 " pdb=" N9 ATP T1001 " ideal model delta sigma weight residual 1.374 1.312 0.062 1.00e-02 1.00e+04 3.82e+01 bond pdb=" C5 ATP U1001 " pdb=" N7 ATP U1001 " ideal model delta sigma weight residual 1.387 1.326 0.061 1.00e-02 1.00e+04 3.69e+01 ... (remaining 34407 not shown) Histogram of bond angle deviations from ideal: 97.61 - 105.56: 713 105.56 - 113.51: 19660 113.51 - 121.46: 18686 121.46 - 129.41: 7475 129.41 - 137.36: 104 Bond angle restraints: 46638 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 118.16 21.71 1.00e+00 1.00e+00 4.71e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 118.48 21.39 1.00e+00 1.00e+00 4.58e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 118.94 20.93 1.00e+00 1.00e+00 4.38e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 119.81 17.02 1.00e+00 1.00e+00 2.90e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 122.46 14.37 1.00e+00 1.00e+00 2.06e+02 ... (remaining 46633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.67: 19768 26.67 - 53.35: 947 53.35 - 80.02: 85 80.02 - 106.69: 22 106.69 - 133.36: 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 -124.97 -55.03 0 5.00e+00 4.00e-02 1.21e+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 -126.66 -53.34 0 5.00e+00 4.00e-02 1.14e+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 -126.91 -53.09 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 20820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4237 0.070 - 0.141: 1127 0.141 - 0.211: 142 0.211 - 0.281: 10 0.281 - 0.352: 3 Chirality restraints: 5519 Sorted by residual: chirality pdb=" CB ILE D 95 " pdb=" CA ILE D 95 " pdb=" CG1 ILE D 95 " pdb=" CG2 ILE D 95 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB ILE E 95 " pdb=" CA ILE E 95 " pdb=" CG1 ILE E 95 " pdb=" CG2 ILE E 95 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB ILE J 95 " pdb=" CA ILE J 95 " pdb=" CG1 ILE J 95 " pdb=" CG2 ILE J 95 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.41e+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 5.91e-02 3.50e+01 pdb=" C ALA Z 503 " -0.102 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA X 350 " -0.060 5.00e-02 4.00e+02 9.06e-02 1.31e+01 pdb=" N PRO X 351 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO X 351 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO X 351 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE U 203 " 0.025 2.00e-02 2.50e+03 2.53e-02 1.12e+01 pdb=" CG PHE U 203 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE U 203 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE U 203 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE U 203 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE U 203 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE U 203 " 0.002 2.00e-02 2.50e+03 ... (remaining 5994 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 504 2.62 - 3.19: 29635 3.19 - 3.76: 54096 3.76 - 4.33: 76591 4.33 - 4.90: 124958 Nonbonded interactions: 285784 Sorted by model distance: nonbonded pdb=" OE1 GLU Y 215 " pdb="MG MG Y 602 " model vdw 2.050 2.170 nonbonded pdb=" OE2 GLU X 215 " pdb="MG MG X 602 " model vdw 2.060 2.170 nonbonded pdb=" O2B ATP T1001 " pdb="MG MG T1002 " model vdw 2.138 2.170 nonbonded pdb=" O ALA S 125 " pdb=" OG1 THR S 129 " model vdw 2.241 2.440 nonbonded pdb=" O GLY V 225 " pdb=" OG1 THR V 385 " model vdw 2.243 2.440 ... (remaining 285779 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 25.900 Check model and map are aligned: 0.490 Set scattering table: 0.310 Process input model: 89.650 Find NCS groups from input model: 2.610 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 0.130 34412 Z= 0.697 Angle : 1.076 21.706 46638 Z= 0.619 Chirality : 0.062 0.352 5519 Planarity : 0.008 0.091 5997 Dihedral : 15.267 133.362 12663 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.96 % Favored : 93.77 % Rotamer: Outliers : 0.51 % Allowed : 11.84 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (0.10), residues: 4461 helix: -3.32 (0.07), residues: 2113 sheet: -2.07 (0.20), residues: 563 loop : -2.34 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP X 141 HIS 0.009 0.002 HIS Y 204 PHE 0.059 0.003 PHE U 203 TYR 0.023 0.003 TYR Z 487 ARG 0.010 0.001 ARG T 360 *********************** 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 838 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 820 time to evaluate : 4.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.7761 (tp) cc_final: 0.7422 (mt) REVERT: A 61 MET cc_start: 0.8010 (mmt) cc_final: 0.7709 (mmt) REVERT: A 94 ASN cc_start: 0.7746 (m110) cc_final: 0.7432 (m-40) REVERT: A 124 ILE cc_start: 0.7979 (pt) cc_final: 0.7628 (pt) REVERT: C 111 GLU cc_start: 0.7482 (tp30) cc_final: 0.7123 (tt0) REVERT: E 60 LYS cc_start: 0.6622 (mtmt) cc_final: 0.6099 (mttp) REVERT: F 94 ASN cc_start: 0.8416 (m-40) cc_final: 0.8187 (t0) REVERT: G 94 ASN cc_start: 0.7792 (t0) cc_final: 0.7549 (t0) REVERT: H 61 MET cc_start: 0.7519 (mmt) cc_final: 0.7265 (mmt) REVERT: I 69 ILE cc_start: 0.7459 (mm) cc_final: 0.7243 (mm) REVERT: J 60 LYS cc_start: 0.6721 (mtmt) cc_final: 0.6308 (pttt) REVERT: P 136 GLU cc_start: 0.6593 (tt0) cc_final: 0.6152 (tt0) REVERT: Q 35 PHE cc_start: 0.7948 (m-80) cc_final: 0.7569 (m-10) REVERT: Q 42 ARG cc_start: 0.7054 (ptp90) cc_final: 0.6382 (mtm-85) REVERT: Q 52 TYR cc_start: 0.6047 (m-10) cc_final: 0.5636 (m-10) REVERT: R 31 LYS cc_start: 0.7180 (tmmt) cc_final: 0.6324 (mptt) REVERT: R 68 ASP cc_start: 0.5619 (m-30) cc_final: 0.5151 (m-30) REVERT: R 88 THR cc_start: 0.5944 (t) cc_final: 0.5476 (p) REVERT: S 62 MET cc_start: 0.7598 (ptm) cc_final: 0.7202 (ptt) REVERT: S 124 ARG cc_start: 0.8176 (ptm-80) cc_final: 0.7973 (ptm160) REVERT: T 101 LYS cc_start: 0.8599 (tptt) cc_final: 0.8374 (mttp) REVERT: T 271 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7431 (mt0) REVERT: T 357 LEU cc_start: 0.8842 (tp) cc_final: 0.8559 (tp) REVERT: T 453 TYR cc_start: 0.7269 (t80) cc_final: 0.6980 (t80) REVERT: T 502 TYR cc_start: 0.7565 (t80) cc_final: 0.7289 (t80) REVERT: T 506 LYS cc_start: 0.6415 (mmtp) cc_final: 0.6019 (mmtt) REVERT: T 515 GLN cc_start: 0.7589 (tt0) cc_final: 0.7384 (mm-40) REVERT: U 112 ASP cc_start: 0.7672 (t0) cc_final: 0.7414 (t0) REVERT: U 215 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8708 (mp) REVERT: U 384 GLU cc_start: 0.7218 (tt0) cc_final: 0.6820 (mt-10) REVERT: U 511 LYS cc_start: 0.7831 (tttt) cc_final: 0.7061 (mmtp) REVERT: V 94 ILE cc_start: 0.9377 (mm) cc_final: 0.9158 (tp) REVERT: V 98 TYR cc_start: 0.8424 (t80) cc_final: 0.8150 (t80) REVERT: V 165 ASP cc_start: 0.7840 (t0) cc_final: 0.7600 (t0) REVERT: V 316 THR cc_start: 0.6881 (p) cc_final: 0.6664 (p) REVERT: V 492 ILE cc_start: 0.8613 (mt) cc_final: 0.8103 (tt) REVERT: V 513 ARG cc_start: 0.6867 (mtm180) cc_final: 0.6466 (mtp180) REVERT: V 551 LYS cc_start: 0.7899 (tttp) cc_final: 0.7184 (mttt) REVERT: X 243 LYS cc_start: 0.8844 (mmmm) cc_final: 0.8571 (mmtm) REVERT: X 573 LYS cc_start: 0.6372 (ttmt) cc_final: 0.6149 (mmmt) REVERT: Y 405 LYS cc_start: 0.8184 (tptt) cc_final: 0.7593 (ttpp) REVERT: Y 494 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7413 (tp30) REVERT: Y 550 LYS cc_start: 0.6223 (mmtt) cc_final: 0.5875 (pptt) REVERT: Z 222 ASP cc_start: 0.7366 (m-30) cc_final: 0.7149 (m-30) REVERT: Z 370 GLU cc_start: 0.6811 (mm-30) cc_final: 0.5918 (mm-30) REVERT: Z 385 ARG cc_start: 0.6870 (ttm-80) cc_final: 0.6426 (ttm170) REVERT: Z 547 GLU cc_start: 0.5487 (mp0) cc_final: 0.4744 (pm20) outliers start: 18 outliers final: 11 residues processed: 835 average time/residue: 0.4936 time to fit residues: 648.4837 Evaluate side-chains 539 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 527 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain U residue 215 ILE Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Z residue 334 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 2.9990 chunk 335 optimal weight: 0.0570 chunk 185 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 225 optimal weight: 0.8980 chunk 178 optimal weight: 8.9990 chunk 346 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 210 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 401 optimal weight: 2.9990 overall best weight: 1.0900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 GLN F 98 GLN G 94 ASN G 98 GLN J 98 GLN ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN Q 67 ASN R 38 ASN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 GLN S 195 ASN S 250 HIS S 262 ASN S 297 GLN ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 405 GLN ** T 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 497 GLN U 134 ASN ** U 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 241 HIS U 319 HIS U 386 GLN U 441 GLN U 529 ASN V 64 GLN V 134 ASN V 169 GLN V 196 GLN V 242 GLN V 244 ASN V 271 GLN V 278 GLN V 488 GLN V 497 GLN V 539 ASN X 199 ASN X 337 GLN ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 514 ASN ** Z 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 252 ASN Z 404 GLN Z 414 GLN Z 471 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34412 Z= 0.192 Angle : 0.605 12.632 46638 Z= 0.311 Chirality : 0.044 0.174 5519 Planarity : 0.005 0.097 5997 Dihedral : 7.289 104.328 4933 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.74 % Favored : 95.99 % Rotamer: Outliers : 2.72 % Allowed : 16.95 % Favored : 80.33 % 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: -2.74 (0.11), residues: 4461 helix: -1.73 (0.10), residues: 2093 sheet: -1.74 (0.22), residues: 526 loop : -1.73 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 37 HIS 0.004 0.001 HIS U 61 PHE 0.024 0.001 PHE V 489 TYR 0.024 0.001 TYR Z 271 ARG 0.007 0.000 ARG V 314 *********************** 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 737 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 640 time to evaluate : 3.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.7531 (m110) cc_final: 0.7236 (m-40) REVERT: C 111 GLU cc_start: 0.6997 (tp30) cc_final: 0.6440 (tt0) REVERT: C 113 ILE cc_start: 0.8018 (mt) cc_final: 0.7780 (mm) REVERT: E 60 LYS cc_start: 0.6545 (mtmt) cc_final: 0.5965 (mttp) REVERT: E 81 MET cc_start: 0.7945 (tmm) cc_final: 0.7725 (tmm) REVERT: H 61 MET cc_start: 0.7508 (mmt) cc_final: 0.7043 (mmt) REVERT: P 50 SER cc_start: 0.8026 (p) cc_final: 0.7634 (m) REVERT: P 136 GLU cc_start: 0.6639 (tt0) cc_final: 0.6342 (tt0) REVERT: P 140 ASN cc_start: 0.8396 (m110) cc_final: 0.8176 (m110) REVERT: P 145 MET cc_start: 0.8135 (ttm) cc_final: 0.7790 (tpp) REVERT: Q 35 PHE cc_start: 0.7833 (m-80) cc_final: 0.7574 (m-80) REVERT: Q 42 ARG cc_start: 0.7108 (ptp90) cc_final: 0.6615 (mtm-85) REVERT: Q 52 TYR cc_start: 0.6027 (m-10) cc_final: 0.5732 (m-10) REVERT: R 31 LYS cc_start: 0.6849 (tmmt) cc_final: 0.6173 (mttm) REVERT: R 88 THR cc_start: 0.5722 (t) cc_final: 0.5045 (p) REVERT: S 124 ARG cc_start: 0.8176 (ptm-80) cc_final: 0.7766 (ptm160) REVERT: S 159 GLN cc_start: 0.7343 (tp40) cc_final: 0.6976 (tm-30) REVERT: T 273 VAL cc_start: 0.9060 (m) cc_final: 0.8840 (t) REVERT: T 304 TYR cc_start: 0.8649 (m-80) cc_final: 0.8417 (m-80) REVERT: T 389 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.7860 (m-30) REVERT: T 455 GLU cc_start: 0.6187 (pm20) cc_final: 0.5771 (pt0) REVERT: T 509 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7518 (mm) REVERT: U 112 ASP cc_start: 0.7584 (t0) cc_final: 0.7233 (t0) REVERT: U 121 ASN cc_start: 0.8790 (p0) cc_final: 0.7904 (p0) REVERT: U 260 VAL cc_start: 0.9215 (t) cc_final: 0.8947 (m) REVERT: U 429 ARG cc_start: 0.7734 (ptm160) cc_final: 0.7521 (ptm-80) REVERT: U 511 LYS cc_start: 0.7628 (tttt) cc_final: 0.6991 (mmtp) REVERT: U 550 LEU cc_start: 0.8704 (mt) cc_final: 0.8205 (mt) REVERT: V 98 TYR cc_start: 0.8350 (t80) cc_final: 0.8026 (t80) REVERT: V 316 THR cc_start: 0.6878 (p) cc_final: 0.6572 (p) REVERT: V 384 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6748 (pp20) REVERT: V 492 ILE cc_start: 0.8464 (mt) cc_final: 0.7959 (tt) REVERT: V 551 LYS cc_start: 0.7852 (tttp) cc_final: 0.7146 (mttt) REVERT: X 56 LEU cc_start: 0.8837 (mp) cc_final: 0.8588 (mp) REVERT: X 456 THR cc_start: 0.8523 (m) cc_final: 0.8086 (p) REVERT: X 573 LYS cc_start: 0.5714 (ttmt) cc_final: 0.5142 (tptt) REVERT: Y 405 LYS cc_start: 0.8190 (tptt) cc_final: 0.7738 (tttm) REVERT: Y 494 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7402 (tp30) REVERT: Y 550 LYS cc_start: 0.6059 (mmtt) cc_final: 0.5728 (pptt) REVERT: Z 49 ASP cc_start: 0.8607 (m-30) cc_final: 0.8361 (m-30) REVERT: Z 366 ARG cc_start: 0.7070 (tpt170) cc_final: 0.6652 (tpt170) REVERT: Z 370 GLU cc_start: 0.7004 (mm-30) cc_final: 0.5861 (mm-30) REVERT: Z 385 ARG cc_start: 0.6833 (ttm-80) cc_final: 0.6313 (ttm170) REVERT: Z 438 LYS cc_start: 0.8153 (ptpp) cc_final: 0.6798 (mttm) outliers start: 97 outliers final: 49 residues processed: 707 average time/residue: 0.4601 time to fit residues: 530.4838 Evaluate side-chains 581 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 530 time to evaluate : 4.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 112 SER Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 188 GLN Chi-restraints excluded: chain S residue 262 ASN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 389 ASP Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain U residue 101 LYS Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 277 THR Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 465 ASP Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 415 ASP Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Y residue 539 ILE Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 564 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 223 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 334 optimal weight: 0.0010 chunk 273 optimal weight: 0.6980 chunk 110 optimal weight: 8.9990 chunk 402 optimal weight: 8.9990 chunk 434 optimal weight: 4.9990 chunk 358 optimal weight: 3.9990 chunk 398 optimal weight: 8.9990 chunk 137 optimal weight: 9.9990 chunk 322 optimal weight: 2.9990 overall best weight: 2.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN C 98 GLN G 98 GLN I 98 GLN ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 GLN S 191 GLN S 262 ASN T 104 GLN ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN T 405 GLN U 123 GLN U 134 ASN ** U 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN V 169 GLN V 278 GLN V 486 GLN X 408 GLN X 412 ASN Y 42 GLN Y 174 GLN Y 198 ASN ** Z 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 471 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 34412 Z= 0.293 Angle : 0.623 11.870 46638 Z= 0.317 Chirality : 0.045 0.198 5519 Planarity : 0.005 0.057 5997 Dihedral : 7.048 103.462 4925 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.93 % Favored : 94.80 % Rotamer: Outliers : 4.24 % Allowed : 18.57 % Favored : 77.19 % 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: -2.22 (0.12), residues: 4461 helix: -1.25 (0.11), residues: 2124 sheet: -1.48 (0.22), residues: 528 loop : -1.55 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 37 HIS 0.005 0.001 HIS S 250 PHE 0.028 0.002 PHE Y 290 TYR 0.020 0.002 TYR Z 271 ARG 0.007 0.000 ARG V 314 *********************** 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 712 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 561 time to evaluate : 3.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.7536 (m110) cc_final: 0.7209 (m-40) REVERT: C 111 GLU cc_start: 0.7136 (tp30) cc_final: 0.6601 (tt0) REVERT: C 113 ILE cc_start: 0.8068 (mt) cc_final: 0.7769 (mm) REVERT: E 123 LEU cc_start: 0.8271 (mt) cc_final: 0.7541 (tt) REVERT: H 61 MET cc_start: 0.7467 (mmt) cc_final: 0.6971 (mmt) REVERT: P 50 SER cc_start: 0.8016 (p) cc_final: 0.7664 (m) REVERT: P 110 LYS cc_start: 0.6924 (mmmt) cc_final: 0.6636 (mmmm) REVERT: P 140 ASN cc_start: 0.8427 (m110) cc_final: 0.8194 (m-40) REVERT: Q 42 ARG cc_start: 0.7210 (ptp90) cc_final: 0.6603 (mtm-85) REVERT: R 31 LYS cc_start: 0.6975 (tmmt) cc_final: 0.6115 (mtmm) REVERT: R 88 THR cc_start: 0.5709 (t) cc_final: 0.5182 (p) REVERT: S 68 MET cc_start: 0.8431 (ttp) cc_final: 0.8088 (ttt) REVERT: S 248 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: T 304 TYR cc_start: 0.8707 (m-80) cc_final: 0.8443 (m-80) REVERT: T 389 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8108 (m-30) REVERT: T 509 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7686 (mm) REVERT: U 112 ASP cc_start: 0.7694 (t0) cc_final: 0.7339 (t0) REVERT: U 260 VAL cc_start: 0.9235 (t) cc_final: 0.8933 (m) REVERT: U 429 ARG cc_start: 0.7962 (ptm160) cc_final: 0.7664 (ptm-80) REVERT: U 511 LYS cc_start: 0.7651 (tttt) cc_final: 0.7008 (mmtp) REVERT: U 550 LEU cc_start: 0.8664 (mt) cc_final: 0.8143 (mt) REVERT: V 98 TYR cc_start: 0.8370 (t80) cc_final: 0.8034 (t80) REVERT: V 316 THR cc_start: 0.6958 (p) cc_final: 0.6715 (p) REVERT: V 384 GLU cc_start: 0.7165 (tm-30) cc_final: 0.6769 (pp20) REVERT: V 492 ILE cc_start: 0.8414 (mt) cc_final: 0.7875 (tt) REVERT: V 551 LYS cc_start: 0.7876 (tttp) cc_final: 0.7341 (mttm) REVERT: X 39 TYR cc_start: 0.7474 (p90) cc_final: 0.7155 (p90) REVERT: X 49 ASP cc_start: 0.8108 (m-30) cc_final: 0.7883 (m-30) REVERT: X 56 LEU cc_start: 0.8898 (mp) cc_final: 0.8628 (mp) REVERT: X 304 ILE cc_start: 0.8952 (mp) cc_final: 0.8581 (mm) REVERT: X 456 THR cc_start: 0.8462 (m) cc_final: 0.7971 (p) REVERT: X 502 MET cc_start: 0.6946 (ptp) cc_final: 0.6472 (ptp) REVERT: X 573 LYS cc_start: 0.5933 (ttmt) cc_final: 0.5307 (tptt) REVERT: Y 405 LYS cc_start: 0.8174 (tptt) cc_final: 0.7731 (tttm) REVERT: Y 494 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7490 (tp30) REVERT: Y 550 LYS cc_start: 0.6162 (mmtt) cc_final: 0.5858 (pptt) REVERT: Z 80 MET cc_start: 0.8323 (mmt) cc_final: 0.7987 (mmt) REVERT: Z 385 ARG cc_start: 0.6897 (ttm-80) cc_final: 0.6439 (ttm170) REVERT: Z 423 ASP cc_start: 0.4491 (OUTLIER) cc_final: 0.3978 (t0) REVERT: Z 438 LYS cc_start: 0.8262 (ptpp) cc_final: 0.6825 (mttm) outliers start: 151 outliers final: 98 residues processed: 659 average time/residue: 0.4412 time to fit residues: 478.4238 Evaluate side-chains 612 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 510 time to evaluate : 3.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 112 SER Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain S residue 188 GLN Chi-restraints excluded: chain S residue 248 GLU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 262 ASN Chi-restraints excluded: chain T residue 137 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 222 LEU Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 389 ASP Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 101 LYS Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 147 THR Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 204 THR Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 277 THR Chi-restraints excluded: chain U residue 307 CYS Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 492 ILE Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 226 ASP Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 155 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 251 MET Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 415 ASP Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Y residue 505 ASP Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 423 ASP Chi-restraints excluded: chain Z residue 454 THR Chi-restraints excluded: chain Z residue 559 VAL Chi-restraints excluded: chain Z residue 564 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 397 optimal weight: 3.9990 chunk 302 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 270 optimal weight: 0.9980 chunk 403 optimal weight: 4.9990 chunk 427 optimal weight: 2.9990 chunk 210 optimal weight: 0.2980 chunk 382 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 94 ASN G 98 GLN ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN R 73 ASN R 83 GLN S 262 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 435 GLN U 134 ASN U 140 GLN ** U 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 529 ASN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 278 GLN X 412 ASN Y 388 ASN Y 390 ASN Z 199 ASN Z 471 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34412 Z= 0.202 Angle : 0.567 10.603 46638 Z= 0.287 Chirality : 0.043 0.162 5519 Planarity : 0.004 0.047 5997 Dihedral : 6.635 98.143 4925 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.19 % Favored : 95.65 % Rotamer: Outliers : 3.98 % Allowed : 20.43 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.12), residues: 4461 helix: -0.82 (0.11), residues: 2120 sheet: -1.31 (0.22), residues: 536 loop : -1.38 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 73 HIS 0.006 0.001 HIS U 61 PHE 0.018 0.001 PHE Y 290 TYR 0.020 0.001 TYR Z 271 ARG 0.007 0.000 ARG Y 435 *********************** 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 709 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 567 time to evaluate : 3.709 Fit side-chains revert: symmetry clash REVERT: A 94 ASN cc_start: 0.7633 (m110) cc_final: 0.7377 (m-40) REVERT: C 111 GLU cc_start: 0.6950 (tp30) cc_final: 0.6459 (tt0) REVERT: C 113 ILE cc_start: 0.7940 (mt) cc_final: 0.7648 (mm) REVERT: E 81 MET cc_start: 0.7996 (tmm) cc_final: 0.7758 (tmm) REVERT: E 116 PHE cc_start: 0.5072 (m-80) cc_final: 0.4823 (m-80) REVERT: E 123 LEU cc_start: 0.8243 (mt) cc_final: 0.7575 (tt) REVERT: H 61 MET cc_start: 0.7447 (mmt) cc_final: 0.6891 (mmt) REVERT: H 87 ASN cc_start: 0.7769 (p0) cc_final: 0.7568 (t0) REVERT: J 111 GLU cc_start: 0.7404 (tp30) cc_final: 0.7147 (tp30) REVERT: P 50 SER cc_start: 0.7993 (p) cc_final: 0.7530 (m) REVERT: P 110 LYS cc_start: 0.6814 (mmmt) cc_final: 0.6548 (mmmm) REVERT: P 140 ASN cc_start: 0.8435 (m110) cc_final: 0.8190 (m-40) REVERT: Q 42 ARG cc_start: 0.7194 (ptp90) cc_final: 0.6609 (mtm-85) REVERT: R 31 LYS cc_start: 0.7067 (tmmt) cc_final: 0.6102 (mtmm) REVERT: R 177 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6590 (mt-10) REVERT: S 124 ARG cc_start: 0.7989 (ptm160) cc_final: 0.7222 (ttp80) REVERT: S 248 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: T 389 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8118 (m-30) REVERT: T 509 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7640 (mm) REVERT: U 112 ASP cc_start: 0.7663 (t0) cc_final: 0.7236 (t0) REVERT: U 210 ASP cc_start: 0.7792 (m-30) cc_final: 0.7587 (m-30) REVERT: U 260 VAL cc_start: 0.9180 (t) cc_final: 0.8914 (m) REVERT: U 371 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7437 (pm20) REVERT: U 511 LYS cc_start: 0.7580 (tttt) cc_final: 0.6938 (mmtp) REVERT: V 98 TYR cc_start: 0.8347 (t80) cc_final: 0.8002 (t80) REVERT: V 316 THR cc_start: 0.6956 (p) cc_final: 0.6732 (p) REVERT: V 384 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6665 (pp20) REVERT: V 551 LYS cc_start: 0.7833 (tttp) cc_final: 0.7133 (mttt) REVERT: X 49 ASP cc_start: 0.8086 (m-30) cc_final: 0.7863 (m-30) REVERT: X 56 LEU cc_start: 0.8853 (mp) cc_final: 0.8581 (mp) REVERT: X 304 ILE cc_start: 0.8888 (mp) cc_final: 0.8568 (mm) REVERT: X 456 THR cc_start: 0.8487 (m) cc_final: 0.8039 (p) REVERT: X 502 MET cc_start: 0.6924 (ptp) cc_final: 0.6437 (ptp) REVERT: X 573 LYS cc_start: 0.5828 (ttmt) cc_final: 0.5228 (tptt) REVERT: Y 194 MET cc_start: 0.8317 (tpp) cc_final: 0.7541 (mmm) REVERT: Y 401 ARG cc_start: 0.7377 (mmm160) cc_final: 0.6646 (mmm-85) REVERT: Y 405 LYS cc_start: 0.8185 (tptt) cc_final: 0.7773 (tttm) REVERT: Y 550 LYS cc_start: 0.6138 (mmtt) cc_final: 0.5812 (pptt) REVERT: Z 80 MET cc_start: 0.8278 (mmt) cc_final: 0.8059 (mmt) REVERT: Z 359 ASP cc_start: 0.8040 (m-30) cc_final: 0.7809 (m-30) REVERT: Z 366 ARG cc_start: 0.7108 (tpt-90) cc_final: 0.6216 (tpt170) REVERT: Z 370 GLU cc_start: 0.6643 (mm-30) cc_final: 0.6064 (mm-30) REVERT: Z 438 LYS cc_start: 0.8210 (ptpp) cc_final: 0.6903 (mttm) REVERT: Z 502 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7549 (mmm) outliers start: 142 outliers final: 100 residues processed: 669 average time/residue: 0.4378 time to fit residues: 485.4443 Evaluate side-chains 615 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 509 time to evaluate : 3.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 112 SER Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain S residue 188 GLN Chi-restraints excluded: chain S residue 248 GLU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 262 ASN Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 137 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 222 LEU Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 389 ASP Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 535 ILE Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 101 LYS Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 204 THR Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 277 THR Chi-restraints excluded: chain U residue 371 GLU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 226 ASP Chi-restraints excluded: chain V residue 356 TYR Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 484 MET Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 155 THR Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 251 MET Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 353 THR Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 415 ASP Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 564 GLU 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: 8.9990 chunk 6 optimal weight: 0.9980 chunk 318 optimal weight: 6.9990 chunk 176 optimal weight: 0.6980 chunk 364 optimal weight: 4.9990 chunk 295 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 218 optimal weight: 0.9980 chunk 383 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 94 ASN G 98 GLN P 140 ASN Q 49 GLN ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 ASN ** U 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 388 ASN Z 157 GLN Z 408 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34412 Z= 0.224 Angle : 0.577 10.760 46638 Z= 0.291 Chirality : 0.043 0.225 5519 Planarity : 0.004 0.045 5997 Dihedral : 6.526 95.115 4924 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.66 % Favored : 95.16 % Rotamer: Outliers : 4.41 % Allowed : 21.27 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.12), residues: 4461 helix: -0.61 (0.11), residues: 2121 sheet: -1.22 (0.22), residues: 549 loop : -1.27 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 73 HIS 0.007 0.001 HIS T 358 PHE 0.028 0.001 PHE V 459 TYR 0.017 0.001 TYR Z 271 ARG 0.006 0.000 ARG U 555 *********************** 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 693 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 536 time to evaluate : 3.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.7563 (m110) cc_final: 0.7326 (m-40) REVERT: C 111 GLU cc_start: 0.7045 (tp30) cc_final: 0.6542 (tt0) REVERT: C 113 ILE cc_start: 0.7986 (mt) cc_final: 0.7675 (mm) REVERT: E 116 PHE cc_start: 0.5163 (m-80) cc_final: 0.4902 (m-80) REVERT: E 123 LEU cc_start: 0.8239 (mt) cc_final: 0.7580 (tt) REVERT: H 61 MET cc_start: 0.7337 (mmt) cc_final: 0.6775 (mmt) REVERT: P 50 SER cc_start: 0.8104 (p) cc_final: 0.7593 (m) REVERT: P 136 GLU cc_start: 0.6770 (tt0) cc_final: 0.6281 (tt0) REVERT: P 143 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7633 (mm-30) REVERT: R 31 LYS cc_start: 0.6896 (tmmt) cc_final: 0.6122 (mtmm) REVERT: R 177 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6631 (mt-10) REVERT: S 68 MET cc_start: 0.8427 (ttp) cc_final: 0.8113 (ttt) REVERT: S 124 ARG cc_start: 0.8023 (ptm160) cc_final: 0.7212 (ttp80) REVERT: S 183 ILE cc_start: 0.8622 (mt) cc_final: 0.8308 (mt) REVERT: S 248 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: T 389 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8142 (m-30) REVERT: T 439 MET cc_start: 0.8179 (tpp) cc_final: 0.7595 (tpp) REVERT: T 509 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7686 (mm) REVERT: U 112 ASP cc_start: 0.7719 (t0) cc_final: 0.7293 (t0) REVERT: U 203 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.6505 (m-80) REVERT: U 210 ASP cc_start: 0.7827 (m-30) cc_final: 0.7427 (m-30) REVERT: U 260 VAL cc_start: 0.9201 (t) cc_final: 0.8919 (m) REVERT: U 371 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7412 (pm20) REVERT: U 511 LYS cc_start: 0.7609 (tttt) cc_final: 0.6955 (mmtp) REVERT: V 98 TYR cc_start: 0.8336 (t80) cc_final: 0.7981 (t80) REVERT: V 316 THR cc_start: 0.7010 (p) cc_final: 0.6772 (p) REVERT: V 384 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6621 (pp20) REVERT: V 551 LYS cc_start: 0.7835 (tttp) cc_final: 0.7138 (mttt) REVERT: X 39 TYR cc_start: 0.7400 (p90) cc_final: 0.7153 (p90) REVERT: X 56 LEU cc_start: 0.8859 (mp) cc_final: 0.8613 (mp) REVERT: X 304 ILE cc_start: 0.8945 (mp) cc_final: 0.8659 (mm) REVERT: X 456 THR cc_start: 0.8512 (m) cc_final: 0.8060 (p) REVERT: X 502 MET cc_start: 0.6864 (ptp) cc_final: 0.6392 (ptp) REVERT: X 573 LYS cc_start: 0.5764 (ttmt) cc_final: 0.5147 (tptt) REVERT: Y 194 MET cc_start: 0.8345 (tpp) cc_final: 0.7605 (mmm) REVERT: Y 405 LYS cc_start: 0.8170 (tptt) cc_final: 0.7732 (tttm) REVERT: Y 550 LYS cc_start: 0.6153 (mmtt) cc_final: 0.5834 (pptt) REVERT: Z 80 MET cc_start: 0.8279 (mmt) cc_final: 0.8049 (mmt) REVERT: Z 271 TYR cc_start: 0.8688 (t80) cc_final: 0.8225 (t80) REVERT: Z 366 ARG cc_start: 0.7278 (tpt-90) cc_final: 0.7071 (tpt170) REVERT: Z 502 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7573 (mmm) outliers start: 157 outliers final: 125 residues processed: 648 average time/residue: 0.4156 time to fit residues: 452.7905 Evaluate side-chains 642 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 510 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 112 SER Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain S residue 188 GLN Chi-restraints excluded: chain S residue 248 GLU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 262 ASN Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 137 VAL Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 389 ASP Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 535 ILE Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 101 LYS Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 147 THR Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 203 PHE Chi-restraints excluded: chain U residue 207 LYS Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 277 THR Chi-restraints excluded: chain U residue 307 CYS Chi-restraints excluded: chain U residue 371 GLU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 224 ILE Chi-restraints excluded: chain V residue 226 ASP Chi-restraints excluded: chain V residue 356 TYR Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 484 MET Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 155 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 251 MET Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 353 THR Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 415 ASP Chi-restraints excluded: chain Y residue 449 VAL Chi-restraints excluded: chain Y residue 452 VAL Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Y residue 505 ASP Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 191 VAL Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 564 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 143 optimal weight: 0.8980 chunk 384 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 250 optimal weight: 0.9990 chunk 105 optimal weight: 0.0270 chunk 427 optimal weight: 0.9980 chunk 355 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 224 optimal weight: 6.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN Q 49 GLN ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 ASN S 267 HIS S 293 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 358 HIS U 123 GLN U 134 ASN ** U 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 529 ASN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 388 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3049 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= 0.153 Angle : 0.544 10.459 46638 Z= 0.273 Chirality : 0.042 0.200 5519 Planarity : 0.004 0.043 5997 Dihedral : 6.208 92.847 4924 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.19 % Favored : 95.67 % Rotamer: Outliers : 3.82 % Allowed : 23.01 % Favored : 73.18 % Cbeta Deviations : 0.00 % 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: -1.22 (0.13), residues: 4461 helix: -0.36 (0.11), residues: 2131 sheet: -1.02 (0.23), residues: 547 loop : -1.12 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 73 HIS 0.005 0.001 HIS T 358 PHE 0.025 0.001 PHE A 82 TYR 0.021 0.001 TYR T 312 ARG 0.006 0.000 ARG U 555 *********************** 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 679 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 543 time to evaluate : 3.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.7476 (m110) cc_final: 0.7270 (m-40) REVERT: C 111 GLU cc_start: 0.6947 (tp30) cc_final: 0.6404 (tt0) REVERT: H 61 MET cc_start: 0.7510 (mmt) cc_final: 0.7099 (mmt) REVERT: P 50 SER cc_start: 0.7948 (p) cc_final: 0.7414 (m) REVERT: P 110 LYS cc_start: 0.6852 (mmmt) cc_final: 0.6569 (mmmm) REVERT: P 122 PHE cc_start: 0.7907 (m-80) cc_final: 0.7639 (m-80) REVERT: P 136 GLU cc_start: 0.6962 (tt0) cc_final: 0.6511 (tt0) REVERT: P 141 TYR cc_start: 0.9186 (t80) cc_final: 0.8959 (t80) REVERT: P 143 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7625 (mm-30) REVERT: Q 42 ARG cc_start: 0.7242 (ptp90) cc_final: 0.6674 (mtm-85) REVERT: R 31 LYS cc_start: 0.6931 (tmmt) cc_final: 0.6182 (mtmm) REVERT: R 32 GLU cc_start: 0.7688 (tm-30) cc_final: 0.6528 (tt0) REVERT: R 177 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6371 (mt-10) REVERT: S 52 ASN cc_start: 0.7107 (t0) cc_final: 0.6527 (t0) REVERT: S 68 MET cc_start: 0.8408 (ttp) cc_final: 0.8154 (ttt) REVERT: S 124 ARG cc_start: 0.8022 (ptm160) cc_final: 0.7213 (ttp80) REVERT: S 183 ILE cc_start: 0.8587 (mt) cc_final: 0.8316 (mt) REVERT: S 248 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: T 389 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8113 (m-30) REVERT: T 439 MET cc_start: 0.8172 (tpp) cc_final: 0.7585 (tpp) REVERT: T 509 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7603 (mm) REVERT: U 112 ASP cc_start: 0.7633 (t0) cc_final: 0.7213 (t0) REVERT: U 203 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.6183 (m-80) REVERT: U 210 ASP cc_start: 0.7779 (m-30) cc_final: 0.7318 (m-30) REVERT: U 260 VAL cc_start: 0.9157 (t) cc_final: 0.8902 (m) REVERT: U 371 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7309 (pm20) REVERT: U 511 LYS cc_start: 0.7558 (tttt) cc_final: 0.6917 (mmtp) REVERT: V 98 TYR cc_start: 0.8279 (t80) cc_final: 0.7908 (t80) REVERT: V 316 THR cc_start: 0.6938 (p) cc_final: 0.6683 (p) REVERT: V 384 GLU cc_start: 0.6937 (tm-30) cc_final: 0.6588 (pp20) REVERT: V 439 MET cc_start: 0.8664 (tpp) cc_final: 0.8459 (tpp) REVERT: V 551 LYS cc_start: 0.7832 (tttp) cc_final: 0.7208 (mttt) REVERT: X 49 ASP cc_start: 0.8092 (m-30) cc_final: 0.7865 (m-30) REVERT: X 56 LEU cc_start: 0.8833 (mp) cc_final: 0.8559 (mp) REVERT: X 304 ILE cc_start: 0.8847 (mp) cc_final: 0.8556 (mm) REVERT: X 456 THR cc_start: 0.8487 (m) cc_final: 0.8034 (p) REVERT: X 502 MET cc_start: 0.6884 (ptp) cc_final: 0.6417 (ptp) REVERT: X 573 LYS cc_start: 0.5736 (ttmt) cc_final: 0.5137 (tptt) REVERT: Y 194 MET cc_start: 0.8308 (tpp) cc_final: 0.7545 (mmm) REVERT: Y 197 ILE cc_start: 0.8705 (mt) cc_final: 0.8485 (mt) REVERT: Y 401 ARG cc_start: 0.7294 (mmm160) cc_final: 0.6614 (mmm-85) REVERT: Y 405 LYS cc_start: 0.8242 (tptt) cc_final: 0.7762 (tttp) REVERT: Y 550 LYS cc_start: 0.6092 (mmtt) cc_final: 0.5828 (pptt) REVERT: Z 80 MET cc_start: 0.8245 (mmt) cc_final: 0.8036 (mmt) REVERT: Z 196 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8826 (mt) REVERT: Z 271 TYR cc_start: 0.8635 (t80) cc_final: 0.8270 (t80) REVERT: Z 441 ARG cc_start: 0.8395 (mmt90) cc_final: 0.8189 (mmm-85) REVERT: Z 502 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7548 (mmm) outliers start: 136 outliers final: 105 residues processed: 635 average time/residue: 0.4294 time to fit residues: 457.7412 Evaluate side-chains 622 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 509 time to evaluate : 3.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain S residue 188 GLN Chi-restraints excluded: chain S residue 248 GLU Chi-restraints excluded: chain S residue 262 ASN Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 137 VAL Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 222 LEU Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 389 ASP Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 535 ILE Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 147 THR Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 203 PHE Chi-restraints excluded: chain U residue 207 LYS Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 277 THR Chi-restraints excluded: chain U residue 307 CYS Chi-restraints excluded: chain U residue 371 GLU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 485 LYS Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 224 ILE Chi-restraints excluded: chain V residue 226 ASP Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 355 PHE Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 484 MET Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 155 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 353 THR Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 449 VAL Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Y residue 539 ILE Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 196 LEU Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 564 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 412 optimal weight: 0.5980 chunk 48 optimal weight: 10.0000 chunk 243 optimal weight: 5.9990 chunk 312 optimal weight: 8.9990 chunk 241 optimal weight: 0.6980 chunk 359 optimal weight: 0.9990 chunk 238 optimal weight: 5.9990 chunk 426 optimal weight: 4.9990 chunk 266 optimal weight: 0.9990 chunk 259 optimal weight: 0.7980 chunk 196 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 94 ASN G 98 GLN Q 49 GLN ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 ASN ** U 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 388 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 0.002 0.036 34412 Z= 0.158 Angle : 0.539 10.078 46638 Z= 0.271 Chirality : 0.042 0.163 5519 Planarity : 0.004 0.043 5997 Dihedral : 6.017 89.894 4924 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.19 % Favored : 95.70 % Rotamer: Outliers : 3.79 % Allowed : 23.23 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 4461 helix: -0.18 (0.12), residues: 2111 sheet: -0.88 (0.23), residues: 541 loop : -1.00 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 73 HIS 0.004 0.001 HIS U 61 PHE 0.041 0.001 PHE E 116 TYR 0.030 0.001 TYR V 312 ARG 0.005 0.000 ARG S 294 *********************** 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 669 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 534 time to evaluate : 3.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.7552 (m110) cc_final: 0.7340 (m-40) REVERT: B 99 LEU cc_start: 0.8616 (mp) cc_final: 0.8415 (mt) REVERT: C 111 GLU cc_start: 0.6946 (tp30) cc_final: 0.6394 (tt0) REVERT: H 61 MET cc_start: 0.7624 (mmt) cc_final: 0.7179 (mmt) REVERT: P 50 SER cc_start: 0.7840 (p) cc_final: 0.7427 (m) REVERT: P 77 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7971 (t80) REVERT: P 136 GLU cc_start: 0.6958 (tt0) cc_final: 0.6621 (tt0) REVERT: Q 42 ARG cc_start: 0.7187 (ptp90) cc_final: 0.6805 (mtm-85) REVERT: R 31 LYS cc_start: 0.6944 (tmmt) cc_final: 0.6179 (mtmm) REVERT: R 177 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6329 (mt-10) REVERT: S 68 MET cc_start: 0.8421 (ttp) cc_final: 0.8212 (ttp) REVERT: S 124 ARG cc_start: 0.8036 (ptm160) cc_final: 0.7186 (ttp80) REVERT: S 183 ILE cc_start: 0.8520 (mt) cc_final: 0.8289 (mt) REVERT: S 248 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: T 389 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8134 (m-30) REVERT: T 439 MET cc_start: 0.8194 (tpp) cc_final: 0.7598 (tpp) REVERT: T 509 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7568 (mm) REVERT: U 112 ASP cc_start: 0.7645 (t0) cc_final: 0.7227 (t0) REVERT: U 210 ASP cc_start: 0.7727 (m-30) cc_final: 0.7222 (m-30) REVERT: U 260 VAL cc_start: 0.9181 (t) cc_final: 0.8926 (m) REVERT: U 371 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7297 (pm20) REVERT: U 511 LYS cc_start: 0.7646 (tttt) cc_final: 0.6974 (mmtp) REVERT: V 98 TYR cc_start: 0.8265 (t80) cc_final: 0.7894 (t80) REVERT: V 316 THR cc_start: 0.7109 (p) cc_final: 0.6840 (p) REVERT: V 384 GLU cc_start: 0.6934 (tm-30) cc_final: 0.6554 (pp20) REVERT: V 551 LYS cc_start: 0.7804 (tttp) cc_final: 0.7155 (mttt) REVERT: X 49 ASP cc_start: 0.8105 (m-30) cc_final: 0.7860 (m-30) REVERT: X 56 LEU cc_start: 0.8827 (mp) cc_final: 0.8549 (mp) REVERT: X 304 ILE cc_start: 0.8841 (mp) cc_final: 0.8550 (mm) REVERT: X 456 THR cc_start: 0.8555 (m) cc_final: 0.8098 (p) REVERT: X 502 MET cc_start: 0.6840 (ptp) cc_final: 0.6427 (ptp) REVERT: X 573 LYS cc_start: 0.5641 (ttmt) cc_final: 0.5078 (tptt) REVERT: Y 194 MET cc_start: 0.8328 (tpp) cc_final: 0.7542 (mmm) REVERT: Y 197 ILE cc_start: 0.8696 (mt) cc_final: 0.8477 (mt) REVERT: Y 405 LYS cc_start: 0.8264 (tptt) cc_final: 0.7770 (tttp) REVERT: Y 550 LYS cc_start: 0.6026 (mmtt) cc_final: 0.5792 (pptt) REVERT: Z 196 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8814 (mt) REVERT: Z 271 TYR cc_start: 0.8631 (t80) cc_final: 0.8296 (t80) REVERT: Z 502 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7551 (mmm) outliers start: 135 outliers final: 106 residues processed: 629 average time/residue: 0.4376 time to fit residues: 464.8523 Evaluate side-chains 617 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 503 time to evaluate : 4.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain S residue 188 GLN Chi-restraints excluded: chain S residue 248 GLU Chi-restraints excluded: chain S residue 262 ASN Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 137 VAL Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 222 LEU Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 389 ASP Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 535 ILE Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 147 THR Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 207 LYS Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 277 THR Chi-restraints excluded: chain U residue 371 GLU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 224 ILE Chi-restraints excluded: chain V residue 226 ASP Chi-restraints excluded: chain V residue 359 SER Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 345 ASP Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 484 MET Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 155 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 251 MET Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 353 THR Chi-restraints excluded: chain Y residue 449 VAL Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 196 LEU Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 564 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 263 optimal weight: 0.7980 chunk 170 optimal weight: 6.9990 chunk 254 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 270 optimal weight: 0.9980 chunk 290 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 334 optimal weight: 0.0050 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 94 ASN Q 49 GLN R 64 GLN ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 422 ASN U 134 ASN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN Y 388 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3279 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= 0.179 Angle : 0.551 11.954 46638 Z= 0.277 Chirality : 0.043 0.166 5519 Planarity : 0.004 0.043 5997 Dihedral : 5.938 89.676 4924 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.44 % Favored : 95.47 % Rotamer: Outliers : 3.98 % Allowed : 23.40 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.13), residues: 4461 helix: -0.15 (0.12), residues: 2127 sheet: -0.84 (0.23), residues: 543 loop : -0.98 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 73 HIS 0.004 0.001 HIS T 358 PHE 0.038 0.001 PHE E 116 TYR 0.026 0.001 TYR V 312 ARG 0.004 0.000 ARG U 555 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 513 time to evaluate : 3.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 LEU cc_start: 0.8613 (mp) cc_final: 0.8310 (mt) REVERT: H 61 MET cc_start: 0.7480 (mmt) cc_final: 0.6833 (mmt) REVERT: J 81 MET cc_start: 0.8143 (tmm) cc_final: 0.7818 (tmm) REVERT: P 50 SER cc_start: 0.7802 (p) cc_final: 0.7512 (m) REVERT: P 77 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7857 (t80) REVERT: P 110 LYS cc_start: 0.6727 (mmmt) cc_final: 0.6289 (mmmm) REVERT: R 31 LYS cc_start: 0.6949 (tmmt) cc_final: 0.6188 (mtmm) REVERT: R 32 GLU cc_start: 0.7674 (tm-30) cc_final: 0.6414 (tt0) REVERT: R 177 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6249 (mt-10) REVERT: S 68 MET cc_start: 0.8418 (ttp) cc_final: 0.8191 (ttp) REVERT: S 124 ARG cc_start: 0.8046 (ptm160) cc_final: 0.7178 (ttp80) REVERT: S 183 ILE cc_start: 0.8523 (mt) cc_final: 0.8280 (mt) REVERT: S 248 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: S 274 MET cc_start: 0.7679 (mmm) cc_final: 0.7430 (mtt) REVERT: T 389 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8146 (m-30) REVERT: T 439 MET cc_start: 0.8225 (tpp) cc_final: 0.7637 (tpp) REVERT: T 509 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7464 (mm) REVERT: U 112 ASP cc_start: 0.7676 (t0) cc_final: 0.7299 (t0) REVERT: U 203 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.6143 (m-80) REVERT: U 210 ASP cc_start: 0.7774 (m-30) cc_final: 0.7257 (m-30) REVERT: U 260 VAL cc_start: 0.9194 (t) cc_final: 0.8941 (m) REVERT: U 371 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7300 (pm20) REVERT: U 511 LYS cc_start: 0.7652 (tttt) cc_final: 0.6972 (mmtp) REVERT: V 98 TYR cc_start: 0.8267 (t80) cc_final: 0.7892 (t80) REVERT: V 316 THR cc_start: 0.7188 (p) cc_final: 0.6933 (p) REVERT: V 384 GLU cc_start: 0.6919 (tm-30) cc_final: 0.6553 (pp20) REVERT: V 551 LYS cc_start: 0.7796 (tttp) cc_final: 0.7138 (mttt) REVERT: X 39 TYR cc_start: 0.7368 (p90) cc_final: 0.7077 (p90) REVERT: X 56 LEU cc_start: 0.8832 (mp) cc_final: 0.8575 (mp) REVERT: X 270 GLU cc_start: 0.8180 (mp0) cc_final: 0.7690 (mp0) REVERT: X 304 ILE cc_start: 0.8863 (mp) cc_final: 0.8576 (mm) REVERT: X 456 THR cc_start: 0.8533 (m) cc_final: 0.8047 (p) REVERT: X 502 MET cc_start: 0.6807 (ptp) cc_final: 0.6434 (ptp) REVERT: X 573 LYS cc_start: 0.5801 (ttmt) cc_final: 0.5180 (tptt) REVERT: Y 194 MET cc_start: 0.8297 (tpp) cc_final: 0.7517 (mmm) REVERT: Y 197 ILE cc_start: 0.8800 (mt) cc_final: 0.8554 (mt) REVERT: Y 405 LYS cc_start: 0.8248 (tptt) cc_final: 0.7772 (tttp) REVERT: Y 550 LYS cc_start: 0.6056 (mmtt) cc_final: 0.5790 (pptt) REVERT: Z 58 SER cc_start: 0.8764 (m) cc_final: 0.8520 (m) REVERT: Z 196 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8829 (mt) REVERT: Z 271 TYR cc_start: 0.8620 (t80) cc_final: 0.8354 (t80) REVERT: Z 502 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7555 (mmm) outliers start: 142 outliers final: 115 residues processed: 614 average time/residue: 0.4187 time to fit residues: 431.8672 Evaluate side-chains 630 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 506 time to evaluate : 3.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain S residue 188 GLN Chi-restraints excluded: chain S residue 248 GLU Chi-restraints excluded: chain S residue 262 ASN Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 137 VAL Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 222 LEU Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 389 ASP Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 535 ILE Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 147 THR Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 203 PHE Chi-restraints excluded: chain U residue 207 LYS Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 277 THR Chi-restraints excluded: chain U residue 307 CYS Chi-restraints excluded: chain U residue 371 GLU Chi-restraints excluded: chain U residue 390 VAL Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 485 LYS Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 224 ILE Chi-restraints excluded: chain V residue 226 ASP Chi-restraints excluded: chain V residue 356 TYR Chi-restraints excluded: chain V residue 359 SER Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 345 ASP Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 484 MET Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 155 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 251 MET Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 353 THR Chi-restraints excluded: chain Y residue 449 VAL Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 196 LEU Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 341 VAL Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 564 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 387 optimal weight: 0.3980 chunk 408 optimal weight: 0.6980 chunk 372 optimal weight: 3.9990 chunk 396 optimal weight: 0.9990 chunk 238 optimal weight: 7.9990 chunk 172 optimal weight: 0.5980 chunk 311 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 358 optimal weight: 0.0470 chunk 375 optimal weight: 1.9990 chunk 395 optimal weight: 2.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 GLN G 94 ASN G 98 GLN Q 49 GLN R 64 GLN ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN S 262 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 ASN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 388 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3456 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= 0.147 Angle : 0.547 11.552 46638 Z= 0.274 Chirality : 0.042 0.169 5519 Planarity : 0.004 0.043 5997 Dihedral : 5.740 85.531 4923 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.76 % Rotamer: Outliers : 3.28 % Allowed : 24.27 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), residues: 4461 helix: 0.00 (0.12), residues: 2107 sheet: -0.79 (0.23), residues: 545 loop : -0.87 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 73 HIS 0.004 0.001 HIS R 66 PHE 0.040 0.001 PHE V 489 TYR 0.023 0.001 TYR V 312 ARG 0.008 0.000 ARG T 418 *********************** 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 661 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 544 time to evaluate : 4.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 105 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.5758 (mm) REVERT: H 61 MET cc_start: 0.7600 (mmt) cc_final: 0.7135 (mmt) REVERT: J 81 MET cc_start: 0.8136 (tmm) cc_final: 0.7816 (tmm) REVERT: P 50 SER cc_start: 0.7694 (p) cc_final: 0.7394 (m) REVERT: P 77 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7916 (t80) REVERT: P 110 LYS cc_start: 0.6790 (mmmt) cc_final: 0.6419 (mmmm) REVERT: R 31 LYS cc_start: 0.6949 (tmmt) cc_final: 0.6186 (mtmm) REVERT: R 177 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6166 (mt-10) REVERT: S 68 MET cc_start: 0.8434 (ttp) cc_final: 0.8212 (ttp) REVERT: S 124 ARG cc_start: 0.8023 (ptm160) cc_final: 0.7311 (ttp80) REVERT: S 180 GLU cc_start: 0.6788 (pp20) cc_final: 0.6572 (pp20) REVERT: S 274 MET cc_start: 0.7642 (mmm) cc_final: 0.7381 (mtt) REVERT: T 389 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8098 (m-30) REVERT: T 439 MET cc_start: 0.8225 (tpp) cc_final: 0.7662 (tpp) REVERT: T 509 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7439 (mm) REVERT: U 112 ASP cc_start: 0.7659 (t0) cc_final: 0.7290 (t0) REVERT: U 121 ASN cc_start: 0.8744 (p0) cc_final: 0.8218 (p0) REVERT: U 203 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.6005 (m-80) REVERT: U 210 ASP cc_start: 0.7653 (m-30) cc_final: 0.7177 (m-30) REVERT: U 260 VAL cc_start: 0.9169 (t) cc_final: 0.8907 (m) REVERT: U 371 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7290 (pm20) REVERT: U 511 LYS cc_start: 0.7745 (tttt) cc_final: 0.6944 (mmtp) REVERT: V 98 TYR cc_start: 0.8242 (t80) cc_final: 0.7929 (t80) REVERT: V 316 THR cc_start: 0.7127 (p) cc_final: 0.6878 (p) REVERT: V 384 GLU cc_start: 0.6902 (tm-30) cc_final: 0.6539 (pp20) REVERT: V 551 LYS cc_start: 0.7744 (tttp) cc_final: 0.7126 (mttt) REVERT: X 56 LEU cc_start: 0.8804 (mp) cc_final: 0.8533 (mp) REVERT: X 270 GLU cc_start: 0.8089 (mp0) cc_final: 0.7821 (mp0) REVERT: X 304 ILE cc_start: 0.8849 (mp) cc_final: 0.8571 (mm) REVERT: X 456 THR cc_start: 0.8556 (m) cc_final: 0.8086 (p) REVERT: X 502 MET cc_start: 0.6699 (ptp) cc_final: 0.6350 (ptp) REVERT: X 573 LYS cc_start: 0.5761 (ttmt) cc_final: 0.5129 (tptt) REVERT: Y 194 MET cc_start: 0.8211 (tpp) cc_final: 0.7612 (mmm) REVERT: Y 197 ILE cc_start: 0.8795 (mt) cc_final: 0.8585 (mt) REVERT: Y 405 LYS cc_start: 0.8257 (tptt) cc_final: 0.7770 (tttp) REVERT: Y 550 LYS cc_start: 0.5980 (mmtt) cc_final: 0.5717 (pptt) REVERT: Z 196 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8790 (mt) REVERT: Z 271 TYR cc_start: 0.8595 (t80) cc_final: 0.8374 (t80) REVERT: Z 502 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7508 (mmm) outliers start: 117 outliers final: 93 residues processed: 620 average time/residue: 0.4548 time to fit residues: 468.2898 Evaluate side-chains 611 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 509 time to evaluate : 3.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 154 GLN Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain S residue 262 ASN Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 222 LEU Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 389 ASP Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 535 ILE Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 147 THR Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 203 PHE Chi-restraints excluded: chain U residue 207 LYS Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 307 CYS Chi-restraints excluded: chain U residue 371 GLU Chi-restraints excluded: chain U residue 390 VAL Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 485 LYS Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 224 ILE Chi-restraints excluded: chain V residue 226 ASP Chi-restraints excluded: chain V residue 359 SER Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 484 MET Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 251 MET Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 353 THR Chi-restraints excluded: chain Y residue 449 VAL Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 539 ILE Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 196 LEU Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 341 VAL Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 564 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 260 optimal weight: 4.9990 chunk 419 optimal weight: 0.9990 chunk 256 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 291 optimal weight: 0.0570 chunk 440 optimal weight: 4.9990 chunk 405 optimal weight: 8.9990 chunk 350 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 270 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 94 ASN G 98 GLN Q 49 GLN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 195 ASN S 262 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 ASN ** U 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN Y 388 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3530 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= 0.166 Angle : 0.561 11.448 46638 Z= 0.281 Chirality : 0.042 0.154 5519 Planarity : 0.004 0.044 5997 Dihedral : 5.702 84.826 4922 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.37 % Favored : 95.56 % Rotamer: Outliers : 3.09 % Allowed : 25.00 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.13), residues: 4461 helix: 0.05 (0.12), residues: 2112 sheet: -0.75 (0.23), residues: 541 loop : -0.86 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 73 HIS 0.004 0.001 HIS U 61 PHE 0.027 0.001 PHE V 489 TYR 0.022 0.001 TYR V 312 ARG 0.009 0.000 ARG T 418 ********************** 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 621 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 511 time to evaluate : 4.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 105 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.5682 (mm) REVERT: H 61 MET cc_start: 0.7589 (mmt) cc_final: 0.7125 (mmt) REVERT: J 81 MET cc_start: 0.8142 (tmm) cc_final: 0.7813 (tmm) REVERT: P 50 SER cc_start: 0.7753 (p) cc_final: 0.7350 (m) REVERT: P 77 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7835 (t80) REVERT: P 79 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7746 (mm-30) REVERT: R 31 LYS cc_start: 0.6962 (tmmt) cc_final: 0.6198 (mtmm) REVERT: R 32 GLU cc_start: 0.7720 (tm-30) cc_final: 0.6515 (tt0) REVERT: R 177 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6107 (mt-10) REVERT: S 68 MET cc_start: 0.8415 (ttp) cc_final: 0.8192 (ttp) REVERT: S 124 ARG cc_start: 0.8032 (ptm160) cc_final: 0.7311 (ttp80) REVERT: S 274 MET cc_start: 0.7644 (mmm) cc_final: 0.7394 (mtt) REVERT: T 439 MET cc_start: 0.8253 (tpp) cc_final: 0.7693 (tpp) REVERT: T 509 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7482 (mm) REVERT: U 112 ASP cc_start: 0.7692 (t0) cc_final: 0.7358 (t0) REVERT: U 203 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6030 (m-80) REVERT: U 210 ASP cc_start: 0.7697 (m-30) cc_final: 0.7243 (m-30) REVERT: U 260 VAL cc_start: 0.9174 (t) cc_final: 0.8892 (m) REVERT: U 371 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7284 (pm20) REVERT: U 511 LYS cc_start: 0.7743 (tttt) cc_final: 0.7011 (mmtp) REVERT: V 98 TYR cc_start: 0.8240 (t80) cc_final: 0.7926 (t80) REVERT: V 316 THR cc_start: 0.7100 (p) cc_final: 0.6849 (p) REVERT: V 384 GLU cc_start: 0.6892 (tm-30) cc_final: 0.6537 (pp20) REVERT: V 476 ARG cc_start: 0.7795 (tpp80) cc_final: 0.7549 (tpp80) REVERT: V 551 LYS cc_start: 0.7754 (tttp) cc_final: 0.7127 (mttt) REVERT: X 56 LEU cc_start: 0.8805 (mp) cc_final: 0.8533 (mp) REVERT: X 270 GLU cc_start: 0.8108 (mp0) cc_final: 0.7808 (mp0) REVERT: X 304 ILE cc_start: 0.8890 (mp) cc_final: 0.8598 (mm) REVERT: X 401 ARG cc_start: 0.8378 (mmt-90) cc_final: 0.8035 (tpp-160) REVERT: X 456 THR cc_start: 0.8532 (m) cc_final: 0.8049 (p) REVERT: X 502 MET cc_start: 0.6666 (ptp) cc_final: 0.6343 (ptp) REVERT: X 573 LYS cc_start: 0.5791 (ttmt) cc_final: 0.5154 (tptt) REVERT: Y 194 MET cc_start: 0.8292 (tpp) cc_final: 0.7657 (mmm) REVERT: Y 405 LYS cc_start: 0.8264 (tptt) cc_final: 0.7762 (tttp) REVERT: Y 550 LYS cc_start: 0.5934 (mmtt) cc_final: 0.5716 (pptt) REVERT: Z 196 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8799 (mt) REVERT: Z 271 TYR cc_start: 0.8487 (t80) cc_final: 0.8276 (t80) REVERT: Z 502 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7557 (mmm) outliers start: 110 outliers final: 94 residues processed: 589 average time/residue: 0.4448 time to fit residues: 440.9978 Evaluate side-chains 607 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 505 time to evaluate : 3.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 195 ASN Chi-restraints excluded: chain S residue 262 ASN Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 222 LEU Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 442 VAL 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 U residue 127 VAL Chi-restraints excluded: chain U residue 147 THR Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 203 PHE Chi-restraints excluded: chain U residue 207 LYS Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 307 CYS Chi-restraints excluded: chain U residue 371 GLU Chi-restraints excluded: chain U residue 390 VAL Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 485 LYS Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 226 ASP Chi-restraints excluded: chain V residue 359 SER Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 484 MET Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 251 MET Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 353 THR Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 449 VAL Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Z residue 196 LEU Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 341 VAL Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 533 GLU Chi-restraints excluded: chain Z residue 564 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 278 optimal weight: 5.9990 chunk 373 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 323 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 351 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 360 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 94 ASN G 98 GLN S 195 ASN S 262 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 ASN ** U 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN Y 388 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116423 restraints weight = 58340.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118757 restraints weight = 33805.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.119242 restraints weight = 22757.527| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34412 Z= 0.213 Angle : 0.579 11.009 46638 Z= 0.290 Chirality : 0.043 0.158 5519 Planarity : 0.004 0.044 5997 Dihedral : 5.788 85.597 4922 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.75 % Favored : 95.16 % Rotamer: Outliers : 3.37 % Allowed : 24.58 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), residues: 4461 helix: -0.02 (0.12), residues: 2124 sheet: -0.79 (0.23), residues: 548 loop : -0.86 (0.15), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP V 73 HIS 0.004 0.001 HIS T 358 PHE 0.033 0.002 PHE V 459 TYR 0.023 0.001 TYR R 188 ARG 0.008 0.000 ARG T 418 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8557.15 seconds wall clock time: 156 minutes 36.89 seconds (9396.89 seconds total)