Starting phenix.real_space_refine on Fri Jul 26 15:19:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6red_4850/07_2024/6red_4850_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6red_4850/07_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_4850/07_2024/6red_4850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6red_4850/07_2024/6red_4850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6red_4850/07_2024/6red_4850_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6red_4850/07_2024/6red_4850_neut.cif" } 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-5388/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: 19.80, per 1000 atoms: 0.58 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: 14.99 Conformation dependent library (CDL) restraints added in 7.1 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... Secondary structure from input PDB file: 190 helices and 0 sheets defined 52.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 54 through 68 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) Processing helix chain 'A' and resid 70 through 92 removed outlier: 3.776A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 119 removed outlier: 4.240A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'B' and resid 55 through 68 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) Processing helix chain 'B' and resid 69 through 92 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 95 through 126 removed outlier: 4.483A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 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) Processing helix chain 'C' and resid 69 through 92 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 95 through 126 removed outlier: 4.783A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 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) Processing helix chain 'D' and resid 70 through 92 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 95 through 126 removed outlier: 4.256A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 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) Processing helix chain 'E' and resid 70 through 92 Processing helix chain 'E' and resid 95 through 126 removed outlier: 4.495A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 4.042A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 90 removed outlier: 3.569A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 95 through 126 removed outlier: 3.507A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 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) Processing helix chain 'G' and resid 70 through 92 removed outlier: 3.680A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 126 removed outlier: 3.571A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA G 114 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 66 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 69 through 92 removed outlier: 4.336A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 124 removed outlier: 4.206A pdb=" N SER H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 removed outlier: 3.539A pdb=" N GLY I 65 " --> pdb=" O MET I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 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 95 through 127 removed outlier: 4.235A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU I 125 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 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) Processing helix chain 'J' and resid 69 through 92 removed outlier: 4.238A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 126 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 50 through 62 Processing helix chain 'P' and resid 66 through 84 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 84 through 93 removed outlier: 3.797A pdb=" N ARG P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) 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 97 through 109 removed outlier: 4.030A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 128 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) removed outlier: 3.619A pdb=" N GLU P 128 " --> pdb=" O ALA P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 132 No H-bonds generated for 'chain 'P' and resid 130 through 132' Processing helix chain 'P' and resid 133 through 147 removed outlier: 3.932A pdb=" N VAL P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 13 Processing helix chain 'Q' and resid 15 through 29 Processing helix chain 'Q' and resid 32 through 40 removed outlier: 4.329A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN Q 40 " --> pdb=" O LYS Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 44 removed outlier: 3.783A pdb=" N ALA Q 44 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 41 through 44' Processing helix chain 'R' and resid 29 through 41 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 50 through 55 Processing helix chain 'R' and resid 153 through 155 No H-bonds generated for 'chain 'R' and resid 153 through 155' Processing helix chain 'R' and resid 156 through 168 removed outlier: 3.818A pdb=" N VAL R 160 " --> pdb=" O ASP R 156 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 196 removed outlier: 3.508A pdb=" N GLU R 196 " --> pdb=" O GLU R 192 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 71 removed outlier: 3.652A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 79 Processing helix chain 'S' and resid 81 through 89 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 115 through 128 removed outlier: 3.787A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 151 removed outlier: 3.501A pdb=" N ARG S 147 " --> pdb=" O GLY S 143 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN S 149 " --> pdb=" O LYS S 145 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR S 151 " --> pdb=" O ARG S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 183 Processing helix chain 'S' and resid 238 through 313 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) removed outlier: 3.518A pdb=" N ALA S 313 " --> pdb=" O ALA S 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 4.076A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 160 Processing helix chain 'T' and resid 206 through 212 Processing helix chain 'T' and resid 230 through 247 removed outlier: 3.735A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 280 removed outlier: 3.514A pdb=" N VAL T 269 " --> pdb=" O LYS T 265 " (cutoff:3.500A) 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 295 through 315 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 326 through 341 removed outlier: 3.528A pdb=" N GLN T 330 " --> pdb=" O ASP T 326 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 346 through 350 Processing helix chain 'T' and resid 351 through 352 No H-bonds generated for 'chain 'T' and resid 351 through 352' Processing helix chain 'T' and resid 353 through 363 Processing helix chain 'T' and resid 392 through 402 Processing helix chain 'T' and resid 410 through 415 Processing helix chain 'T' and resid 430 through 435 removed outlier: 3.879A pdb=" N ALA T 433 " --> pdb=" O VAL T 430 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 430 through 435' Processing helix chain 'T' and resid 436 through 456 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) removed outlier: 3.532A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) Processing helix chain 'T' and resid 458 through 462 Processing helix chain 'T' and resid 469 through 482 removed outlier: 3.968A pdb=" N VAL T 473 " --> pdb=" O ALA T 469 " (cutoff:3.500A) Processing helix chain 'T' and resid 493 through 506 removed outlier: 3.635A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 522 through 528 Processing helix chain 'T' and resid 530 through 540 Processing helix chain 'T' and resid 543 through 556 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) removed outlier: 4.036A pdb=" N LYS T 556 " --> pdb=" O ALA T 552 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 48 removed outlier: 3.639A pdb=" N LEU U 45 " --> pdb=" O ASP U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 73 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) Processing helix chain 'U' and resid 74 through 77 Processing helix chain 'U' and resid 134 through 138 removed outlier: 3.940A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE U 138 " --> pdb=" O ASP U 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 134 through 138' Processing helix chain 'U' and resid 156 through 160 removed outlier: 3.578A pdb=" N THR U 159 " --> pdb=" O GLY U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 212 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.790A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 279 Processing helix chain 'U' and resid 280 through 283 removed outlier: 3.727A pdb=" N ARG U 283 " --> pdb=" O GLY U 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 280 through 283' Processing helix chain 'U' and resid 295 through 316 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 326 through 341 removed outlier: 3.718A pdb=" N GLN U 330 " --> pdb=" O ASP U 326 " (cutoff:3.500A) 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 346 through 350 Processing helix chain 'U' and resid 351 through 352 No H-bonds generated for 'chain 'U' and resid 351 through 352' Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.788A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 369 through 373 Processing helix chain 'U' and resid 392 through 402 Processing helix chain 'U' and resid 412 through 416 removed outlier: 3.877A pdb=" N GLY U 416 " --> pdb=" O PHE U 413 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 455 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) Processing helix chain 'U' and resid 456 through 460 removed outlier: 3.725A pdb=" N ALA U 460 " --> pdb=" O ALA U 457 " (cutoff:3.500A) Processing helix chain 'U' and resid 465 through 469 removed outlier: 4.385A pdb=" N ALA U 468 " --> pdb=" O ASP U 465 " (cutoff:3.500A) Processing helix chain 'U' and resid 472 through 484 removed outlier: 4.107A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 501 Processing helix chain 'U' and resid 501 through 506 Processing helix chain 'U' and resid 513 through 515 No H-bonds generated for 'chain 'U' and resid 513 through 515' Processing helix chain 'U' and resid 516 through 528 removed outlier: 4.215A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA U 523 " --> pdb=" O ALA U 519 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL U 528 " --> pdb=" O VAL U 524 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 540 removed outlier: 4.056A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 removed outlier: 3.899A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 48 removed outlier: 3.732A pdb=" N GLU V 47 " --> pdb=" O ALA V 44 " (cutoff:3.500A) Processing helix chain 'V' and resid 58 through 67 removed outlier: 3.683A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 138 removed outlier: 3.664A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE V 138 " --> pdb=" O ASP V 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 134 through 138' Processing helix chain 'V' and resid 156 through 160 Processing helix chain 'V' and resid 206 through 213 Processing helix chain 'V' and resid 230 through 247 removed outlier: 3.943A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 250 through 253 Processing helix chain 'V' and resid 265 through 279 Processing helix chain 'V' and resid 280 through 283 Processing helix chain 'V' and resid 295 through 316 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 326 through 340 removed outlier: 3.549A pdb=" N GLN V 330 " --> pdb=" O ASP V 326 " (cutoff:3.500A) Processing helix chain 'V' and resid 346 through 350 removed outlier: 3.517A pdb=" N ALA V 349 " --> pdb=" O GLY V 346 " (cutoff:3.500A) Processing helix chain 'V' and resid 351 through 352 No H-bonds generated for 'chain 'V' and resid 351 through 352' Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.832A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU V 361 " --> pdb=" O LEU V 357 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.936A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 400 Processing helix chain 'V' and resid 409 through 414 Processing helix chain 'V' and resid 438 through 454 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) Processing helix chain 'V' and resid 455 through 457 No H-bonds generated for 'chain 'V' and resid 455 through 457' Processing helix chain 'V' and resid 470 through 485 removed outlier: 4.036A pdb=" N ARG V 479 " --> pdb=" O GLU V 475 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 Processing helix chain 'V' and resid 513 through 515 No H-bonds generated for 'chain 'V' and resid 513 through 515' Processing helix chain 'V' and resid 516 through 528 removed outlier: 3.536A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 530 through 540 removed outlier: 3.803A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) Processing helix chain 'V' and resid 545 through 555 removed outlier: 4.148A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG V 555 " --> pdb=" O LYS V 551 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 Processing helix chain 'X' and resid 166 through 171 Processing helix chain 'X' and resid 188 through 201 Processing helix chain 'X' and resid 216 through 229 Processing helix chain 'X' and resid 235 through 242 removed outlier: 4.114A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) 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 254 through 259 Processing helix chain 'X' and resid 260 through 275 Processing helix chain 'X' and resid 287 through 297 removed outlier: 3.737A pdb=" N THR X 291 " --> pdb=" O ILE X 287 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL X 297 " --> pdb=" O ALA X 293 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 342 through 345 Processing helix chain 'X' and resid 348 through 355 removed outlier: 3.608A pdb=" N THR X 354 " --> pdb=" O ALA X 350 " (cutoff:3.500A) Processing helix chain 'X' and resid 365 through 370 removed outlier: 3.613A pdb=" N ALA X 369 " --> pdb=" O SER X 365 " (cutoff:3.500A) Processing helix chain 'X' and resid 393 through 421 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 430 through 443 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 447 through 451 removed outlier: 3.864A pdb=" N GLU X 451 " --> pdb=" O GLN X 448 " (cutoff:3.500A) Processing helix chain 'X' and resid 462 through 476 Processing helix chain 'X' and resid 482 through 487 removed outlier: 3.645A pdb=" N PHE X 486 " --> pdb=" O GLU X 483 " (cutoff:3.500A) Processing helix chain 'X' and resid 491 through 508 removed outlier: 4.005A pdb=" N VAL X 495 " --> pdb=" O ASP X 491 " (cutoff:3.500A) 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 526 through 533 Processing helix chain 'Y' and resid 114 through 118 Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 188 through 204 Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 3.601A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) 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 254 through 275 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 286 through 301 Processing helix chain 'Y' and resid 313 through 323 removed outlier: 3.730A pdb=" N LEU Y 321 " --> pdb=" O ASP Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 341 through 345 removed outlier: 3.721A pdb=" N ASP Y 344 " --> pdb=" O VAL Y 341 " (cutoff:3.500A) Processing helix chain 'Y' and resid 348 through 355 Processing helix chain 'Y' and resid 365 through 371 removed outlier: 3.611A pdb=" N LEU Y 371 " --> pdb=" O SER Y 367 " (cutoff:3.500A) Processing helix chain 'Y' and resid 388 through 412 removed outlier: 7.242A pdb=" N ALA Y 394 " --> pdb=" O ASN Y 390 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N GLU Y 395 " --> pdb=" O VAL Y 391 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N HIS Y 396 " --> pdb=" O ILE Y 392 " (cutoff:3.500A) Processing helix chain 'Y' and resid 412 through 420 removed outlier: 4.065A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 427 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 462 through 476 removed outlier: 3.959A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 491 through 504 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) Processing helix chain 'Y' and resid 505 through 508 Processing helix chain 'Y' and resid 518 through 522 removed outlier: 3.589A pdb=" N LEU Y 521 " --> pdb=" O SER Y 518 " (cutoff:3.500A) Processing helix chain 'Y' and resid 544 through 554 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 114 through 118 Processing helix chain 'Z' and resid 149 through 153 removed outlier: 3.521A pdb=" N GLN Z 153 " --> pdb=" O PHE Z 150 " (cutoff:3.500A) Processing helix chain 'Z' and resid 164 through 171 removed outlier: 3.578A pdb=" N ALA Z 171 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 201 Processing helix chain 'Z' and resid 216 through 229 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 4.117A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 259 Processing helix chain 'Z' and resid 260 through 275 removed outlier: 3.587A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 298 removed outlier: 3.855A pdb=" N THR Z 291 " --> pdb=" O ILE Z 287 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 Processing helix chain 'Z' and resid 348 through 355 removed outlier: 3.602A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) Processing helix chain 'Z' and resid 356 through 358 No H-bonds generated for 'chain 'Z' and resid 356 through 358' Processing helix chain 'Z' and resid 365 through 372 removed outlier: 3.527A pdb=" N ALA Z 369 " --> pdb=" O SER Z 365 " (cutoff:3.500A) Processing helix chain 'Z' and resid 388 through 393 Processing helix chain 'Z' and resid 393 through 412 removed outlier: 3.620A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 420 Processing helix chain 'Z' and resid 421 through 425 removed outlier: 4.077A pdb=" N GLU Z 424 " --> pdb=" O GLY Z 421 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU Z 425 " --> pdb=" O MET Z 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 421 through 425' Processing helix chain 'Z' and resid 429 through 440 Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.690A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 482 through 486 Processing helix chain 'Z' and resid 492 through 500 removed outlier: 3.641A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) Processing helix chain 'Z' and resid 500 through 508 removed outlier: 3.579A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) Processing helix chain 'Z' and resid 509 through 511 No H-bonds generated for 'chain 'Z' and resid 509 through 511' Processing helix chain 'Z' and resid 527 through 533 1434 hydrogen bonds defined for protein. 4149 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: 10.22 Time building geometry restraints manager: 16.60 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: 1129 2.69 - 3.24: 32604 3.24 - 3.80: 57093 3.80 - 4.35: 76930 4.35 - 4.90: 126582 Nonbonded interactions: 294338 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 294333 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: 7.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.330 Check model and map are aligned: 0.280 Set scattering table: 0.360 Process input model: 92.460 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.080 ------------------------------------------------------------------------------- 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= 0.789 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 : 3.464 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: 1.1929 time to fit residues: 495.0730 Evaluate side-chains 209 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 205 time to evaluate : 3.271 ------------------------------------------------------------------------------- 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: 0.7980 chunk 335 optimal weight: 3.9990 chunk 185 optimal weight: 0.5980 chunk 114 optimal weight: 8.9990 chunk 225 optimal weight: 3.9990 chunk 178 optimal weight: 0.0670 chunk 346 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 257 optimal weight: 0.0970 chunk 401 optimal weight: 5.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- 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 D 94 ASN E 94 ASN E 98 GLN G 92 ASN G 94 ASN G 98 GLN J 98 GLN P 52 GLN ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN T 386 GLN T 435 GLN ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 319 HIS U 386 GLN U 435 GLN U 497 GLN ** V 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 139 HIS ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 244 ASN V 278 GLN V 386 GLN V 435 GLN V 452 GLN V 486 GLN V 497 GLN X 241 ASN X 388 ASN X 390 ASN X 398 ASN Y 157 GLN Y 199 ASN Y 278 GLN Y 286 ASN Y 294 ASN ** Y 322 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 398 ASN Y 404 GLN Y 414 GLN Z 42 GLN Z 68 HIS Z 199 ASN Z 337 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0494 moved from start: 0.2146 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= 0.167 Angle : 0.583 8.987 46649 Z= 0.296 Chirality : 0.043 0.381 5520 Planarity : 0.005 0.054 5999 Dihedral : 7.362 152.736 4925 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.18 % Favored : 96.68 % Rotamer: Outliers : 1.68 % Allowed : 11.28 % Favored : 87.04 % 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: -1.97 (0.12), residues: 4462 helix: -1.18 (0.10), residues: 2158 sheet: -0.76 (0.22), residues: 491 loop : -1.44 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 141 HIS 0.003 0.001 HIS Z 396 PHE 0.030 0.001 PHE Y 288 TYR 0.016 0.001 TYR Z 340 ARG 0.008 0.000 ARG V 254 *********************** 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 288 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 228 time to evaluate : 3.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: -0.0683 (mmt) cc_final: -0.1489 (pmm) REVERT: B 81 MET cc_start: 0.2536 (tmm) cc_final: 0.1516 (mtm) REVERT: C 61 MET cc_start: -0.1450 (mmt) cc_final: -0.1890 (mtt) REVERT: C 81 MET cc_start: 0.4555 (OUTLIER) cc_final: 0.4326 (tpp) REVERT: E 95 ILE cc_start: 0.1085 (mm) cc_final: -0.1056 (tp) REVERT: S 223 VAL cc_start: -0.0015 (OUTLIER) cc_final: -0.0445 (t) REVERT: T 138 ILE cc_start: 0.0494 (mt) cc_final: 0.0277 (mt) REVERT: T 313 PHE cc_start: 0.3205 (m-10) cc_final: 0.2532 (m-10) REVERT: T 483 MET cc_start: 0.1012 (pp-130) cc_final: -0.0031 (ptt) REVERT: T 488 GLN cc_start: 0.3938 (OUTLIER) cc_final: 0.3030 (tt0) REVERT: U 118 MET cc_start: 0.2023 (ttt) cc_final: 0.1470 (mtt) REVERT: U 282 MET cc_start: -0.1377 (mmt) cc_final: -0.1681 (ptm) REVERT: V 241 HIS cc_start: 0.0431 (t70) cc_final: 0.0110 (t70) REVERT: V 258 VAL cc_start: 0.4458 (t) cc_final: 0.4212 (t) REVERT: V 321 LEU cc_start: 0.2918 (OUTLIER) cc_final: 0.1432 (mp) REVERT: X 80 MET cc_start: 0.0650 (mtm) cc_final: 0.0308 (mtm) REVERT: X 422 MET cc_start: 0.1297 (pp-130) cc_final: -0.0153 (ptt) REVERT: Y 52 PHE cc_start: 0.2131 (m-80) cc_final: 0.0570 (t80) REVERT: Y 64 GLU cc_start: 0.1711 (mm-30) cc_final: 0.0717 (mp0) REVERT: Y 194 MET cc_start: 0.1340 (mtm) cc_final: -0.1380 (pp-130) REVERT: Y 207 PHE cc_start: 0.3515 (m-80) cc_final: 0.2051 (m-80) REVERT: Y 246 LEU cc_start: 0.1765 (OUTLIER) cc_final: 0.0984 (mt) REVERT: Y 286 ASN cc_start: 0.0603 (OUTLIER) cc_final: -0.0890 (t0) REVERT: Y 386 MET cc_start: 0.2576 (mmp) cc_final: -0.0712 (mmp) REVERT: Y 422 MET cc_start: -0.2142 (ttt) cc_final: -0.3047 (mpt) REVERT: Z 80 MET cc_start: 0.0104 (mmm) cc_final: -0.0116 (ttt) REVERT: Z 224 TYR cc_start: 0.1970 (t80) cc_final: 0.0828 (t80) REVERT: Z 251 MET cc_start: -0.0406 (ptp) cc_final: -0.1172 (mtt) REVERT: Z 422 MET cc_start: 0.0227 (tpp) cc_final: -0.0306 (tpp) REVERT: Z 424 GLU cc_start: 0.4221 (pp20) cc_final: 0.2723 (tm-30) REVERT: Z 486 PHE cc_start: 0.2809 (m-80) cc_final: 0.2181 (m-80) REVERT: Z 502 MET cc_start: 0.0013 (mtp) cc_final: -0.1581 (tpt) outliers start: 60 outliers final: 23 residues processed: 267 average time/residue: 1.1127 time to fit residues: 374.2727 Evaluate side-chains 223 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 3.445 ------------------------------------------------------------------------------- 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 R residue 65 VAL 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 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 180 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 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: 10.0000 chunk 124 optimal weight: 10.0000 chunk 334 optimal weight: 5.9990 chunk 273 optimal weight: 7.9990 chunk 110 optimal weight: 0.1980 chunk 402 optimal weight: 5.9990 chunk 434 optimal weight: 4.9990 chunk 358 optimal weight: 0.8980 chunk 398 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 322 optimal weight: 5.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN F 98 GLN G 98 GLN P 52 GLN P 76 GLN S 52 ASN ** S 70 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 T 104 GLN ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 336 GLN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 386 GLN ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 250 GLN ** X 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 388 ASN Y 79 HIS ** 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 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1492 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 34420 Z= 0.346 Angle : 0.887 15.894 46649 Z= 0.454 Chirality : 0.050 0.273 5520 Planarity : 0.007 0.094 5999 Dihedral : 7.970 163.667 4921 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 23.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.47 % Favored : 94.44 % Rotamer: Outliers : 3.76 % Allowed : 13.32 % Favored : 82.92 % 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: -2.05 (0.12), residues: 4462 helix: -1.12 (0.10), residues: 2136 sheet: -1.09 (0.23), residues: 481 loop : -1.56 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Y 141 HIS 0.011 0.002 HIS T 139 PHE 0.050 0.003 PHE U 380 TYR 0.039 0.003 TYR T 284 ARG 0.011 0.001 ARG U 429 *********************** 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 389 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 255 time to evaluate : 3.356 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: B 60 LYS cc_start: 0.1324 (OUTLIER) cc_final: 0.0638 (mtmt) REVERT: C 61 MET cc_start: -0.0594 (mmt) cc_final: -0.0803 (mmp) REVERT: J 81 MET cc_start: 0.1911 (ptt) cc_final: 0.1400 (ptm) REVERT: Q 14 MET cc_start: -0.1608 (ttt) cc_final: -0.3662 (mmm) REVERT: S 223 VAL cc_start: -0.0453 (OUTLIER) cc_final: -0.0789 (t) REVERT: S 259 MET cc_start: 0.2629 (mmt) cc_final: 0.1685 (tmt) REVERT: T 118 MET cc_start: 0.2096 (ttt) cc_final: 0.1723 (ttp) REVERT: T 159 THR cc_start: 0.0336 (OUTLIER) cc_final: -0.0843 (p) REVERT: T 278 GLN cc_start: -0.0684 (OUTLIER) cc_final: -0.1725 (mm-40) REVERT: T 483 MET cc_start: 0.0468 (pp-130) cc_final: -0.0400 (tpt) REVERT: U 476 ARG cc_start: -0.0054 (OUTLIER) cc_final: -0.0532 (tpt-90) REVERT: V 240 ILE cc_start: 0.4233 (mt) cc_final: 0.2129 (tt) REVERT: V 241 HIS cc_start: 0.1530 (t70) cc_final: 0.0972 (t70) REVERT: V 475 GLU cc_start: 0.0219 (OUTLIER) cc_final: -0.0262 (mm-30) REVERT: X 253 GLU cc_start: 0.2246 (OUTLIER) cc_final: 0.1315 (mt-10) REVERT: X 422 MET cc_start: 0.0871 (pp-130) cc_final: -0.1021 (ptt) REVERT: Y 52 PHE cc_start: 0.4124 (m-80) cc_final: 0.2036 (t80) REVERT: Y 286 ASN cc_start: -0.0016 (OUTLIER) cc_final: -0.0571 (t0) REVERT: Y 337 GLN cc_start: 0.4023 (OUTLIER) cc_final: 0.1361 (mt0) REVERT: Y 422 MET cc_start: -0.2126 (ttt) cc_final: -0.4100 (mpp) REVERT: Y 536 GLU cc_start: 0.3552 (OUTLIER) cc_final: 0.3226 (pm20) REVERT: Y 550 LYS cc_start: 0.2981 (OUTLIER) cc_final: 0.1670 (mttp) REVERT: Z 43 VAL cc_start: 0.2691 (t) cc_final: 0.2258 (p) REVERT: Z 52 PHE cc_start: 0.1253 (m-80) cc_final: 0.0917 (m-80) REVERT: Z 324 ARG cc_start: 0.3024 (mtp180) cc_final: 0.2402 (mpt-90) REVERT: Z 383 THR cc_start: 0.2128 (p) cc_final: 0.1918 (t) REVERT: Z 422 MET cc_start: 0.0976 (tpp) cc_final: 0.0048 (tpp) REVERT: Z 502 MET cc_start: 0.0080 (mtp) cc_final: -0.1551 (tpt) outliers start: 134 outliers final: 58 residues processed: 359 average time/residue: 1.0852 time to fit residues: 493.9338 Evaluate side-chains 277 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 208 time to evaluate : 3.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 90 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 258 VAL Chi-restraints excluded: chain T residue 278 GLN Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 446 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain U residue 121 ASN 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 287 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 U residue 476 ARG Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 184 LEU 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 337 MET Chi-restraints excluded: chain V residue 475 GLU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 164 ILE 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 308 VAL Chi-restraints excluded: chain X residue 339 VAL Chi-restraints excluded: chain X residue 383 THR 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 140 ILE Chi-restraints excluded: chain Y residue 162 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 337 GLN Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Y residue 465 ASP Chi-restraints excluded: chain Y residue 536 GLU Chi-restraints excluded: chain Y residue 550 LYS Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 91 ASP Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 361 THR 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: 1.9990 chunk 302 optimal weight: 5.9990 chunk 208 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 191 optimal weight: 0.9980 chunk 270 optimal weight: 0.5980 chunk 403 optimal weight: 0.6980 chunk 427 optimal weight: 2.9990 chunk 210 optimal weight: 0.5980 chunk 382 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 52 GLN ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 257 ASN ** T 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 264 GLN U 405 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 152 ASN V 241 HIS ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 294 ASN X 322 GLN X 388 ASN Y 174 GLN Y 204 HIS Y 286 ASN ** Y 311 GLN ** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1333 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34420 Z= 0.171 Angle : 0.607 10.546 46649 Z= 0.305 Chirality : 0.043 0.276 5520 Planarity : 0.004 0.052 5999 Dihedral : 6.911 158.895 4921 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.92 % Favored : 95.94 % Rotamer: Outliers : 2.78 % Allowed : 16.04 % Favored : 81.18 % 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: -1.30 (0.12), residues: 4462 helix: -0.41 (0.11), residues: 2140 sheet: -0.86 (0.23), residues: 493 loop : -1.26 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Y 141 HIS 0.009 0.001 HIS X 144 PHE 0.024 0.002 PHE S 203 TYR 0.020 0.002 TYR U 393 ARG 0.005 0.000 ARG X 260 *********************** 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 314 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 215 time to evaluate : 3.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: -0.1031 (mmt) cc_final: -0.1798 (pmm) REVERT: C 61 MET cc_start: -0.0580 (mmt) cc_final: -0.1027 (mtt) REVERT: J 122 PHE cc_start: 0.0016 (t80) cc_final: -0.1002 (t80) REVERT: S 223 VAL cc_start: -0.0909 (OUTLIER) cc_final: -0.1209 (t) REVERT: S 259 MET cc_start: 0.2620 (mmt) cc_final: 0.1569 (tmt) REVERT: S 279 LYS cc_start: 0.1880 (OUTLIER) cc_final: 0.1665 (mmpt) REVERT: T 118 MET cc_start: 0.1317 (ttt) cc_final: 0.1068 (ttp) REVERT: T 313 PHE cc_start: 0.3493 (m-10) cc_final: 0.3202 (m-10) REVERT: T 483 MET cc_start: 0.0404 (pp-130) cc_final: -0.0076 (tpt) REVERT: U 46 ASP cc_start: 0.4169 (t0) cc_final: 0.3944 (t0) REVERT: U 60 GLN cc_start: 0.2196 (pp30) cc_final: 0.1846 (pm20) REVERT: U 282 MET cc_start: 0.0137 (mmt) cc_final: -0.1109 (ptm) REVERT: V 223 ILE cc_start: -0.3587 (OUTLIER) cc_final: -0.3846 (mt) REVERT: V 241 HIS cc_start: 0.1686 (t-90) cc_final: 0.0843 (t-90) REVERT: V 475 GLU cc_start: 0.0267 (OUTLIER) cc_final: -0.0269 (mm-30) REVERT: X 189 LYS cc_start: 0.1133 (OUTLIER) cc_final: 0.0759 (mtmt) REVERT: X 194 MET cc_start: 0.0673 (OUTLIER) cc_final: -0.0075 (mpp) REVERT: X 422 MET cc_start: 0.1166 (pp-130) cc_final: -0.0496 (ptt) REVERT: Y 52 PHE cc_start: 0.3149 (m-80) cc_final: 0.1329 (t80) REVERT: Y 65 VAL cc_start: 0.2866 (t) cc_final: 0.2618 (t) REVERT: Y 194 MET cc_start: -0.0593 (mtm) cc_final: -0.1586 (mtm) REVERT: Y 286 ASN cc_start: 0.1277 (OUTLIER) cc_final: 0.0446 (t0) REVERT: Y 422 MET cc_start: -0.2072 (ttt) cc_final: -0.3943 (mpt) REVERT: Z 52 PHE cc_start: 0.1446 (m-80) cc_final: 0.1077 (m-80) REVERT: Z 324 ARG cc_start: 0.2967 (mtp180) cc_final: 0.2357 (mpt180) REVERT: Z 355 PHE cc_start: -0.1243 (OUTLIER) cc_final: -0.4081 (m-10) REVERT: Z 488 MET cc_start: 0.2161 (mmt) cc_final: -0.0721 (ptm) REVERT: Z 502 MET cc_start: 0.0081 (mtp) cc_final: -0.1547 (tpt) outliers start: 99 outliers final: 51 residues processed: 285 average time/residue: 1.1470 time to fit residues: 415.6057 Evaluate side-chains 258 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 199 time to evaluate : 3.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain S residue 279 LYS Chi-restraints excluded: chain T residue 144 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 439 MET 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 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 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 383 ILE Chi-restraints excluded: chain U residue 386 GLN Chi-restraints excluded: chain U residue 389 ASP Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 184 LEU 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 223 ILE 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 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 189 LYS 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 383 THR Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 103 VAL 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 Z residue 141 TRP Chi-restraints excluded: chain Z residue 355 PHE 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: 0.2980 chunk 242 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 318 optimal weight: 0.4980 chunk 176 optimal weight: 4.9990 chunk 364 optimal weight: 0.4980 chunk 295 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 218 optimal weight: 7.9990 chunk 383 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 98 GLN ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN ** S 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 297 GLN ** T 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 336 GLN ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 152 ASN ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 322 GLN ** 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: 0.1344 moved from start: 0.5416 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= 0.159 Angle : 0.583 9.821 46649 Z= 0.291 Chirality : 0.042 0.238 5520 Planarity : 0.004 0.059 5999 Dihedral : 6.414 127.420 4921 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.39 % Favored : 95.47 % Rotamer: Outliers : 3.39 % Allowed : 16.44 % 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: -0.87 (0.12), residues: 4462 helix: -0.01 (0.11), residues: 2126 sheet: -0.80 (0.24), residues: 479 loop : -1.06 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 141 HIS 0.007 0.001 HIS X 144 PHE 0.024 0.001 PHE I 82 TYR 0.015 0.001 TYR Z 340 ARG 0.008 0.000 ARG V 146 *********************** 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 331 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 210 time to evaluate : 3.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.2621 (OUTLIER) cc_final: 0.1200 (tpt) REVERT: C 61 MET cc_start: -0.1017 (mmt) cc_final: -0.1465 (mtt) REVERT: G 123 LEU cc_start: 0.5322 (OUTLIER) cc_final: 0.5011 (pp) REVERT: S 118 ASN cc_start: 0.3569 (m-40) cc_final: 0.3246 (m110) REVERT: S 203 PHE cc_start: 0.2515 (p90) cc_final: 0.2261 (p90) REVERT: S 223 VAL cc_start: -0.1121 (OUTLIER) cc_final: -0.1396 (t) REVERT: S 259 MET cc_start: 0.2631 (mmt) cc_final: 0.1596 (tmt) REVERT: T 118 MET cc_start: 0.1147 (ttt) cc_final: 0.0814 (ttp) REVERT: T 313 PHE cc_start: 0.3557 (m-10) cc_final: 0.3343 (m-10) REVERT: T 371 GLU cc_start: 0.1665 (OUTLIER) cc_final: -0.0291 (tt0) REVERT: T 403 ASP cc_start: -0.1084 (OUTLIER) cc_final: -0.1899 (t70) REVERT: T 439 MET cc_start: 0.2425 (mtt) cc_final: 0.1752 (mtt) REVERT: T 483 MET cc_start: -0.0083 (pp-130) cc_final: -0.0290 (tpt) REVERT: T 559 LEU cc_start: -0.1331 (OUTLIER) cc_final: -0.1584 (pt) REVERT: U 60 GLN cc_start: 0.2603 (pp30) cc_final: 0.2151 (pm20) REVERT: U 282 MET cc_start: -0.0141 (mmt) cc_final: -0.1085 (ptm) REVERT: U 513 ARG cc_start: 0.3379 (tpp-160) cc_final: 0.3074 (tpt170) REVERT: V 241 HIS cc_start: 0.1638 (t-90) cc_final: 0.0778 (t-90) REVERT: V 475 GLU cc_start: 0.0343 (OUTLIER) cc_final: -0.0148 (mm-30) REVERT: X 189 LYS cc_start: 0.1351 (OUTLIER) cc_final: 0.0942 (mtmt) REVERT: X 194 MET cc_start: 0.0459 (OUTLIER) cc_final: -0.0212 (mpp) REVERT: X 290 PHE cc_start: -0.0569 (OUTLIER) cc_final: -0.1843 (t80) REVERT: X 422 MET cc_start: 0.1071 (pp-130) cc_final: -0.0596 (ptt) REVERT: Y 52 PHE cc_start: 0.3197 (m-80) cc_final: 0.1278 (t80) REVERT: Y 194 MET cc_start: -0.0229 (mtm) cc_final: -0.0533 (mtm) REVERT: Y 286 ASN cc_start: -0.0384 (OUTLIER) cc_final: -0.1363 (t0) REVERT: Y 422 MET cc_start: -0.2000 (ttt) cc_final: -0.3900 (mpt) REVERT: Z 43 VAL cc_start: 0.1714 (t) cc_final: 0.1414 (p) REVERT: Z 52 PHE cc_start: 0.1440 (m-80) cc_final: 0.1053 (m-80) REVERT: Z 224 TYR cc_start: 0.3056 (t80) cc_final: 0.1469 (t80) REVERT: Z 324 ARG cc_start: 0.3038 (mtp180) cc_final: 0.2379 (mpt180) REVERT: Z 355 PHE cc_start: -0.1311 (OUTLIER) cc_final: -0.3961 (m-80) REVERT: Z 422 MET cc_start: 0.1977 (mpp) cc_final: 0.1110 (tpp) REVERT: Z 488 MET cc_start: 0.1747 (mmt) cc_final: -0.0804 (ptm) REVERT: Z 502 MET cc_start: -0.0273 (mtp) cc_final: -0.2054 (tpt) outliers start: 121 outliers final: 60 residues processed: 301 average time/residue: 1.0363 time to fit residues: 398.1063 Evaluate side-chains 272 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 200 time to evaluate : 3.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 65 VAL 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 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 287 MET Chi-restraints excluded: chain T residue 357 LEU 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 T residue 559 LEU Chi-restraints excluded: chain U residue 121 ASN 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 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 389 ASP Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain V residue 134 ASN 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 223 ILE Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 475 GLU Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 494 ILE Chi-restraints excluded: chain V residue 521 GLU Chi-restraints excluded: chain X residue 60 LEU 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 155 THR Chi-restraints excluded: chain X residue 165 LYS Chi-restraints excluded: chain X residue 189 LYS Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 290 PHE Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 190 THR 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 Z residue 91 ASP Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 213 VAL Chi-restraints excluded: chain Z residue 355 PHE Chi-restraints excluded: chain Z residue 383 THR 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: 0.0270 chunk 84 optimal weight: 0.0980 chunk 250 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 427 optimal weight: 2.9990 chunk 355 optimal weight: 0.7980 chunk 198 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 141 optimal weight: 0.4980 chunk 224 optimal weight: 0.0870 overall best weight: 0.2616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 ASN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN ** S 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 123 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 152 ASN ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 388 ASN Y 286 ASN ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 278 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1228 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34420 Z= 0.136 Angle : 0.546 10.817 46649 Z= 0.270 Chirality : 0.041 0.210 5520 Planarity : 0.004 0.049 5999 Dihedral : 5.835 91.680 4921 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.12 % Favored : 96.75 % Rotamer: Outliers : 3.00 % Allowed : 17.62 % Favored : 79.38 % 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: -0.51 (0.13), residues: 4462 helix: 0.29 (0.12), residues: 2140 sheet: -0.71 (0.24), residues: 470 loop : -0.86 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 141 HIS 0.007 0.001 HIS V 83 PHE 0.053 0.001 PHE R 70 TYR 0.014 0.001 TYR Y 487 ARG 0.008 0.000 ARG Z 435 *********************** 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 326 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 219 time to evaluate : 3.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.2556 (OUTLIER) cc_final: 0.1158 (tpt) REVERT: C 61 MET cc_start: -0.0981 (mmt) cc_final: -0.1329 (mtt) REVERT: E 95 ILE cc_start: 0.2128 (mp) cc_final: 0.1619 (mm) REVERT: G 123 LEU cc_start: 0.5123 (tm) cc_final: 0.4824 (pp) REVERT: S 118 ASN cc_start: 0.3136 (m-40) cc_final: 0.2764 (m110) REVERT: S 223 VAL cc_start: -0.1102 (OUTLIER) cc_final: -0.1352 (t) REVERT: S 259 MET cc_start: 0.2617 (mmt) cc_final: 0.1578 (tmt) REVERT: S 279 LYS cc_start: 0.1664 (OUTLIER) cc_final: 0.1433 (mmpt) REVERT: T 118 MET cc_start: 0.1037 (ttt) cc_final: 0.0797 (ttp) REVERT: T 207 LYS cc_start: 0.0708 (OUTLIER) cc_final: 0.0231 (pttm) REVERT: T 371 GLU cc_start: 0.1459 (OUTLIER) cc_final: -0.0256 (mt-10) REVERT: T 403 ASP cc_start: -0.1205 (OUTLIER) cc_final: -0.2000 (t0) REVERT: T 483 MET cc_start: 0.0115 (pp-130) cc_final: -0.0096 (tmm) REVERT: T 559 LEU cc_start: -0.1617 (OUTLIER) cc_final: -0.1836 (pt) REVERT: U 186 GLU cc_start: 0.2745 (tp30) cc_final: 0.2095 (mm-30) REVERT: U 282 MET cc_start: -0.0425 (mmt) cc_final: -0.1130 (ptm) REVERT: U 411 GLU cc_start: 0.0605 (OUTLIER) cc_final: -0.0666 (mm-30) REVERT: U 466 LEU cc_start: -0.4224 (OUTLIER) cc_final: -0.4552 (mp) REVERT: V 126 HIS cc_start: 0.2817 (p90) cc_final: 0.2508 (p90) REVERT: V 241 HIS cc_start: 0.1525 (t-90) cc_final: 0.0717 (t-90) REVERT: X 160 LEU cc_start: 0.2360 (OUTLIER) cc_final: 0.1863 (tp) REVERT: X 189 LYS cc_start: 0.1106 (OUTLIER) cc_final: 0.0765 (mtmt) REVERT: X 194 MET cc_start: 0.0399 (OUTLIER) cc_final: -0.0457 (mpp) REVERT: X 290 PHE cc_start: -0.0654 (OUTLIER) cc_final: -0.1922 (t80) REVERT: X 422 MET cc_start: 0.1335 (pp-130) cc_final: -0.0056 (ptt) REVERT: Y 52 PHE cc_start: 0.2934 (m-80) cc_final: 0.1064 (t80) REVERT: Y 135 ILE cc_start: 0.0539 (OUTLIER) cc_final: 0.0336 (mm) REVERT: Y 286 ASN cc_start: 0.1360 (OUTLIER) cc_final: 0.0106 (t0) REVERT: Y 422 MET cc_start: -0.1902 (ttt) cc_final: -0.3857 (mpt) REVERT: Z 52 PHE cc_start: 0.1387 (m-80) cc_final: 0.1004 (m-80) REVERT: Z 224 TYR cc_start: 0.2548 (t80) cc_final: 0.1143 (t80) REVERT: Z 324 ARG cc_start: 0.2869 (mtp180) cc_final: 0.2309 (mpt-90) REVERT: Z 355 PHE cc_start: -0.1506 (OUTLIER) cc_final: -0.4284 (m-10) REVERT: Z 422 MET cc_start: 0.1665 (mpp) cc_final: 0.1264 (tpp) REVERT: Z 486 PHE cc_start: 0.2109 (m-80) cc_final: 0.1053 (m-80) REVERT: Z 488 MET cc_start: 0.1428 (mmt) cc_final: -0.0874 (ptm) REVERT: Z 502 MET cc_start: -0.0244 (mtp) cc_final: -0.2122 (tpt) outliers start: 107 outliers final: 60 residues processed: 301 average time/residue: 1.1025 time to fit residues: 422.2171 Evaluate side-chains 277 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 201 time to evaluate : 3.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 96 ASN 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 S residue 279 LYS Chi-restraints excluded: chain T residue 121 ASN Chi-restraints excluded: chain T residue 165 ASP Chi-restraints excluded: chain T residue 172 ASP Chi-restraints excluded: chain T residue 207 LYS 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 287 MET 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 T residue 559 LEU Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 121 ASN 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 337 MET Chi-restraints excluded: chain U residue 383 ILE Chi-restraints excluded: chain U residue 389 ASP Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 466 LEU Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain V residue 134 ASN 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 337 MET Chi-restraints excluded: chain V residue 521 GLU Chi-restraints excluded: chain X residue 60 LEU 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 155 THR Chi-restraints excluded: chain X residue 160 LEU Chi-restraints excluded: chain X residue 165 LYS Chi-restraints excluded: chain X residue 189 LYS Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 290 PHE Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 562 ASN Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 190 THR Chi-restraints excluded: chain Y residue 251 MET 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 Z residue 44 ILE Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 355 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 412 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 243 optimal weight: 0.9980 chunk 312 optimal weight: 3.9990 chunk 241 optimal weight: 0.0070 chunk 359 optimal weight: 0.7980 chunk 238 optimal weight: 0.9980 chunk 426 optimal weight: 0.0270 chunk 266 optimal weight: 0.1980 chunk 259 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN ** S 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 121 ASN V 152 ASN V 242 GLN ** X 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.1275 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 34420 Z= 0.138 Angle : 0.554 14.049 46649 Z= 0.272 Chirality : 0.041 0.243 5520 Planarity : 0.004 0.048 5999 Dihedral : 5.684 76.105 4921 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.99 % Favored : 95.88 % Rotamer: Outliers : 2.89 % Allowed : 18.01 % Favored : 79.10 % 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: -0.26 (0.13), residues: 4462 helix: 0.52 (0.12), residues: 2162 sheet: -0.67 (0.24), residues: 471 loop : -0.75 (0.15), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 58 HIS 0.006 0.001 HIS V 83 PHE 0.024 0.001 PHE V 489 TYR 0.011 0.001 TYR Z 340 ARG 0.008 0.000 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 305 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 202 time to evaluate : 3.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.2591 (OUTLIER) cc_final: 0.1103 (tpt) REVERT: C 61 MET cc_start: -0.0891 (mmt) cc_final: -0.1275 (mtt) REVERT: E 95 ILE cc_start: 0.2168 (mp) cc_final: 0.1684 (mm) REVERT: G 123 LEU cc_start: 0.4957 (OUTLIER) cc_final: 0.4584 (pp) REVERT: S 223 VAL cc_start: -0.1066 (OUTLIER) cc_final: -0.1318 (t) REVERT: S 259 MET cc_start: 0.2546 (mmt) cc_final: 0.1463 (tmt) REVERT: T 118 MET cc_start: 0.0847 (ttt) cc_final: 0.0480 (ttp) REVERT: T 207 LYS cc_start: 0.0717 (OUTLIER) cc_final: 0.0234 (pttm) REVERT: T 371 GLU cc_start: 0.1577 (OUTLIER) cc_final: -0.0154 (tt0) REVERT: T 403 ASP cc_start: -0.0903 (OUTLIER) cc_final: -0.1944 (t0) REVERT: T 559 LEU cc_start: -0.1397 (OUTLIER) cc_final: -0.1649 (pt) REVERT: U 282 MET cc_start: -0.0558 (mmt) cc_final: -0.1195 (ptm) REVERT: U 411 GLU cc_start: 0.0641 (OUTLIER) cc_final: -0.0747 (mm-30) REVERT: U 466 LEU cc_start: -0.4285 (OUTLIER) cc_final: -0.4610 (mp) REVERT: V 126 HIS cc_start: 0.2900 (p90) cc_final: 0.2589 (p90) REVERT: V 132 PHE cc_start: -0.0590 (OUTLIER) cc_final: -0.1456 (m-80) REVERT: V 215 ILE cc_start: -0.0415 (OUTLIER) cc_final: -0.0913 (tt) REVERT: V 241 HIS cc_start: 0.1419 (t-90) cc_final: 0.0655 (t-90) REVERT: V 282 MET cc_start: 0.1713 (tpt) cc_final: 0.0084 (tpt) REVERT: X 194 MET cc_start: 0.0432 (OUTLIER) cc_final: -0.0484 (mpp) REVERT: X 290 PHE cc_start: -0.0717 (OUTLIER) cc_final: -0.2304 (t80) REVERT: X 422 MET cc_start: 0.1258 (pp-130) cc_final: -0.0099 (ptt) REVERT: Y 52 PHE cc_start: 0.3022 (m-80) cc_final: 0.1099 (t80) REVERT: Y 135 ILE cc_start: 0.0933 (OUTLIER) cc_final: 0.0502 (mm) REVERT: Y 251 MET cc_start: 0.0783 (OUTLIER) cc_final: -0.0298 (mmt) REVERT: Y 422 MET cc_start: -0.1588 (ttt) cc_final: -0.3758 (mpt) REVERT: Y 488 MET cc_start: 0.5005 (pp-130) cc_final: 0.3428 (ptm) REVERT: Z 224 TYR cc_start: 0.2679 (t80) cc_final: 0.1133 (t80) REVERT: Z 324 ARG cc_start: 0.2970 (mtp180) cc_final: 0.2648 (mpt-90) REVERT: Z 355 PHE cc_start: -0.1449 (OUTLIER) cc_final: -0.4056 (m-80) REVERT: Z 422 MET cc_start: 0.1580 (mpp) cc_final: 0.1297 (tpp) REVERT: Z 488 MET cc_start: 0.1523 (mmt) cc_final: -0.0969 (ptp) REVERT: Z 502 MET cc_start: -0.0695 (mtp) cc_final: -0.2486 (tpt) outliers start: 103 outliers final: 66 residues processed: 277 average time/residue: 1.1271 time to fit residues: 394.8540 Evaluate side-chains 282 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 200 time to evaluate : 3.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 56 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 P residue 146 LEU Chi-restraints excluded: chain R residue 100 VAL 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 121 ASN Chi-restraints excluded: chain T residue 165 ASP Chi-restraints excluded: chain T residue 172 ASP Chi-restraints excluded: chain T residue 207 LYS 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 287 MET Chi-restraints excluded: chain T residue 357 LEU 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 T residue 559 LEU Chi-restraints excluded: chain U residue 121 ASN 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 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 383 ILE Chi-restraints excluded: chain U residue 389 ASP Chi-restraints excluded: chain U residue 403 ASP Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 466 LEU Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain V residue 134 ASN 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 215 ILE Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 489 PHE Chi-restraints excluded: chain V residue 521 GLU Chi-restraints excluded: chain X residue 60 LEU 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 155 THR Chi-restraints excluded: chain X residue 160 LEU Chi-restraints excluded: chain X residue 189 LYS Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 227 MET Chi-restraints excluded: chain X residue 290 PHE Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 251 MET Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 80 MET Chi-restraints excluded: chain Z residue 91 ASP Chi-restraints excluded: chain Z residue 355 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 263 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 254 optimal weight: 0.0970 chunk 128 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 270 optimal weight: 10.0000 chunk 290 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 334 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 297 GLN ** T 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 144 HIS ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1455 moved from start: 0.6349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 34420 Z= 0.167 Angle : 0.593 16.244 46649 Z= 0.293 Chirality : 0.043 0.281 5520 Planarity : 0.004 0.046 5999 Dihedral : 5.824 81.242 4921 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.55 % Favored : 95.32 % Rotamer: Outliers : 3.20 % Allowed : 18.18 % Favored : 78.63 % 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: -0.27 (0.13), residues: 4462 helix: 0.55 (0.12), residues: 2145 sheet: -0.88 (0.24), residues: 481 loop : -0.74 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 58 HIS 0.008 0.001 HIS S 250 PHE 0.050 0.002 PHE R 70 TYR 0.014 0.001 TYR P 75 ARG 0.010 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 321 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 207 time to evaluate : 3.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.2846 (OUTLIER) cc_final: 0.1319 (tpt) REVERT: C 61 MET cc_start: -0.0758 (mmt) cc_final: -0.1384 (mtt) REVERT: S 62 MET cc_start: 0.3134 (tmm) cc_final: 0.2597 (tmm) REVERT: S 118 ASN cc_start: 0.2959 (m-40) cc_final: 0.2712 (p0) REVERT: T 118 MET cc_start: 0.1134 (ttt) cc_final: -0.1251 (mtp) REVERT: T 278 GLN cc_start: -0.1197 (OUTLIER) cc_final: -0.1633 (mm-40) REVERT: T 371 GLU cc_start: 0.2008 (OUTLIER) cc_final: 0.0272 (mm-30) REVERT: T 403 ASP cc_start: -0.0451 (OUTLIER) cc_final: -0.1785 (t70) REVERT: T 483 MET cc_start: 0.0771 (OUTLIER) cc_final: -0.0972 (pmm) REVERT: T 559 LEU cc_start: -0.1384 (OUTLIER) cc_final: -0.1629 (pt) REVERT: U 282 MET cc_start: -0.0447 (mmt) cc_final: -0.1137 (ptm) REVERT: U 411 GLU cc_start: 0.1223 (OUTLIER) cc_final: -0.0522 (mm-30) REVERT: U 466 LEU cc_start: -0.3767 (OUTLIER) cc_final: -0.4147 (mp) REVERT: V 126 HIS cc_start: 0.3201 (p90) cc_final: 0.2926 (p90) REVERT: V 132 PHE cc_start: -0.0233 (OUTLIER) cc_final: -0.0961 (m-80) REVERT: V 215 ILE cc_start: -0.0339 (OUTLIER) cc_final: -0.0826 (tt) REVERT: V 223 ILE cc_start: -0.3571 (OUTLIER) cc_final: -0.4502 (mt) REVERT: V 241 HIS cc_start: 0.1441 (t-90) cc_final: 0.0954 (t-90) REVERT: V 282 MET cc_start: 0.1763 (tpt) cc_final: 0.0067 (tpt) REVERT: V 492 ILE cc_start: -0.1460 (OUTLIER) cc_final: -0.1781 (mm) REVERT: X 110 LYS cc_start: 0.4397 (ttmm) cc_final: 0.4135 (ptpt) REVERT: X 189 LYS cc_start: 0.1705 (OUTLIER) cc_final: 0.0759 (mtmt) REVERT: X 194 MET cc_start: 0.0406 (OUTLIER) cc_final: -0.0588 (mpp) REVERT: X 290 PHE cc_start: -0.0834 (OUTLIER) cc_final: -0.2550 (t80) REVERT: X 422 MET cc_start: 0.0645 (pp-130) cc_final: -0.0866 (ptt) REVERT: Y 52 PHE cc_start: 0.3339 (m-80) cc_final: 0.1282 (t80) REVERT: Y 251 MET cc_start: 0.1946 (mpt) cc_final: 0.0584 (mmt) REVERT: Y 422 MET cc_start: -0.1311 (ttt) cc_final: -0.3691 (mpt) REVERT: Z 43 VAL cc_start: 0.2196 (t) cc_final: 0.1947 (p) REVERT: Z 224 TYR cc_start: 0.2815 (t80) cc_final: 0.1342 (t80) REVERT: Z 324 ARG cc_start: 0.3172 (mtp180) cc_final: 0.2619 (mpt180) REVERT: Z 422 MET cc_start: 0.1645 (mpp) cc_final: 0.1296 (tpp) REVERT: Z 486 PHE cc_start: 0.2124 (m-80) cc_final: 0.0958 (m-80) REVERT: Z 488 MET cc_start: 0.1678 (mmt) cc_final: -0.0821 (ptp) REVERT: Z 502 MET cc_start: -0.0404 (mtp) cc_final: -0.2333 (tpt) outliers start: 114 outliers final: 70 residues processed: 296 average time/residue: 1.0846 time to fit residues: 407.4711 Evaluate side-chains 273 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 188 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 121 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 322 ILE Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 371 GLU Chi-restraints excluded: chain T residue 403 ASP Chi-restraints excluded: chain T residue 483 MET 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 239 ILE 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 383 ILE Chi-restraints excluded: chain U residue 389 ASP Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 466 LEU Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 152 ASN 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 215 ILE Chi-restraints excluded: chain V residue 223 ILE Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 427 VAL 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 V residue 521 GLU Chi-restraints excluded: chain X residue 60 LEU 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 155 THR Chi-restraints excluded: chain X residue 160 LEU Chi-restraints excluded: chain X residue 189 LYS Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 227 MET Chi-restraints excluded: chain X residue 290 PHE Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 103 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 465 ASP Chi-restraints excluded: chain Z residue 44 ILE 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 213 VAL Chi-restraints excluded: chain Z residue 252 ASN 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: 0.7980 chunk 408 optimal weight: 0.3980 chunk 372 optimal weight: 0.9990 chunk 396 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 311 optimal weight: 4.9990 chunk 121 optimal weight: 0.3980 chunk 358 optimal weight: 1.9990 chunk 375 optimal weight: 3.9990 chunk 395 optimal weight: 0.4980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 388 ASN ** X 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1432 moved from start: 0.6588 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= 0.153 Angle : 0.587 16.039 46649 Z= 0.288 Chirality : 0.042 0.214 5520 Planarity : 0.004 0.054 5999 Dihedral : 5.728 86.535 4921 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.19 % Favored : 95.67 % Rotamer: Outliers : 2.55 % Allowed : 18.88 % Favored : 78.57 % 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: -0.14 (0.13), residues: 4462 helix: 0.69 (0.12), residues: 2139 sheet: -0.86 (0.24), residues: 489 loop : -0.70 (0.15), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 58 HIS 0.004 0.001 HIS U 126 PHE 0.024 0.001 PHE V 489 TYR 0.010 0.001 TYR Z 340 ARG 0.012 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 288 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 197 time to evaluate : 3.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.2851 (OUTLIER) cc_final: 0.1351 (tpt) REVERT: C 61 MET cc_start: -0.0605 (mmt) cc_final: -0.1229 (mtt) REVERT: C 81 MET cc_start: 0.5065 (ppp) cc_final: 0.4804 (ppp) REVERT: F 61 MET cc_start: 0.1545 (mmt) cc_final: 0.1028 (tpt) REVERT: P 146 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.7066 (mm) REVERT: S 118 ASN cc_start: 0.2533 (m-40) cc_final: 0.2287 (p0) REVERT: T 118 MET cc_start: 0.1044 (ttt) cc_final: -0.1059 (mtp) REVERT: T 371 GLU cc_start: 0.1922 (OUTLIER) cc_final: 0.0549 (mm-30) REVERT: T 403 ASP cc_start: -0.0569 (OUTLIER) cc_final: -0.1783 (t70) REVERT: T 483 MET cc_start: 0.1333 (OUTLIER) cc_final: -0.0841 (pmm) REVERT: U 282 MET cc_start: -0.0125 (mmt) cc_final: -0.0718 (ptm) REVERT: U 411 GLU cc_start: 0.1386 (OUTLIER) cc_final: -0.0445 (mm-30) REVERT: U 466 LEU cc_start: -0.3866 (OUTLIER) cc_final: -0.4262 (mp) REVERT: V 126 HIS cc_start: 0.3248 (p90) cc_final: 0.2960 (p90) REVERT: V 132 PHE cc_start: -0.0741 (OUTLIER) cc_final: -0.1301 (m-80) REVERT: V 215 ILE cc_start: -0.0074 (OUTLIER) cc_final: -0.0551 (tt) REVERT: V 241 HIS cc_start: 0.1454 (t-90) cc_final: 0.0975 (t-90) REVERT: V 282 MET cc_start: 0.1652 (tpt) cc_final: -0.0115 (tpt) REVERT: V 492 ILE cc_start: -0.1508 (OUTLIER) cc_final: -0.1780 (mm) REVERT: X 110 LYS cc_start: 0.4260 (ttmm) cc_final: 0.4003 (ptpt) REVERT: X 189 LYS cc_start: 0.1363 (OUTLIER) cc_final: 0.0401 (mtmm) REVERT: X 194 MET cc_start: 0.0413 (tpt) cc_final: -0.0601 (mpp) REVERT: X 290 PHE cc_start: -0.0709 (OUTLIER) cc_final: -0.2482 (t80) REVERT: X 422 MET cc_start: 0.0883 (pp-130) cc_final: -0.0542 (ptt) REVERT: Y 52 PHE cc_start: 0.3279 (m-80) cc_final: 0.1249 (t80) REVERT: Y 251 MET cc_start: 0.1909 (OUTLIER) cc_final: 0.0507 (mmt) REVERT: Y 422 MET cc_start: -0.1243 (ttt) cc_final: -0.3727 (mpt) REVERT: Z 43 VAL cc_start: 0.1935 (t) cc_final: 0.1683 (p) REVERT: Z 90 MET cc_start: 0.0345 (ppp) cc_final: -0.0588 (ttm) REVERT: Z 224 TYR cc_start: 0.2743 (t80) cc_final: 0.1293 (t80) REVERT: Z 253 GLU cc_start: 0.2298 (OUTLIER) cc_final: -0.0591 (tp30) REVERT: Z 324 ARG cc_start: 0.3498 (mtp180) cc_final: 0.2682 (mpt180) REVERT: Z 422 MET cc_start: 0.1775 (mpp) cc_final: 0.1423 (tpp) REVERT: Z 488 MET cc_start: 0.1500 (mmt) cc_final: -0.0962 (ptp) REVERT: Z 502 MET cc_start: -0.0499 (mtp) cc_final: -0.2462 (tpt) outliers start: 91 outliers final: 62 residues processed: 267 average time/residue: 1.1367 time to fit residues: 384.7240 Evaluate side-chains 272 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 196 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 121 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 371 GLU Chi-restraints excluded: chain T residue 403 ASP Chi-restraints excluded: chain T residue 483 MET 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 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 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 383 ILE Chi-restraints excluded: chain U residue 389 ASP Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 466 LEU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 146 ARG Chi-restraints excluded: chain V residue 177 LEU 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 215 ILE Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 489 PHE Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 521 GLU Chi-restraints excluded: chain X residue 60 LEU 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 155 THR Chi-restraints excluded: chain X residue 189 LYS Chi-restraints excluded: chain X residue 227 MET Chi-restraints excluded: chain X residue 290 PHE Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 562 ASN Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 251 MET Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 465 ASP Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 91 ASP Chi-restraints excluded: chain Z residue 122 MET 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 347 THR 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: 2.9990 chunk 419 optimal weight: 0.0270 chunk 256 optimal weight: 0.0970 chunk 199 optimal weight: 0.9990 chunk 291 optimal weight: 2.9990 chunk 440 optimal weight: 1.9990 chunk 405 optimal weight: 10.0000 chunk 350 optimal weight: 0.0980 chunk 36 optimal weight: 40.0000 chunk 270 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 336 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 388 ASN ** X 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1474 moved from start: 0.6881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 34420 Z= 0.160 Angle : 0.595 15.022 46649 Z= 0.291 Chirality : 0.042 0.262 5520 Planarity : 0.004 0.049 5999 Dihedral : 5.743 89.203 4920 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.64 % Favored : 95.23 % Rotamer: Outliers : 2.33 % Allowed : 19.27 % Favored : 78.40 % 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: -0.14 (0.13), residues: 4462 helix: 0.72 (0.12), residues: 2140 sheet: -0.87 (0.24), residues: 484 loop : -0.74 (0.15), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 58 HIS 0.004 0.001 HIS U 126 PHE 0.050 0.001 PHE R 70 TYR 0.015 0.001 TYR T 304 ARG 0.013 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 289 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 206 time to evaluate : 3.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.2837 (OUTLIER) cc_final: 0.1269 (tpt) REVERT: C 61 MET cc_start: -0.0452 (mmt) cc_final: -0.1071 (mtt) REVERT: F 61 MET cc_start: 0.1796 (mmt) cc_final: 0.1328 (tpt) REVERT: G 123 LEU cc_start: 0.4085 (tm) cc_final: 0.3637 (pp) REVERT: H 61 MET cc_start: 0.5386 (ppp) cc_final: 0.4777 (pmm) REVERT: P 146 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.7092 (mm) REVERT: S 62 MET cc_start: 0.2747 (mmm) cc_final: 0.1722 (mmm) REVERT: S 118 ASN cc_start: 0.2678 (m-40) cc_final: 0.2412 (p0) REVERT: S 259 MET cc_start: 0.0292 (tmt) cc_final: -0.0180 (mmt) REVERT: T 118 MET cc_start: 0.1203 (ttt) cc_final: -0.1473 (mtp) REVERT: T 371 GLU cc_start: 0.2211 (OUTLIER) cc_final: 0.0923 (mm-30) REVERT: T 403 ASP cc_start: -0.0443 (OUTLIER) cc_final: -0.1779 (t0) REVERT: T 483 MET cc_start: 0.0960 (OUTLIER) cc_final: -0.1064 (pmm) REVERT: T 559 LEU cc_start: -0.1070 (OUTLIER) cc_final: -0.1294 (pt) REVERT: U 282 MET cc_start: -0.0028 (mmt) cc_final: -0.0649 (ptm) REVERT: U 411 GLU cc_start: 0.1319 (OUTLIER) cc_final: -0.0159 (tt0) REVERT: U 439 MET cc_start: 0.1653 (ptp) cc_final: -0.1110 (ttm) REVERT: U 466 LEU cc_start: -0.3851 (OUTLIER) cc_final: -0.4279 (mp) REVERT: V 126 HIS cc_start: 0.3256 (p90) cc_final: 0.2984 (p90) REVERT: V 132 PHE cc_start: -0.0754 (OUTLIER) cc_final: -0.1272 (m-80) REVERT: V 215 ILE cc_start: -0.0331 (OUTLIER) cc_final: -0.0843 (tt) REVERT: V 223 ILE cc_start: -0.3363 (OUTLIER) cc_final: -0.4232 (mt) REVERT: V 240 ILE cc_start: 0.4207 (mt) cc_final: 0.3621 (pt) REVERT: V 241 HIS cc_start: 0.1594 (t-90) cc_final: 0.1108 (t-90) REVERT: V 282 MET cc_start: 0.1637 (tpt) cc_final: -0.0137 (tpt) REVERT: V 492 ILE cc_start: -0.1471 (OUTLIER) cc_final: -0.1702 (mm) REVERT: X 110 LYS cc_start: 0.4192 (ttmm) cc_final: 0.3903 (ptpt) REVERT: X 189 LYS cc_start: 0.0945 (OUTLIER) cc_final: 0.0114 (mtmm) REVERT: X 194 MET cc_start: 0.0543 (tpt) cc_final: -0.0511 (mpp) REVERT: X 290 PHE cc_start: -0.0574 (OUTLIER) cc_final: -0.2490 (t80) REVERT: X 422 MET cc_start: 0.0659 (pp-130) cc_final: -0.0859 (ptt) REVERT: Y 52 PHE cc_start: 0.3429 (m-80) cc_final: 0.1336 (t80) REVERT: Y 118 LEU cc_start: 0.1844 (mt) cc_final: 0.1593 (mt) REVERT: Y 251 MET cc_start: 0.1949 (mpt) cc_final: 0.0559 (mmt) REVERT: Y 422 MET cc_start: -0.1092 (ttt) cc_final: -0.3619 (mpt) REVERT: Z 43 VAL cc_start: 0.2245 (t) cc_final: 0.2018 (p) REVERT: Z 90 MET cc_start: 0.0481 (ppp) cc_final: 0.0198 (ppp) REVERT: Z 224 TYR cc_start: 0.2928 (t80) cc_final: 0.1320 (t80) REVERT: Z 253 GLU cc_start: 0.2398 (OUTLIER) cc_final: -0.0343 (tp30) REVERT: Z 324 ARG cc_start: 0.3325 (mtp180) cc_final: 0.2520 (mpt180) REVERT: Z 422 MET cc_start: 0.1852 (mpp) cc_final: 0.1410 (tpp) REVERT: Z 486 PHE cc_start: 0.2286 (m-80) cc_final: 0.0922 (m-80) REVERT: Z 488 MET cc_start: 0.1531 (mmt) cc_final: -0.0887 (ptp) REVERT: Z 502 MET cc_start: -0.0607 (mtp) cc_final: -0.2342 (tpt) outliers start: 83 outliers final: 58 residues processed: 271 average time/residue: 1.1923 time to fit residues: 406.7037 Evaluate side-chains 273 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 200 time to evaluate : 3.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 172 PHE Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 121 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 371 GLU Chi-restraints excluded: chain T residue 403 ASP Chi-restraints excluded: chain T residue 483 MET 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 239 ILE 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 383 ILE Chi-restraints excluded: chain U residue 389 ASP Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 466 LEU Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 152 ASN 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 215 ILE Chi-restraints excluded: chain V residue 223 ILE Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 427 VAL 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 V residue 521 GLU Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 189 LYS Chi-restraints excluded: chain X residue 227 MET Chi-restraints excluded: chain X residue 290 PHE Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 562 ASN Chi-restraints excluded: chain Y residue 87 CYS 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 465 ASP Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 91 ASP Chi-restraints excluded: chain Z residue 122 MET 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: 0.0980 chunk 373 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 323 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 351 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 chunk 360 optimal weight: 0.0370 chunk 44 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 ** S 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5096 r_free = 0.5096 target = 0.287282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.258044 restraints weight = 60902.928| |-----------------------------------------------------------------------------| r_work (start): 0.4846 rms_B_bonded: 2.38 r_work: 0.4776 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1343 moved from start: 0.7077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 34420 Z= 0.149 Angle : 0.590 14.740 46649 Z= 0.285 Chirality : 0.042 0.211 5520 Planarity : 0.004 0.050 5999 Dihedral : 5.591 85.445 4920 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.06 % Favored : 95.81 % Rotamer: Outliers : 2.19 % Allowed : 19.66 % Favored : 78.15 % 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: -0.02 (0.13), residues: 4462 helix: 0.86 (0.12), residues: 2131 sheet: -0.80 (0.25), residues: 472 loop : -0.73 (0.15), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 141 HIS 0.004 0.001 HIS U 126 PHE 0.025 0.001 PHE V 489 TYR 0.010 0.001 TYR T 304 ARG 0.011 0.000 ARG Z 435 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9149.61 seconds wall clock time: 162 minutes 52.44 seconds (9772.44 seconds total)