Starting phenix.real_space_refine on Mon Apr 15 04:46:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6red_4850/04_2024/6red_4850_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6red_4850/04_2024/6red_4850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6red_4850/04_2024/6red_4850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6red_4850/04_2024/6red_4850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6red_4850/04_2024/6red_4850_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6red_4850/04_2024/6red_4850_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 116 5.16 5 C 21545 2.51 5 N 5796 2.21 5 O 6424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 91": "NH1" <-> "NH2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "G PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "P PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 111": "OD1" <-> "OD2" Residue "P ASP 127": "OD1" <-> "OD2" Residue "P GLU 143": "OE1" <-> "OE2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 25": "OD1" <-> "OD2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 54": "OD1" <-> "OD2" Residue "Q GLU 66": "OE1" <-> "OE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 62": "OE1" <-> "OE2" Residue "R PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 174": "OD1" <-> "OD2" Residue "R PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 83": "OD1" <-> "OD2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S GLU 133": "OE1" <-> "OE2" Residue "S ASP 144": "OD1" <-> "OD2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ARG 96": "NH1" <-> "NH2" Residue "T ASP 112": "OD1" <-> "OD2" Residue "T TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ASP 172": "OD1" <-> "OD2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 226": "OD1" <-> "OD2" Residue "T TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 325": "OD1" <-> "OD2" Residue "T PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 389": "OD1" <-> "OD2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 418": "NH1" <-> "NH2" Residue "T ARG 429": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 475": "OE1" <-> "OE2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 495": "OE1" <-> "OE2" Residue "T ASP 516": "OD1" <-> "OD2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ASP 46": "OD1" <-> "OD2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 72": "OE1" <-> "OE2" Residue "U TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 135": "OD1" <-> "OD2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U ASP 326": "OD1" <-> "OD2" Residue "U ARG 342": "NH1" <-> "NH2" Residue "U ARG 343": "NH1" <-> "NH2" Residue "U ARG 364": "NH1" <-> "NH2" Residue "U PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 389": "OD1" <-> "OD2" Residue "U GLU 409": "OE1" <-> "OE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U GLU 455": "OE1" <-> "OE2" Residue "U PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 510": "OD1" <-> "OD2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U ASP 516": "OD1" <-> "OD2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 142": "OD1" <-> "OD2" Residue "V TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V TYR 256": "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 360": "NH1" <-> "NH2" Residue "V PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 403": "OD1" <-> "OD2" Residue "V GLU 409": "OE1" <-> "OE2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V GLU 455": "OE1" <-> "OE2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 467": "OD1" <-> "OD2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V ASP 516": "OD1" <-> "OD2" Residue "V ASP 547": "OD1" <-> "OD2" Residue "V GLU 553": "OE1" <-> "OE2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X ASP 36": "OD1" <-> "OD2" Residue "X TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 71": "NH1" <-> "NH2" Residue "X ASP 82": "OD1" <-> "OD2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X ASP 94": "OD1" <-> "OD2" Residue "X ASP 104": "OD1" <-> "OD2" Residue "X ARG 115": "NH1" <-> "NH2" Residue "X ARG 120": "NH1" <-> "NH2" Residue "X ASP 139": "OD1" <-> "OD2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 168": "OD1" <-> "OD2" Residue "X TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 215": "OE1" <-> "OE2" Residue "X ARG 258": "NH1" <-> "NH2" Residue "X GLU 270": "OE1" <-> "OE2" Residue "X TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 348": "OD1" <-> "OD2" Residue "X ASP 359": "OD1" <-> "OD2" Residue "X ARG 366": "NH1" <-> "NH2" Residue "X TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X ASP 423": "OD1" <-> "OD2" Residue "X GLU 451": "OE1" <-> "OE2" Residue "X PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 479": "OD1" <-> "OD2" Residue "X ASP 480": "OD1" <-> "OD2" Residue "X TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 505": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X GLU 536": "OE1" <-> "OE2" Residue "X GLU 541": "OE1" <-> "OE2" Residue "X ASP 542": "OD1" <-> "OD2" Residue "X GLU 546": "OE1" <-> "OE2" Residue "X GLU 557": "OE1" <-> "OE2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y GLU 55": "OE1" <-> "OE2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y ASP 82": "OD1" <-> "OD2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ASP 94": "OD1" <-> "OD2" Residue "Y ARG 98": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y ASP 136": "OD1" <-> "OD2" Residue "Y GLU 149": "OE1" <-> "OE2" Residue "Y PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 216": "NH1" <-> "NH2" Residue "Y GLU 226": "OE1" <-> "OE2" Residue "Y GLU 229": "OE1" <-> "OE2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y ASP 285": "OD1" <-> "OD2" Residue "Y ARG 289": "NH1" <-> "NH2" Residue "Y GLU 323": "OE1" <-> "OE2" Residue "Y ASP 345": "OD1" <-> "OD2" Residue "Y PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 378": "OD1" <-> "OD2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y ARG 401": "NH1" <-> "NH2" Residue "Y TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 435": "NH1" <-> "NH2" Residue "Y ARG 437": "NH1" <-> "NH2" Residue "Y PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 479": "OD1" <-> "OD2" Residue "Y PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 505": "OD1" <-> "OD2" Residue "Y ARG 509": "NH1" <-> "NH2" Residue "Y ASP 542": "OD1" <-> "OD2" Residue "Y ASP 548": "OD1" <-> "OD2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "Z ASP 91": "OD1" <-> "OD2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z ASP 136": "OD1" <-> "OD2" Residue "Z PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 218": "NH1" <-> "NH2" Residue "Z GLU 219": "OE1" <-> "OE2" Residue "Z ARG 225": "NH1" <-> "NH2" Residue "Z GLU 226": "OE1" <-> "OE2" Residue "Z ARG 239": "NH1" <-> "NH2" Residue "Z TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 253": "OE1" <-> "OE2" Residue "Z GLU 296": "OE1" <-> "OE2" Residue "Z TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 378": "OD1" <-> "OD2" Residue "Z ASP 381": "OD1" <-> "OD2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z GLU 428": "OE1" <-> "OE2" Residue "Z PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z ASP 548": "OD1" <-> "OD2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 552": "OE1" <-> "OE2" Residue "Z GLU 557": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 33899 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: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} 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: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.20, per 1000 atoms: 0.51 Number of scatterers: 33899 At special positions: 0 Unit cell: (164.16, 135, 209.52, 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 6424 8.00 N 5796 7.00 C 21545 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: 13.54 Conformation dependent library (CDL) restraints added in 6.2 seconds 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8162 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 169 helices and 28 sheets defined 47.2% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.68 Creating SS restraints... Processing helix chain 'A' and resid 55 through 91 removed outlier: 4.337A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 118 removed outlier: 3.790A pdb=" N ALA A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYS A 97 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 112 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.756A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 125 removed outlier: 5.771A pdb=" N LYS B 97 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 110 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B 119 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 120 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL B 121 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 124 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 125 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 91 removed outlier: 4.409A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 126 removed outlier: 3.890A pdb=" N ALA C 96 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LYS C 97 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 111 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER C 112 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 119 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE C 124 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU C 125 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE C 126 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 91 removed outlier: 4.220A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 125 removed outlier: 3.585A pdb=" N ALA D 96 " --> pdb=" O PRO D 93 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LYS D 97 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 105 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 91 removed outlier: 4.458A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 125 removed outlier: 3.823A pdb=" N ALA E 96 " --> pdb=" O PRO E 93 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LYS E 97 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA E 108 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N GLU E 111 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER E 112 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU E 118 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU E 125 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 91 removed outlier: 4.042A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 125 removed outlier: 3.540A pdb=" N ALA F 96 " --> pdb=" O PRO F 93 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL F 100 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU F 104 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU F 111 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE F 113 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER F 117 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU F 118 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU F 125 " --> pdb=" O PHE F 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 91 removed outlier: 3.985A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 125 removed outlier: 3.710A pdb=" N ALA G 96 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU G 104 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU G 109 " --> pdb=" O GLY G 106 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU G 111 " --> pdb=" O ALA G 108 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU G 115 " --> pdb=" O SER G 112 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU G 125 " --> pdb=" O PHE G 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 65 removed outlier: 3.953A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 91 removed outlier: 3.538A pdb=" N GLY H 73 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY H 77 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY H 88 " --> pdb=" O LEU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 125 removed outlier: 5.583A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU H 119 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE H 124 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU H 125 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 91 removed outlier: 3.539A pdb=" N GLY I 65 " --> pdb=" O MET I 61 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ALA I 70 " --> pdb=" O CYS I 66 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA I 72 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 126 removed outlier: 3.667A pdb=" N ALA I 96 " --> pdb=" O PRO I 93 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LYS I 97 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU I 104 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER I 112 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU I 115 " --> pdb=" O SER I 112 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE I 124 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE I 126 " --> pdb=" O LEU I 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 91 removed outlier: 3.904A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS J 66 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 125 removed outlier: 4.663A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL J 120 " --> pdb=" O PHE J 116 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL J 121 " --> pdb=" O SER J 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 63 removed outlier: 3.581A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 83 removed outlier: 4.047A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 92 removed outlier: 3.997A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 108 removed outlier: 4.030A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 127 removed outlier: 3.901A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA P 124 " --> pdb=" O LYS P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 148 removed outlier: 3.767A pdb=" N LEU P 134 " --> pdb=" O LEU P 131 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU P 146 " --> pdb=" O GLU P 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 12 No H-bonds generated for 'chain 'Q' and resid 10 through 12' Processing helix chain 'Q' and resid 16 through 30 removed outlier: 4.271A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 39 removed outlier: 4.329A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 43 No H-bonds generated for 'chain 'Q' and resid 41 through 43' Processing helix chain 'R' and resid 30 through 40 removed outlier: 3.730A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 54 Processing helix chain 'R' and resid 152 through 154 No H-bonds generated for 'chain 'R' and resid 152 through 154' Processing helix chain 'R' and resid 157 through 167 removed outlier: 3.831A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 195 Processing helix chain 'S' and resid 42 through 70 removed outlier: 3.652A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 78 Processing helix chain 'S' and resid 81 through 88 removed outlier: 4.466A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 116 through 127 removed outlier: 3.787A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 150 removed outlier: 3.668A 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 239 through 312 removed outlier: 3.769A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 137 No H-bonds generated for 'chain 'T' and resid 135 through 137' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 207 through 211 Processing helix chain 'T' and resid 231 through 246 Processing helix chain 'T' and resid 266 through 279 removed outlier: 3.520A pdb=" N ALA T 270 " --> pdb=" O ARG T 266 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN T 271 " --> pdb=" O SER T 267 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 296 through 314 Proline residue: T 303 - end of helix removed outlier: 4.168A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 340 removed outlier: 3.777A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 347 through 349 No H-bonds generated for 'chain 'T' and resid 347 through 349' Processing helix chain 'T' and resid 352 through 362 removed outlier: 4.441A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER T 359 " --> pdb=" O TYR T 356 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 401 Processing helix chain 'T' and resid 411 through 414 No H-bonds generated for 'chain 'T' and resid 411 through 414' Processing helix chain 'T' and resid 431 through 434 removed outlier: 3.505A 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 455 removed outlier: 3.723A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL T 442 " --> pdb=" O GLY T 438 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY T 444 " --> pdb=" O LYS T 440 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR T 445 " --> pdb=" O GLN T 441 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) Processing helix chain 'T' and resid 459 through 461 No H-bonds generated for 'chain 'T' and resid 459 through 461' Processing helix chain 'T' and resid 471 through 483 Processing helix chain 'T' and resid 494 through 505 removed outlier: 3.635A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 523 through 527 Processing helix chain 'T' and resid 531 through 539 Processing helix chain 'T' and resid 544 through 555 removed outlier: 3.810A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG T 555 " --> pdb=" O LYS T 551 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 47 Processing helix chain 'U' and resid 59 through 76 removed outlier: 3.651A pdb=" N SER U 63 " --> pdb=" O ILE U 59 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix removed outlier: 3.592A pdb=" N GLU U 72 " --> pdb=" O PRO U 68 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP U 73 " --> pdb=" O ALA U 69 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LYS U 75 " --> pdb=" O LYS U 71 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER U 76 " --> pdb=" O GLU U 72 " (cutoff:3.500A) 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 211 Processing helix chain 'U' and resid 231 through 246 Processing helix chain 'U' and resid 266 through 278 Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 296 through 315 Proline residue: U 303 - end of helix removed outlier: 3.793A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG U 314 " --> pdb=" O ALA U 310 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 removed outlier: 3.659A pdb=" N SER U 331 " --> pdb=" O LEU U 327 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 347 through 349 No H-bonds generated for 'chain 'U' and resid 347 through 349' Processing helix chain 'U' and resid 352 through 364 removed outlier: 4.336A pdb=" N PHE U 355 " --> pdb=" O GLY U 352 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU U 357 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG U 360 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU U 363 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 370 through 372 No H-bonds generated for 'chain 'U' and resid 370 through 372' Processing helix chain 'U' and resid 393 through 401 Processing helix chain 'U' and resid 413 through 415 No H-bonds generated for 'chain 'U' and resid 413 through 415' Processing helix chain 'U' and resid 437 through 459 removed outlier: 3.590A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU U 449 " --> pdb=" O THR U 445 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL U 456 " --> pdb=" O GLN U 452 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA U 457 " --> pdb=" O TYR U 453 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA U 458 " --> pdb=" O ARG U 454 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N PHE U 459 " --> pdb=" O GLU U 455 " (cutoff:3.500A) Processing helix chain 'U' and resid 466 through 468 No H-bonds generated for 'chain 'U' and resid 466 through 468' Processing helix chain 'U' and resid 472 through 483 removed outlier: 4.107A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 500 Processing helix chain 'U' and resid 502 through 505 No H-bonds generated for 'chain 'U' and resid 502 through 505' Processing helix chain 'U' and resid 514 through 527 removed outlier: 4.167A pdb=" N ILE U 517 " --> pdb=" O VAL U 514 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL U 518 " --> pdb=" O GLN U 515 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA U 519 " --> pdb=" O ASP U 516 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU U 521 " --> pdb=" O VAL U 518 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER U 526 " --> pdb=" O ALA U 523 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN U 527 " --> pdb=" O VAL U 524 " (cutoff:3.500A) Processing helix chain 'U' and resid 531 through 539 removed outlier: 3.536A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 544 through 553 removed outlier: 3.899A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 47 No H-bonds generated for 'chain 'V' and resid 45 through 47' Processing helix chain 'V' and resid 59 through 66 Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 212 Processing helix chain 'V' and resid 231 through 246 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 281 through 283 No H-bonds generated for 'chain 'V' and resid 281 through 283' Processing helix chain 'V' and resid 296 through 315 Proline residue: V 303 - end of helix removed outlier: 4.385A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 340 Processing helix chain 'V' and resid 347 through 349 No H-bonds generated for 'chain 'V' and resid 347 through 349' Processing helix chain 'V' and resid 352 through 364 removed outlier: 4.362A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR V 356 " --> pdb=" O ASP V 353 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU V 363 " --> pdb=" O ARG V 360 " (cutoff:3.500A) removed outlier: 3.570A 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 399 Processing helix chain 'V' and resid 410 through 415 Processing helix chain 'V' and resid 439 through 456 removed outlier: 3.617A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL V 456 " --> pdb=" O GLN V 452 " (cutoff:3.500A) Processing helix chain 'V' and resid 471 through 484 removed outlier: 4.036A pdb=" N ARG V 479 " --> pdb=" O GLU V 475 " (cutoff:3.500A) Processing helix chain 'V' and resid 494 through 505 Processing helix chain 'V' and resid 514 through 527 removed outlier: 4.001A pdb=" N ILE V 517 " --> pdb=" O VAL V 514 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL V 518 " --> pdb=" O GLN V 515 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU V 521 " --> pdb=" O VAL V 518 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU V 522 " --> pdb=" O ALA V 519 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER V 526 " --> pdb=" O ALA V 523 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN V 527 " --> pdb=" O VAL V 524 " (cutoff:3.500A) Processing helix chain 'V' and resid 531 through 539 Processing helix chain 'V' and resid 546 through 554 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 167 through 170 No H-bonds generated for 'chain 'X' and resid 167 through 170' Processing helix chain 'X' and resid 189 through 200 Processing helix chain 'X' and resid 217 through 228 Processing helix chain 'X' and resid 236 through 241 removed outlier: 3.645A pdb=" N ARG X 239 " --> pdb=" O GLY X 236 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 255 through 258 No H-bonds generated for 'chain 'X' and resid 255 through 258' Processing helix chain 'X' and resid 261 through 274 Processing helix chain 'X' and resid 288 through 296 Processing helix chain 'X' and resid 314 through 324 removed outlier: 4.339A pdb=" N ARG X 324 " --> pdb=" O GLY X 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 342 through 344 No H-bonds generated for 'chain 'X' and resid 342 through 344' Processing helix chain 'X' and resid 349 through 354 removed outlier: 3.608A pdb=" N THR X 354 " --> pdb=" O ALA X 350 " (cutoff:3.500A) Processing helix chain 'X' and resid 366 through 371 removed outlier: 3.695A pdb=" N LEU X 371 " --> pdb=" O SER X 367 " (cutoff:3.500A) Processing helix chain 'X' and resid 394 through 420 removed outlier: 3.523A pdb=" N VAL X 399 " --> pdb=" O GLU X 395 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE X 419 " --> pdb=" O ASP X 415 " (cutoff:3.500A) Processing helix chain 'X' and resid 431 through 442 removed outlier: 3.593A pdb=" N ALA X 436 " --> pdb=" O THR X 432 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG X 441 " --> pdb=" O ARG X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 448 through 450 No H-bonds generated for 'chain 'X' and resid 448 through 450' Processing helix chain 'X' and resid 463 through 475 Processing helix chain 'X' and resid 483 through 486 removed outlier: 3.645A pdb=" N PHE X 486 " --> pdb=" O GLU X 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 483 through 486' Processing helix chain 'X' and resid 492 through 507 removed outlier: 3.825A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 532 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 203 Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 3.641A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 274 removed outlier: 5.091A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 300 Processing helix chain 'Y' and resid 314 through 322 removed outlier: 3.730A pdb=" N LEU Y 321 " --> pdb=" O ASP Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 342 through 344 No H-bonds generated for 'chain 'Y' and resid 342 through 344' Processing helix chain 'Y' and resid 349 through 356 removed outlier: 3.774A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 370 Processing helix chain 'Y' and resid 393 through 411 Processing helix chain 'Y' and resid 413 through 419 removed outlier: 3.790A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 428 through 442 removed outlier: 4.616A pdb=" N VAL Y 433 " --> pdb=" O ASP Y 429 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS Y 438 " --> pdb=" O ALA Y 434 " (cutoff:3.500A) Processing helix chain 'Y' and resid 463 through 475 removed outlier: 3.959A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 492 through 507 removed outlier: 3.742A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU Y 497 " --> pdb=" O LYS Y 493 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP Y 505 " --> pdb=" O LYS Y 501 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ILE Y 506 " --> pdb=" O MET Y 502 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA Y 507 " --> pdb=" O ALA Y 503 " (cutoff:3.500A) Processing helix chain 'Y' and resid 519 through 521 No H-bonds generated for 'chain 'Y' and resid 519 through 521' Processing helix chain 'Y' and resid 545 through 553 removed outlier: 4.175A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU Y 552 " --> pdb=" O ASP Y 548 " (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 150 through 152 No H-bonds generated for 'chain 'Z' and resid 150 through 152' Processing helix chain 'Z' and resid 165 through 170 Processing helix chain 'Z' and resid 191 through 200 Processing helix chain 'Z' and resid 217 through 228 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 4.705A 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 removed outlier: 3.587A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 288 through 298 Processing helix chain 'Z' and resid 314 through 324 removed outlier: 4.414A pdb=" N ARG Z 324 " --> pdb=" O GLY Z 320 " (cutoff:3.500A) Processing helix chain 'Z' and resid 349 through 357 removed outlier: 3.602A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA Z 356 " --> pdb=" O ALA Z 352 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N HIS Z 357 " --> pdb=" O THR Z 353 " (cutoff:3.500A) Processing helix chain 'Z' and resid 366 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: 3.620A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU Z 413 " --> pdb=" O ASP Z 409 " (cutoff:3.500A) Processing helix chain 'Z' and resid 416 through 419 No H-bonds generated for 'chain 'Z' and resid 416 through 419' Processing helix chain 'Z' and resid 422 through 424 No H-bonds generated for 'chain 'Z' and resid 422 through 424' Processing helix chain 'Z' and resid 430 through 441 removed outlier: 3.506A pdb=" N ARG Z 441 " --> pdb=" O ARG Z 437 " (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: 3.690A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 483 through 486 Processing helix chain 'Z' and resid 492 through 499 removed outlier: 3.641A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) Processing helix chain 'Z' and resid 501 through 510 removed outlier: 3.579A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG Z 509 " --> pdb=" O ASP Z 505 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYS Z 510 " --> pdb=" O ILE Z 506 " (cutoff:3.500A) Processing helix chain 'Z' and resid 528 through 532 Processing sheet with id= A, first strand: chain 'Q' and resid 45 through 49 Processing sheet with id= B, first strand: chain 'R' and resid 72 through 75 removed outlier: 6.987A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE R 144 " --> pdb=" O TYR R 75 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'R' and resid 96 through 100 removed outlier: 3.620A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY R 114 " --> pdb=" O VAL R 129 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 203 through 211 removed outlier: 5.205A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.584A 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: 6.608A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN T 121 " --> pdb=" O GLY T 128 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'T' and resid 152 through 155 Processing sheet with id= G, first strand: chain 'T' and resid 404 through 408 removed outlier: 3.548A pdb=" N LEU T 222 " --> pdb=" O GLY T 404 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'T' and resid 376 through 381 Processing sheet with id= I, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.574A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'U' and resid 109 through 111 Processing sheet with id= K, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= L, first strand: chain 'U' and resid 404 through 408 Processing sheet with id= M, first strand: chain 'U' and resid 285 through 290 removed outlier: 8.732A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE U 380 " --> pdb=" O TYR U 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'V' and resid 84 through 86 removed outlier: 6.457A pdb=" N GLY V 128 " --> pdb=" O LEU V 120 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU V 122 " --> pdb=" O HIS V 126 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N HIS V 126 " --> pdb=" O LEU V 122 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N TYR V 98 " --> pdb=" O VAL V 87 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL V 87 " --> pdb=" O TYR V 98 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= P, first strand: chain 'V' and resid 404 through 408 Processing sheet with id= Q, first strand: chain 'V' and resid 285 through 290 removed outlier: 8.740A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N PHE V 380 " --> pdb=" O TYR V 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'X' and resid 38 through 44 removed outlier: 6.298A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'X' and resid 158 through 160 removed outlier: 4.772A pdb=" N GLU X 158 " --> pdb=" O ARG X 175 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR X 173 " --> pdb=" O LEU X 160 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'X' and resid 360 through 363 removed outlier: 7.629A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N GLY X 183 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL X 339 " --> pdb=" O GLY X 183 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N PHE X 207 " --> pdb=" O LEU X 281 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N PHE X 283 " --> pdb=" O PHE X 207 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL X 209 " --> pdb=" O PHE X 283 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ASP X 285 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ALA X 211 " --> pdb=" O ASP X 285 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= V, first strand: chain 'Y' and resid 39 through 44 removed outlier: 6.283A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Y' and resid 110 through 113 Processing sheet with id= X, first strand: chain 'Y' and resid 244 through 250 removed outlier: 6.624A pdb=" N SER Y 208 " --> pdb=" O THR Y 245 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL Y 247 " --> pdb=" O SER Y 208 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE Y 210 " --> pdb=" O VAL Y 247 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLY Y 249 " --> pdb=" O PHE Y 210 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLY Y 212 " --> pdb=" O GLY Y 249 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N VAL Y 209 " --> pdb=" O ASP Y 279 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU Y 281 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ALA Y 211 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE Y 283 " --> pdb=" O ALA Y 211 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL Y 213 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 213 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU Y 215 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER Y 332 " --> pdb=" O VAL Y 280 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU Y 282 " --> pdb=" O SER Y 332 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR Y 334 " --> pdb=" O LEU Y 282 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL Y 284 " --> pdb=" O THR Y 334 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL Y 336 " --> pdb=" O VAL Y 284 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLY Y 180 " --> pdb=" O ASP Y 359 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR Y 361 " --> pdb=" O GLY Y 180 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N PHE Y 182 " --> pdb=" O THR Y 361 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL Y 363 " --> pdb=" O PHE Y 182 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Z' and resid 37 through 39 removed outlier: 6.480A pdb=" N ARG Z 86 " --> pdb=" O ALA Z 77 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N HIS Z 79 " --> pdb=" O THR Z 84 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR Z 84 " --> pdb=" O HIS Z 79 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG Z 51 " --> pdb=" O VAL Z 40 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL Z 40 " --> pdb=" O ARG Z 51 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Z' and resid 110 through 113 removed outlier: 3.558A pdb=" N ASP Z 139 " --> pdb=" O VAL Z 113 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Z' and resid 360 through 363 removed outlier: 7.216A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N GLY Z 183 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL Z 339 " --> pdb=" O GLY Z 183 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N PHE Z 207 " --> pdb=" O LEU Z 281 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N PHE Z 283 " --> pdb=" O PHE Z 207 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL Z 209 " --> pdb=" O PHE Z 283 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASP Z 285 " --> pdb=" O VAL Z 209 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA Z 211 " --> pdb=" O ASP Z 285 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Z' and resid 559 through 561 1426 hydrogen bonds defined for protein. 3432 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.77 Time building geometry restraints manager: 14.59 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: 8626 1.33 - 1.45: 5919 1.45 - 1.57: 19654 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34420 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.84e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.74e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.54e+01 bond pdb=" C5 ATP V1001 " pdb=" N7 ATP V1001 " ideal model delta sigma weight residual 1.387 1.326 0.061 1.00e-02 1.00e+04 3.67e+01 bond pdb=" C5 ATP T1001 " pdb=" N7 ATP T1001 " ideal model delta sigma weight residual 1.387 1.331 0.056 1.00e-02 1.00e+04 3.14e+01 ... (remaining 34415 not shown) Histogram of bond angle deviations from ideal: 97.04 - 104.83: 582 104.83 - 112.61: 18135 112.61 - 120.40: 15573 120.40 - 128.19: 12191 128.19 - 135.97: 168 Bond angle restraints: 46649 Sorted by residual: angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 122.20 17.67 1.00e+00 1.00e+00 3.12e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 122.55 17.32 1.00e+00 1.00e+00 3.00e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 124.31 15.56 1.00e+00 1.00e+00 2.42e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 123.78 13.05 1.00e+00 1.00e+00 1.70e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 125.03 11.80 1.00e+00 1.00e+00 1.39e+02 ... (remaining 46644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.25: 20149 30.25 - 60.49: 628 60.49 - 90.74: 47 90.74 - 120.98: 0 120.98 - 151.23: 4 Dihedral angle restraints: 20828 sinusoidal: 8068 harmonic: 12760 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 -122.78 -57.22 0 5.00e+00 4.00e-02 1.31e+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 -133.09 -46.91 0 5.00e+00 4.00e-02 8.80e+01 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual -180.00 -134.41 -45.59 0 5.00e+00 4.00e-02 8.31e+01 ... (remaining 20825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4352 0.076 - 0.152: 1053 0.152 - 0.228: 101 0.228 - 0.304: 11 0.304 - 0.380: 3 Chirality restraints: 5520 Sorted by residual: chirality pdb=" CB VAL V 180 " pdb=" CA VAL V 180 " pdb=" CG1 VAL V 180 " pdb=" CG2 VAL V 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CB ILE Y 524 " pdb=" CA ILE Y 524 " pdb=" CG1 ILE Y 524 " pdb=" CG2 ILE Y 524 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CG LEU U 202 " pdb=" CB LEU U 202 " pdb=" CD1 LEU U 202 " pdb=" CD2 LEU U 202 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 5517 not shown) Planarity restraints: 5999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 6.22e-02 3.86e+01 pdb=" C ALA Z 503 " -0.108 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.040 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA X 503 " -0.030 2.00e-02 2.50e+03 5.78e-02 3.34e+01 pdb=" C ALA X 503 " 0.100 2.00e-02 2.50e+03 pdb=" O ALA X 503 " -0.037 2.00e-02 2.50e+03 pdb=" N LYS X 504 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL Z 341 " -0.057 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO Z 342 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO Z 342 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO Z 342 " -0.047 5.00e-02 4.00e+02 ... (remaining 5996 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1098 2.69 - 3.24: 32767 3.24 - 3.80: 56790 3.80 - 4.35: 77106 4.35 - 4.90: 126609 Nonbonded interactions: 294370 Sorted by model distance: nonbonded pdb=" OG1 THR X 190 " pdb="MG MG X 602 " model vdw 2.140 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.197 2.170 nonbonded pdb=" O3G ATP U1001 " pdb="MG MG U1002 " model vdw 2.217 2.170 nonbonded pdb=" OG SER Q 15 " pdb=" OE1 GLU S 248 " model vdw 2.243 2.440 nonbonded pdb=" OG SER X 295 " pdb=" OE1 GLN X 311 " model vdw 2.268 2.440 ... (remaining 294365 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 36 through 556) selection = chain 'Y' selection = (chain 'Z' and resid 36 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 25.220 Check model and map are aligned: 0.450 Set scattering table: 0.270 Process input model: 89.320 Find NCS groups from input model: 2.530 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0191 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 : 0.012 0.121 34420 Z= 0.784 Angle : 1.043 17.672 46649 Z= 0.595 Chirality : 0.064 0.380 5520 Planarity : 0.008 0.086 5999 Dihedral : 14.607 151.228 12666 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.73 % Favored : 95.16 % Rotamer: Outliers : 0.31 % Allowed : 6.82 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.10), residues: 4462 helix: -3.03 (0.08), residues: 2162 sheet: -1.38 (0.21), residues: 547 loop : -2.04 (0.13), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP Y 141 HIS 0.011 0.002 HIS R 104 PHE 0.034 0.003 PHE R 74 TYR 0.024 0.003 TYR Q 52 ARG 0.007 0.001 ARG T 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 323 time to evaluate : 3.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 MET cc_start: -0.1054 (mmt) cc_final: -0.1572 (mtt) REVERT: G 99 LEU cc_start: 0.3804 (mt) cc_final: 0.3229 (mt) REVERT: S 183 ILE cc_start: -0.0113 (OUTLIER) cc_final: -0.0875 (mp) REVERT: T 367 LYS cc_start: 0.1617 (tptp) cc_final: 0.0687 (tttp) REVERT: T 501 VAL cc_start: -0.0756 (t) cc_final: -0.1086 (p) REVERT: U 118 MET cc_start: 0.1813 (ttt) cc_final: 0.0978 (mtt) REVERT: V 408 LEU cc_start: 0.2177 (mt) cc_final: 0.1179 (mp) REVERT: Y 52 PHE cc_start: 0.2508 (m-80) cc_final: 0.0540 (t80) REVERT: Y 64 GLU cc_start: 0.0628 (mm-30) cc_final: 0.0183 (mt-10) REVERT: Y 207 PHE cc_start: 0.2325 (m-80) cc_final: 0.1374 (m-80) REVERT: Y 386 MET cc_start: 0.2348 (mmp) cc_final: -0.1212 (mmm) REVERT: Y 422 MET cc_start: -0.2470 (ttt) cc_final: -0.3081 (mpp) REVERT: Z 80 MET cc_start: -0.0173 (mmm) cc_final: -0.0542 (ttt) REVERT: Z 251 MET cc_start: -0.1408 (ptp) cc_final: -0.1834 (mtt) REVERT: Z 411 LYS cc_start: 0.1479 (ttpt) cc_final: 0.0881 (tmtm) REVERT: Z 424 GLU cc_start: 0.3631 (pp20) cc_final: 0.2848 (tt0) REVERT: Z 486 PHE cc_start: 0.2418 (m-80) cc_final: 0.1585 (m-80) REVERT: Z 502 MET cc_start: 0.0073 (mtp) cc_final: -0.1533 (tpt) outliers start: 11 outliers final: 3 residues processed: 334 average time/residue: 1.2590 time to fit residues: 521.0053 Evaluate side-chains 209 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 205 time to evaluate : 3.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain V residue 137 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 0.9990 chunk 335 optimal weight: 0.9990 chunk 185 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 225 optimal weight: 0.0770 chunk 178 optimal weight: 3.9990 chunk 346 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 257 optimal weight: 0.6980 chunk 401 optimal weight: 4.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN C 87 ASN E 94 ASN E 98 GLN F 98 GLN G 92 ASN G 94 ASN G 98 GLN P 52 GLN Q 46 HIS R 38 ASN R 53 ASN R 66 HIS R 73 ASN R 83 GLN R 85 GLN R 154 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 98 ASN S 116 ASN S 174 GLN ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN T 241 HIS T 386 GLN T 435 GLN U 123 GLN U 319 HIS U 386 GLN U 435 GLN ** V 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 139 HIS ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 244 ASN V 278 GLN V 435 GLN V 452 GLN V 486 GLN V 497 GLN X 241 ASN X 322 GLN X 390 ASN X 398 ASN Y 199 ASN Y 278 GLN Y 286 ASN Y 294 ASN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 398 ASN Y 404 GLN Y 414 GLN Z 42 GLN Z 199 ASN Z 337 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0599 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 34420 Z= 0.177 Angle : 0.606 10.766 46649 Z= 0.311 Chirality : 0.043 0.401 5520 Planarity : 0.005 0.054 5999 Dihedral : 7.384 156.925 4925 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.38 % Favored : 96.46 % Rotamer: Outliers : 1.85 % Allowed : 11.30 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.12), residues: 4462 helix: -1.41 (0.10), residues: 2129 sheet: -0.86 (0.22), residues: 534 loop : -1.40 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 141 HIS 0.005 0.001 HIS T 139 PHE 0.025 0.002 PHE E 122 TYR 0.017 0.001 TYR Z 340 ARG 0.007 0.001 ARG Z 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 225 time to evaluate : 3.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: -0.0656 (mmt) cc_final: -0.1449 (pmm) REVERT: B 81 MET cc_start: 0.2216 (tmm) cc_final: 0.1268 (mtp) REVERT: C 61 MET cc_start: -0.1243 (mmt) cc_final: -0.1738 (mtt) REVERT: E 95 ILE cc_start: 0.2036 (mm) cc_final: 0.0223 (tp) REVERT: S 223 VAL cc_start: 0.0068 (OUTLIER) cc_final: -0.0356 (t) REVERT: T 138 ILE cc_start: 0.0436 (mt) cc_final: 0.0211 (mt) REVERT: T 313 PHE cc_start: 0.3370 (m-10) cc_final: 0.2852 (m-10) REVERT: T 488 GLN cc_start: 0.4039 (OUTLIER) cc_final: 0.3013 (tp40) REVERT: U 118 MET cc_start: 0.2139 (ttt) cc_final: 0.1471 (mtt) REVERT: U 282 MET cc_start: -0.1324 (mmt) cc_final: -0.1729 (ptm) REVERT: V 241 HIS cc_start: 0.0488 (t70) cc_final: 0.0045 (t70) REVERT: V 321 LEU cc_start: 0.3011 (OUTLIER) cc_final: 0.1472 (mp) REVERT: X 422 MET cc_start: 0.1212 (pp-130) cc_final: -0.0091 (ptt) REVERT: Y 52 PHE cc_start: 0.2387 (m-80) cc_final: 0.0759 (t80) REVERT: Y 207 PHE cc_start: 0.3695 (m-80) cc_final: 0.2165 (m-80) REVERT: Y 246 LEU cc_start: 0.1690 (OUTLIER) cc_final: 0.1099 (mt) REVERT: Y 286 ASN cc_start: 0.0404 (OUTLIER) cc_final: -0.0844 (t0) REVERT: Y 386 MET cc_start: 0.2620 (mmp) cc_final: 0.0559 (mmp) REVERT: Y 422 MET cc_start: -0.2165 (ttt) cc_final: -0.3052 (mpt) REVERT: Z 224 TYR cc_start: 0.2257 (t80) cc_final: 0.1017 (t80) REVERT: Z 251 MET cc_start: 0.0088 (ptp) cc_final: -0.0204 (mmt) REVERT: Z 422 MET cc_start: 0.0238 (tpp) cc_final: -0.0208 (tpp) REVERT: Z 424 GLU cc_start: 0.4236 (pp20) cc_final: 0.2247 (tm-30) REVERT: Z 486 PHE cc_start: 0.2836 (m-80) cc_final: 0.2200 (m-80) REVERT: Z 502 MET cc_start: -0.0020 (mtp) cc_final: -0.1629 (tpt) outliers start: 66 outliers final: 27 residues processed: 269 average time/residue: 1.2023 time to fit residues: 407.3443 Evaluate side-chains 222 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 3.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain H residue 98 GLN Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 118 MET Chi-restraints excluded: chain T residue 165 ASP Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 488 GLN Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 321 LEU Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 251 MET Chi-restraints excluded: chain Y residue 246 LEU Chi-restraints excluded: chain Y residue 286 ASN Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 454 THR Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 223 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 334 optimal weight: 0.0270 chunk 273 optimal weight: 0.0570 chunk 110 optimal weight: 20.0000 chunk 402 optimal weight: 7.9990 chunk 434 optimal weight: 6.9990 chunk 358 optimal weight: 0.9990 chunk 398 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 322 optimal weight: 7.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 ASN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN P 71 GLN P 76 GLN S 52 ASN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 72 GLN ** S 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 104 GLN ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 264 GLN ** U 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 497 GLN V 121 ASN V 123 GLN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 397 ASN X 42 GLN X 294 ASN ** X 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 294 ASN ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 396 HIS Z 42 GLN ** Z 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 292 GLN Z 337 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1266 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 34420 Z= 0.254 Angle : 0.725 12.935 46649 Z= 0.373 Chirality : 0.047 0.286 5520 Planarity : 0.006 0.071 5999 Dihedral : 7.293 172.197 4921 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.42 % Favored : 95.45 % Rotamer: Outliers : 3.23 % Allowed : 13.41 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.12), residues: 4462 helix: -1.15 (0.11), residues: 2087 sheet: -0.86 (0.22), residues: 529 loop : -1.30 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Y 141 HIS 0.011 0.002 HIS T 139 PHE 0.036 0.002 PHE U 380 TYR 0.028 0.002 TYR T 284 ARG 0.014 0.001 ARG I 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 244 time to evaluate : 3.452 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: C 61 MET cc_start: -0.0284 (mmt) cc_final: -0.1054 (mmp) REVERT: G 61 MET cc_start: 0.1059 (mmt) cc_final: 0.0742 (mmp) REVERT: S 118 ASN cc_start: 0.3263 (m-40) cc_final: 0.2888 (p0) REVERT: S 223 VAL cc_start: -0.0321 (OUTLIER) cc_final: -0.0626 (t) REVERT: S 259 MET cc_start: 0.2835 (mmt) cc_final: 0.1496 (tmt) REVERT: T 159 THR cc_start: 0.0152 (OUTLIER) cc_final: -0.1063 (m) REVERT: T 483 MET cc_start: 0.1186 (pp-130) cc_final: 0.0025 (tpt) REVERT: U 118 MET cc_start: 0.2261 (ttt) cc_final: 0.1650 (mtt) REVERT: U 394 ILE cc_start: 0.2783 (mm) cc_final: 0.2338 (mm) REVERT: V 241 HIS cc_start: 0.1211 (t70) cc_final: 0.0720 (t70) REVERT: V 475 GLU cc_start: -0.0138 (OUTLIER) cc_final: -0.0520 (mm-30) REVERT: X 251 MET cc_start: 0.1266 (mtp) cc_final: 0.0895 (mtm) REVERT: X 422 MET cc_start: 0.1375 (pp-130) cc_final: 0.0081 (ptt) REVERT: Y 52 PHE cc_start: 0.3328 (m-80) cc_final: 0.1174 (t80) REVERT: Y 286 ASN cc_start: -0.0706 (OUTLIER) cc_final: -0.1268 (t0) REVERT: Y 422 MET cc_start: -0.2136 (ttt) cc_final: -0.3873 (mpt) REVERT: Y 536 GLU cc_start: 0.3209 (pm20) cc_final: 0.2927 (pm20) REVERT: Y 550 LYS cc_start: 0.3037 (OUTLIER) cc_final: 0.1897 (mttp) REVERT: Z 91 ASP cc_start: 0.2145 (OUTLIER) cc_final: 0.1209 (t70) REVERT: Z 224 TYR cc_start: 0.3170 (t80) cc_final: 0.1575 (t80) REVERT: Z 414 GLN cc_start: -0.0320 (OUTLIER) cc_final: -0.0704 (pt0) REVERT: Z 422 MET cc_start: 0.0827 (tpp) cc_final: -0.0100 (tpp) REVERT: Z 486 PHE cc_start: 0.2708 (m-80) cc_final: 0.2197 (m-80) REVERT: Z 502 MET cc_start: 0.0034 (mtp) cc_final: -0.1482 (tpt) outliers start: 115 outliers final: 59 residues processed: 333 average time/residue: 1.1916 time to fit residues: 499.3443 Evaluate side-chains 274 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 208 time to evaluate : 3.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 152 ASN Chi-restraints excluded: chain T residue 159 THR Chi-restraints excluded: chain T residue 165 ASP Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 446 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 403 ASP Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 475 GLU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 223 ILE Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 475 GLU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 253 GLU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 339 VAL Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 90 MET Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 162 THR Chi-restraints excluded: chain Y residue 190 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 286 ASN Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Y residue 465 ASP Chi-restraints excluded: chain Y residue 550 LYS Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 91 ASP Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 361 THR Chi-restraints excluded: chain Z residue 414 GLN Chi-restraints excluded: chain Z residue 454 THR Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 397 optimal weight: 0.8980 chunk 302 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 270 optimal weight: 0.9990 chunk 403 optimal weight: 0.7980 chunk 427 optimal weight: 0.0050 chunk 210 optimal weight: 0.5980 chunk 382 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 52 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 72 GLN ** S 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 405 GLN U 497 GLN V 152 ASN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 397 ASN ** X 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 250 GLN X 388 ASN Y 204 HIS Y 286 ASN ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 322 GLN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1167 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 34420 Z= 0.152 Angle : 0.563 9.796 46649 Z= 0.286 Chirality : 0.042 0.237 5520 Planarity : 0.004 0.092 5999 Dihedral : 6.447 141.009 4921 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.50 % Favored : 96.37 % Rotamer: Outliers : 2.69 % Allowed : 16.19 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.12), residues: 4462 helix: -0.77 (0.11), residues: 2082 sheet: -0.71 (0.22), residues: 553 loop : -1.02 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 141 HIS 0.005 0.001 HIS X 144 PHE 0.016 0.001 PHE Z 290 TYR 0.013 0.001 TYR T 284 ARG 0.019 0.000 ARG Z 435 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 219 time to evaluate : 3.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: -0.1120 (mmt) cc_final: -0.1391 (pmm) REVERT: C 61 MET cc_start: -0.0282 (mmt) cc_final: -0.0882 (mtt) REVERT: F 81 MET cc_start: 0.1058 (OUTLIER) cc_final: 0.0542 (ttt) REVERT: J 105 LEU cc_start: 0.2327 (mt) cc_final: 0.1076 (tp) REVERT: S 223 VAL cc_start: -0.0523 (OUTLIER) cc_final: -0.0805 (t) REVERT: T 278 GLN cc_start: -0.1272 (OUTLIER) cc_final: -0.2042 (mm-40) REVERT: T 483 MET cc_start: 0.0901 (pp-130) cc_final: 0.0091 (tpt) REVERT: T 559 LEU cc_start: -0.1433 (OUTLIER) cc_final: -0.1681 (pt) REVERT: U 46 ASP cc_start: 0.4563 (t0) cc_final: 0.4269 (t0) REVERT: U 282 MET cc_start: -0.0297 (mmt) cc_final: -0.1334 (ptm) REVERT: U 513 ARG cc_start: 0.3103 (tpp-160) cc_final: 0.2763 (tpm170) REVERT: V 187 VAL cc_start: -0.1017 (OUTLIER) cc_final: -0.1319 (t) REVERT: V 241 HIS cc_start: 0.1194 (t70) cc_final: 0.0693 (t70) REVERT: V 475 GLU cc_start: -0.0066 (OUTLIER) cc_final: -0.0489 (mm-30) REVERT: X 143 ILE cc_start: 0.1085 (pt) cc_final: 0.0817 (pt) REVERT: X 194 MET cc_start: 0.0414 (OUTLIER) cc_final: -0.0648 (mpp) REVERT: X 330 LYS cc_start: 0.1210 (mttt) cc_final: 0.0434 (tppt) REVERT: X 422 MET cc_start: 0.1153 (pp-130) cc_final: -0.0005 (ptt) REVERT: Y 52 PHE cc_start: 0.2927 (m-80) cc_final: 0.0928 (t80) REVERT: Y 194 MET cc_start: 0.0783 (mtm) cc_final: -0.3279 (pp-130) REVERT: Y 286 ASN cc_start: 0.0582 (OUTLIER) cc_final: -0.0989 (t0) REVERT: Y 422 MET cc_start: -0.1789 (ttt) cc_final: -0.3580 (mpt) REVERT: Y 488 MET cc_start: 0.4628 (pp-130) cc_final: 0.2964 (ptm) REVERT: Y 536 GLU cc_start: 0.3269 (pm20) cc_final: 0.2990 (pm20) REVERT: Y 550 LYS cc_start: 0.3253 (OUTLIER) cc_final: 0.1822 (mptp) REVERT: Z 224 TYR cc_start: 0.3017 (t80) cc_final: 0.1522 (t80) REVERT: Z 486 PHE cc_start: 0.2547 (m-80) cc_final: 0.2012 (m-80) REVERT: Z 502 MET cc_start: 0.0006 (mtp) cc_final: -0.1681 (tpt) outliers start: 96 outliers final: 48 residues processed: 290 average time/residue: 1.2505 time to fit residues: 455.6273 Evaluate side-chains 264 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 207 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain H residue 98 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 172 PHE Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 165 ASP Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 264 GLN Chi-restraints excluded: chain T residue 278 GLN Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 446 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 299 GLN Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 449 GLU Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 499 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 231 LYS Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 475 GLU Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 190 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 286 ASN Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 526 SER Chi-restraints excluded: chain Y residue 550 LYS Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 454 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 355 optimal weight: 0.9990 chunk 242 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 318 optimal weight: 4.9990 chunk 176 optimal weight: 0.0020 chunk 364 optimal weight: 0.5980 chunk 295 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 218 optimal weight: 0.7980 chunk 383 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 71 GLN ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 72 GLN S 96 ASN ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 140 GLN V 242 GLN Y 286 ASN ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 440 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1171 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 34420 Z= 0.149 Angle : 0.551 11.254 46649 Z= 0.279 Chirality : 0.042 0.320 5520 Planarity : 0.004 0.066 5999 Dihedral : 6.018 103.493 4921 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 2.95 % Allowed : 16.89 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.12), residues: 4462 helix: -0.44 (0.11), residues: 2069 sheet: -0.51 (0.22), residues: 550 loop : -0.91 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 141 HIS 0.008 0.001 HIS R 78 PHE 0.042 0.001 PHE S 172 TYR 0.016 0.001 TYR U 256 ARG 0.007 0.000 ARG U 476 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 201 time to evaluate : 3.569 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: C 61 MET cc_start: -0.0219 (mmt) cc_final: -0.0848 (mtt) REVERT: E 95 ILE cc_start: 0.2419 (mp) cc_final: 0.1768 (tp) REVERT: F 81 MET cc_start: 0.0860 (OUTLIER) cc_final: 0.0355 (ttt) REVERT: G 61 MET cc_start: -0.1016 (mmp) cc_final: -0.1829 (mmt) REVERT: G 112 SER cc_start: 0.6367 (OUTLIER) cc_final: 0.6069 (m) REVERT: H 95 ILE cc_start: -0.1284 (OUTLIER) cc_final: -0.1575 (mm) REVERT: J 105 LEU cc_start: 0.2472 (mt) cc_final: 0.1194 (tp) REVERT: S 223 VAL cc_start: -0.0932 (OUTLIER) cc_final: -0.1223 (t) REVERT: T 278 GLN cc_start: -0.1158 (OUTLIER) cc_final: -0.1910 (mm-40) REVERT: T 403 ASP cc_start: -0.1569 (OUTLIER) cc_final: -0.2148 (t70) REVERT: T 483 MET cc_start: 0.0635 (pp-130) cc_final: -0.0059 (tpt) REVERT: T 559 LEU cc_start: -0.1426 (OUTLIER) cc_final: -0.1662 (pt) REVERT: U 46 ASP cc_start: 0.4531 (t70) cc_final: 0.4232 (t0) REVERT: U 60 GLN cc_start: 0.2526 (pp30) cc_final: 0.2216 (pm20) REVERT: U 282 MET cc_start: -0.0320 (mmt) cc_final: -0.1255 (ptm) REVERT: V 241 HIS cc_start: 0.1146 (t70) cc_final: 0.0673 (t70) REVERT: V 475 GLU cc_start: -0.0068 (OUTLIER) cc_final: -0.0466 (mm-30) REVERT: X 194 MET cc_start: 0.0370 (OUTLIER) cc_final: -0.0520 (mpp) REVERT: X 330 LYS cc_start: 0.0977 (mttt) cc_final: 0.0523 (tptm) REVERT: X 358 LEU cc_start: 0.0786 (mt) cc_final: 0.0573 (mt) REVERT: X 422 MET cc_start: 0.1091 (pp-130) cc_final: -0.0035 (ptt) REVERT: Y 52 PHE cc_start: 0.2713 (m-80) cc_final: 0.0808 (t80) REVERT: Y 194 MET cc_start: 0.0468 (mtm) cc_final: -0.3466 (pp-130) REVERT: Y 422 MET cc_start: -0.1470 (ttt) cc_final: -0.3437 (mpt) REVERT: Y 536 GLU cc_start: 0.3393 (OUTLIER) cc_final: 0.3061 (pm20) REVERT: Z 52 PHE cc_start: 0.0728 (m-80) cc_final: 0.0489 (m-80) REVERT: Z 224 TYR cc_start: 0.2961 (t80) cc_final: 0.1403 (t80) REVERT: Z 422 MET cc_start: 0.1845 (mpp) cc_final: 0.0735 (tpp) REVERT: Z 486 PHE cc_start: 0.2411 (m-80) cc_final: 0.1907 (m-80) REVERT: Z 502 MET cc_start: -0.0110 (mtp) cc_final: -0.1760 (tpt) outliers start: 105 outliers final: 59 residues processed: 283 average time/residue: 1.1819 time to fit residues: 421.2681 Evaluate side-chains 255 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 186 time to evaluate : 3.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain S residue 215 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 165 ASP Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 264 GLN Chi-restraints excluded: chain T residue 278 GLN Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 403 ASP Chi-restraints excluded: chain T residue 446 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 299 GLN Chi-restraints excluded: chain U residue 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 403 ASP Chi-restraints excluded: chain U residue 449 GLU Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 499 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 475 GLU Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 196 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 190 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 348 ASP Chi-restraints excluded: chain Y residue 536 GLU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 91 ASP Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 454 THR Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 143 optimal weight: 0.5980 chunk 384 optimal weight: 0.3980 chunk 84 optimal weight: 0.0060 chunk 250 optimal weight: 0.7980 chunk 105 optimal weight: 0.3980 chunk 427 optimal weight: 8.9990 chunk 355 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 224 optimal weight: 6.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 98 GLN ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN S 174 GLN ** S 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 336 GLN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 204 HIS X 322 GLN ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1174 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 34420 Z= 0.138 Angle : 0.538 10.841 46649 Z= 0.270 Chirality : 0.041 0.182 5520 Planarity : 0.004 0.077 5999 Dihedral : 5.758 81.471 4921 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.29 % Favored : 96.57 % Rotamer: Outliers : 2.72 % Allowed : 17.73 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 4462 helix: -0.19 (0.12), residues: 2067 sheet: -0.44 (0.23), residues: 539 loop : -0.77 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 73 HIS 0.003 0.001 HIS Z 396 PHE 0.050 0.001 PHE R 70 TYR 0.011 0.001 TYR V 334 ARG 0.006 0.000 ARG U 476 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 201 time to evaluate : 3.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 MET cc_start: -0.0403 (mmt) cc_final: -0.0959 (mtt) REVERT: E 95 ILE cc_start: 0.2552 (mp) cc_final: 0.1925 (tp) REVERT: F 81 MET cc_start: 0.0826 (OUTLIER) cc_final: 0.0284 (ttt) REVERT: G 112 SER cc_start: 0.6417 (t) cc_final: 0.6175 (m) REVERT: J 105 LEU cc_start: 0.2489 (mt) cc_final: 0.1215 (tp) REVERT: S 223 VAL cc_start: -0.0892 (OUTLIER) cc_final: -0.1178 (t) REVERT: T 278 GLN cc_start: -0.1253 (OUTLIER) cc_final: -0.1936 (mm-40) REVERT: T 313 PHE cc_start: 0.3594 (m-10) cc_final: 0.3301 (m-10) REVERT: T 403 ASP cc_start: -0.1268 (OUTLIER) cc_final: -0.2001 (OUTLIER) REVERT: T 483 MET cc_start: 0.0556 (pp-130) cc_final: -0.0035 (tpt) REVERT: T 536 LEU cc_start: 0.3442 (OUTLIER) cc_final: 0.3194 (tt) REVERT: T 559 LEU cc_start: -0.1431 (OUTLIER) cc_final: -0.1656 (pt) REVERT: U 46 ASP cc_start: 0.4419 (t70) cc_final: 0.4146 (t0) REVERT: U 60 GLN cc_start: 0.2501 (pp30) cc_final: 0.2060 (pm20) REVERT: U 282 MET cc_start: -0.0507 (mmt) cc_final: -0.1279 (ptm) REVERT: U 513 ARG cc_start: 0.3142 (tpp-160) cc_final: 0.2836 (tpt170) REVERT: V 241 HIS cc_start: 0.1224 (t70) cc_final: 0.0715 (t70) REVERT: V 316 THR cc_start: 0.2064 (m) cc_final: 0.0757 (t) REVERT: V 475 GLU cc_start: -0.0082 (OUTLIER) cc_final: -0.0457 (mm-30) REVERT: X 194 MET cc_start: 0.0665 (OUTLIER) cc_final: -0.0381 (mpp) REVERT: X 330 LYS cc_start: 0.1027 (mttt) cc_final: 0.0308 (ttmt) REVERT: X 358 LEU cc_start: 0.0657 (mt) cc_final: 0.0357 (mt) REVERT: X 422 MET cc_start: 0.1188 (pp-130) cc_final: 0.0115 (ptt) REVERT: Y 52 PHE cc_start: 0.2688 (m-80) cc_final: 0.0777 (t80) REVERT: Y 194 MET cc_start: 0.0323 (mtm) cc_final: -0.1631 (pp-130) REVERT: Y 422 MET cc_start: -0.1637 (ttt) cc_final: -0.3572 (mpt) REVERT: Y 536 GLU cc_start: 0.3231 (OUTLIER) cc_final: 0.3022 (pm20) REVERT: Z 52 PHE cc_start: 0.0952 (m-80) cc_final: 0.0589 (OUTLIER) REVERT: Z 224 TYR cc_start: 0.2874 (t80) cc_final: 0.1329 (t80) REVERT: Z 251 MET cc_start: -0.1722 (mmt) cc_final: -0.1949 (ptp) REVERT: Z 383 THR cc_start: 0.1875 (p) cc_final: 0.1530 (t) REVERT: Z 422 MET cc_start: 0.1391 (mpp) cc_final: 0.0710 (tpp) REVERT: Z 486 PHE cc_start: 0.2393 (m-80) cc_final: 0.1856 (m-80) REVERT: Z 502 MET cc_start: -0.0337 (mtp) cc_final: -0.1839 (tpt) outliers start: 97 outliers final: 63 residues processed: 279 average time/residue: 1.1656 time to fit residues: 412.0528 Evaluate side-chains 260 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 190 time to evaluate : 3.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 215 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 165 ASP Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 264 GLN Chi-restraints excluded: chain T residue 278 GLN Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 403 ASP Chi-restraints excluded: chain T residue 446 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 536 LEU Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 260 VAL Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 403 ASP Chi-restraints excluded: chain U residue 439 MET Chi-restraints excluded: chain U residue 449 GLU Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 475 GLU Chi-restraints excluded: chain V residue 489 PHE Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 196 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 162 THR Chi-restraints excluded: chain Y residue 190 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 536 GLU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 91 ASP Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 454 THR Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 412 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 chunk 312 optimal weight: 0.8980 chunk 241 optimal weight: 3.9990 chunk 359 optimal weight: 0.9980 chunk 238 optimal weight: 0.0070 chunk 426 optimal weight: 1.9990 chunk 266 optimal weight: 0.8980 chunk 259 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN ** S 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 497 GLN V 104 GLN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 397 ASN X 204 HIS X 388 ASN ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 292 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1346 moved from start: 0.5793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34420 Z= 0.162 Angle : 0.583 10.033 46649 Z= 0.292 Chirality : 0.042 0.212 5520 Planarity : 0.004 0.048 5999 Dihedral : 5.850 72.507 4921 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.28 % Favored : 95.58 % Rotamer: Outliers : 3.06 % Allowed : 17.62 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 4462 helix: -0.13 (0.12), residues: 2033 sheet: -0.54 (0.23), residues: 536 loop : -0.74 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 73 HIS 0.004 0.001 HIS S 250 PHE 0.017 0.001 PHE X 355 TYR 0.016 0.001 TYR V 98 ARG 0.008 0.001 ARG Z 435 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 204 time to evaluate : 3.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.1320 (pmm) cc_final: 0.0923 (pmm) REVERT: C 61 MET cc_start: -0.0053 (mmt) cc_final: -0.0274 (mtt) REVERT: E 95 ILE cc_start: 0.2510 (mp) cc_final: 0.2053 (tp) REVERT: G 112 SER cc_start: 0.6679 (OUTLIER) cc_final: 0.6404 (m) REVERT: J 105 LEU cc_start: 0.2469 (mt) cc_final: 0.1151 (tp) REVERT: S 166 TYR cc_start: 0.4820 (m-80) cc_final: 0.4476 (m-80) REVERT: S 223 VAL cc_start: -0.1136 (OUTLIER) cc_final: -0.1402 (t) REVERT: T 90 VAL cc_start: -0.0156 (OUTLIER) cc_final: -0.0392 (t) REVERT: T 278 GLN cc_start: -0.1236 (OUTLIER) cc_final: -0.2010 (mm-40) REVERT: T 371 GLU cc_start: 0.1959 (OUTLIER) cc_final: 0.0140 (tt0) REVERT: T 403 ASP cc_start: -0.0702 (OUTLIER) cc_final: -0.2003 (t70) REVERT: T 483 MET cc_start: 0.0337 (pp-130) cc_final: -0.0092 (tpt) REVERT: U 46 ASP cc_start: 0.4426 (t70) cc_final: 0.4157 (t0) REVERT: U 282 MET cc_start: -0.0369 (mmt) cc_final: -0.1203 (ptm) REVERT: U 411 GLU cc_start: 0.0599 (OUTLIER) cc_final: -0.0746 (mm-30) REVERT: U 466 LEU cc_start: -0.3641 (OUTLIER) cc_final: -0.3927 (mp) REVERT: V 126 HIS cc_start: 0.3371 (p90) cc_final: 0.2971 (p90) REVERT: V 241 HIS cc_start: 0.1418 (t70) cc_final: 0.0832 (t70) REVERT: V 475 GLU cc_start: -0.0190 (OUTLIER) cc_final: -0.0430 (mm-30) REVERT: X 194 MET cc_start: 0.0516 (tpt) cc_final: -0.0559 (mpp) REVERT: X 290 PHE cc_start: -0.0745 (OUTLIER) cc_final: -0.2425 (t80) REVERT: X 386 MET cc_start: 0.2685 (tpp) cc_final: 0.1766 (mpp) REVERT: X 422 MET cc_start: 0.0802 (OUTLIER) cc_final: -0.0116 (ptt) REVERT: Y 52 PHE cc_start: 0.3182 (m-80) cc_final: 0.1062 (t80) REVERT: Y 68 HIS cc_start: 0.3073 (OUTLIER) cc_final: 0.2869 (t-170) REVERT: Y 422 MET cc_start: -0.1551 (ttt) cc_final: -0.3737 (mpt) REVERT: Y 536 GLU cc_start: 0.3136 (pm20) cc_final: 0.2915 (pm20) REVERT: Z 52 PHE cc_start: 0.1230 (m-80) cc_final: 0.0909 (m-80) REVERT: Z 224 TYR cc_start: 0.2858 (t80) cc_final: 0.1499 (t80) REVERT: Z 251 MET cc_start: -0.1544 (mmt) cc_final: -0.2008 (ptp) REVERT: Z 324 ARG cc_start: 0.3007 (mtp180) cc_final: 0.2307 (mpt-90) REVERT: Z 383 THR cc_start: 0.2289 (p) cc_final: 0.1913 (t) REVERT: Z 486 PHE cc_start: 0.2501 (m-80) cc_final: 0.1992 (m-80) REVERT: Z 502 MET cc_start: -0.0553 (mtp) cc_final: -0.1679 (tpt) outliers start: 109 outliers final: 73 residues processed: 292 average time/residue: 1.1626 time to fit residues: 430.5572 Evaluate side-chains 279 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 194 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 215 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 165 ASP Chi-restraints excluded: chain T residue 172 ASP Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 264 GLN Chi-restraints excluded: chain T residue 278 GLN Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 371 GLU Chi-restraints excluded: chain T residue 403 ASP Chi-restraints excluded: chain T residue 446 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 299 GLN Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 383 ILE Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 439 MET Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 466 LEU Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 475 GLU Chi-restraints excluded: chain V residue 489 PHE Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 196 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 290 PHE Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 422 MET Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 68 HIS Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 162 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Y residue 526 SER Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 91 ASP Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 253 GLU Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 454 THR Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 263 optimal weight: 0.8980 chunk 170 optimal weight: 0.1980 chunk 254 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 270 optimal weight: 4.9990 chunk 290 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 334 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN ** S 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 297 GLN ** U 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 497 GLN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 388 ASN ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1390 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34420 Z= 0.159 Angle : 0.578 13.264 46649 Z= 0.288 Chirality : 0.042 0.212 5520 Planarity : 0.004 0.051 5999 Dihedral : 5.790 73.138 4921 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.83 % Favored : 96.03 % Rotamer: Outliers : 2.81 % Allowed : 18.18 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.13), residues: 4462 helix: -0.09 (0.12), residues: 2052 sheet: -0.60 (0.23), residues: 545 loop : -0.75 (0.15), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 73 HIS 0.007 0.001 HIS X 144 PHE 0.053 0.001 PHE R 70 TYR 0.015 0.001 TYR P 141 ARG 0.014 0.000 ARG Z 435 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 194 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.1759 (pmm) cc_final: 0.1506 (pmm) REVERT: E 118 LEU cc_start: 0.4217 (tm) cc_final: 0.3940 (tt) REVERT: G 112 SER cc_start: 0.6849 (OUTLIER) cc_final: 0.6647 (m) REVERT: J 105 LEU cc_start: 0.2467 (mt) cc_final: 0.1134 (tp) REVERT: S 166 TYR cc_start: 0.4763 (m-80) cc_final: 0.4512 (m-80) REVERT: S 223 VAL cc_start: -0.1076 (OUTLIER) cc_final: -0.1342 (t) REVERT: T 278 GLN cc_start: -0.1394 (OUTLIER) cc_final: -0.2067 (mm-40) REVERT: T 403 ASP cc_start: -0.0720 (OUTLIER) cc_final: -0.2113 (t70) REVERT: T 483 MET cc_start: 0.0406 (pp-130) cc_final: -0.0016 (tpt) REVERT: T 559 LEU cc_start: -0.1185 (OUTLIER) cc_final: -0.1401 (pt) REVERT: U 46 ASP cc_start: 0.4426 (t70) cc_final: 0.4148 (t0) REVERT: U 118 MET cc_start: 0.1083 (ttt) cc_final: 0.0755 (ttm) REVERT: U 282 MET cc_start: -0.0423 (mmt) cc_final: -0.1155 (ptm) REVERT: U 466 LEU cc_start: -0.3633 (OUTLIER) cc_final: -0.3931 (mp) REVERT: V 126 HIS cc_start: 0.3449 (p90) cc_final: 0.3052 (p90) REVERT: V 241 HIS cc_start: 0.1453 (t70) cc_final: 0.0933 (t70) REVERT: V 282 MET cc_start: 0.1412 (tpt) cc_final: -0.0229 (tpt) REVERT: V 475 GLU cc_start: -0.0078 (OUTLIER) cc_final: -0.0339 (mm-30) REVERT: X 189 LYS cc_start: 0.1760 (OUTLIER) cc_final: 0.1126 (mtmt) REVERT: X 194 MET cc_start: 0.0514 (OUTLIER) cc_final: -0.0549 (mpp) REVERT: X 290 PHE cc_start: -0.0696 (OUTLIER) cc_final: -0.2401 (t80) REVERT: X 386 MET cc_start: 0.2842 (tpp) cc_final: 0.1872 (mpp) REVERT: X 422 MET cc_start: 0.0779 (OUTLIER) cc_final: -0.0117 (ptt) REVERT: X 488 MET cc_start: -0.0211 (mmt) cc_final: -0.1537 (ttp) REVERT: Y 52 PHE cc_start: 0.3212 (m-80) cc_final: 0.1067 (t80) REVERT: Y 80 MET cc_start: -0.0831 (mmm) cc_final: -0.2211 (pmm) REVERT: Y 422 MET cc_start: -0.1199 (ttt) cc_final: -0.3466 (mpt) REVERT: Y 536 GLU cc_start: 0.3201 (pm20) cc_final: 0.2932 (pm20) REVERT: Y 538 VAL cc_start: -0.1093 (OUTLIER) cc_final: -0.1358 (p) REVERT: Z 224 TYR cc_start: 0.2999 (t80) cc_final: 0.1462 (t80) REVERT: Z 251 MET cc_start: -0.0985 (mmt) cc_final: -0.1716 (ptp) REVERT: Z 324 ARG cc_start: 0.3368 (mtp180) cc_final: 0.2709 (mpt-90) REVERT: Z 486 PHE cc_start: 0.2473 (m-80) cc_final: 0.1875 (m-80) REVERT: Z 502 MET cc_start: 0.0037 (mtp) cc_final: -0.1400 (tpt) outliers start: 100 outliers final: 73 residues processed: 276 average time/residue: 1.1617 time to fit residues: 403.3759 Evaluate side-chains 268 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 183 time to evaluate : 3.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain S residue 96 ASN Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 152 ASN Chi-restraints excluded: chain T residue 165 ASP Chi-restraints excluded: chain T residue 172 ASP Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 264 GLN Chi-restraints excluded: chain T residue 278 GLN Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 403 ASP Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 299 GLN Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 439 MET Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 466 LEU Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 475 GLU Chi-restraints excluded: chain V residue 489 PHE Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 189 LYS Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 290 PHE Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 422 MET Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 190 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Y residue 526 SER Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 55 GLU Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 91 ASP Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 253 GLU Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 415 ASP Chi-restraints excluded: chain Z residue 454 THR Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 387 optimal weight: 0.0870 chunk 408 optimal weight: 0.9980 chunk 372 optimal weight: 0.2980 chunk 396 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 172 optimal weight: 0.4980 chunk 311 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 358 optimal weight: 0.9990 chunk 375 optimal weight: 7.9990 chunk 395 optimal weight: 0.3980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 76 GLN ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN ** S 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 397 ASN X 388 ASN Y 294 ASN ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1336 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 34420 Z= 0.141 Angle : 0.555 9.906 46649 Z= 0.276 Chirality : 0.042 0.194 5520 Planarity : 0.004 0.049 5999 Dihedral : 5.588 71.868 4921 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.70 % Favored : 96.17 % Rotamer: Outliers : 2.33 % Allowed : 18.85 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.13), residues: 4462 helix: 0.05 (0.12), residues: 2055 sheet: -0.55 (0.23), residues: 549 loop : -0.65 (0.15), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 73 HIS 0.005 0.001 HIS X 144 PHE 0.023 0.001 PHE G 82 TYR 0.012 0.001 TYR P 141 ARG 0.013 0.000 ARG Z 435 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 190 time to evaluate : 3.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.1646 (pmm) cc_final: 0.1101 (pmm) REVERT: E 95 ILE cc_start: 0.3171 (mm) cc_final: 0.2779 (mt) REVERT: E 118 LEU cc_start: 0.4266 (tm) cc_final: 0.3944 (tt) REVERT: J 61 MET cc_start: 0.0781 (tmt) cc_final: 0.0214 (tmm) REVERT: J 105 LEU cc_start: 0.2463 (mt) cc_final: 0.1137 (tp) REVERT: S 166 TYR cc_start: 0.4688 (m-80) cc_final: 0.4416 (m-80) REVERT: T 278 GLN cc_start: -0.1050 (OUTLIER) cc_final: -0.1816 (mm-40) REVERT: T 403 ASP cc_start: -0.0549 (OUTLIER) cc_final: -0.2002 (t0) REVERT: T 483 MET cc_start: 0.0315 (pp-130) cc_final: -0.0078 (tpt) REVERT: T 559 LEU cc_start: -0.1078 (OUTLIER) cc_final: -0.1312 (pt) REVERT: U 46 ASP cc_start: 0.4358 (t70) cc_final: 0.4094 (t0) REVERT: U 118 MET cc_start: 0.1810 (ttt) cc_final: 0.1377 (ttm) REVERT: U 282 MET cc_start: -0.0663 (mmt) cc_final: -0.1231 (ptm) REVERT: U 411 GLU cc_start: 0.1023 (OUTLIER) cc_final: -0.0720 (mt-10) REVERT: U 466 LEU cc_start: -0.3622 (OUTLIER) cc_final: -0.3919 (mp) REVERT: U 513 ARG cc_start: 0.3376 (tpp-160) cc_final: 0.3091 (tpm170) REVERT: V 241 HIS cc_start: 0.1445 (t70) cc_final: 0.0941 (t70) REVERT: V 282 MET cc_start: 0.1256 (tpt) cc_final: -0.0411 (tpt) REVERT: V 475 GLU cc_start: 0.0156 (OUTLIER) cc_final: -0.0227 (mm-30) REVERT: X 194 MET cc_start: 0.0668 (OUTLIER) cc_final: -0.0440 (mpp) REVERT: X 386 MET cc_start: 0.2511 (tpp) cc_final: 0.1967 (pmm) REVERT: X 422 MET cc_start: 0.0755 (OUTLIER) cc_final: -0.0185 (ptt) REVERT: X 488 MET cc_start: -0.0333 (mmt) cc_final: -0.1560 (ttp) REVERT: Y 52 PHE cc_start: 0.3062 (m-80) cc_final: 0.1075 (t80) REVERT: Y 422 MET cc_start: -0.1162 (ttt) cc_final: -0.3430 (mpt) REVERT: Z 224 TYR cc_start: 0.2800 (t80) cc_final: 0.1407 (t80) REVERT: Z 251 MET cc_start: -0.1080 (mmt) cc_final: -0.1843 (pp-130) REVERT: Z 253 GLU cc_start: 0.3344 (OUTLIER) cc_final: 0.0974 (tp30) REVERT: Z 383 THR cc_start: 0.1780 (p) cc_final: 0.1484 (t) REVERT: Z 486 PHE cc_start: 0.2484 (m-80) cc_final: 0.1928 (m-80) REVERT: Z 488 MET cc_start: 0.1950 (mmt) cc_final: -0.0688 (ptm) REVERT: Z 502 MET cc_start: -0.0034 (mtp) cc_final: -0.1484 (tpt) outliers start: 83 outliers final: 57 residues processed: 258 average time/residue: 1.2504 time to fit residues: 408.7841 Evaluate side-chains 245 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 179 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 152 ASN Chi-restraints excluded: chain T residue 165 ASP Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 264 GLN Chi-restraints excluded: chain T residue 278 GLN Chi-restraints excluded: chain T residue 403 ASP Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 299 GLN Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 439 MET Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 466 LEU Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 475 GLU Chi-restraints excluded: chain V residue 489 PHE Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 422 MET Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 526 SER Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 91 ASP Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 253 GLU Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 415 ASP Chi-restraints excluded: chain Z residue 454 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 260 optimal weight: 0.9980 chunk 419 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 199 optimal weight: 0.9990 chunk 291 optimal weight: 0.3980 chunk 440 optimal weight: 7.9990 chunk 405 optimal weight: 0.0670 chunk 350 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 270 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN ** S 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 257 ASN ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 397 ASN ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 79 HIS ** Z 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 292 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1427 moved from start: 0.6706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34420 Z= 0.157 Angle : 0.587 14.539 46649 Z= 0.288 Chirality : 0.042 0.182 5520 Planarity : 0.004 0.049 5999 Dihedral : 5.689 74.390 4921 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.19 % Favored : 95.67 % Rotamer: Outliers : 2.27 % Allowed : 19.05 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 4462 helix: 0.06 (0.12), residues: 2053 sheet: -0.57 (0.23), residues: 537 loop : -0.68 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 73 HIS 0.004 0.001 HIS Y 204 PHE 0.048 0.001 PHE R 70 TYR 0.013 0.001 TYR T 304 ARG 0.008 0.000 ARG Z 435 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 195 time to evaluate : 3.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.2749 (tmm) cc_final: 0.2410 (tmm) REVERT: E 95 ILE cc_start: 0.3100 (mm) cc_final: 0.2778 (mt) REVERT: E 118 LEU cc_start: 0.4379 (tm) cc_final: 0.4095 (tt) REVERT: F 121 VAL cc_start: 0.3477 (t) cc_final: 0.3203 (t) REVERT: H 61 MET cc_start: 0.5513 (ppp) cc_final: 0.4641 (pmm) REVERT: J 61 MET cc_start: 0.0852 (tmt) cc_final: 0.0281 (tmm) REVERT: J 81 MET cc_start: 0.3052 (ptm) cc_final: 0.2696 (ptm) REVERT: J 105 LEU cc_start: 0.1986 (mt) cc_final: 0.0719 (tp) REVERT: S 259 MET cc_start: 0.1450 (mmt) cc_final: 0.0293 (tmt) REVERT: T 371 GLU cc_start: 0.1825 (OUTLIER) cc_final: 0.0561 (mm-30) REVERT: T 403 ASP cc_start: -0.0358 (OUTLIER) cc_final: -0.2082 (t0) REVERT: T 483 MET cc_start: 0.0499 (pp-130) cc_final: -0.0002 (tpt) REVERT: U 46 ASP cc_start: 0.4364 (t70) cc_final: 0.4096 (t0) REVERT: U 118 MET cc_start: 0.1837 (ttt) cc_final: 0.1424 (ttm) REVERT: U 282 MET cc_start: -0.0618 (mmt) cc_final: -0.1203 (ptm) REVERT: U 411 GLU cc_start: 0.1298 (OUTLIER) cc_final: -0.0624 (mt-10) REVERT: U 466 LEU cc_start: -0.3586 (OUTLIER) cc_final: -0.3914 (mp) REVERT: V 240 ILE cc_start: 0.4209 (mt) cc_final: 0.3606 (pt) REVERT: V 241 HIS cc_start: 0.1415 (t70) cc_final: 0.1017 (t70) REVERT: V 282 MET cc_start: 0.1512 (tpt) cc_final: -0.0199 (tpt) REVERT: V 475 GLU cc_start: 0.0060 (OUTLIER) cc_final: -0.0273 (mm-30) REVERT: X 189 LYS cc_start: 0.1254 (OUTLIER) cc_final: 0.0632 (mtmt) REVERT: X 194 MET cc_start: 0.0718 (OUTLIER) cc_final: -0.0400 (mpp) REVERT: X 290 PHE cc_start: -0.0471 (OUTLIER) cc_final: -0.2431 (t80) REVERT: X 422 MET cc_start: 0.0761 (OUTLIER) cc_final: -0.0215 (ptt) REVERT: X 488 MET cc_start: -0.0422 (mmt) cc_final: -0.1551 (ttp) REVERT: Y 386 MET cc_start: 0.3383 (mmp) cc_final: 0.3107 (mmp) REVERT: Y 422 MET cc_start: -0.0979 (ttt) cc_final: -0.3506 (mpt) REVERT: Z 52 PHE cc_start: 0.1006 (m-80) cc_final: 0.0782 (m-10) REVERT: Z 227 MET cc_start: 0.2291 (mtt) cc_final: 0.1700 (mtt) REVERT: Z 251 MET cc_start: -0.0736 (mmt) cc_final: -0.1636 (pp-130) REVERT: Z 253 GLU cc_start: 0.3377 (OUTLIER) cc_final: 0.1119 (tp30) REVERT: Z 383 THR cc_start: 0.1865 (p) cc_final: 0.1620 (t) REVERT: Z 486 PHE cc_start: 0.2294 (m-80) cc_final: 0.1796 (m-80) REVERT: Z 488 MET cc_start: 0.1948 (mmt) cc_final: -0.0671 (ptm) REVERT: Z 502 MET cc_start: -0.0050 (mtp) cc_final: -0.1446 (tpt) outliers start: 81 outliers final: 61 residues processed: 263 average time/residue: 1.2078 time to fit residues: 400.7754 Evaluate side-chains 258 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 187 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 152 ASN Chi-restraints excluded: chain T residue 165 ASP Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 264 GLN Chi-restraints excluded: chain T residue 371 GLU Chi-restraints excluded: chain T residue 403 ASP Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 299 GLN Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 439 MET Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 466 LEU Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 475 GLU Chi-restraints excluded: chain V residue 489 PHE Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 189 LYS Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 290 PHE Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 422 MET Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Y residue 526 SER Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 55 GLU Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 79 HIS Chi-restraints excluded: chain Z residue 91 ASP Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 253 GLU Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 454 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 278 optimal weight: 0.8980 chunk 373 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 323 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 351 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 360 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN ** S 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 ASN T 139 HIS ** U 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 497 GLN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5097 r_free = 0.5097 target = 0.286921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.259981 restraints weight = 61224.238| |-----------------------------------------------------------------------------| r_work (start): 0.4873 rms_B_bonded: 2.33 r_work: 0.4805 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1586 moved from start: 0.7270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 34420 Z= 0.248 Angle : 0.703 13.062 46649 Z= 0.352 Chirality : 0.045 0.233 5520 Planarity : 0.005 0.064 5999 Dihedral : 6.331 79.384 4921 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.45 % Favored : 94.42 % Rotamer: Outliers : 2.27 % Allowed : 19.33 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.12), residues: 4462 helix: -0.22 (0.11), residues: 2046 sheet: -1.03 (0.23), residues: 484 loop : -0.97 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP V 73 HIS 0.071 0.002 HIS Z 79 PHE 0.026 0.002 PHE X 355 TYR 0.020 0.002 TYR T 304 ARG 0.008 0.001 ARG U 429 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9250.65 seconds wall clock time: 169 minutes 0.26 seconds (10140.26 seconds total)