Starting phenix.real_space_refine on Thu Feb 22 09:59:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rer_4854/02_2024/6rer_4854_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rer_4854/02_2024/6rer_4854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rer_4854/02_2024/6rer_4854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rer_4854/02_2024/6rer_4854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rer_4854/02_2024/6rer_4854_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rer_4854/02_2024/6rer_4854_updated.pdb" } resolution = 2.9 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= 0.005 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 "B GLU 111": "OE1" <-> "OE2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "G PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "I GLU 111": "OE1" <-> "OE2" Residue "P PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P GLU 143": "OE1" <-> "OE2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 68": "OD1" <-> "OD2" Residue "R ASP 95": "OD1" <-> "OD2" Residue "R ASP 143": "OD1" <-> "OD2" Residue "R ASP 156": "OD1" <-> "OD2" Residue "R PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 214": "OD1" <-> "OD2" Residue "S ASP 232": "OD1" <-> "OD2" Residue "S ASP 241": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ARG 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 GLU 186": "OE1" <-> "OE2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 247": "OE1" <-> "OE2" Residue "T TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 455": "OE1" <-> "OE2" Residue "T PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 311": "OE1" <-> "OE2" Residue "U PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U ARG 342": "NH1" <-> "NH2" Residue "U ARG 343": "NH1" <-> "NH2" Residue "U ARG 364": "NH1" <-> "NH2" Residue "U PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 409": "OE1" <-> "OE2" Residue "U GLU 411": "OE1" <-> "OE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 454": "NH1" <-> "NH2" 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 GLU 521": "OE1" <-> "OE2" 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 PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V ASP 467": "OD1" <-> "OD2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 71": "NH1" <-> "NH2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X ASP 104": "OD1" <-> "OD2" Residue "X ARG 115": "NH1" <-> "NH2" Residue "X ARG 120": "NH1" <-> "NH2" Residue "X ASP 136": "OD1" <-> "OD2" 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 GLU 215": "OE1" <-> "OE2" Residue "X GLU 253": "OE1" <-> "OE2" Residue "X ARG 258": "NH1" <-> "NH2" Residue "X GLU 270": "OE1" <-> "OE2" Residue "X TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 366": "NH1" <-> "NH2" Residue "X GLU 370": "OE1" <-> "OE2" Residue "X TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 378": "OD1" <-> "OD2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 462": "OD1" <-> "OD2" Residue "X PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 479": "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 520": "OE1" <-> "OE2" Residue "X GLU 533": "OE1" <-> "OE2" Residue "X ASP 542": "OD1" <-> "OD2" Residue "X ASP 543": "OD1" <-> "OD2" Residue "Y TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 49": "OD1" <-> "OD2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y GLU 55": "OE1" <-> "OE2" Residue "Y GLU 66": "OE1" <-> "OE2" Residue "Y ARG 71": "NH1" <-> "NH2" 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 PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 216": "NH1" <-> "NH2" Residue "Y GLU 226": "OE1" <-> "OE2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 289": "NH1" <-> "NH2" Residue "Y ASP 345": "OD1" <-> "OD2" Residue "Y PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 497": "OE1" <-> "OE2" Residue "Y ASP 500": "OD1" <-> "OD2" Residue "Y ASP 505": "OD1" <-> "OD2" Residue "Y ARG 509": "NH1" <-> "NH2" Residue "Y ASP 528": "OD1" <-> "OD2" Residue "Y ASP 542": "OD1" <-> "OD2" Residue "Y GLU 546": "OE1" <-> "OE2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 49": "OD1" <-> "OD2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "Z ASP 82": "OD1" <-> "OD2" Residue "Z GLU 131": "OE1" <-> "OE2" 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 ARG 218": "NH1" <-> "NH2" Residue "Z GLU 219": "OE1" <-> "OE2" Residue "Z ARG 225": "NH1" <-> "NH2" Residue "Z GLU 238": "OE1" <-> "OE2" Residue "Z ARG 239": "NH1" <-> "NH2" Residue "Z TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 296": "OE1" <-> "OE2" Residue "Z TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 378": "OD1" <-> "OD2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z ASP 415": "OD1" <-> "OD2" Residue "Z PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z ASP 513": "OD1" <-> "OD2" Residue "Z ASP 528": "OD1" <-> "OD2" Residue "Z GLU 541": "OE1" <-> "OE2" Residue "Z ASP 542": "OD1" <-> "OD2" Residue "Z ASP 543": "OD1" <-> "OD2" Residue "Z GLU 547": "OE1" <-> "OE2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 552": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33899 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "P" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 895 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3609 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 456} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.73, per 1000 atoms: 0.52 Number of scatterers: 33899 At special positions: 0 Unit cell: (163.215, 134.784, 206.388, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 13 15.00 Mg 5 11.99 O 6424 8.00 N 5796 7.00 C 21545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.25 Conformation dependent library (CDL) restraints added in 6.6 seconds 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8162 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 169 helices and 27 sheets defined 47.3% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.88 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 removed outlier: 4.056A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 91 removed outlier: 4.112A pdb=" N GLY A 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 74 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 82 " --> pdb=" O GLY A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 125 removed outlier: 3.617A pdb=" N ALA A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LYS A 97 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 100 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER A 112 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 119 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 122 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 125 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.932A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 125 removed outlier: 3.543A pdb=" N ALA B 96 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LYS B 97 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 106 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 119 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 121 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 124 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 125 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 91 removed outlier: 4.113A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 126 removed outlier: 4.053A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 91 removed outlier: 3.942A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 126 removed outlier: 3.659A pdb=" N ALA D 96 " --> pdb=" O PRO D 93 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LYS D 97 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU D 104 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 119 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE D 126 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 91 removed outlier: 4.452A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 126 removed outlier: 3.930A pdb=" N ALA E 96 " --> pdb=" O PRO E 93 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LYS E 97 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA E 108 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLU E 111 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER E 112 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 118 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU E 125 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE E 126 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 91 removed outlier: 3.749A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 125 removed outlier: 3.632A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 91 removed outlier: 4.013A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 110 removed outlier: 3.564A pdb=" N ALA G 96 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU G 104 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR G 110 " --> pdb=" O PHE G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 125 removed outlier: 3.589A pdb=" N SER G 117 " --> pdb=" O ILE G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 91 removed outlier: 3.822A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ALA H 70 " --> pdb=" O CYS H 66 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ALA H 72 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 125 removed outlier: 5.310A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU H 119 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE H 124 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU H 125 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 91 removed outlier: 3.894A pdb=" N GLY I 65 " --> pdb=" O MET I 61 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ALA I 70 " --> pdb=" O CYS I 66 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA I 72 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY I 79 " --> pdb=" O GLY I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 95 No H-bonds generated for 'chain 'I' and resid 93 through 95' Processing helix chain 'I' and resid 98 through 123 removed outlier: 3.505A pdb=" N LEU I 105 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 91 removed outlier: 3.804A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS J 66 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 95 No H-bonds generated for 'chain 'J' and resid 93 through 95' Processing helix chain 'J' and resid 98 through 125 removed outlier: 4.105A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 63 removed outlier: 3.583A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 83 removed outlier: 3.935A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 92 No H-bonds generated for 'chain 'P' and resid 89 through 92' Processing helix chain 'P' and resid 98 through 108 Processing helix chain 'P' and resid 116 through 125 removed outlier: 3.758A pdb=" N ALA P 124 " --> pdb=" O LYS P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 146 removed outlier: 3.823A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU P 146 " --> pdb=" O GLU P 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 30 removed outlier: 4.281A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 37 Processing helix chain 'R' and resid 30 through 40 removed outlier: 4.148A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 53 No H-bonds generated for 'chain 'R' and resid 51 through 53' Processing helix chain 'R' and resid 158 through 168 removed outlier: 3.790A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 195 Processing helix chain 'S' and resid 42 through 78 removed outlier: 3.672A pdb=" N ASN S 52 " --> pdb=" O ARG S 48 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL S 75 " --> pdb=" O ALA S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 88 removed outlier: 4.465A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 118 through 129 removed outlier: 3.760A pdb=" N THR S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 150 No H-bonds generated for 'chain 'S' and resid 147 through 150' Processing helix chain 'S' and resid 172 through 182 Processing helix chain 'S' and resid 213 through 216 No H-bonds generated for 'chain 'S' and resid 213 through 216' Processing helix chain 'S' and resid 239 through 314 removed outlier: 3.753A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA S 313 " --> pdb=" O ALA S 309 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU S 314 " --> pdb=" O GLY S 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 137 No H-bonds generated for 'chain 'T' and resid 135 through 137' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 207 through 211 Processing helix chain 'T' and resid 231 through 247 removed outlier: 3.773A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 268 through 279 removed outlier: 3.585A pdb=" N VAL T 273 " --> pdb=" O VAL T 269 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 296 through 315 Proline residue: T 303 - end of helix removed outlier: 4.155A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 340 removed outlier: 3.769A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 347 through 349 No H-bonds generated for 'chain 'T' and resid 347 through 349' Processing helix chain 'T' and resid 354 through 364 removed outlier: 4.263A pdb=" N ARG T 364 " --> pdb=" O ARG T 360 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 401 Processing helix chain 'T' and resid 410 through 414 removed outlier: 3.574A pdb=" N TYR T 414 " --> pdb=" O THR T 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 410 through 414' Processing helix chain 'T' and resid 431 through 434 Processing helix chain 'T' and resid 437 through 440 No H-bonds generated for 'chain 'T' and resid 437 through 440' Processing helix chain 'T' and resid 443 through 455 removed outlier: 3.621A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) Processing helix chain 'T' and resid 459 through 461 No H-bonds generated for 'chain 'T' and resid 459 through 461' Processing helix chain 'T' and resid 470 through 483 removed outlier: 3.781A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU T 482 " --> pdb=" O ALA T 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 505 removed outlier: 3.660A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 523 through 527 Processing helix chain 'T' and resid 531 through 539 Processing helix chain 'T' and resid 547 through 555 Processing helix chain 'U' and resid 42 through 49 removed outlier: 4.332A pdb=" N ARG U 49 " --> pdb=" O LEU U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 73 removed outlier: 4.459A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix removed outlier: 3.864A pdb=" N GLU U 72 " --> pdb=" O PRO U 68 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TRP U 73 " --> pdb=" O ALA U 69 " (cutoff:3.500A) Processing helix chain 'U' and resid 135 through 137 No H-bonds generated for 'chain 'U' and resid 135 through 137' Processing helix chain 'U' and resid 157 through 159 No H-bonds generated for 'chain 'U' and resid 157 through 159' Processing helix chain 'U' and resid 207 through 212 Processing helix chain 'U' and resid 231 through 246 Processing helix chain 'U' and resid 266 through 278 Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 296 through 315 Proline residue: U 303 - end of helix removed outlier: 3.787A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 removed outlier: 3.661A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 347 through 349 No H-bonds generated for 'chain 'U' and resid 347 through 349' Processing helix chain 'U' and resid 352 through 364 removed outlier: 4.305A pdb=" N PHE U 355 " --> pdb=" O GLY U 352 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU U 357 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG U 360 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU U 363 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 370 through 372 No H-bonds generated for 'chain 'U' and resid 370 through 372' Processing helix chain 'U' and resid 393 through 401 Processing helix chain 'U' and resid 410 through 413 No H-bonds generated for 'chain 'U' and resid 410 through 413' Processing helix chain 'U' and resid 437 through 459 removed outlier: 3.560A pdb=" N GLN U 441 " --> pdb=" O PRO U 437 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA U 451 " --> pdb=" O LYS U 447 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL U 456 " --> pdb=" O GLN U 452 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA U 458 " --> pdb=" O ARG U 454 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N PHE U 459 " --> pdb=" O GLU U 455 " (cutoff:3.500A) Processing helix chain 'U' and resid 466 through 468 No H-bonds generated for 'chain 'U' and resid 466 through 468' Processing helix chain 'U' and resid 470 through 483 removed outlier: 3.677A pdb=" N LEU U 474 " --> pdb=" O THR U 470 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG U 479 " --> pdb=" O GLU U 475 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 500 removed outlier: 3.604A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 502 through 505 No H-bonds generated for 'chain 'U' and resid 502 through 505' Processing helix chain 'U' and resid 517 through 527 removed outlier: 3.938A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 531 through 539 Processing helix chain 'U' and resid 546 through 553 Processing helix chain 'V' and resid 46 through 48 No H-bonds generated for 'chain 'V' and resid 46 through 48' Processing helix chain 'V' and resid 58 through 66 removed outlier: 3.750A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 212 Processing helix chain 'V' and resid 231 through 246 Processing helix chain 'V' and resid 251 through 253 No H-bonds generated for 'chain 'V' and resid 251 through 253' Processing helix chain 'V' and resid 266 through 278 Processing helix chain 'V' and resid 281 through 284 Processing helix chain 'V' and resid 296 through 315 Proline residue: V 303 - end of helix removed outlier: 4.265A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 340 Processing helix chain 'V' and resid 347 through 349 No H-bonds generated for 'chain 'V' and resid 347 through 349' Processing helix chain 'V' and resid 352 through 364 removed outlier: 4.386A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR V 356 " --> pdb=" O ASP V 353 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU V 362 " --> pdb=" O SER V 359 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU V 363 " --> pdb=" O ARG V 360 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG V 364 " --> pdb=" O LEU V 361 " (cutoff:3.500A) Processing helix chain 'V' and resid 370 through 372 No H-bonds generated for 'chain 'V' and resid 370 through 372' Processing helix chain 'V' and resid 393 through 399 Processing helix chain 'V' and resid 410 through 414 removed outlier: 3.825A pdb=" N TYR V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 410 through 414' Processing helix chain 'V' and resid 439 through 453 removed outlier: 4.087A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) Processing helix chain 'V' and resid 471 through 484 removed outlier: 4.570A pdb=" N ARG V 479 " --> pdb=" O GLU V 475 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU V 484 " --> pdb=" O LEU V 480 " (cutoff:3.500A) Processing helix chain 'V' and resid 494 through 506 removed outlier: 3.775A pdb=" N VAL V 499 " --> pdb=" O GLU V 495 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA V 500 " --> pdb=" O ARG V 496 " (cutoff:3.500A) Processing helix chain 'V' and resid 514 through 527 removed outlier: 3.921A pdb=" N ILE V 517 " --> pdb=" O VAL V 514 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL V 518 " --> pdb=" O GLN V 515 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU V 521 " --> pdb=" O VAL V 518 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN V 527 " --> pdb=" O VAL V 524 " (cutoff:3.500A) Processing helix chain 'V' and resid 531 through 539 Processing helix chain 'V' and resid 546 through 554 Processing helix chain 'X' and resid 115 through 117 No H-bonds generated for 'chain 'X' and resid 115 through 117' Processing helix chain 'X' and resid 167 through 170 No H-bonds generated for 'chain 'X' and resid 167 through 170' Processing helix chain 'X' and resid 189 through 200 Processing helix chain 'X' and resid 217 through 229 Processing helix chain 'X' and resid 236 through 241 removed outlier: 3.524A pdb=" N ARG X 239 " --> pdb=" O GLY X 236 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 255 through 259 Processing helix chain 'X' and resid 261 through 274 Processing helix chain 'X' and resid 287 through 298 removed outlier: 3.523A pdb=" N GLN X 292 " --> pdb=" O ARG X 289 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU X 296 " --> pdb=" O ALA X 293 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL X 297 " --> pdb=" O ASN X 294 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER X 298 " --> pdb=" O SER X 295 " (cutoff:3.500A) Processing helix chain 'X' and resid 314 through 324 removed outlier: 4.321A pdb=" N ARG X 324 " --> pdb=" O GLY X 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 342 through 344 No H-bonds generated for 'chain 'X' and resid 342 through 344' Processing helix chain 'X' and resid 349 through 357 removed outlier: 3.629A pdb=" N THR X 354 " --> pdb=" O ALA X 350 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA X 356 " --> pdb=" O ALA X 352 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N HIS X 357 " --> pdb=" O THR X 353 " (cutoff:3.500A) Processing helix chain 'X' and resid 366 through 371 Processing helix chain 'X' and resid 389 through 392 No H-bonds generated for 'chain 'X' and resid 389 through 392' Processing helix chain 'X' and resid 396 through 418 removed outlier: 4.419A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA X 418 " --> pdb=" O GLN X 414 " (cutoff:3.500A) Processing helix chain 'X' and resid 431 through 443 Processing helix chain 'X' and resid 451 through 454 No H-bonds generated for 'chain 'X' and resid 451 through 454' Processing helix chain 'X' and resid 463 through 475 removed outlier: 3.534A pdb=" N SER X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY X 469 " --> pdb=" O ASP X 465 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL X 473 " --> pdb=" O GLY X 469 " (cutoff:3.500A) Processing helix chain 'X' and resid 484 through 486 No H-bonds generated for 'chain 'X' and resid 484 through 486' Processing helix chain 'X' and resid 492 through 506 removed outlier: 3.823A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP X 500 " --> pdb=" O LYS X 496 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 533 removed outlier: 3.629A pdb=" N VAL X 531 " --> pdb=" O LEU X 527 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU X 533 " --> pdb=" O LYS X 529 " (cutoff:3.500A) Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 165 through 169 Processing helix chain 'Y' and resid 189 through 203 Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 238 through 241 Processing helix chain 'Y' and resid 255 through 274 removed outlier: 4.838A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 300 Processing helix chain 'Y' and resid 314 through 322 removed outlier: 3.817A pdb=" N LEU Y 321 " --> pdb=" O ASP Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 342 through 344 No H-bonds generated for 'chain 'Y' and resid 342 through 344' Processing helix chain 'Y' and resid 349 through 354 Processing helix chain 'Y' and resid 366 through 370 Processing helix chain 'Y' and resid 393 through 419 removed outlier: 4.540A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) Processing helix chain 'Y' and resid 431 through 442 removed outlier: 4.095A pdb=" N LYS Y 438 " --> pdb=" O ALA Y 434 " (cutoff:3.500A) Processing helix chain 'Y' and resid 448 through 454 removed outlier: 4.686A pdb=" N VAL Y 452 " --> pdb=" O VAL Y 449 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR Y 454 " --> pdb=" O GLU Y 451 " (cutoff:3.500A) Processing helix chain 'Y' and resid 463 through 475 removed outlier: 3.912A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 483 through 485 No H-bonds generated for 'chain 'Y' and resid 483 through 485' Processing helix chain 'Y' and resid 493 through 509 removed outlier: 4.004A pdb=" N GLU Y 497 " --> pdb=" O LYS Y 493 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS Y 504 " --> pdb=" O ASP Y 500 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP Y 505 " --> pdb=" O LYS Y 501 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE Y 506 " --> pdb=" O MET Y 502 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA Y 507 " --> pdb=" O ALA Y 503 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER Y 508 " --> pdb=" O LYS Y 504 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG Y 509 " --> pdb=" O ASP Y 505 " (cutoff:3.500A) Processing helix chain 'Y' and resid 519 through 522 No H-bonds generated for 'chain 'Y' and resid 519 through 522' Processing helix chain 'Y' and resid 527 through 533 removed outlier: 3.669A pdb=" N SER Y 532 " --> pdb=" O ASP Y 528 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU Y 533 " --> pdb=" O LYS Y 529 " (cutoff:3.500A) Processing helix chain 'Y' and resid 545 through 553 removed outlier: 4.081A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU Y 552 " --> pdb=" O ASP Y 548 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 117 No H-bonds generated for 'chain 'Z' and resid 115 through 117' Processing helix chain 'Z' and resid 150 through 152 No H-bonds generated for 'chain 'Z' and resid 150 through 152' Processing helix chain 'Z' and resid 165 through 170 Processing helix chain 'Z' and resid 189 through 203 removed outlier: 4.543A pdb=" N LYS Z 202 " --> pdb=" O ASN Z 198 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA Z 203 " --> pdb=" O ASN Z 199 " (cutoff:3.500A) Processing helix chain 'Z' and resid 217 through 230 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 3.651A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 274 removed outlier: 3.643A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 288 through 298 Processing helix chain 'Z' and resid 314 through 324 removed outlier: 4.417A pdb=" N ARG Z 324 " --> pdb=" O GLY Z 320 " (cutoff:3.500A) Processing helix chain 'Z' and resid 349 through 357 removed outlier: 4.412A pdb=" N ALA Z 356 " --> pdb=" O ALA Z 352 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N HIS Z 357 " --> pdb=" O THR Z 353 " (cutoff:3.500A) Processing helix chain 'Z' and resid 366 through 370 Processing helix chain 'Z' and resid 394 through 420 removed outlier: 3.506A pdb=" N LEU Z 413 " --> pdb=" O ASP Z 409 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA Z 418 " --> pdb=" O GLN Z 414 " (cutoff:3.500A) Processing helix chain 'Z' and resid 422 through 424 No H-bonds generated for 'chain 'Z' and resid 422 through 424' Processing helix chain 'Z' and resid 427 through 442 removed outlier: 3.706A pdb=" N LEU Z 431 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG Z 441 " --> pdb=" O ARG Z 437 " (cutoff:3.500A) Processing helix chain 'Z' and resid 451 through 454 No H-bonds generated for 'chain 'Z' and resid 451 through 454' Processing helix chain 'Z' and resid 463 through 475 Processing helix chain 'Z' and resid 483 through 485 No H-bonds generated for 'chain 'Z' and resid 483 through 485' Processing helix chain 'Z' and resid 492 through 499 removed outlier: 3.702A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) Processing helix chain 'Z' and resid 501 through 507 removed outlier: 3.970A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) Processing helix chain 'Z' and resid 528 through 532 removed outlier: 3.521A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 528 through 532' Processing sheet with id= A, first strand: chain 'Q' and resid 45 through 49 Processing sheet with id= B, first strand: chain 'R' and resid 96 through 100 removed outlier: 3.865A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY R 114 " --> pdb=" O VAL R 129 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'R' and resid 107 through 110 Processing sheet with id= D, first strand: chain 'S' and resid 203 through 211 removed outlier: 5.262A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN S 159 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALA S 161 " --> pdb=" O SER S 141 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'T' and resid 86 through 91 removed outlier: 6.719A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN T 121 " --> pdb=" O GLY T 128 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'T' and resid 152 through 155 Processing sheet with id= G, first strand: chain 'T' and resid 404 through 408 removed outlier: 3.680A pdb=" N LEU T 222 " --> pdb=" O GLY T 404 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'T' and resid 376 through 381 removed outlier: 3.550A pdb=" N VAL T 262 " --> pdb=" O ASP T 325 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.678A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU U 107 " --> pdb=" O ALA U 119 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= K, first strand: chain 'U' and resid 404 through 408 Processing sheet with id= L, first strand: chain 'U' and resid 285 through 290 removed outlier: 8.544A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE U 380 " --> pdb=" O TYR U 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'V' and resid 143 through 145 removed outlier: 6.481A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL V 90 " --> pdb=" O ILE V 94 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE V 94 " --> pdb=" O VAL V 90 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLN V 149 " --> pdb=" O LEU V 108 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N CYS V 110 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR V 147 " --> pdb=" O CYS V 110 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= O, first strand: chain 'V' and resid 404 through 408 Processing sheet with id= P, first strand: chain 'V' and resid 285 through 290 removed outlier: 8.749A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE V 380 " --> pdb=" O TYR V 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'X' and resid 38 through 44 removed outlier: 6.468A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU X 72 " --> pdb=" O VAL X 65 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'X' and resid 158 through 160 removed outlier: 4.753A pdb=" N GLU X 158 " --> pdb=" O ARG X 175 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR X 173 " --> pdb=" O LEU X 160 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'X' and resid 360 through 363 removed outlier: 7.684A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLY X 183 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL X 339 " --> pdb=" O GLY X 183 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= U, first strand: chain 'Y' and resid 38 through 44 removed outlier: 6.359A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'Y' and resid 110 through 113 removed outlier: 3.547A pdb=" N ASP Y 139 " --> pdb=" O VAL Y 113 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Y' and resid 360 through 363 removed outlier: 8.355A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Z' and resid 101 through 103 removed outlier: 6.640A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER Z 61 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER Z 107 " --> pdb=" O SER Z 62 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N GLU Z 64 " --> pdb=" O THR Z 105 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR Z 105 " --> pdb=" O GLU Z 64 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id= Z, first strand: chain 'Z' and resid 360 through 363 removed outlier: 7.491A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLY Z 183 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL Z 339 " --> pdb=" O GLY Z 183 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE Z 207 " --> pdb=" O LEU Z 281 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N PHE Z 283 " --> pdb=" O PHE Z 207 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL Z 209 " --> pdb=" O PHE Z 283 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ASP Z 285 " --> pdb=" O VAL Z 209 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA Z 211 " --> pdb=" O ASP Z 285 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Z' and resid 559 through 561 1453 hydrogen bonds defined for protein. 3768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.56 Time building geometry restraints manager: 14.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10763 1.34 - 1.45: 4548 1.45 - 1.57: 18888 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34420 Sorted by residual: bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.01e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.95e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.87e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.59e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.52e+01 ... (remaining 34415 not shown) Histogram of bond angle deviations from ideal: 97.78 - 105.45: 676 105.45 - 113.12: 19037 113.12 - 120.79: 16385 120.79 - 128.47: 10427 128.47 - 136.14: 124 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 139.87 121.45 18.42 1.00e+00 1.00e+00 3.39e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 122.40 17.47 1.00e+00 1.00e+00 3.05e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 122.52 17.35 1.00e+00 1.00e+00 3.01e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 121.20 15.63 1.00e+00 1.00e+00 2.44e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 122.20 14.63 1.00e+00 1.00e+00 2.14e+02 ... (remaining 46644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.89: 20289 31.89 - 63.78: 487 63.78 - 95.67: 47 95.67 - 127.56: 1 127.56 - 159.45: 4 Dihedral angle restraints: 20828 sinusoidal: 8068 harmonic: 12760 Sorted by residual: dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual -180.00 -126.90 -53.10 0 5.00e+00 4.00e-02 1.13e+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 -128.27 -51.73 0 5.00e+00 4.00e-02 1.07e+02 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 -128.91 -51.09 0 5.00e+00 4.00e-02 1.04e+02 ... (remaining 20825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4307 0.061 - 0.123: 1046 0.123 - 0.184: 152 0.184 - 0.246: 10 0.246 - 0.307: 5 Chirality restraints: 5520 Sorted by residual: chirality pdb=" CB ILE H 95 " pdb=" CA ILE H 95 " pdb=" CG1 ILE H 95 " pdb=" CG2 ILE H 95 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.36e+00 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 -2.32 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB ILE S 183 " pdb=" CA ILE S 183 " pdb=" CG1 ILE S 183 " pdb=" CG2 ILE S 183 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 5517 not shown) Planarity restraints: 5999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA X 503 " -0.033 2.00e-02 2.50e+03 6.35e-02 4.03e+01 pdb=" C ALA X 503 " 0.110 2.00e-02 2.50e+03 pdb=" O ALA X 503 " -0.041 2.00e-02 2.50e+03 pdb=" N LYS X 504 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 6.06e-02 3.67e+01 pdb=" C ALA Z 503 " -0.105 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP Y 348 " -0.047 5.00e-02 4.00e+02 7.21e-02 8.31e+00 pdb=" N PRO Y 349 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO Y 349 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO Y 349 " -0.040 5.00e-02 4.00e+02 ... (remaining 5996 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4899 2.76 - 3.29: 32185 3.29 - 3.83: 59422 3.83 - 4.36: 73338 4.36 - 4.90: 122683 Nonbonded interactions: 292527 Sorted by model distance: nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.219 2.170 nonbonded pdb=" OG1 THR V 232 " pdb="MG MG V1002 " model vdw 2.225 2.170 nonbonded pdb=" O3G ATP U1001 " pdb="MG MG U1002 " model vdw 2.230 2.170 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.241 2.170 nonbonded pdb=" OG1 THR X 190 " pdb="MG MG X 602 " model vdw 2.253 2.170 ... (remaining 292522 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: 14.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 22.910 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 92.070 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 0.006 0.083 34420 Z= 0.393 Angle : 0.881 18.419 46649 Z= 0.517 Chirality : 0.054 0.307 5520 Planarity : 0.007 0.072 5999 Dihedral : 14.408 159.451 12666 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.28 % Favored : 95.61 % Rotamer: Outliers : 0.17 % Allowed : 5.47 % Favored : 94.36 % 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: -3.68 (0.10), residues: 4462 helix: -2.94 (0.08), residues: 2134 sheet: -1.37 (0.22), residues: 485 loop : -1.88 (0.13), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Z 141 HIS 0.008 0.001 HIS R 104 PHE 0.028 0.002 PHE A 122 TYR 0.017 0.002 TYR U 57 ARG 0.009 0.001 ARG U 217 *********************** 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 717 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 711 time to evaluate : 4.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8330 (t0) cc_final: 0.8052 (t0) REVERT: E 91 ARG cc_start: 0.7714 (mtt-85) cc_final: 0.7411 (mtm180) REVERT: E 95 ILE cc_start: 0.8132 (pt) cc_final: 0.7860 (pt) REVERT: E 119 LEU cc_start: 0.6988 (tp) cc_final: 0.6647 (mt) REVERT: G 102 TYR cc_start: 0.6903 (m-10) cc_final: 0.6684 (m-80) REVERT: P 66 GLN cc_start: 0.7215 (tt0) cc_final: 0.6951 (mm-40) REVERT: P 145 MET cc_start: 0.8939 (mmm) cc_final: 0.8565 (mmm) REVERT: Q 43 GLN cc_start: 0.8701 (tt0) cc_final: 0.8491 (tt0) REVERT: R 110 GLN cc_start: 0.8662 (tt0) cc_final: 0.8326 (tt0) REVERT: R 115 VAL cc_start: 0.8697 (p) cc_final: 0.8446 (t) REVERT: S 188 GLN cc_start: 0.7785 (mt0) cc_final: 0.7189 (mp10) REVERT: S 219 GLN cc_start: 0.7884 (mt0) cc_final: 0.7659 (mt0) REVERT: S 248 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7263 (mt-10) REVERT: S 261 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7961 (mm-30) REVERT: S 271 MET cc_start: 0.8429 (ttp) cc_final: 0.8181 (ttp) REVERT: T 530 PRO cc_start: 0.8170 (Cg_exo) cc_final: 0.7827 (Cg_endo) REVERT: U 50 LYS cc_start: 0.6508 (mppt) cc_final: 0.6249 (mptt) REVERT: U 337 MET cc_start: 0.8527 (ttp) cc_final: 0.8242 (ttp) REVERT: U 471 GLN cc_start: 0.7357 (tp-100) cc_final: 0.6947 (tm-30) REVERT: U 474 LEU cc_start: 0.7207 (pp) cc_final: 0.6809 (pp) REVERT: U 487 LYS cc_start: 0.7855 (mtmt) cc_final: 0.7588 (mmtm) REVERT: U 502 TYR cc_start: 0.7949 (t80) cc_final: 0.7700 (t80) REVERT: U 537 LYS cc_start: 0.8112 (tptt) cc_final: 0.7839 (tptp) REVERT: U 551 LYS cc_start: 0.7715 (mttt) cc_final: 0.7452 (mtpt) REVERT: U 559 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6597 (pp) REVERT: V 65 LYS cc_start: 0.8341 (mmtm) cc_final: 0.7929 (mmtt) REVERT: V 467 ASP cc_start: 0.6090 (m-30) cc_final: 0.5700 (t0) REVERT: X 502 MET cc_start: 0.7670 (mtp) cc_final: 0.7451 (mtm) REVERT: Y 493 LYS cc_start: 0.8076 (tmmt) cc_final: 0.7660 (tmtm) REVERT: Z 82 ASP cc_start: 0.7530 (t0) cc_final: 0.7233 (t0) REVERT: Z 386 MET cc_start: 0.8185 (mmm) cc_final: 0.7882 (mmm) REVERT: Z 502 MET cc_start: 0.7829 (mtp) cc_final: 0.7550 (mtm) outliers start: 6 outliers final: 1 residues processed: 713 average time/residue: 1.4743 time to fit residues: 1258.3217 Evaluate side-chains 401 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 399 time to evaluate : 3.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain U residue 559 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 2.9990 chunk 335 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 225 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 chunk 346 optimal weight: 0.8980 chunk 134 optimal weight: 0.5980 chunk 210 optimal weight: 5.9990 chunk 257 optimal weight: 0.7980 chunk 401 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 98 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN H 87 ASN ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN R 53 ASN R 73 ASN R 83 GLN R 85 GLN R 119 HIS R 137 HIS S 174 GLN S 262 ASN T 134 ASN T 241 HIS T 253 GLN T 358 HIS T 386 GLN ** T 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 60 GLN U 64 GLN U 78 GLN U 83 HIS U 126 HIS ** U 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 241 HIS U 242 GLN U 319 HIS U 497 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 64 GLN V 123 GLN V 126 HIS V 134 ASN V 139 HIS V 152 ASN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 242 GLN V 244 ASN V 435 GLN V 441 GLN V 486 GLN V 497 GLN X 157 GLN X 204 HIS X 278 GLN Y 157 GLN Y 199 ASN Y 278 GLN Y 294 ASN Y 322 GLN Y 337 GLN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN Z 42 GLN Z 83 ASN Z 199 ASN Z 440 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34420 Z= 0.168 Angle : 0.545 9.084 46649 Z= 0.281 Chirality : 0.042 0.260 5520 Planarity : 0.005 0.058 5999 Dihedral : 7.474 153.043 4923 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.12 % Favored : 96.71 % Rotamer: Outliers : 2.95 % Allowed : 13.58 % Favored : 83.48 % 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: -1.99 (0.12), residues: 4462 helix: -1.21 (0.10), residues: 2135 sheet: -1.07 (0.21), residues: 561 loop : -1.32 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Z 141 HIS 0.003 0.001 HIS V 61 PHE 0.021 0.001 PHE F 107 TYR 0.019 0.001 TYR C 102 ARG 0.007 0.000 ARG S 124 *********************** 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 571 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 466 time to evaluate : 3.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 TYR cc_start: 0.8012 (m-80) cc_final: 0.7805 (m-80) REVERT: E 91 ARG cc_start: 0.7788 (mtt-85) cc_final: 0.7523 (mtm180) REVERT: E 92 ASN cc_start: 0.7971 (t0) cc_final: 0.7762 (t0) REVERT: I 115 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6106 (pp) REVERT: P 145 MET cc_start: 0.9068 (mmm) cc_final: 0.8861 (mmm) REVERT: Q 43 GLN cc_start: 0.8661 (tt0) cc_final: 0.8436 (tt0) REVERT: Q 48 ARG cc_start: 0.8087 (ptt-90) cc_final: 0.7549 (ptt180) REVERT: R 110 GLN cc_start: 0.8650 (tt0) cc_final: 0.8313 (tt0) REVERT: R 171 GLN cc_start: 0.6232 (OUTLIER) cc_final: 0.6005 (pp30) REVERT: S 144 ASP cc_start: 0.8074 (p0) cc_final: 0.7841 (p0) REVERT: S 147 ARG cc_start: 0.7037 (ptt90) cc_final: 0.6516 (ptm-80) REVERT: S 248 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7204 (mt-10) REVERT: S 271 MET cc_start: 0.8427 (ttp) cc_final: 0.8183 (ttp) REVERT: T 456 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8231 (p) REVERT: U 45 LEU cc_start: 0.7828 (mt) cc_final: 0.7623 (mp) REVERT: U 482 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7174 (tm-30) REVERT: U 537 LYS cc_start: 0.8066 (tptt) cc_final: 0.7815 (tptp) REVERT: U 551 LYS cc_start: 0.7636 (mttt) cc_final: 0.7378 (mtpt) REVERT: V 479 ARG cc_start: 0.7967 (mtt-85) cc_final: 0.7740 (mtt-85) REVERT: V 549 HIS cc_start: 0.6260 (m-70) cc_final: 0.6011 (m90) REVERT: X 502 MET cc_start: 0.7771 (mtp) cc_final: 0.7566 (mtm) REVERT: Y 411 LYS cc_start: 0.7989 (tttm) cc_final: 0.7613 (ttpt) REVERT: Y 430 LYS cc_start: 0.6390 (ttmt) cc_final: 0.6186 (mtmt) REVERT: Y 501 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6834 (tmtp) REVERT: Z 82 ASP cc_start: 0.7741 (t0) cc_final: 0.7400 (t0) REVERT: Z 502 MET cc_start: 0.7746 (mtp) cc_final: 0.7512 (mtm) REVERT: Z 550 LYS cc_start: 0.6602 (tppt) cc_final: 0.6157 (tptp) outliers start: 105 outliers final: 31 residues processed: 530 average time/residue: 1.3402 time to fit residues: 861.5847 Evaluate side-chains 405 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 369 time to evaluate : 3.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain R residue 161 LYS Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 143 LEU Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 475 GLU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 511 LYS Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 487 LYS Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 416 ILE Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain Y residue 82 ASP Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 426 SER Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Y residue 532 SER Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 456 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 223 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 334 optimal weight: 0.9980 chunk 273 optimal weight: 0.5980 chunk 110 optimal weight: 8.9990 chunk 402 optimal weight: 8.9990 chunk 434 optimal weight: 0.9990 chunk 358 optimal weight: 0.7980 chunk 398 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 322 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN F 87 ASN H 87 ASN I 94 ASN R 53 ASN ** T 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 60 GLN U 64 GLN U 83 HIS ** U 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 ASN Y 83 ASN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2255 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= 0.179 Angle : 0.532 9.110 46649 Z= 0.270 Chirality : 0.042 0.260 5520 Planarity : 0.004 0.054 5999 Dihedral : 6.901 154.198 4919 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.23 % Favored : 96.62 % Rotamer: Outliers : 3.00 % Allowed : 15.40 % Favored : 81.60 % 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: -1.27 (0.12), residues: 4462 helix: -0.55 (0.11), residues: 2129 sheet: -0.80 (0.21), residues: 580 loop : -1.01 (0.15), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Z 141 HIS 0.006 0.001 HIS U 83 PHE 0.023 0.001 PHE A 107 TYR 0.021 0.001 TYR P 75 ARG 0.004 0.000 ARG G 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 426 time to evaluate : 3.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6278 (mp) REVERT: B 81 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.7153 (ptm) REVERT: D 113 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7586 (mp) REVERT: E 91 ARG cc_start: 0.7821 (mtt-85) cc_final: 0.7531 (mtm180) REVERT: E 92 ASN cc_start: 0.8114 (t0) cc_final: 0.7871 (t0) REVERT: I 115 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6059 (pp) REVERT: P 68 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.6940 (m-30) REVERT: Q 38 LYS cc_start: 0.7951 (mttt) cc_final: 0.7493 (mmtm) REVERT: Q 43 GLN cc_start: 0.8606 (tt0) cc_final: 0.8354 (tt0) REVERT: Q 48 ARG cc_start: 0.8051 (ptt-90) cc_final: 0.7544 (ptt180) REVERT: R 110 GLN cc_start: 0.8654 (tt0) cc_final: 0.8349 (tt0) REVERT: R 171 GLN cc_start: 0.6326 (OUTLIER) cc_final: 0.6061 (pp30) REVERT: S 144 ASP cc_start: 0.8052 (p0) cc_final: 0.7780 (p0) REVERT: S 147 ARG cc_start: 0.7137 (ptt90) cc_final: 0.6619 (ptm-80) REVERT: S 243 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7933 (mp) REVERT: S 248 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7270 (mt-10) REVERT: S 271 MET cc_start: 0.8408 (ttp) cc_final: 0.8115 (ttp) REVERT: T 86 ARG cc_start: 0.7806 (mpp-170) cc_final: 0.7561 (mtt90) REVERT: T 456 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8208 (p) REVERT: T 475 GLU cc_start: 0.6646 (tm-30) cc_final: 0.6373 (mm-30) REVERT: U 199 ARG cc_start: 0.7125 (mtt90) cc_final: 0.6922 (mtt90) REVERT: U 475 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.6383 (pp20) REVERT: U 482 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7251 (tm-30) REVERT: U 511 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.6106 (mtmt) REVERT: U 537 LYS cc_start: 0.8109 (tptt) cc_final: 0.7811 (tptp) REVERT: U 551 LYS cc_start: 0.7577 (mttt) cc_final: 0.7315 (mtpt) REVERT: X 502 MET cc_start: 0.7854 (mtp) cc_final: 0.7601 (mtm) REVERT: Y 411 LYS cc_start: 0.7987 (tttm) cc_final: 0.7609 (ttpt) REVERT: Y 430 LYS cc_start: 0.6399 (ttmt) cc_final: 0.6184 (mtmt) REVERT: Y 487 TYR cc_start: 0.6957 (t80) cc_final: 0.6736 (t80) REVERT: Y 488 MET cc_start: 0.7087 (mmm) cc_final: 0.6630 (mpt) REVERT: Z 82 ASP cc_start: 0.7762 (t0) cc_final: 0.7392 (t0) REVERT: Z 422 MET cc_start: 0.8014 (mtp) cc_final: 0.7773 (mmm) REVERT: Z 546 GLU cc_start: 0.5437 (pm20) cc_final: 0.5205 (tm-30) REVERT: Z 550 LYS cc_start: 0.6659 (tppt) cc_final: 0.6219 (tptp) REVERT: Z 572 LYS cc_start: 0.8041 (tppt) cc_final: 0.7412 (mmtm) outliers start: 107 outliers final: 32 residues processed: 497 average time/residue: 1.3638 time to fit residues: 823.8822 Evaluate side-chains 403 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 360 time to evaluate : 3.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 288 LEU Chi-restraints excluded: chain T residue 101 LYS Chi-restraints excluded: chain T residue 143 LEU Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 475 GLU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 511 LYS Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 426 SER Chi-restraints excluded: chain Y residue 492 ILE Chi-restraints excluded: chain Y residue 532 SER Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 456 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 397 optimal weight: 5.9990 chunk 302 optimal weight: 3.9990 chunk 208 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 403 optimal weight: 0.9990 chunk 427 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 382 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN D 98 GLN H 87 ASN P 76 GLN T 441 GLN T 497 GLN U 60 GLN ** U 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 ASN Y 278 GLN Y 311 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34420 Z= 0.214 Angle : 0.545 8.723 46649 Z= 0.276 Chirality : 0.043 0.260 5520 Planarity : 0.004 0.053 5999 Dihedral : 6.810 153.623 4919 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.36 % Favored : 96.46 % Rotamer: Outliers : 3.53 % Allowed : 16.61 % Favored : 79.86 % 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: -0.88 (0.12), residues: 4462 helix: -0.21 (0.11), residues: 2126 sheet: -0.65 (0.21), residues: 560 loop : -0.83 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 58 HIS 0.003 0.001 HIS T 241 PHE 0.019 0.001 PHE R 127 TYR 0.025 0.001 TYR U 453 ARG 0.006 0.000 ARG G 91 *********************** 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 539 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 413 time to evaluate : 4.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 LEU cc_start: 0.5616 (OUTLIER) cc_final: 0.5184 (tm) REVERT: B 81 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.7211 (ptm) REVERT: D 56 LEU cc_start: 0.5204 (OUTLIER) cc_final: 0.4992 (tt) REVERT: E 61 MET cc_start: 0.4187 (mtp) cc_final: 0.3948 (mtp) REVERT: E 91 ARG cc_start: 0.7807 (mtt-85) cc_final: 0.7605 (mmm160) REVERT: E 92 ASN cc_start: 0.8118 (t0) cc_final: 0.7875 (t0) REVERT: E 107 PHE cc_start: 0.7812 (t80) cc_final: 0.7491 (t80) REVERT: H 126 PHE cc_start: 0.6322 (m-80) cc_final: 0.5233 (p90) REVERT: I 119 LEU cc_start: 0.5521 (OUTLIER) cc_final: 0.5314 (mt) REVERT: P 66 GLN cc_start: 0.7259 (tt0) cc_final: 0.7038 (mm-40) REVERT: P 68 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6888 (m-30) REVERT: Q 43 GLN cc_start: 0.8570 (tt0) cc_final: 0.8321 (tt0) REVERT: Q 48 ARG cc_start: 0.7996 (ptt-90) cc_final: 0.7431 (ptt180) REVERT: R 110 GLN cc_start: 0.8688 (tt0) cc_final: 0.8350 (tt0) REVERT: R 171 GLN cc_start: 0.6278 (OUTLIER) cc_final: 0.6061 (pp30) REVERT: S 144 ASP cc_start: 0.8034 (p0) cc_final: 0.7721 (p0) REVERT: S 147 ARG cc_start: 0.7062 (ptt90) cc_final: 0.6645 (ptm-80) REVERT: S 243 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7885 (mp) REVERT: S 248 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7383 (mt-10) REVERT: S 271 MET cc_start: 0.8365 (ttp) cc_final: 0.8130 (ttp) REVERT: T 86 ARG cc_start: 0.7809 (mpp-170) cc_final: 0.7577 (mtt90) REVERT: T 200 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: T 448 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7932 (tp) REVERT: T 456 VAL cc_start: 0.8661 (OUTLIER) cc_final: 0.8283 (p) REVERT: U 57 TYR cc_start: 0.6993 (p90) cc_final: 0.6525 (p90) REVERT: U 118 MET cc_start: 0.8757 (ttm) cc_final: 0.8537 (ttm) REVERT: U 482 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7260 (tm-30) REVERT: U 537 LYS cc_start: 0.8124 (tptt) cc_final: 0.7864 (tptp) REVERT: U 551 LYS cc_start: 0.7609 (mttt) cc_final: 0.7255 (mtpt) REVERT: X 51 ARG cc_start: 0.8580 (ttt90) cc_final: 0.8301 (ttt-90) REVERT: X 502 MET cc_start: 0.7865 (mtp) cc_final: 0.7624 (mtm) REVERT: Y 430 LYS cc_start: 0.6508 (ttmt) cc_final: 0.6265 (mtmt) REVERT: Y 487 TYR cc_start: 0.7043 (t80) cc_final: 0.6625 (t80) REVERT: Y 488 MET cc_start: 0.7243 (mmm) cc_final: 0.6737 (mpt) REVERT: Y 501 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.6758 (tmtp) REVERT: Y 528 ASP cc_start: 0.6379 (p0) cc_final: 0.6150 (p0) REVERT: Z 82 ASP cc_start: 0.7855 (t0) cc_final: 0.7442 (t0) REVERT: Z 422 MET cc_start: 0.8040 (mtp) cc_final: 0.7785 (mmm) REVERT: Z 502 MET cc_start: 0.8046 (mtp) cc_final: 0.7709 (mtm) REVERT: Z 504 LYS cc_start: 0.7117 (ptpt) cc_final: 0.6881 (pptt) REVERT: Z 546 GLU cc_start: 0.5312 (pm20) cc_final: 0.5092 (tm-30) REVERT: Z 550 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6381 (tptp) outliers start: 126 outliers final: 51 residues processed: 495 average time/residue: 1.4006 time to fit residues: 840.5904 Evaluate side-chains 436 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 372 time to evaluate : 3.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 288 LEU Chi-restraints excluded: chain T residue 101 LYS Chi-restraints excluded: chain T residue 143 LEU Chi-restraints excluded: chain T residue 200 GLU Chi-restraints excluded: chain T residue 421 LEU Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 193 ILE Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 558 LYS Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 487 LYS Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 390 ASN Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 344 ASP Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 415 ASP Chi-restraints excluded: chain Y residue 426 SER Chi-restraints excluded: chain Y residue 492 ILE Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Y residue 532 SER Chi-restraints excluded: chain Z residue 161 VAL Chi-restraints excluded: chain Z residue 306 SER Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 527 LEU Chi-restraints excluded: chain Z residue 550 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 355 optimal weight: 3.9990 chunk 242 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 318 optimal weight: 0.0270 chunk 176 optimal weight: 2.9990 chunk 364 optimal weight: 4.9990 chunk 295 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 218 optimal weight: 1.9990 chunk 383 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN D 98 GLN H 87 ASN H 98 GLN T 104 GLN T 497 GLN U 60 GLN U 83 HIS ** U 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 ASN Z 440 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 34420 Z= 0.184 Angle : 0.540 17.133 46649 Z= 0.269 Chirality : 0.043 0.246 5520 Planarity : 0.004 0.052 5999 Dihedral : 6.625 154.025 4919 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.23 % Favored : 96.62 % Rotamer: Outliers : 3.39 % Allowed : 17.81 % Favored : 78.79 % 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: -0.59 (0.13), residues: 4462 helix: 0.04 (0.12), residues: 2124 sheet: -0.57 (0.21), residues: 562 loop : -0.68 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 58 HIS 0.004 0.001 HIS U 61 PHE 0.019 0.001 PHE R 127 TYR 0.024 0.001 TYR U 453 ARG 0.007 0.000 ARG A 91 *********************** 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 543 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 422 time to evaluate : 3.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.5641 (mmt) cc_final: 0.4892 (tpp) REVERT: B 56 LEU cc_start: 0.5539 (OUTLIER) cc_final: 0.5094 (tm) REVERT: B 81 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.7172 (ptm) REVERT: D 113 ILE cc_start: 0.7487 (mt) cc_final: 0.7272 (mp) REVERT: E 92 ASN cc_start: 0.8087 (t0) cc_final: 0.7811 (t0) REVERT: P 66 GLN cc_start: 0.7175 (tt0) cc_final: 0.6920 (mm-40) REVERT: P 68 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.6964 (m-30) REVERT: P 146 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8247 (tm) REVERT: Q 43 GLN cc_start: 0.8570 (tt0) cc_final: 0.8319 (tt0) REVERT: Q 48 ARG cc_start: 0.7977 (ptt-90) cc_final: 0.7437 (ptt180) REVERT: R 31 LYS cc_start: 0.7733 (pmtt) cc_final: 0.7027 (ttpp) REVERT: R 110 GLN cc_start: 0.8673 (tt0) cc_final: 0.8347 (tt0) REVERT: R 171 GLN cc_start: 0.6245 (OUTLIER) cc_final: 0.6031 (pp30) REVERT: S 144 ASP cc_start: 0.7969 (p0) cc_final: 0.7727 (p0) REVERT: S 147 ARG cc_start: 0.7036 (ptt90) cc_final: 0.6648 (ptm-80) REVERT: S 243 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7931 (mp) REVERT: S 248 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7423 (mt-10) REVERT: S 271 MET cc_start: 0.8351 (ttp) cc_final: 0.8083 (ttp) REVERT: T 86 ARG cc_start: 0.7777 (mpp-170) cc_final: 0.7540 (mtt90) REVERT: T 200 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: T 456 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8268 (p) REVERT: U 60 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.6819 (mp-120) REVERT: U 199 ARG cc_start: 0.7103 (mtt90) cc_final: 0.6895 (mtt90) REVERT: U 471 GLN cc_start: 0.7711 (tp-100) cc_final: 0.7332 (tm-30) REVERT: U 482 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7254 (tm-30) REVERT: U 537 LYS cc_start: 0.8103 (tptt) cc_final: 0.7843 (tptp) REVERT: U 551 LYS cc_start: 0.7590 (mttt) cc_final: 0.7374 (mtpt) REVERT: X 502 MET cc_start: 0.7877 (mtp) cc_final: 0.7646 (mtm) REVERT: Y 227 MET cc_start: 0.9024 (mtt) cc_final: 0.8780 (mtt) REVERT: Y 430 LYS cc_start: 0.6542 (ttmt) cc_final: 0.6305 (mtmt) REVERT: Y 487 TYR cc_start: 0.7023 (t80) cc_final: 0.6642 (t80) REVERT: Y 488 MET cc_start: 0.7254 (mmm) cc_final: 0.6782 (mpt) REVERT: Y 501 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6756 (tmtp) REVERT: Y 528 ASP cc_start: 0.6315 (p0) cc_final: 0.6061 (p0) REVERT: Z 51 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7261 (ttm110) REVERT: Z 82 ASP cc_start: 0.7854 (t0) cc_final: 0.7575 (t0) REVERT: Z 422 MET cc_start: 0.8004 (mtp) cc_final: 0.7793 (mmm) REVERT: Z 502 MET cc_start: 0.8063 (mtp) cc_final: 0.7733 (mtm) REVERT: Z 504 LYS cc_start: 0.7165 (ptpt) cc_final: 0.6896 (pptt) REVERT: Z 572 LYS cc_start: 0.8086 (tppt) cc_final: 0.7455 (mmtm) outliers start: 121 outliers final: 59 residues processed: 503 average time/residue: 1.3440 time to fit residues: 820.3488 Evaluate side-chains 443 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 373 time to evaluate : 3.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 288 LEU Chi-restraints excluded: chain T residue 101 LYS Chi-restraints excluded: chain T residue 143 LEU Chi-restraints excluded: chain T residue 200 GLU Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 325 ASP Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain U residue 60 GLN Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 511 LYS Chi-restraints excluded: chain U residue 558 LYS Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 390 ASN Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain Y residue 136 ASP Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 344 ASP Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 415 ASP Chi-restraints excluded: chain Y residue 484 MET Chi-restraints excluded: chain Y residue 492 ILE Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Y residue 532 SER Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 161 VAL Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 428 GLU Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 527 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 143 optimal weight: 0.9980 chunk 384 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 250 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 427 optimal weight: 4.9990 chunk 355 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 35 optimal weight: 0.0010 chunk 141 optimal weight: 0.9980 chunk 224 optimal weight: 0.5980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN H 87 ASN H 98 GLN S 195 ASN T 196 GLN T 497 GLN U 60 GLN ** U 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 452 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 64 GLN V 241 HIS V 529 ASN Z 440 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 34420 Z= 0.161 Angle : 0.529 9.944 46649 Z= 0.264 Chirality : 0.042 0.267 5520 Planarity : 0.003 0.051 5999 Dihedral : 6.434 157.518 4919 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.32 % Favored : 96.53 % Rotamer: Outliers : 3.17 % Allowed : 18.71 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.13), residues: 4462 helix: 0.21 (0.12), residues: 2121 sheet: -0.44 (0.21), residues: 570 loop : -0.55 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 58 HIS 0.008 0.001 HIS U 61 PHE 0.020 0.001 PHE R 127 TYR 0.023 0.001 TYR U 453 ARG 0.006 0.000 ARG T 199 *********************** 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 522 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 409 time to evaluate : 3.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.5629 (mmt) cc_final: 0.4902 (tpp) REVERT: B 81 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7179 (ptm) REVERT: D 113 ILE cc_start: 0.7495 (mt) cc_final: 0.7285 (mp) REVERT: E 92 ASN cc_start: 0.8035 (t0) cc_final: 0.7811 (t0) REVERT: H 118 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6070 (mt) REVERT: P 66 GLN cc_start: 0.7123 (tt0) cc_final: 0.6897 (mm-40) REVERT: P 68 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.6947 (m-30) REVERT: P 79 GLU cc_start: 0.7474 (tt0) cc_final: 0.7029 (tp30) REVERT: P 146 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8262 (tm) REVERT: Q 48 ARG cc_start: 0.7869 (ptt-90) cc_final: 0.7337 (ptt180) REVERT: R 31 LYS cc_start: 0.7715 (pmtt) cc_final: 0.7030 (ttpp) REVERT: R 110 GLN cc_start: 0.8629 (tt0) cc_final: 0.8311 (tt0) REVERT: S 144 ASP cc_start: 0.7891 (p0) cc_final: 0.7654 (p0) REVERT: S 147 ARG cc_start: 0.7028 (ptt90) cc_final: 0.6642 (ptm-80) REVERT: S 243 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7991 (mp) REVERT: S 248 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7436 (mt-10) REVERT: S 271 MET cc_start: 0.8336 (ttp) cc_final: 0.8077 (ttp) REVERT: T 86 ARG cc_start: 0.7783 (mpp-170) cc_final: 0.7550 (mtt90) REVERT: T 449 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7072 (mt-10) REVERT: T 456 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8255 (p) REVERT: U 60 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6646 (mm-40) REVERT: U 204 THR cc_start: 0.8956 (p) cc_final: 0.8656 (t) REVERT: U 411 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: U 482 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7218 (tm-30) REVERT: U 511 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.5967 (mtmt) REVERT: U 537 LYS cc_start: 0.8116 (tptt) cc_final: 0.7825 (tptp) REVERT: V 539 ASN cc_start: 0.8259 (m110) cc_final: 0.8016 (m110) REVERT: X 502 MET cc_start: 0.7871 (mtp) cc_final: 0.7654 (mtm) REVERT: Y 487 TYR cc_start: 0.7008 (t80) cc_final: 0.6646 (t80) REVERT: Y 488 MET cc_start: 0.7269 (mmm) cc_final: 0.6811 (mpt) REVERT: Y 501 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6725 (tmtp) REVERT: Z 51 ARG cc_start: 0.7837 (ttm-80) cc_final: 0.7211 (ttm110) REVERT: Z 82 ASP cc_start: 0.7821 (t0) cc_final: 0.7559 (t0) REVERT: Z 502 MET cc_start: 0.8009 (mtp) cc_final: 0.7675 (mtm) REVERT: Z 504 LYS cc_start: 0.7199 (ptpt) cc_final: 0.6911 (pptt) REVERT: Z 550 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6546 (tptp) REVERT: Z 572 LYS cc_start: 0.8096 (tppt) cc_final: 0.7426 (mmtm) outliers start: 113 outliers final: 51 residues processed: 487 average time/residue: 1.3327 time to fit residues: 788.1708 Evaluate side-chains 430 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 367 time to evaluate : 3.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 288 LEU Chi-restraints excluded: chain T residue 101 LYS Chi-restraints excluded: chain T residue 143 LEU Chi-restraints excluded: chain T residue 421 LEU Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain U residue 60 GLN Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 511 LYS Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 487 LYS Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 525 ILE Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 390 ASN Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 344 ASP Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 415 ASP Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Y residue 532 SER Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 161 VAL Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 527 LEU Chi-restraints excluded: chain Z residue 550 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 412 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 243 optimal weight: 0.0470 chunk 312 optimal weight: 6.9990 chunk 241 optimal weight: 0.2980 chunk 359 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 426 optimal weight: 0.8980 chunk 266 optimal weight: 1.9990 chunk 259 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 overall best weight: 0.6482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 ASN P 83 GLN Q 43 GLN T 179 ASN T 497 GLN U 60 GLN ** U 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 471 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 440 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34420 Z= 0.161 Angle : 0.533 12.536 46649 Z= 0.265 Chirality : 0.042 0.248 5520 Planarity : 0.003 0.051 5999 Dihedral : 6.325 167.054 4919 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.09 % Favored : 96.75 % Rotamer: Outliers : 2.92 % Allowed : 19.35 % Favored : 77.73 % 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: -0.21 (0.13), residues: 4462 helix: 0.32 (0.12), residues: 2129 sheet: -0.35 (0.22), residues: 566 loop : -0.46 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 73 HIS 0.005 0.001 HIS U 61 PHE 0.022 0.001 PHE R 127 TYR 0.024 0.001 TYR U 453 ARG 0.004 0.000 ARG T 199 *********************** 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 503 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 399 time to evaluate : 3.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.7178 (ptm) REVERT: E 92 ASN cc_start: 0.8002 (t0) cc_final: 0.7775 (t0) REVERT: H 118 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6273 (mt) REVERT: P 66 GLN cc_start: 0.7079 (tt0) cc_final: 0.6858 (mm-40) REVERT: P 68 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6971 (m-30) REVERT: P 77 PHE cc_start: 0.8150 (m-80) cc_final: 0.7001 (m-80) REVERT: P 146 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8186 (tm) REVERT: Q 48 ARG cc_start: 0.7858 (ptt-90) cc_final: 0.7341 (ptt180) REVERT: R 31 LYS cc_start: 0.7692 (pmtt) cc_final: 0.7024 (ttpp) REVERT: R 110 GLN cc_start: 0.8618 (tt0) cc_final: 0.8302 (tt0) REVERT: S 144 ASP cc_start: 0.7831 (p0) cc_final: 0.7603 (p0) REVERT: S 147 ARG cc_start: 0.7072 (ptt90) cc_final: 0.6681 (ptm-80) REVERT: S 243 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8061 (mp) REVERT: S 248 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7428 (mt-10) REVERT: S 271 MET cc_start: 0.8345 (ttp) cc_final: 0.8094 (ttp) REVERT: T 86 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7562 (mtt90) REVERT: T 448 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7925 (tp) REVERT: T 456 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8252 (p) REVERT: U 60 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6538 (mm-40) REVERT: U 204 THR cc_start: 0.8973 (p) cc_final: 0.8678 (t) REVERT: U 482 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7260 (tm-30) REVERT: U 511 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.5959 (mtmt) REVERT: U 537 LYS cc_start: 0.8115 (tptt) cc_final: 0.7824 (tptp) REVERT: V 539 ASN cc_start: 0.8215 (m110) cc_final: 0.7984 (m110) REVERT: X 502 MET cc_start: 0.7881 (mtp) cc_final: 0.7638 (mtm) REVERT: Y 487 TYR cc_start: 0.7031 (t80) cc_final: 0.6666 (t80) REVERT: Y 488 MET cc_start: 0.7331 (mmm) cc_final: 0.6850 (mpt) REVERT: Y 501 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6731 (tmtp) REVERT: Y 528 ASP cc_start: 0.6370 (p0) cc_final: 0.6141 (p0) REVERT: Z 51 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7194 (ttm110) REVERT: Z 82 ASP cc_start: 0.7798 (t0) cc_final: 0.7541 (t0) REVERT: Z 502 MET cc_start: 0.8017 (mtp) cc_final: 0.7685 (mtm) REVERT: Z 504 LYS cc_start: 0.7197 (ptpt) cc_final: 0.6905 (pptt) REVERT: Z 550 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6445 (tptp) REVERT: Z 572 LYS cc_start: 0.8107 (tppt) cc_final: 0.7443 (mmtm) outliers start: 104 outliers final: 51 residues processed: 474 average time/residue: 1.3890 time to fit residues: 797.5873 Evaluate side-chains 426 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 362 time to evaluate : 3.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 288 LEU Chi-restraints excluded: chain T residue 86 ARG Chi-restraints excluded: chain T residue 101 LYS Chi-restraints excluded: chain T residue 143 LEU Chi-restraints excluded: chain T residue 207 LYS Chi-restraints excluded: chain T residue 325 ASP Chi-restraints excluded: chain T residue 421 LEU Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain U residue 60 GLN Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 511 LYS Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 487 LYS Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 390 ASN Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 344 ASP Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Y residue 532 SER Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 161 VAL Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 428 GLU Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 527 LEU Chi-restraints excluded: chain Z residue 550 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 263 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 254 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 270 optimal weight: 3.9990 chunk 290 optimal weight: 2.9990 chunk 210 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 334 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN H 87 ASN T 179 ASN T 441 GLN T 497 GLN U 60 GLN ** U 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 471 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 157 GLN Z 440 GLN Z 574 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34420 Z= 0.186 Angle : 0.552 12.301 46649 Z= 0.274 Chirality : 0.043 0.233 5520 Planarity : 0.004 0.052 5999 Dihedral : 6.298 172.188 4919 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.32 % Favored : 96.53 % Rotamer: Outliers : 2.89 % Allowed : 19.61 % Favored : 77.50 % 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: -0.14 (0.13), residues: 4462 helix: 0.36 (0.12), residues: 2137 sheet: -0.29 (0.22), residues: 566 loop : -0.41 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 58 HIS 0.012 0.001 HIS U 61 PHE 0.022 0.001 PHE R 127 TYR 0.019 0.001 TYR T 502 ARG 0.007 0.000 ARG T 199 *********************** 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 490 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 387 time to evaluate : 3.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 LEU cc_start: 0.5665 (OUTLIER) cc_final: 0.5097 (tm) REVERT: B 81 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.7197 (ptm) REVERT: E 92 ASN cc_start: 0.8016 (t0) cc_final: 0.7776 (t0) REVERT: E 123 LEU cc_start: 0.6043 (OUTLIER) cc_final: 0.5653 (mt) REVERT: H 118 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6228 (mt) REVERT: P 66 GLN cc_start: 0.7113 (tt0) cc_final: 0.6893 (mm-40) REVERT: P 68 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.7031 (m-30) REVERT: P 79 GLU cc_start: 0.7415 (tt0) cc_final: 0.6988 (tp30) REVERT: P 146 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8189 (tm) REVERT: P 150 LYS cc_start: 0.6533 (mmtp) cc_final: 0.6063 (mmmt) REVERT: R 31 LYS cc_start: 0.7730 (pmtt) cc_final: 0.7048 (ttpp) REVERT: R 110 GLN cc_start: 0.8620 (tt0) cc_final: 0.8299 (tt0) REVERT: S 144 ASP cc_start: 0.7871 (p0) cc_final: 0.7630 (p0) REVERT: S 147 ARG cc_start: 0.7088 (ptt90) cc_final: 0.6683 (ptm-80) REVERT: S 243 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8008 (mp) REVERT: S 248 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7429 (mt-10) REVERT: S 271 MET cc_start: 0.8355 (ttp) cc_final: 0.8106 (ttp) REVERT: T 86 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7555 (mtt90) REVERT: T 449 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7074 (mt-10) REVERT: T 456 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8296 (p) REVERT: U 60 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6495 (mm-40) REVERT: U 482 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7156 (tm-30) REVERT: U 511 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.5954 (mtmt) REVERT: U 537 LYS cc_start: 0.8115 (tptt) cc_final: 0.7848 (tptp) REVERT: V 539 ASN cc_start: 0.8232 (m110) cc_final: 0.7933 (m110) REVERT: X 51 ARG cc_start: 0.8531 (ttt90) cc_final: 0.8192 (ttt-90) REVERT: X 158 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: X 502 MET cc_start: 0.7910 (mtp) cc_final: 0.7666 (mtm) REVERT: Y 487 TYR cc_start: 0.7100 (t80) cc_final: 0.6825 (t80) REVERT: Y 488 MET cc_start: 0.7364 (mmm) cc_final: 0.6908 (mpt) REVERT: Y 501 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6692 (tmtp) REVERT: Z 51 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7220 (ttm110) REVERT: Z 82 ASP cc_start: 0.7853 (t0) cc_final: 0.7584 (t0) REVERT: Z 502 MET cc_start: 0.8028 (mtp) cc_final: 0.7695 (mtm) REVERT: Z 504 LYS cc_start: 0.7199 (ptpt) cc_final: 0.6920 (pptt) REVERT: Z 550 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6492 (tptp) REVERT: Z 572 LYS cc_start: 0.8114 (tppt) cc_final: 0.7457 (mmtm) outliers start: 103 outliers final: 56 residues processed: 457 average time/residue: 1.3971 time to fit residues: 769.9389 Evaluate side-chains 434 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 363 time to evaluate : 3.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 288 LEU Chi-restraints excluded: chain T residue 86 ARG Chi-restraints excluded: chain T residue 101 LYS Chi-restraints excluded: chain T residue 143 LEU Chi-restraints excluded: chain T residue 207 LYS Chi-restraints excluded: chain T residue 325 ASP Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain U residue 60 GLN Chi-restraints excluded: chain U residue 101 LYS Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 511 LYS Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 487 LYS Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 390 ASN Chi-restraints excluded: chain X residue 419 ILE Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 344 ASP Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 413 LEU Chi-restraints excluded: chain Y residue 426 SER Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Y residue 532 SER Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 161 VAL Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 527 LEU Chi-restraints excluded: chain Z residue 550 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 387 optimal weight: 2.9990 chunk 408 optimal weight: 0.7980 chunk 372 optimal weight: 4.9990 chunk 396 optimal weight: 4.9990 chunk 238 optimal weight: 7.9990 chunk 172 optimal weight: 0.4980 chunk 311 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 358 optimal weight: 0.8980 chunk 375 optimal weight: 2.9990 chunk 395 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 ASN T 497 GLN U 60 GLN ** U 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 471 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 157 GLN Z 440 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34420 Z= 0.230 Angle : 0.575 12.028 46649 Z= 0.286 Chirality : 0.044 0.230 5520 Planarity : 0.004 0.070 5999 Dihedral : 6.274 147.354 4919 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.52 % Favored : 96.32 % Rotamer: Outliers : 2.50 % Allowed : 20.31 % Favored : 77.19 % 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: -0.17 (0.13), residues: 4462 helix: 0.32 (0.12), residues: 2136 sheet: -0.26 (0.22), residues: 547 loop : -0.42 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 37 HIS 0.011 0.001 HIS U 61 PHE 0.023 0.001 PHE R 127 TYR 0.020 0.001 TYR P 75 ARG 0.008 0.000 ARG T 199 *********************** 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 470 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 381 time to evaluate : 3.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 LEU cc_start: 0.5597 (OUTLIER) cc_final: 0.5079 (tm) REVERT: B 81 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7268 (ptm) REVERT: E 92 ASN cc_start: 0.8065 (t0) cc_final: 0.7795 (t0) REVERT: E 123 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.5625 (mt) REVERT: H 118 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6202 (mt) REVERT: P 79 GLU cc_start: 0.7430 (tt0) cc_final: 0.6961 (tp30) REVERT: P 82 LYS cc_start: 0.8249 (mtpp) cc_final: 0.7939 (mtpp) REVERT: P 146 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8202 (tm) REVERT: P 150 LYS cc_start: 0.6729 (mmtp) cc_final: 0.5762 (tttm) REVERT: R 110 GLN cc_start: 0.8642 (tt0) cc_final: 0.8332 (tt0) REVERT: S 144 ASP cc_start: 0.7911 (p0) cc_final: 0.7660 (p0) REVERT: S 147 ARG cc_start: 0.7064 (ptt90) cc_final: 0.6671 (ptm-80) REVERT: S 243 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7945 (mp) REVERT: S 271 MET cc_start: 0.8372 (ttp) cc_final: 0.8133 (ttp) REVERT: T 86 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7546 (mtt90) REVERT: T 449 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7052 (mt-10) REVERT: T 456 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8319 (p) REVERT: U 60 GLN cc_start: 0.7135 (OUTLIER) cc_final: 0.6716 (mm-40) REVERT: U 453 TYR cc_start: 0.6995 (t80) cc_final: 0.6436 (t80) REVERT: U 482 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7192 (tm-30) REVERT: U 537 LYS cc_start: 0.8169 (tptt) cc_final: 0.7897 (tptp) REVERT: V 539 ASN cc_start: 0.8266 (m110) cc_final: 0.7904 (m110) REVERT: X 158 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7473 (tt0) REVERT: X 491 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6840 (p0) REVERT: X 502 MET cc_start: 0.7834 (mtp) cc_final: 0.7564 (mtm) REVERT: Y 487 TYR cc_start: 0.7149 (t80) cc_final: 0.6695 (t80) REVERT: Y 488 MET cc_start: 0.7372 (mmm) cc_final: 0.6910 (mpt) REVERT: Y 501 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6693 (tmtp) REVERT: Z 51 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7253 (ttm110) REVERT: Z 82 ASP cc_start: 0.7908 (t0) cc_final: 0.7613 (t0) REVERT: Z 441 ARG cc_start: 0.8217 (mmt-90) cc_final: 0.8008 (mmt-90) REVERT: Z 504 LYS cc_start: 0.7245 (ptpt) cc_final: 0.6959 (pptt) REVERT: Z 550 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6511 (tptp) REVERT: Z 572 LYS cc_start: 0.8105 (tppt) cc_final: 0.7504 (mmtm) outliers start: 89 outliers final: 63 residues processed: 446 average time/residue: 1.4434 time to fit residues: 779.0461 Evaluate side-chains 440 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 363 time to evaluate : 3.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 288 LEU Chi-restraints excluded: chain T residue 86 ARG Chi-restraints excluded: chain T residue 101 LYS Chi-restraints excluded: chain T residue 143 LEU Chi-restraints excluded: chain T residue 207 LYS Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain U residue 60 GLN Chi-restraints excluded: chain U residue 101 LYS Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 511 LYS Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 487 LYS Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 390 ASN Chi-restraints excluded: chain X residue 419 ILE Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 344 ASP Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 413 LEU Chi-restraints excluded: chain Y residue 415 ASP Chi-restraints excluded: chain Y residue 426 SER Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Y residue 532 SER Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 161 VAL Chi-restraints excluded: chain Z residue 428 GLU Chi-restraints excluded: chain Z residue 431 LEU Chi-restraints excluded: chain Z residue 440 GLN Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 550 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 260 optimal weight: 0.6980 chunk 419 optimal weight: 0.2980 chunk 256 optimal weight: 0.5980 chunk 199 optimal weight: 0.9990 chunk 291 optimal weight: 2.9990 chunk 440 optimal weight: 0.7980 chunk 405 optimal weight: 2.9990 chunk 350 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 270 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 ASN T 497 GLN U 60 GLN ** U 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS Y 157 GLN Z 440 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34420 Z= 0.165 Angle : 0.558 13.165 46649 Z= 0.276 Chirality : 0.042 0.230 5520 Planarity : 0.004 0.067 5999 Dihedral : 5.950 128.568 4919 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.73 % Rotamer: Outliers : 2.22 % Allowed : 20.76 % Favored : 77.03 % 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: -0.05 (0.13), residues: 4462 helix: 0.42 (0.12), residues: 2128 sheet: -0.24 (0.22), residues: 566 loop : -0.35 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 58 HIS 0.008 0.001 HIS U 61 PHE 0.022 0.001 PHE R 127 TYR 0.019 0.001 TYR X 410 ARG 0.008 0.000 ARG T 199 ********************** 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 456 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 377 time to evaluate : 3.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.7107 (ptm) REVERT: C 118 LEU cc_start: 0.6730 (tp) cc_final: 0.6501 (tm) REVERT: G 81 MET cc_start: 0.7030 (tmm) cc_final: 0.6827 (tmm) REVERT: G 97 LYS cc_start: 0.7363 (mttm) cc_final: 0.7087 (tptt) REVERT: H 118 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6149 (mt) REVERT: P 79 GLU cc_start: 0.7409 (tt0) cc_final: 0.6947 (tp30) REVERT: P 82 LYS cc_start: 0.8280 (mtpp) cc_final: 0.7980 (mtpp) REVERT: P 146 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8216 (tm) REVERT: P 150 LYS cc_start: 0.6717 (mmtp) cc_final: 0.5769 (tttm) REVERT: Q 52 TYR cc_start: 0.7256 (m-10) cc_final: 0.6962 (m-10) REVERT: R 31 LYS cc_start: 0.7711 (pmtt) cc_final: 0.7033 (ttpp) REVERT: R 110 GLN cc_start: 0.8603 (tt0) cc_final: 0.8291 (tt0) REVERT: S 144 ASP cc_start: 0.7850 (p0) cc_final: 0.7612 (p0) REVERT: S 147 ARG cc_start: 0.7071 (ptt90) cc_final: 0.6677 (ptm-80) REVERT: S 243 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8073 (mp) REVERT: S 271 MET cc_start: 0.8359 (ttp) cc_final: 0.8110 (ttp) REVERT: T 86 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7526 (mtt90) REVERT: T 449 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7088 (mt-10) REVERT: T 456 VAL cc_start: 0.8647 (OUTLIER) cc_final: 0.8281 (p) REVERT: U 60 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.6722 (mm-40) REVERT: U 204 THR cc_start: 0.8975 (p) cc_final: 0.8697 (t) REVERT: U 411 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: U 453 TYR cc_start: 0.6950 (t80) cc_final: 0.6442 (t80) REVERT: U 482 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7227 (tm-30) REVERT: U 511 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6058 (mtmt) REVERT: U 537 LYS cc_start: 0.8140 (tptt) cc_final: 0.7912 (tptp) REVERT: V 539 ASN cc_start: 0.8222 (m110) cc_final: 0.7918 (m110) REVERT: X 491 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6685 (p0) REVERT: X 502 MET cc_start: 0.7899 (mtp) cc_final: 0.7663 (mtm) REVERT: Y 487 TYR cc_start: 0.7112 (t80) cc_final: 0.6861 (t80) REVERT: Y 488 MET cc_start: 0.7371 (mmm) cc_final: 0.6943 (mpt) REVERT: Y 501 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6685 (tmtp) REVERT: Z 51 ARG cc_start: 0.7842 (ttm-80) cc_final: 0.7318 (ttm110) REVERT: Z 82 ASP cc_start: 0.7834 (t0) cc_final: 0.7560 (t0) REVERT: Z 484 MET cc_start: 0.7713 (mmm) cc_final: 0.7510 (tmm) REVERT: Z 502 MET cc_start: 0.7804 (mtp) cc_final: 0.7450 (mtm) REVERT: Z 504 LYS cc_start: 0.7215 (ptpt) cc_final: 0.6914 (pptt) REVERT: Z 550 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6503 (tptp) REVERT: Z 572 LYS cc_start: 0.8070 (tppt) cc_final: 0.7500 (mmtm) outliers start: 79 outliers final: 50 residues processed: 433 average time/residue: 1.4039 time to fit residues: 736.0124 Evaluate side-chains 420 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 357 time to evaluate : 4.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 288 LEU Chi-restraints excluded: chain T residue 86 ARG Chi-restraints excluded: chain T residue 101 LYS Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain U residue 60 GLN Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 511 LYS Chi-restraints excluded: chain U residue 558 LYS Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 487 LYS Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 390 ASN Chi-restraints excluded: chain X residue 419 ILE Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 344 ASP Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 426 SER Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Y residue 532 SER Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 161 VAL Chi-restraints excluded: chain Z residue 440 GLN Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 550 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 278 optimal weight: 1.9990 chunk 373 optimal weight: 0.4980 chunk 107 optimal weight: 4.9990 chunk 323 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 351 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 360 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN T 179 ASN T 497 GLN U 60 GLN ** U 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 157 GLN Z 440 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.146771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109042 restraints weight = 49050.047| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.94 r_work: 0.3211 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34420 Z= 0.190 Angle : 0.571 12.938 46649 Z= 0.283 Chirality : 0.043 0.250 5520 Planarity : 0.004 0.068 5999 Dihedral : 5.873 111.512 4919 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.32 % Favored : 96.53 % Rotamer: Outliers : 2.16 % Allowed : 21.12 % Favored : 76.72 % 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: 0.44 (0.12), residues: 2125 sheet: -0.21 (0.22), residues: 565 loop : -0.33 (0.15), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 58 HIS 0.003 0.001 HIS V 241 PHE 0.023 0.001 PHE R 127 TYR 0.022 0.001 TYR P 75 ARG 0.008 0.000 ARG T 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13453.17 seconds wall clock time: 240 minutes 21.06 seconds (14421.06 seconds total)