Starting phenix.real_space_refine on Thu Feb 22 11:16:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdg_4817/02_2024/6rdg_4817_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdg_4817/02_2024/6rdg_4817.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/6rdg_4817/02_2024/6rdg_4817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdg_4817/02_2024/6rdg_4817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdg_4817/02_2024/6rdg_4817_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdg_4817/02_2024/6rdg_4817_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 21567 2.51 5 N 5801 2.21 5 O 6462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 91": "NH1" <-> "NH2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "G PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "I GLU 111": "OE1" <-> "OE2" Residue "J 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 "Q ASP 54": "OD1" <-> "OD2" Residue "Q GLU 64": "OE1" <-> "OE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 174": "OD1" <-> "OD2" Residue "R PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 186": "OE1" <-> "OE2" Residue "R GLU 196": "OE1" <-> "OE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S ASP 136": "OD1" <-> "OD2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 232": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ARG 96": "NH1" <-> "NH2" Residue "T ASP 112": "OD1" <-> "OD2" Residue "T TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ASP 172": "OD1" <-> "OD2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 237": "OD1" <-> "OD2" 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 380": "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 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 495": "OE1" <-> "OE2" Residue "T TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 510": "OD1" <-> "OD2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 135": "OD1" <-> "OD2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 311": "OE1" <-> "OE2" Residue "U PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U ARG 342": "NH1" <-> "NH2" Residue "U ARG 343": "NH1" <-> "NH2" Residue "U ARG 364": "NH1" <-> "NH2" Residue "U PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 409": "OE1" <-> "OE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U 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 ARG 513": "NH1" <-> "NH2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 547": "OD1" <-> "OD2" 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 ASP 326": "OD1" <-> "OD2" Residue "V ARG 335": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "V ARG 360": "NH1" <-> "NH2" Residue "V PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 403": "OD1" <-> "OD2" Residue "V PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V GLU 455": "OE1" <-> "OE2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V GLU 553": "OE1" <-> "OE2" 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 139": "OD1" <-> "OD2" Residue "X GLU 146": "OE1" <-> "OE2" 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 ARG 258": "NH1" <-> "NH2" Residue "X GLU 270": "OE1" <-> "OE2" Residue "X ASP 279": "OD1" <-> "OD2" 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 GLU 451": "OE1" <-> "OE2" Residue "X PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 465": "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 491": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X ASP 543": "OD1" <-> "OD2" Residue "X GLU 547": "OE1" <-> "OE2" Residue "X GLU 557": "OE1" <-> "OE2" Residue "Y ASP 49": "OD1" <-> "OD2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y GLU 55": "OE1" <-> "OE2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ARG 98": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y GLU 149": "OE1" <-> "OE2" Residue "Y PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 216": "NH1" <-> "NH2" Residue "Y GLU 226": "OE1" <-> "OE2" Residue "Y GLU 229": "OE1" <-> "OE2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y ARG 289": "NH1" <-> "NH2" Residue "Y ASP 344": "OD1" <-> "OD2" Residue "Y ASP 345": "OD1" <-> "OD2" Residue "Y PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 378": "OD1" <-> "OD2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y ARG 401": "NH1" <-> "NH2" Residue "Y TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 415": "OD1" <-> "OD2" Residue "Y ARG 435": "NH1" <-> "NH2" Residue "Y ARG 437": "NH1" <-> "NH2" Residue "Y PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 465": "OD1" <-> "OD2" Residue "Y ASP 479": "OD1" <-> "OD2" Residue "Y ARG 509": "NH1" <-> "NH2" Residue "Y ASP 542": "OD1" <-> "OD2" Residue "Y GLU 546": "OE1" <-> "OE2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 36": "OD1" <-> "OD2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "Z ASP 53": "OD1" <-> "OD2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z ASP 139": "OD1" <-> "OD2" Residue "Z PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 218": "NH1" <-> "NH2" Residue "Z GLU 219": "OE1" <-> "OE2" Residue "Z ARG 225": "NH1" <-> "NH2" Residue "Z ARG 239": "NH1" <-> "NH2" Residue "Z TYR 248": "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 GLU 424": "OE1" <-> "OE2" Residue "Z GLU 427": "OE1" <-> "OE2" Residue "Z PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z GLU 541": "OE1" <-> "OE2" Residue "Z ASP 543": "OD1" <-> "OD2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33964 Number of models: 1 Model: "" Number of chains: 31 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: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 886 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} 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: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3649 Classifications: {'peptide': 483} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 461} 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} Chain: "T" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "U" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "V" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "X" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 16.91, per 1000 atoms: 0.50 Number of scatterers: 33964 At special positions: 0 Unit cell: (164.268, 135.837, 207.441, 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 6462 8.00 N 5801 7.00 C 21567 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: 12.62 Conformation dependent library (CDL) restraints added in 6.0 seconds 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8170 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 27 sheets defined 46.4% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.76 Creating SS restraints... Processing helix chain 'A' and resid 55 through 91 removed outlier: 4.158A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 124 removed outlier: 4.772A pdb=" N LYS A 97 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 99 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL A 100 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU A 104 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 105 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 109 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR A 110 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 111 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 112 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 117 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 118 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 119 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 120 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 121 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 122 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE A 124 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.967A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 125 removed outlier: 5.267A pdb=" N LYS B 97 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B 100 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU B 104 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 105 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 107 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 108 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU B 111 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 115 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B 119 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 120 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL B 121 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE B 124 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU B 125 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 65 removed outlier: 4.508A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 91 removed outlier: 3.670A pdb=" N LEU C 71 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 74 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA C 76 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C 78 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY C 79 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE C 82 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 83 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA C 89 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG C 91 " --> pdb=" O GLY C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 124 removed outlier: 3.505A pdb=" N VAL C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL C 121 " --> pdb=" O SER C 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 91 removed outlier: 3.855A pdb=" N LYS D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 125 removed outlier: 3.566A pdb=" N ALA D 96 " --> pdb=" O PRO D 93 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LYS D 97 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU D 99 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 100 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU D 104 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU D 105 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE D 107 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA D 108 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 109 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR D 110 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU D 111 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 115 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL D 120 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE D 122 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE D 124 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 removed outlier: 4.668A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 91 removed outlier: 3.628A pdb=" N GLY E 79 " --> pdb=" O GLY E 75 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG E 91 " --> pdb=" O ASN E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 108 removed outlier: 3.812A pdb=" N ALA E 96 " --> pdb=" O PRO E 93 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS E 97 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL E 100 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU E 104 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU E 105 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE E 107 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.592A pdb=" N VAL E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 89 removed outlier: 3.929A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY F 63 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 125 removed outlier: 4.786A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU F 99 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL F 100 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU F 104 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU F 105 " --> pdb=" O TYR F 102 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA F 108 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU F 109 " --> pdb=" O GLY F 106 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU F 111 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER F 117 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL F 121 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE F 122 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU F 125 " --> pdb=" O PHE F 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 91 removed outlier: 4.062A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 110 removed outlier: 3.850A pdb=" N ALA G 96 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU G 99 " --> pdb=" O ALA G 96 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL G 100 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU G 104 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU G 105 " --> pdb=" O TYR G 102 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR G 110 " --> pdb=" O PHE G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 125 Processing helix chain 'H' and resid 55 through 65 removed outlier: 3.741A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 91 removed outlier: 3.993A pdb=" N GLY H 73 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL H 74 " --> pdb=" O LEU H 71 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA H 76 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU H 78 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY H 79 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE H 82 " --> pdb=" O GLY H 79 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU H 85 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY H 88 " --> pdb=" O LEU H 85 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA H 89 " --> pdb=" O ILE H 86 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG H 91 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 125 removed outlier: 5.378A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN H 98 " --> pdb=" O ILE H 95 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL H 100 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU H 104 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU H 105 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA H 108 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR H 110 " --> pdb=" O PHE H 107 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE H 113 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU H 115 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER H 117 " --> pdb=" O ALA H 114 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU H 118 " --> pdb=" O LEU H 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU H 119 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL H 120 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE H 124 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU H 125 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 91 removed outlier: 3.826A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY I 65 " --> pdb=" O MET I 61 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA I 70 " --> pdb=" O CYS I 66 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LEU I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA I 72 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY I 79 " --> pdb=" O GLY I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 126 removed outlier: 3.518A pdb=" N ALA I 96 " --> pdb=" O PRO I 93 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LYS I 97 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU I 99 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU I 104 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU I 105 " --> pdb=" O TYR I 102 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA I 108 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU I 109 " --> pdb=" O GLY I 106 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU I 111 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER I 112 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU I 115 " --> pdb=" O SER I 112 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU I 118 " --> pdb=" O LEU I 115 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU I 119 " --> pdb=" O PHE I 116 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL I 120 " --> pdb=" O SER I 117 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL I 121 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE I 124 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU I 125 " --> pdb=" O PHE I 122 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE I 126 " --> pdb=" O LEU I 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 91 removed outlier: 3.658A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS J 66 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY J 79 " --> pdb=" O GLY J 75 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU J 85 " --> pdb=" O MET J 81 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 125 removed outlier: 3.635A pdb=" N VAL J 100 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY J 101 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR J 102 " --> pdb=" O GLN J 98 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU J 111 " --> pdb=" O PHE J 107 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL J 120 " --> pdb=" O PHE J 116 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL J 121 " --> pdb=" O SER J 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 63 removed outlier: 3.552A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 83 removed outlier: 3.768A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR P 75 " --> pdb=" O GLN P 71 " (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 removed outlier: 3.732A pdb=" N THR P 102 " --> pdb=" O THR P 98 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 127 removed outlier: 4.443A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA P 124 " --> pdb=" O LYS P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 148 removed outlier: 3.959A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL P 137 " --> pdb=" O LEU P 134 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU P 143 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU P 146 " --> pdb=" O GLU P 143 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA P 147 " --> pdb=" O LEU P 144 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 12 No H-bonds generated for 'chain 'Q' and resid 10 through 12' Processing helix chain 'Q' and resid 16 through 30 removed outlier: 4.273A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 38 removed outlier: 4.534A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 37 removed outlier: 3.920A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 54 Processing helix chain 'R' and resid 152 through 154 No H-bonds generated for 'chain 'R' and resid 152 through 154' Processing helix chain 'R' and resid 160 through 165 Processing helix chain 'R' and resid 177 through 196 removed outlier: 3.502A pdb=" N SER R 193 " --> pdb=" O SER R 189 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL R 195 " --> pdb=" O LEU R 191 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 70 removed outlier: 3.815A pdb=" N ASN S 52 " --> pdb=" O ARG S 48 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 81 removed outlier: 4.092A pdb=" N GLY S 80 " --> pdb=" O GLU S 76 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU S 81 " --> pdb=" O GLN S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 88 Processing helix chain 'S' and resid 116 through 127 removed outlier: 3.609A pdb=" N THR S 120 " --> pdb=" O ASN S 116 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 184 removed outlier: 3.555A pdb=" N LEU S 182 " --> pdb=" O ILE S 178 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS S 184 " --> pdb=" O GLU S 180 " (cutoff:3.500A) Processing helix chain 'S' and resid 228 through 230 No H-bonds generated for 'chain 'S' and resid 228 through 230' Processing helix chain 'S' and resid 239 through 312 removed outlier: 3.648A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 137 No H-bonds generated for 'chain 'T' and resid 135 through 137' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 207 through 212 removed outlier: 3.673A pdb=" N LEU T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 231 through 246 removed outlier: 3.513A pdb=" N ALA T 238 " --> pdb=" O VAL T 234 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 279 removed outlier: 3.504A pdb=" N ALA T 270 " --> pdb=" O ARG T 266 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 284 Processing helix chain 'T' and resid 296 through 316 Proline residue: T 303 - end of helix removed outlier: 4.363A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 340 removed outlier: 3.655A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 347 through 349 No H-bonds generated for 'chain 'T' and resid 347 through 349' Processing helix chain 'T' and resid 352 through 364 removed outlier: 4.371A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR T 356 " --> pdb=" O ASP T 353 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER T 359 " --> pdb=" O TYR T 356 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG T 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU T 361 " --> pdb=" O HIS T 358 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU T 362 " --> pdb=" O SER T 359 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU T 363 " --> pdb=" O ARG T 360 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 401 Processing helix chain 'T' and resid 411 through 414 No H-bonds generated for 'chain 'T' and resid 411 through 414' Processing helix chain 'T' and resid 431 through 434 removed outlier: 3.697A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 431 through 434' Processing helix chain 'T' and resid 437 through 440 No H-bonds generated for 'chain 'T' and resid 437 through 440' Processing helix chain 'T' and resid 443 through 455 removed outlier: 4.012A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) Processing helix chain 'T' and resid 459 through 461 No H-bonds generated for 'chain 'T' and resid 459 through 461' Processing helix chain 'T' and resid 471 through 481 removed outlier: 3.566A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 505 removed outlier: 3.658A pdb=" N VAL T 499 " --> pdb=" O GLU T 495 " (cutoff:3.500A) removed outlier: 3.840A 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 removed outlier: 3.580A pdb=" N ALA T 552 " --> pdb=" O ALA T 548 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG T 555 " --> pdb=" O LYS T 551 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 49 removed outlier: 4.042A pdb=" N ARG U 49 " --> pdb=" O LEU U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 70 removed outlier: 3.791A pdb=" N SER U 63 " --> pdb=" O ILE U 59 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix Processing helix chain 'U' and resid 157 through 159 No H-bonds generated for 'chain 'U' and resid 157 through 159' Processing helix chain 'U' and resid 207 through 212 removed outlier: 3.604A pdb=" N LEU U 212 " --> pdb=" O ALA U 208 " (cutoff:3.500A) Processing helix chain 'U' and resid 231 through 246 removed outlier: 3.543A pdb=" N LYS U 243 " --> pdb=" O ILE U 239 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 279 removed outlier: 3.639A pdb=" N LEU U 275 " --> pdb=" O GLN U 271 " (cutoff:3.500A) 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 316 Proline residue: U 303 - end of helix removed outlier: 3.552A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG U 314 " --> pdb=" O ALA U 310 " (cutoff:3.500A) Processing helix chain 'U' and resid 328 through 340 removed outlier: 3.855A 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: 4.337A pdb=" N PHE U 355 " --> pdb=" O GLY U 352 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU U 357 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER U 359 " --> pdb=" O TYR U 356 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG U 360 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU U 361 " --> pdb=" O HIS U 358 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU U 362 " --> pdb=" O SER U 359 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU U 363 " --> pdb=" O ARG U 360 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG U 364 " --> pdb=" O LEU U 361 " (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 442 removed outlier: 3.659A pdb=" N GLN U 441 " --> pdb=" O PRO U 437 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 437 through 442' Processing helix chain 'U' and resid 444 through 459 removed outlier: 3.870A pdb=" N GLU U 449 " --> pdb=" O THR U 445 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA U 451 " --> pdb=" O LYS U 447 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN U 452 " --> pdb=" O LEU U 448 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL U 456 " --> pdb=" O GLN U 452 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA U 458 " --> pdb=" O ARG U 454 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N PHE U 459 " --> pdb=" O GLU U 455 " (cutoff:3.500A) Processing helix chain 'U' and resid 466 through 468 No H-bonds generated for 'chain 'U' and resid 466 through 468' Processing helix chain 'U' and resid 472 through 484 removed outlier: 3.632A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG U 479 " --> pdb=" O GLU U 475 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU U 482 " --> pdb=" O ALA U 478 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET U 483 " --> pdb=" O ARG U 479 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 500 removed outlier: 3.561A 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 520 through 526 Processing helix chain 'U' and resid 531 through 539 removed outlier: 3.516A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 544 through 552 removed outlier: 3.512A pdb=" N ALA U 548 " --> pdb=" O PRO U 544 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) Processing helix chain 'V' and resid 46 through 48 No H-bonds generated for 'chain 'V' and resid 46 through 48' Processing helix chain 'V' and resid 58 through 66 removed outlier: 3.509A 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 210 No H-bonds generated for 'chain 'V' and resid 207 through 210' Processing helix chain 'V' and resid 231 through 246 removed outlier: 3.702A pdb=" N ASP V 237 " --> pdb=" O ALA V 233 " (cutoff:3.500A) Processing helix chain 'V' and resid 251 through 253 No H-bonds generated for 'chain 'V' and resid 251 through 253' Processing helix chain 'V' and resid 266 through 279 Processing helix chain 'V' and resid 281 through 284 Processing helix chain 'V' and resid 296 through 316 Proline residue: V 303 - end of helix removed outlier: 4.590A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG V 314 " --> pdb=" O ALA V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 340 removed outlier: 3.634A pdb=" N SER V 331 " --> pdb=" O LEU V 327 " (cutoff:3.500A) Processing helix chain 'V' and resid 347 through 349 No H-bonds generated for 'chain 'V' and resid 347 through 349' Processing helix chain 'V' and resid 352 through 364 removed outlier: 4.362A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR V 356 " --> pdb=" O ASP V 353 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER V 359 " --> pdb=" O TYR V 356 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU V 362 " --> pdb=" O SER V 359 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU V 363 " --> pdb=" O ARG V 360 " (cutoff:3.500A) removed outlier: 3.560A 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: 3.571A 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 456 removed outlier: 3.600A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL V 456 " --> pdb=" O GLN V 452 " (cutoff:3.500A) Processing helix chain 'V' and resid 471 through 484 removed outlier: 3.544A pdb=" N ALA V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ARG V 479 " --> pdb=" O GLU V 475 " (cutoff:3.500A) Processing helix chain 'V' and resid 494 through 505 removed outlier: 3.987A pdb=" N VAL V 499 " --> pdb=" O GLU V 495 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA V 500 " --> pdb=" O ARG V 496 " (cutoff:3.500A) Processing helix chain 'V' and resid 514 through 527 removed outlier: 4.012A pdb=" N ILE V 517 " --> pdb=" O VAL V 514 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL V 518 " --> pdb=" O GLN V 515 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA V 519 " --> pdb=" O ASP V 516 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU V 521 " --> pdb=" O VAL V 518 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU V 522 " --> pdb=" O ALA V 519 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE V 525 " --> pdb=" O GLU V 522 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER V 526 " --> pdb=" O ALA V 523 " (cutoff:3.500A) removed outlier: 3.518A 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: 4.787A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 255 through 258 No H-bonds generated for 'chain 'X' and resid 255 through 258' Processing helix chain 'X' and resid 261 through 274 Processing helix chain 'X' and resid 288 through 295 Processing helix chain 'X' and resid 314 through 324 removed outlier: 4.226A 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: 3.738A pdb=" N THR X 354 " --> pdb=" O ALA X 350 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE X 355 " --> pdb=" O PRO X 351 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA X 356 " --> pdb=" O ALA X 352 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N HIS X 357 " --> pdb=" O THR X 353 " (cutoff:3.500A) Processing helix chain 'X' and resid 366 through 370 Processing helix chain 'X' and resid 394 through 417 removed outlier: 3.502A pdb=" N ASN X 398 " --> pdb=" O ALA X 394 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL X 399 " --> pdb=" O GLU X 395 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) Processing helix chain 'X' and resid 431 through 443 removed outlier: 3.558A pdb=" N ALA X 436 " --> pdb=" O THR X 432 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG X 441 " --> pdb=" O ARG X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 448 through 450 No H-bonds generated for 'chain 'X' and resid 448 through 450' Processing helix chain 'X' and resid 463 through 475 removed outlier: 3.562A pdb=" N SER X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY X 469 " --> pdb=" O ASP X 465 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL X 473 " --> pdb=" O GLY X 469 " (cutoff:3.500A) Processing helix chain 'X' and resid 483 through 486 removed outlier: 3.651A pdb=" N PHE X 486 " --> pdb=" O GLU X 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 483 through 486' Processing helix chain 'X' and resid 492 through 506 removed outlier: 3.537A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP X 500 " --> pdb=" O LYS X 496 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 533 removed outlier: 3.641A pdb=" N VAL X 531 " --> pdb=" O LEU X 527 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU X 533 " --> pdb=" O LYS X 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 527 through 533' Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 165 through 169 Processing helix chain 'Y' and resid 189 through 203 removed outlier: 3.612A pdb=" N MET Y 194 " --> pdb=" O THR Y 190 " (cutoff:3.500A) Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 3.745A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 274 removed outlier: 4.970A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) removed outlier: 3.568A 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: 3.556A 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 355 Processing helix chain 'Y' and resid 366 through 370 Processing helix chain 'Y' and resid 389 through 411 removed outlier: 7.518A pdb=" N ALA Y 394 " --> pdb=" O ASN Y 390 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N GLU Y 395 " --> pdb=" O VAL Y 391 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N HIS Y 396 " --> pdb=" O ILE Y 392 " (cutoff:3.500A) Processing helix chain 'Y' and resid 414 through 419 removed outlier: 3.793A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 427 through 442 removed outlier: 3.535A pdb=" N LEU Y 431 " --> pdb=" O GLU Y 427 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR Y 432 " --> pdb=" O GLU Y 428 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL Y 433 " --> pdb=" O ASP Y 429 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS Y 438 " --> pdb=" O ALA Y 434 " (cutoff:3.500A) Processing helix chain 'Y' and resid 451 through 454 No H-bonds generated for 'chain 'Y' and resid 451 through 454' Processing helix chain 'Y' and resid 463 through 475 removed outlier: 3.551A pdb=" N SER Y 468 " --> pdb=" O ALA Y 464 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 492 through 503 removed outlier: 4.011A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU Y 497 " --> pdb=" O LYS Y 493 " (cutoff:3.500A) Processing helix chain 'Y' and resid 505 through 507 No H-bonds generated for 'chain 'Y' and resid 505 through 507' Processing helix chain 'Y' and resid 527 through 530 No H-bonds generated for 'chain 'Y' and resid 527 through 530' Processing helix chain 'Y' and resid 545 through 554 removed outlier: 3.540A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) removed outlier: 3.592A 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 removed outlier: 3.581A pdb=" N LEU Z 170 " --> pdb=" O VAL Z 166 " (cutoff:3.500A) Processing helix chain 'Z' and resid 189 through 200 Processing helix chain 'Z' and resid 217 through 229 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 4.624A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 274 removed outlier: 3.572A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 288 through 298 removed outlier: 3.567A pdb=" N VAL Z 297 " --> pdb=" O ALA Z 293 " (cutoff:3.500A) Processing helix chain 'Z' and resid 314 through 324 removed outlier: 4.217A pdb=" N ARG Z 324 " --> pdb=" O GLY Z 320 " (cutoff:3.500A) Processing helix chain 'Z' and resid 349 through 357 removed outlier: 3.569A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA Z 356 " --> pdb=" O ALA Z 352 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N HIS Z 357 " --> pdb=" O THR Z 353 " (cutoff:3.500A) Processing helix chain 'Z' and resid 366 through 371 removed outlier: 3.560A pdb=" N LEU Z 371 " --> pdb=" O SER Z 367 " (cutoff:3.500A) Processing helix chain 'Z' and resid 389 through 392 No H-bonds generated for 'chain 'Z' and resid 389 through 392' Processing helix chain 'Z' and resid 394 through 412 removed outlier: 3.669A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) Processing helix chain 'Z' and resid 416 through 420 Processing helix chain 'Z' and resid 422 through 424 No H-bonds generated for 'chain 'Z' and resid 422 through 424' Processing helix chain 'Z' and resid 430 through 442 removed outlier: 3.774A pdb=" N ARG Z 441 " --> pdb=" O ARG Z 437 " (cutoff:3.500A) Processing helix chain 'Z' and resid 451 through 454 No H-bonds generated for 'chain 'Z' and resid 451 through 454' Processing helix chain 'Z' and resid 463 through 475 removed outlier: 3.564A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU Z 474 " --> pdb=" O PHE Z 470 " (cutoff:3.500A) Processing helix chain 'Z' and resid 492 through 504 removed outlier: 3.877A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS Z 501 " --> pdb=" O GLU Z 497 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA Z 503 " --> pdb=" O ALA Z 499 " (cutoff:3.500A) Processing helix chain 'Z' and resid 508 through 510 No H-bonds generated for 'chain 'Z' and resid 508 through 510' Processing helix chain 'Z' and resid 528 through 532 Processing sheet with id= A, first strand: chain 'Q' and resid 45 through 49 Processing sheet with id= B, first strand: chain 'R' and resid 72 through 75 removed outlier: 6.985A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE R 144 " --> pdb=" O TYR R 75 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY R 132 " --> pdb=" O LEU R 111 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU R 111 " --> pdb=" O GLY R 132 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'R' and resid 96 through 100 removed outlier: 6.572A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU R 125 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 203 through 208 removed outlier: 3.690A pdb=" N SER S 189 " --> pdb=" O LYS S 99 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA S 161 " --> pdb=" O SER S 141 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'T' and resid 84 through 86 removed outlier: 3.889A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS T 116 " --> pdb=" O PHE T 132 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY T 128 " --> pdb=" O LEU T 120 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU T 122 " --> pdb=" O HIS T 126 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N HIS T 126 " --> pdb=" O LEU T 122 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TYR T 98 " --> pdb=" O VAL T 87 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VAL T 87 " --> pdb=" O TYR T 98 " (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 163 through 165 removed outlier: 8.136A pdb=" N THR T 164 " --> pdb=" O THR T 285 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N MET T 287 " --> pdb=" O THR T 164 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N ILE T 286 " --> pdb=" O VAL T 255 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N CYS T 257 " --> pdb=" O ILE T 286 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL T 288 " --> pdb=" O CYS T 257 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR T 259 " --> pdb=" O VAL T 288 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA T 290 " --> pdb=" O TYR T 259 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ALA T 261 " --> pdb=" O ALA T 290 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN T 264 " --> pdb=" O ASP T 325 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N SER T 376 " --> pdb=" O GLY T 320 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE T 322 " --> pdb=" O SER T 376 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE T 380 " --> pdb=" O TYR T 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'T' and resid 404 through 408 Processing sheet with id= I, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.710A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) removed outlier: 3.773A 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: 8.668A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.880A 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 84 through 86 removed outlier: 6.393A pdb=" N GLY V 128 " --> pdb=" O LEU V 120 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LEU V 122 " --> pdb=" O HIS V 126 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N HIS V 126 " --> pdb=" O LEU V 122 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TYR V 98 " --> pdb=" O VAL V 87 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL V 87 " --> pdb=" O TYR V 98 " (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: 8.745A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 6.689A 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: 6.378A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'X' and resid 158 through 160 removed outlier: 4.911A pdb=" N GLU X 158 " --> pdb=" O ARG X 175 " (cutoff:3.500A) removed outlier: 4.314A 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: 7.695A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLY X 183 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL X 339 " --> pdb=" O GLY X 183 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N PHE X 207 " --> pdb=" O LEU X 281 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N PHE X 283 " --> pdb=" O PHE X 207 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL X 209 " --> pdb=" O PHE X 283 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP X 285 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ALA X 211 " --> pdb=" O ASP X 285 " (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 39 through 44 removed outlier: 6.359A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.491A 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: 3.510A pdb=" N ASP Y 139 " --> pdb=" O VAL Y 113 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Y' and resid 244 through 250 removed outlier: 6.808A pdb=" N SER Y 208 " --> pdb=" O THR Y 245 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N VAL Y 247 " --> pdb=" O SER Y 208 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE Y 210 " --> pdb=" O VAL Y 247 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY Y 249 " --> pdb=" O PHE Y 210 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY Y 212 " --> pdb=" O GLY Y 249 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N VAL Y 209 " --> pdb=" O ASP Y 279 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU Y 281 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA Y 211 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE Y 283 " --> pdb=" O ALA Y 211 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL Y 213 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER Y 332 " --> pdb=" O VAL Y 280 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU Y 282 " --> pdb=" O SER Y 332 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR Y 334 " --> pdb=" O LEU Y 282 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL Y 284 " --> pdb=" O THR Y 334 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL Y 336 " --> pdb=" O VAL Y 284 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N GLY Y 180 " --> pdb=" O ASP Y 359 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR Y 361 " --> pdb=" O GLY Y 180 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N PHE Y 182 " --> pdb=" O THR Y 361 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL Y 363 " --> pdb=" O PHE Y 182 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Z' and resid 37 through 39 removed outlier: 6.516A pdb=" N ARG Z 86 " --> pdb=" O ALA Z 77 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N HIS Z 79 " --> pdb=" O THR Z 84 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR Z 84 " --> pdb=" O HIS Z 79 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ARG Z 51 " --> pdb=" O VAL Z 40 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N VAL Z 40 " --> pdb=" O ARG Z 51 " (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: 7.322A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N GLY Z 183 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL Z 339 " --> pdb=" O GLY Z 183 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE Z 207 " --> pdb=" O LEU Z 281 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE Z 283 " --> pdb=" O PHE Z 207 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL Z 209 " --> pdb=" O PHE Z 283 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASP Z 285 " --> pdb=" O VAL Z 209 " (cutoff:3.500A) removed outlier: 7.236A 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 1243 hydrogen bonds defined for protein. 3243 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: 11.36 Time building geometry restraints manager: 13.55 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: 11168 1.34 - 1.46: 5402 1.46 - 1.57: 17662 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34453 Sorted by residual: bond pdb=" C4 ADP X 601 " pdb=" C5 ADP X 601 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C4 ADP Z 601 " pdb=" C5 ADP Z 601 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C5 ADP Z 601 " pdb=" C6 ADP Z 601 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C5 ADP X 601 " pdb=" C6 ADP X 601 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" N ARG Z 216 " pdb=" CA ARG Z 216 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.22e-02 6.72e+03 7.48e+00 ... (remaining 34448 not shown) Histogram of bond angle deviations from ideal: 98.06 - 105.26: 646 105.26 - 112.45: 17459 112.45 - 119.65: 12193 119.65 - 126.84: 16113 126.84 - 134.04: 285 Bond angle restraints: 46696 Sorted by residual: angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 132.51 7.36 1.00e+00 1.00e+00 5.41e+01 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 132.52 7.35 1.00e+00 1.00e+00 5.40e+01 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 132.63 7.24 1.00e+00 1.00e+00 5.24e+01 angle pdb=" N GLU H 111 " pdb=" CA GLU H 111 " pdb=" C GLU H 111 " ideal model delta sigma weight residual 112.89 104.53 8.36 1.24e+00 6.50e-01 4.55e+01 angle pdb=" C GLY P 48 " pdb=" N THR P 49 " pdb=" CA THR P 49 " ideal model delta sigma weight residual 121.54 132.63 -11.09 1.91e+00 2.74e-01 3.37e+01 ... (remaining 46691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.00: 20217 31.00 - 61.99: 571 61.99 - 92.99: 55 92.99 - 123.99: 0 123.99 - 154.99: 3 Dihedral angle restraints: 20846 sinusoidal: 8074 harmonic: 12772 Sorted by residual: dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -122.53 -57.47 0 5.00e+00 4.00e-02 1.32e+02 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual -180.00 -129.08 -50.92 0 5.00e+00 4.00e-02 1.04e+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 -131.25 -48.75 0 5.00e+00 4.00e-02 9.50e+01 ... (remaining 20843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4440 0.063 - 0.126: 946 0.126 - 0.190: 125 0.190 - 0.253: 13 0.253 - 0.316: 3 Chirality restraints: 5527 Sorted by residual: chirality pdb=" CB ILE Y 524 " pdb=" CA ILE Y 524 " pdb=" CG1 ILE Y 524 " pdb=" CG2 ILE Y 524 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.49e+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 -2.34 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ASN Z 286 " pdb=" N ASN Z 286 " pdb=" C ASN Z 286 " pdb=" CB ASN Z 286 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 5524 not shown) Planarity restraints: 6004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA X 503 " -0.031 2.00e-02 2.50e+03 6.07e-02 3.68e+01 pdb=" C ALA X 503 " 0.105 2.00e-02 2.50e+03 pdb=" O ALA X 503 " -0.039 2.00e-02 2.50e+03 pdb=" N LYS X 504 " -0.035 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 6.01e-02 3.61e+01 pdb=" C ALA Z 503 " -0.104 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=" CA THR J 110 " 0.014 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" C THR J 110 " -0.052 2.00e-02 2.50e+03 pdb=" O THR J 110 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU J 111 " 0.018 2.00e-02 2.50e+03 ... (remaining 6001 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 260 2.54 - 3.13: 24433 3.13 - 3.72: 54317 3.72 - 4.31: 82905 4.31 - 4.90: 131561 Nonbonded interactions: 293476 Sorted by model distance: nonbonded pdb=" N LEU V 327 " pdb=" O VAL V 382 " model vdw 1.951 2.520 nonbonded pdb=" NH2 ARG U 227 " pdb=" OD1 ASP Z 381 " model vdw 2.088 2.520 nonbonded pdb=" OE2 GLU H 111 " pdb=" CB ALA H 114 " model vdw 2.097 3.460 nonbonded pdb=" OG1 THR X 190 " pdb="MG MG X 602 " model vdw 2.141 2.170 nonbonded pdb=" O SER V 328 " pdb=" OG SER V 331 " model vdw 2.156 2.440 ... (remaining 293471 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 80 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 80 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: 5.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 25.630 Check model and map are aligned: 0.500 Set scattering table: 0.270 Process input model: 84.710 Find NCS groups from input model: 2.270 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:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.005 0.109 34453 Z= 0.343 Angle : 0.825 14.165 46696 Z= 0.452 Chirality : 0.053 0.316 5527 Planarity : 0.006 0.067 6004 Dihedral : 14.247 154.986 12676 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.61 % Favored : 96.24 % Rotamer: Outliers : 0.22 % Allowed : 5.83 % Favored : 93.95 % 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: -4.83 (0.09), residues: 4466 helix: -4.39 (0.05), residues: 2114 sheet: -1.50 (0.20), residues: 570 loop : -1.91 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP Y 141 HIS 0.008 0.001 HIS R 104 PHE 0.025 0.002 PHE A 122 TYR 0.017 0.002 TYR U 502 ARG 0.006 0.000 ARG X 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 684 time to evaluate : 3.488 Fit side-chains revert: symmetry clash REVERT: A 87 ASN cc_start: 0.8344 (t0) cc_final: 0.8069 (t0) REVERT: C 74 VAL cc_start: 0.8871 (m) cc_final: 0.8555 (p) REVERT: E 61 MET cc_start: 0.8009 (mtm) cc_final: 0.7755 (mtp) REVERT: E 62 VAL cc_start: 0.8591 (p) cc_final: 0.8273 (t) REVERT: F 87 ASN cc_start: 0.8543 (m-40) cc_final: 0.8342 (m-40) REVERT: G 81 MET cc_start: 0.6898 (ttp) cc_final: 0.6628 (ttp) REVERT: I 61 MET cc_start: 0.5783 (mmt) cc_final: 0.5514 (mmt) REVERT: I 118 LEU cc_start: 0.6708 (mt) cc_final: 0.6333 (mp) REVERT: J 87 ASN cc_start: 0.8457 (m-40) cc_final: 0.7885 (m110) REVERT: P 73 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6883 (mt-10) REVERT: P 83 GLN cc_start: 0.8096 (mt0) cc_final: 0.7839 (mt0) REVERT: P 103 LYS cc_start: 0.8023 (mmtt) cc_final: 0.7599 (tttt) REVERT: P 120 LYS cc_start: 0.8456 (mmmt) cc_final: 0.8171 (mttt) REVERT: P 135 LEU cc_start: 0.9236 (tp) cc_final: 0.8998 (mt) REVERT: Q 10 ARG cc_start: 0.7527 (tpp-160) cc_final: 0.7031 (mmt180) REVERT: Q 38 LYS cc_start: 0.7702 (mttp) cc_final: 0.7452 (mmmm) REVERT: Q 48 ARG cc_start: 0.8275 (ptt-90) cc_final: 0.7865 (ptt90) REVERT: Q 49 GLN cc_start: 0.7443 (pt0) cc_final: 0.7090 (pt0) REVERT: Q 52 TYR cc_start: 0.7339 (m-80) cc_final: 0.6992 (m-80) REVERT: S 136 ASP cc_start: 0.6960 (t70) cc_final: 0.6710 (t0) REVERT: S 188 GLN cc_start: 0.8418 (mt0) cc_final: 0.8045 (mt0) REVERT: S 234 GLU cc_start: 0.7597 (tt0) cc_final: 0.7237 (tm-30) REVERT: S 241 ASP cc_start: 0.7481 (m-30) cc_final: 0.7222 (m-30) REVERT: S 291 ASP cc_start: 0.7910 (t70) cc_final: 0.7644 (t0) REVERT: T 447 LYS cc_start: 0.8618 (ptpt) cc_final: 0.8409 (ptpp) REVERT: T 483 MET cc_start: 0.7952 (tpt) cc_final: 0.7721 (tpp) REVERT: T 525 ILE cc_start: 0.8475 (pt) cc_final: 0.8194 (mp) REVERT: U 74 GLU cc_start: 0.7865 (pp20) cc_final: 0.7603 (pm20) REVERT: U 282 MET cc_start: 0.8812 (tpt) cc_final: 0.8329 (tpt) REVERT: U 475 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7195 (mm-30) REVERT: V 411 GLU cc_start: 0.7660 (mp0) cc_final: 0.7418 (mp0) REVERT: X 168 ASP cc_start: 0.8195 (m-30) cc_final: 0.7985 (m-30) REVERT: X 422 MET cc_start: 0.7406 (tmm) cc_final: 0.7124 (ttp) REVERT: Y 292 GLN cc_start: 0.8265 (tt0) cc_final: 0.8027 (tt0) REVERT: Y 430 LYS cc_start: 0.6815 (ptpt) cc_final: 0.6281 (ptpp) REVERT: Y 441 ARG cc_start: 0.8629 (mmt-90) cc_final: 0.8407 (mmt90) REVERT: Z 82 ASP cc_start: 0.7679 (t0) cc_final: 0.7167 (t0) REVERT: Z 140 ILE cc_start: 0.9165 (mm) cc_final: 0.8826 (tp) outliers start: 8 outliers final: 1 residues processed: 691 average time/residue: 1.4086 time to fit residues: 1161.0611 Evaluate side-chains 449 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 448 time to evaluate : 3.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 280 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 374 optimal weight: 3.9990 chunk 335 optimal weight: 4.9990 chunk 186 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 226 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 347 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 211 optimal weight: 0.6980 chunk 258 optimal weight: 0.9980 chunk 402 optimal weight: 3.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN E 94 ASN F 87 ASN G 92 ASN G 98 GLN H 87 ASN I 94 ASN J 94 ASN J 98 GLN P 59 GLN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN R 73 ASN R 85 GLN R 119 HIS ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 GLN S 70 ASN S 77 GLN S 262 ASN S 267 HIS T 126 HIS T 134 ASN T 386 GLN U 78 GLN U 134 ASN U 179 ASN U 242 GLN V 61 HIS V 121 ASN V 123 GLN V 134 ASN V 139 HIS V 152 ASN V 196 GLN V 241 HIS V 242 GLN V 248 GLN V 386 GLN V 435 GLN V 452 GLN V 486 GLN V 497 GLN ** X 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 204 HIS X 390 ASN X 414 GLN Y 199 ASN Y 252 ASN Y 278 GLN Y 294 ASN Y 471 GLN Z 42 GLN Z 199 ASN Z 278 GLN Z 337 GLN Z 388 ASN Z 440 GLN Z 574 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 34453 Z= 0.274 Angle : 0.604 9.463 46696 Z= 0.310 Chirality : 0.045 0.174 5527 Planarity : 0.005 0.052 6004 Dihedral : 7.909 162.900 4924 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.40 % Favored : 96.46 % Rotamer: Outliers : 2.58 % Allowed : 13.45 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.11), residues: 4466 helix: -2.47 (0.09), residues: 2134 sheet: -1.12 (0.20), residues: 588 loop : -1.34 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Y 141 HIS 0.005 0.001 HIS V 83 PHE 0.018 0.001 PHE A 122 TYR 0.020 0.002 TYR U 57 ARG 0.005 0.000 ARG U 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 492 time to evaluate : 4.025 Fit side-chains revert: symmetry clash REVERT: A 81 MET cc_start: 0.8244 (ttp) cc_final: 0.7942 (ttp) REVERT: C 74 VAL cc_start: 0.8854 (m) cc_final: 0.8538 (p) REVERT: C 87 ASN cc_start: 0.7879 (t0) cc_final: 0.7614 (t0) REVERT: E 61 MET cc_start: 0.8049 (mtm) cc_final: 0.7295 (mtt) REVERT: F 123 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6565 (mp) REVERT: I 61 MET cc_start: 0.5950 (mmt) cc_final: 0.5730 (mmt) REVERT: I 118 LEU cc_start: 0.6635 (mt) cc_final: 0.6225 (mp) REVERT: J 87 ASN cc_start: 0.8625 (m-40) cc_final: 0.8424 (m110) REVERT: J 102 TYR cc_start: 0.7921 (m-10) cc_final: 0.7624 (m-10) REVERT: P 79 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7230 (tm-30) REVERT: P 82 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8440 (mmmt) REVERT: P 83 GLN cc_start: 0.7951 (mt0) cc_final: 0.7668 (mt0) REVERT: P 127 ASP cc_start: 0.8330 (t70) cc_final: 0.7973 (t70) REVERT: Q 38 LYS cc_start: 0.7655 (mttp) cc_final: 0.7428 (mmmm) REVERT: Q 52 TYR cc_start: 0.7108 (m-80) cc_final: 0.6553 (m-10) REVERT: R 143 ASP cc_start: 0.8489 (m-30) cc_final: 0.8263 (m-30) REVERT: S 153 ILE cc_start: 0.7260 (tt) cc_final: 0.6600 (pt) REVERT: S 234 GLU cc_start: 0.7570 (tt0) cc_final: 0.6998 (tm-30) REVERT: S 275 GLU cc_start: 0.7188 (pp20) cc_final: 0.6960 (pp20) REVERT: T 447 LYS cc_start: 0.8506 (ptpt) cc_final: 0.8302 (ptpp) REVERT: T 525 ILE cc_start: 0.8499 (pt) cc_final: 0.8214 (mp) REVERT: U 43 LYS cc_start: 0.8433 (tptt) cc_final: 0.7822 (tmmt) REVERT: U 74 GLU cc_start: 0.7960 (pp20) cc_final: 0.7559 (pm20) REVERT: U 282 MET cc_start: 0.8771 (tpt) cc_final: 0.8321 (tpt) REVERT: U 449 GLU cc_start: 0.6620 (tt0) cc_final: 0.6340 (tt0) REVERT: U 475 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7142 (mm-30) REVERT: U 496 ARG cc_start: 0.8651 (mtt-85) cc_final: 0.8284 (mtt-85) REVERT: V 50 LYS cc_start: 0.7213 (pptt) cc_final: 0.7004 (ptpp) REVERT: X 253 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: Y 292 GLN cc_start: 0.8185 (tt0) cc_final: 0.7859 (tt0) REVERT: Y 405 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8141 (ttpp) REVERT: Y 484 MET cc_start: 0.7444 (mmm) cc_final: 0.6972 (mmm) REVERT: Y 488 MET cc_start: 0.8277 (mmm) cc_final: 0.8055 (tpt) REVERT: Z 82 ASP cc_start: 0.7871 (t0) cc_final: 0.7267 (t0) outliers start: 92 outliers final: 39 residues processed: 556 average time/residue: 1.4059 time to fit residues: 942.1371 Evaluate side-chains 483 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 441 time to evaluate : 3.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 445 THR Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 559 LEU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 253 GLU Chi-restraints excluded: chain X residue 306 SER Chi-restraints excluded: chain X residue 411 LYS Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 405 LYS Chi-restraints excluded: chain Y residue 547 GLU Chi-restraints excluded: chain Z residue 406 VAL Chi-restraints excluded: chain Z residue 471 GLN Chi-restraints excluded: chain Z residue 480 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 223 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 334 optimal weight: 8.9990 chunk 273 optimal weight: 0.2980 chunk 110 optimal weight: 3.9990 chunk 403 optimal weight: 4.9990 chunk 435 optimal weight: 0.8980 chunk 358 optimal weight: 0.8980 chunk 399 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 323 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN H 87 ASN J 98 GLN P 59 GLN P 66 GLN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN ** R 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN T 435 GLN T 497 GLN U 134 ASN V 121 ASN V 134 ASN V 452 GLN Y 286 ASN Y 471 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34453 Z= 0.178 Angle : 0.544 10.518 46696 Z= 0.274 Chirality : 0.043 0.153 5527 Planarity : 0.004 0.051 6004 Dihedral : 7.394 168.825 4923 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.13 % Favored : 96.73 % Rotamer: Outliers : 2.72 % Allowed : 16.20 % Favored : 81.09 % 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: -1.94 (0.12), residues: 4466 helix: -1.43 (0.10), residues: 2118 sheet: -1.00 (0.20), residues: 596 loop : -0.91 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 141 HIS 0.006 0.001 HIS V 83 PHE 0.032 0.001 PHE E 107 TYR 0.024 0.001 TYR U 57 ARG 0.005 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 478 time to evaluate : 3.787 Fit side-chains REVERT: A 81 MET cc_start: 0.8203 (ttp) cc_final: 0.7895 (ttp) REVERT: C 74 VAL cc_start: 0.8794 (m) cc_final: 0.8539 (p) REVERT: C 107 PHE cc_start: 0.7542 (t80) cc_final: 0.7279 (t80) REVERT: E 61 MET cc_start: 0.7941 (mtm) cc_final: 0.7146 (mtt) REVERT: E 62 VAL cc_start: 0.8708 (p) cc_final: 0.8329 (t) REVERT: I 61 MET cc_start: 0.5895 (mmt) cc_final: 0.5591 (mmt) REVERT: I 118 LEU cc_start: 0.6869 (mt) cc_final: 0.6508 (mp) REVERT: J 102 TYR cc_start: 0.7894 (m-10) cc_final: 0.7619 (m-10) REVERT: P 79 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7172 (tm-30) REVERT: P 82 LYS cc_start: 0.8688 (mtpt) cc_final: 0.8481 (mtpt) REVERT: P 83 GLN cc_start: 0.7778 (mt0) cc_final: 0.7541 (mt0) REVERT: P 128 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7537 (mt-10) REVERT: Q 38 LYS cc_start: 0.7633 (mttp) cc_final: 0.7398 (mmmm) REVERT: Q 49 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.7064 (pt0) REVERT: Q 52 TYR cc_start: 0.7007 (m-80) cc_final: 0.6597 (m-10) REVERT: S 153 ILE cc_start: 0.7294 (tt) cc_final: 0.6661 (pt) REVERT: S 159 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7389 (mp10) REVERT: S 234 GLU cc_start: 0.7558 (tt0) cc_final: 0.6993 (tm-30) REVERT: S 275 GLU cc_start: 0.7156 (pp20) cc_final: 0.6846 (pp20) REVERT: T 179 ASN cc_start: 0.8321 (t0) cc_final: 0.8106 (t0) REVERT: T 525 ILE cc_start: 0.8521 (pt) cc_final: 0.8296 (mp) REVERT: U 43 LYS cc_start: 0.8505 (tptt) cc_final: 0.7798 (tmmt) REVERT: U 46 ASP cc_start: 0.6751 (OUTLIER) cc_final: 0.6130 (m-30) REVERT: U 74 GLU cc_start: 0.7996 (pp20) cc_final: 0.7467 (pm20) REVERT: U 282 MET cc_start: 0.8785 (tpt) cc_final: 0.8302 (tpt) REVERT: U 475 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7206 (mm-30) REVERT: U 496 ARG cc_start: 0.8629 (mtt-85) cc_final: 0.8408 (mtt-85) REVERT: V 56 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8146 (tptt) REVERT: X 416 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7570 (tt) REVERT: Y 292 GLN cc_start: 0.8134 (tt0) cc_final: 0.7842 (tt0) REVERT: Y 405 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8184 (ttpp) REVERT: Z 82 ASP cc_start: 0.7827 (t0) cc_final: 0.7397 (t0) REVERT: Z 198 ASN cc_start: 0.8432 (t0) cc_final: 0.8043 (t0) REVERT: Z 471 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7551 (mt0) outliers start: 97 outliers final: 42 residues processed: 549 average time/residue: 1.3735 time to fit residues: 914.7643 Evaluate side-chains 473 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 424 time to evaluate : 3.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain V residue 56 LYS Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 411 LYS Chi-restraints excluded: chain X residue 416 ILE Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 286 ASN Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 405 LYS Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 471 GLN Chi-restraints excluded: chain Z residue 473 VAL Chi-restraints excluded: chain Z residue 480 ASP Chi-restraints excluded: chain Z residue 550 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 398 optimal weight: 4.9990 chunk 303 optimal weight: 2.9990 chunk 209 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 404 optimal weight: 1.9990 chunk 428 optimal weight: 4.9990 chunk 211 optimal weight: 0.5980 chunk 383 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN J 98 GLN P 59 GLN P 66 GLN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN ** R 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 HIS ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN T 461 GLN T 488 GLN T 497 GLN T 539 ASN U 134 ASN V 121 ASN V 134 ASN V 452 GLN V 515 GLN Y 286 ASN Y 471 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34453 Z= 0.216 Angle : 0.546 9.424 46696 Z= 0.275 Chirality : 0.043 0.151 5527 Planarity : 0.004 0.050 6004 Dihedral : 7.301 171.976 4923 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.45 % Favored : 96.42 % Rotamer: Outliers : 3.08 % Allowed : 17.01 % Favored : 79.91 % 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: -1.46 (0.12), residues: 4466 helix: -0.98 (0.11), residues: 2111 sheet: -0.90 (0.20), residues: 608 loop : -0.71 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Y 141 HIS 0.005 0.001 HIS V 83 PHE 0.034 0.001 PHE E 107 TYR 0.024 0.001 TYR U 57 ARG 0.009 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 450 time to evaluate : 3.748 Fit side-chains REVERT: A 81 MET cc_start: 0.8216 (ttp) cc_final: 0.7900 (ttp) REVERT: C 74 VAL cc_start: 0.8808 (m) cc_final: 0.8534 (p) REVERT: E 61 MET cc_start: 0.8025 (mtm) cc_final: 0.7210 (mtt) REVERT: E 62 VAL cc_start: 0.8675 (p) cc_final: 0.8264 (t) REVERT: F 123 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6633 (mp) REVERT: G 86 ILE cc_start: 0.8810 (mt) cc_final: 0.8581 (mp) REVERT: I 61 MET cc_start: 0.6007 (mmt) cc_final: 0.5731 (mmt) REVERT: I 118 LEU cc_start: 0.6952 (mt) cc_final: 0.6587 (mp) REVERT: J 102 TYR cc_start: 0.7862 (m-10) cc_final: 0.7589 (m-10) REVERT: P 127 ASP cc_start: 0.8267 (t70) cc_final: 0.7911 (t70) REVERT: Q 38 LYS cc_start: 0.7672 (mttp) cc_final: 0.7405 (mmmm) REVERT: Q 48 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7717 (ppt-90) REVERT: Q 52 TYR cc_start: 0.7051 (m-80) cc_final: 0.6547 (m-10) REVERT: S 124 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6568 (ptm-80) REVERT: S 153 ILE cc_start: 0.7331 (tt) cc_final: 0.6716 (pt) REVERT: S 159 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7391 (mp10) REVERT: S 275 GLU cc_start: 0.7112 (pp20) cc_final: 0.6809 (pp20) REVERT: T 179 ASN cc_start: 0.8439 (t0) cc_final: 0.8085 (t0) REVERT: T 181 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.6843 (ptp90) REVERT: T 525 ILE cc_start: 0.8521 (pt) cc_final: 0.8313 (mp) REVERT: U 43 LYS cc_start: 0.8519 (tptt) cc_final: 0.7789 (tmmt) REVERT: U 46 ASP cc_start: 0.6741 (OUTLIER) cc_final: 0.6205 (m-30) REVERT: U 74 GLU cc_start: 0.7869 (pp20) cc_final: 0.7399 (pm20) REVERT: U 248 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7569 (mt0) REVERT: U 282 MET cc_start: 0.8801 (tpt) cc_final: 0.8333 (tpt) REVERT: U 411 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: U 475 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7149 (mm-30) REVERT: U 496 ARG cc_start: 0.8586 (mtt-85) cc_final: 0.8320 (mtt-85) REVERT: V 52 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7116 (pttm) REVERT: V 56 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8109 (tptt) REVERT: X 195 GLU cc_start: 0.7828 (tp30) cc_final: 0.7565 (tp30) REVERT: Y 292 GLN cc_start: 0.8118 (tt0) cc_final: 0.7830 (tt0) REVERT: Y 366 ARG cc_start: 0.7722 (ttm110) cc_final: 0.7463 (mtp85) REVERT: Y 405 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8195 (ttpp) REVERT: Y 422 MET cc_start: 0.6399 (mmm) cc_final: 0.5906 (mmm) REVERT: Y 552 GLU cc_start: 0.5438 (OUTLIER) cc_final: 0.5172 (pt0) REVERT: Z 82 ASP cc_start: 0.7836 (t0) cc_final: 0.7414 (t0) REVERT: Z 198 ASN cc_start: 0.8457 (t0) cc_final: 0.8064 (t0) REVERT: Z 471 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7461 (mt0) outliers start: 110 outliers final: 56 residues processed: 528 average time/residue: 1.3456 time to fit residues: 862.2340 Evaluate side-chains 498 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 429 time to evaluate : 3.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 48 ARG Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 181 ARG Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 445 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 248 GLN Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain V residue 52 LYS Chi-restraints excluded: chain V residue 56 LYS Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 559 LEU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Y residue 405 LYS Chi-restraints excluded: chain Y residue 547 GLU Chi-restraints excluded: chain Y residue 552 GLU Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 471 GLN Chi-restraints excluded: chain Z residue 473 VAL Chi-restraints excluded: chain Z residue 480 ASP Chi-restraints excluded: chain Z residue 550 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 356 optimal weight: 0.8980 chunk 243 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 318 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 365 optimal weight: 3.9990 chunk 295 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 218 optimal weight: 0.0030 chunk 384 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN G 98 GLN J 98 GLN P 52 GLN P 59 GLN P 66 GLN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN T 497 GLN T 539 ASN U 134 ASN V 121 ASN V 134 ASN V 452 GLN X 414 GLN Y 286 ASN Y 471 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34453 Z= 0.233 Angle : 0.554 10.081 46696 Z= 0.278 Chirality : 0.043 0.154 5527 Planarity : 0.004 0.052 6004 Dihedral : 7.271 179.250 4923 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.61 % Favored : 96.26 % Rotamer: Outliers : 3.03 % Allowed : 18.02 % Favored : 78.96 % 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: -1.16 (0.12), residues: 4466 helix: -0.69 (0.11), residues: 2106 sheet: -0.84 (0.20), residues: 602 loop : -0.59 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Y 141 HIS 0.004 0.001 HIS V 83 PHE 0.036 0.001 PHE E 107 TYR 0.026 0.001 TYR U 57 ARG 0.010 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 440 time to evaluate : 3.426 Fit side-chains REVERT: A 81 MET cc_start: 0.8169 (ttp) cc_final: 0.7865 (ttp) REVERT: D 61 MET cc_start: 0.7137 (mmt) cc_final: 0.6381 (mmt) REVERT: E 61 MET cc_start: 0.8032 (mtm) cc_final: 0.7209 (mtt) REVERT: E 62 VAL cc_start: 0.8721 (p) cc_final: 0.8326 (t) REVERT: F 123 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6679 (mp) REVERT: G 86 ILE cc_start: 0.8824 (mt) cc_final: 0.8616 (mp) REVERT: I 61 MET cc_start: 0.6089 (mmt) cc_final: 0.5780 (mmt) REVERT: I 118 LEU cc_start: 0.6914 (mt) cc_final: 0.6545 (mp) REVERT: J 102 TYR cc_start: 0.7864 (m-10) cc_final: 0.7579 (m-10) REVERT: P 82 LYS cc_start: 0.8512 (mmmt) cc_final: 0.8306 (mmmt) REVERT: P 128 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7614 (mt-10) REVERT: Q 38 LYS cc_start: 0.7715 (mttp) cc_final: 0.7434 (mmmm) REVERT: Q 52 TYR cc_start: 0.7067 (m-80) cc_final: 0.6652 (m-10) REVERT: S 124 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6626 (ptm-80) REVERT: S 147 ARG cc_start: 0.7552 (tmm-80) cc_final: 0.7173 (tmm-80) REVERT: S 159 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7339 (mp10) REVERT: S 275 GLU cc_start: 0.7096 (pp20) cc_final: 0.6805 (pp20) REVERT: T 179 ASN cc_start: 0.8454 (t0) cc_final: 0.8009 (t0) REVERT: T 539 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.7713 (p0) REVERT: U 43 LYS cc_start: 0.8523 (tptt) cc_final: 0.7743 (tmmt) REVERT: U 46 ASP cc_start: 0.7047 (OUTLIER) cc_final: 0.6511 (m-30) REVERT: U 74 GLU cc_start: 0.7833 (pp20) cc_final: 0.7446 (pm20) REVERT: U 475 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7161 (mm-30) REVERT: U 496 ARG cc_start: 0.8550 (mtt-85) cc_final: 0.8221 (mtt-85) REVERT: V 52 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7205 (pttm) REVERT: V 56 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8101 (tptt) REVERT: V 274 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8232 (ttpt) REVERT: X 175 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8178 (ptm160) REVERT: X 195 GLU cc_start: 0.7913 (tp30) cc_final: 0.7669 (tp30) REVERT: Y 292 GLN cc_start: 0.8137 (tt0) cc_final: 0.7845 (tt0) REVERT: Y 366 ARG cc_start: 0.7744 (ttm110) cc_final: 0.7384 (ptp-110) REVERT: Y 405 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8191 (ttpp) REVERT: Y 422 MET cc_start: 0.6346 (mmm) cc_final: 0.5901 (mmm) REVERT: Y 430 LYS cc_start: 0.6640 (ptpt) cc_final: 0.6183 (mtmm) REVERT: Y 453 PHE cc_start: 0.8096 (p90) cc_final: 0.7767 (p90) REVERT: Z 82 ASP cc_start: 0.7853 (t0) cc_final: 0.7429 (t0) REVERT: Z 198 ASN cc_start: 0.8485 (t0) cc_final: 0.8115 (t0) REVERT: Z 480 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7464 (m-30) outliers start: 108 outliers final: 62 residues processed: 515 average time/residue: 1.3712 time to fit residues: 853.1438 Evaluate side-chains 493 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 420 time to evaluate : 3.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain Q residue 5 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 445 THR Chi-restraints excluded: chain T residue 539 ASN Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 287 MET 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 487 LYS Chi-restraints excluded: chain V residue 52 LYS Chi-restraints excluded: chain V residue 56 LYS Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 274 LYS Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 559 LEU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 175 ARG Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 286 ASN Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 405 LYS Chi-restraints excluded: chain Y residue 547 GLU Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 473 VAL Chi-restraints excluded: chain Z residue 480 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 144 optimal weight: 0.6980 chunk 385 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 251 optimal weight: 1.9990 chunk 105 optimal weight: 0.0070 chunk 428 optimal weight: 4.9990 chunk 355 optimal weight: 0.8980 chunk 198 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 141 optimal weight: 0.0010 chunk 225 optimal weight: 0.8980 overall best weight: 0.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN G 98 GLN J 98 GLN P 52 GLN P 59 GLN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN T 461 GLN T 497 GLN U 134 ASN V 121 ASN V 134 ASN V 452 GLN Y 286 ASN Y 471 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 34453 Z= 0.157 Angle : 0.531 10.007 46696 Z= 0.264 Chirality : 0.042 0.149 5527 Planarity : 0.003 0.052 6004 Dihedral : 6.851 163.719 4923 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.27 % Favored : 96.60 % Rotamer: Outliers : 2.89 % Allowed : 18.69 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.13), residues: 4466 helix: -0.40 (0.11), residues: 2109 sheet: -0.78 (0.20), residues: 619 loop : -0.46 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Y 141 HIS 0.005 0.001 HIS V 83 PHE 0.037 0.001 PHE E 107 TYR 0.025 0.001 TYR U 57 ARG 0.012 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 450 time to evaluate : 4.146 Fit side-chains REVERT: D 61 MET cc_start: 0.7109 (mmt) cc_final: 0.6358 (mmt) REVERT: E 61 MET cc_start: 0.8019 (mtm) cc_final: 0.7226 (mtt) REVERT: E 62 VAL cc_start: 0.8755 (p) cc_final: 0.8359 (t) REVERT: F 123 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6619 (mp) REVERT: G 86 ILE cc_start: 0.8839 (mt) cc_final: 0.8594 (mp) REVERT: H 60 LYS cc_start: 0.8231 (tppp) cc_final: 0.7849 (mmmm) REVERT: H 118 LEU cc_start: 0.7035 (mm) cc_final: 0.6787 (mt) REVERT: I 61 MET cc_start: 0.6024 (mmt) cc_final: 0.5700 (mmt) REVERT: I 118 LEU cc_start: 0.6950 (mt) cc_final: 0.6565 (mp) REVERT: J 102 TYR cc_start: 0.7840 (m-10) cc_final: 0.7558 (m-10) REVERT: P 128 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7213 (mt-10) REVERT: Q 38 LYS cc_start: 0.7622 (mttp) cc_final: 0.7363 (mmmm) REVERT: Q 52 TYR cc_start: 0.7083 (m-80) cc_final: 0.6679 (m-10) REVERT: S 124 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6558 (ptm-80) REVERT: S 147 ARG cc_start: 0.7533 (tmm-80) cc_final: 0.7149 (tmm-80) REVERT: S 153 ILE cc_start: 0.7620 (tt) cc_final: 0.6906 (pt) REVERT: S 275 GLU cc_start: 0.7074 (pp20) cc_final: 0.6793 (pp20) REVERT: T 179 ASN cc_start: 0.8422 (t0) cc_final: 0.7929 (t0) REVERT: T 539 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7842 (p0) REVERT: U 43 LYS cc_start: 0.8502 (tptt) cc_final: 0.7743 (tmmt) REVERT: U 46 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6485 (m-30) REVERT: U 74 GLU cc_start: 0.7821 (pp20) cc_final: 0.7430 (pm20) REVERT: U 248 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7461 (mt0) REVERT: U 282 MET cc_start: 0.8782 (tpt) cc_final: 0.8322 (tpt) REVERT: V 61 HIS cc_start: 0.7542 (t-90) cc_final: 0.6872 (t-170) REVERT: X 195 GLU cc_start: 0.7882 (tp30) cc_final: 0.7669 (tp30) REVERT: Y 292 GLN cc_start: 0.8128 (tt0) cc_final: 0.7837 (tt0) REVERT: Y 366 ARG cc_start: 0.7817 (ttm110) cc_final: 0.7320 (ptp-110) REVERT: Y 405 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8418 (ttmt) REVERT: Y 430 LYS cc_start: 0.6641 (ptpt) cc_final: 0.6210 (mtmm) REVERT: Y 453 PHE cc_start: 0.8056 (p90) cc_final: 0.7767 (p90) REVERT: Y 497 GLU cc_start: 0.6997 (mp0) cc_final: 0.6742 (mp0) REVERT: Z 82 ASP cc_start: 0.7806 (t0) cc_final: 0.7391 (t0) REVERT: Z 198 ASN cc_start: 0.8448 (t0) cc_final: 0.8085 (t0) REVERT: Z 480 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7401 (m-30) outliers start: 103 outliers final: 46 residues processed: 529 average time/residue: 1.4012 time to fit residues: 898.0043 Evaluate side-chains 481 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 428 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain Q residue 5 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 445 THR Chi-restraints excluded: chain T residue 539 ASN Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 248 GLN Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 405 LYS Chi-restraints excluded: chain Z residue 473 VAL Chi-restraints excluded: chain Z residue 480 ASP Chi-restraints excluded: chain Z residue 550 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 413 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 313 optimal weight: 0.8980 chunk 242 optimal weight: 2.9990 chunk 360 optimal weight: 3.9990 chunk 239 optimal weight: 0.6980 chunk 426 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN J 98 GLN P 59 GLN Q 43 GLN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 497 GLN T 539 ASN U 134 ASN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 121 ASN V 134 ASN V 452 GLN Y 286 ASN Z 440 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 34453 Z= 0.279 Angle : 0.580 10.161 46696 Z= 0.291 Chirality : 0.044 0.169 5527 Planarity : 0.004 0.052 6004 Dihedral : 6.905 138.734 4923 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.83 % Favored : 96.04 % Rotamer: Outliers : 2.94 % Allowed : 19.33 % Favored : 77.72 % 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: -0.82 (0.13), residues: 4466 helix: -0.38 (0.11), residues: 2119 sheet: -0.72 (0.20), residues: 608 loop : -0.43 (0.16), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 37 HIS 0.005 0.001 HIS V 83 PHE 0.039 0.002 PHE E 107 TYR 0.026 0.001 TYR U 57 ARG 0.011 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 435 time to evaluate : 3.857 Fit side-chains REVERT: D 61 MET cc_start: 0.7192 (mmt) cc_final: 0.6436 (mmt) REVERT: E 61 MET cc_start: 0.8112 (mtm) cc_final: 0.7242 (mtt) REVERT: E 62 VAL cc_start: 0.8746 (p) cc_final: 0.8339 (t) REVERT: F 123 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6689 (mp) REVERT: G 86 ILE cc_start: 0.8862 (mt) cc_final: 0.8655 (mp) REVERT: H 118 LEU cc_start: 0.7120 (mm) cc_final: 0.6893 (tp) REVERT: I 61 MET cc_start: 0.6031 (mmt) cc_final: 0.5781 (mmt) REVERT: I 118 LEU cc_start: 0.6923 (mt) cc_final: 0.6558 (mp) REVERT: J 102 TYR cc_start: 0.7869 (m-10) cc_final: 0.7585 (m-10) REVERT: P 69 LYS cc_start: 0.7772 (tttm) cc_final: 0.7539 (tptt) REVERT: P 73 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6508 (mt-10) REVERT: P 128 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7300 (mt-10) REVERT: Q 38 LYS cc_start: 0.7707 (mttp) cc_final: 0.7352 (mmmm) REVERT: Q 52 TYR cc_start: 0.7100 (m-80) cc_final: 0.6634 (m-10) REVERT: S 124 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6632 (ptm-80) REVERT: S 147 ARG cc_start: 0.7517 (tmm-80) cc_final: 0.7230 (tmm-80) REVERT: S 153 ILE cc_start: 0.7559 (tt) cc_final: 0.6919 (pt) REVERT: S 220 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7748 (mm) REVERT: S 275 GLU cc_start: 0.7100 (pp20) cc_final: 0.6809 (pp20) REVERT: T 179 ASN cc_start: 0.8558 (t0) cc_final: 0.8004 (t0) REVERT: T 181 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.6744 (ptp90) REVERT: T 539 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.7889 (p0) REVERT: U 46 ASP cc_start: 0.7020 (OUTLIER) cc_final: 0.6469 (m-30) REVERT: U 74 GLU cc_start: 0.7833 (pp20) cc_final: 0.7421 (pm20) REVERT: U 150 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8791 (mm) REVERT: U 475 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6890 (mm-30) REVERT: U 496 ARG cc_start: 0.8560 (mtt-85) cc_final: 0.8189 (mtt-85) REVERT: V 61 HIS cc_start: 0.7560 (t-90) cc_final: 0.7027 (t-170) REVERT: V 274 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8223 (ttpt) REVERT: X 195 GLU cc_start: 0.7916 (tp30) cc_final: 0.7701 (tp30) REVERT: Y 292 GLN cc_start: 0.8166 (tt0) cc_final: 0.7907 (tt0) REVERT: Y 370 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6292 (mp0) REVERT: Y 405 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8242 (ttpp) REVERT: Y 422 MET cc_start: 0.6433 (mmm) cc_final: 0.5937 (mmm) REVERT: Y 430 LYS cc_start: 0.6801 (ptpt) cc_final: 0.6334 (mtmm) REVERT: Y 453 PHE cc_start: 0.8122 (p90) cc_final: 0.7870 (p90) REVERT: Y 497 GLU cc_start: 0.7101 (mp0) cc_final: 0.6822 (mp0) REVERT: Z 82 ASP cc_start: 0.7872 (t0) cc_final: 0.7495 (t0) REVERT: Z 198 ASN cc_start: 0.8498 (t0) cc_final: 0.8120 (t0) REVERT: Z 480 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7380 (m-30) outliers start: 105 outliers final: 58 residues processed: 515 average time/residue: 1.3962 time to fit residues: 872.6588 Evaluate side-chains 493 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 424 time to evaluate : 4.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain Q residue 5 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 181 ARG Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 445 THR Chi-restraints excluded: chain T residue 539 ASN Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain U residue 150 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 274 LYS Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 559 LEU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 286 ASN Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 370 GLU Chi-restraints excluded: chain Y residue 405 LYS Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 473 VAL Chi-restraints excluded: chain Z residue 480 ASP Chi-restraints excluded: chain Z residue 535 LYS Chi-restraints excluded: chain Z residue 550 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 264 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 255 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 271 optimal weight: 0.9990 chunk 290 optimal weight: 0.7980 chunk 211 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 335 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN J 98 GLN P 52 GLN P 59 GLN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN T 461 GLN T 497 GLN U 134 ASN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 121 ASN V 134 ASN V 452 GLN ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Z 440 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34453 Z= 0.183 Angle : 0.549 9.699 46696 Z= 0.274 Chirality : 0.043 0.158 5527 Planarity : 0.003 0.054 6004 Dihedral : 6.573 117.030 4923 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.38 % Favored : 96.48 % Rotamer: Outliers : 2.47 % Allowed : 19.81 % Favored : 77.72 % 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: -0.64 (0.13), residues: 4466 helix: -0.19 (0.12), residues: 2110 sheet: -0.67 (0.20), residues: 617 loop : -0.37 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 37 HIS 0.005 0.001 HIS V 83 PHE 0.041 0.001 PHE E 107 TYR 0.027 0.001 TYR U 57 ARG 0.012 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 440 time to evaluate : 3.980 Fit side-chains REVERT: B 107 PHE cc_start: 0.7497 (t80) cc_final: 0.7111 (t80) REVERT: D 61 MET cc_start: 0.7168 (mmt) cc_final: 0.6457 (mmt) REVERT: E 61 MET cc_start: 0.8078 (mtm) cc_final: 0.7237 (mtt) REVERT: E 62 VAL cc_start: 0.8776 (p) cc_final: 0.8356 (t) REVERT: F 123 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6631 (mp) REVERT: G 86 ILE cc_start: 0.8879 (mt) cc_final: 0.8625 (mp) REVERT: I 61 MET cc_start: 0.5985 (mmt) cc_final: 0.5726 (mmt) REVERT: J 81 MET cc_start: 0.7544 (tpp) cc_final: 0.7296 (tpt) REVERT: J 102 TYR cc_start: 0.7865 (m-10) cc_final: 0.7587 (m-10) REVERT: P 82 LYS cc_start: 0.8480 (mmmt) cc_final: 0.8257 (mmmt) REVERT: P 84 HIS cc_start: 0.7627 (m-70) cc_final: 0.7150 (m170) REVERT: P 128 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7211 (mt-10) REVERT: P 145 MET cc_start: 0.8801 (mmm) cc_final: 0.8503 (mmm) REVERT: Q 38 LYS cc_start: 0.7693 (mttp) cc_final: 0.7328 (mmmm) REVERT: Q 52 TYR cc_start: 0.7072 (m-80) cc_final: 0.6676 (m-10) REVERT: S 124 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6471 (ptm-80) REVERT: S 147 ARG cc_start: 0.7532 (tmm-80) cc_final: 0.7247 (tmm-80) REVERT: S 153 ILE cc_start: 0.7604 (tt) cc_final: 0.7027 (pt) REVERT: S 220 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7779 (mm) REVERT: S 234 GLU cc_start: 0.7601 (tt0) cc_final: 0.6895 (tm-30) REVERT: S 275 GLU cc_start: 0.7062 (pp20) cc_final: 0.6777 (pp20) REVERT: T 179 ASN cc_start: 0.8478 (t0) cc_final: 0.7942 (t0) REVERT: T 181 ARG cc_start: 0.7913 (ttp80) cc_final: 0.7515 (ptm160) REVERT: T 445 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8430 (t) REVERT: U 46 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6434 (m-30) REVERT: U 59 ILE cc_start: 0.7995 (mt) cc_final: 0.7721 (mt) REVERT: U 74 GLU cc_start: 0.7812 (pp20) cc_final: 0.7389 (pm20) REVERT: U 150 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8751 (mm) REVERT: U 496 ARG cc_start: 0.8535 (mtt-85) cc_final: 0.8146 (mtt-85) REVERT: V 61 HIS cc_start: 0.7578 (t-90) cc_final: 0.6899 (t-170) REVERT: V 274 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8186 (ttpt) REVERT: X 195 GLU cc_start: 0.7889 (tp30) cc_final: 0.7661 (tp30) REVERT: Y 292 GLN cc_start: 0.8114 (tt0) cc_final: 0.7828 (tt0) REVERT: Y 366 ARG cc_start: 0.7696 (ttm110) cc_final: 0.6775 (ptp-110) REVERT: Y 370 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6239 (mp0) REVERT: Y 405 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8315 (ttpp) REVERT: Y 430 LYS cc_start: 0.6657 (ptpt) cc_final: 0.6224 (mtmm) REVERT: Y 453 PHE cc_start: 0.8074 (p90) cc_final: 0.7794 (p90) REVERT: Y 488 MET cc_start: 0.8318 (mmm) cc_final: 0.8095 (tpt) REVERT: Y 497 GLU cc_start: 0.7105 (mp0) cc_final: 0.6846 (mp0) REVERT: Z 82 ASP cc_start: 0.7828 (t0) cc_final: 0.7420 (t0) REVERT: Z 198 ASN cc_start: 0.8465 (t0) cc_final: 0.8060 (t0) REVERT: Z 480 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7448 (m-30) outliers start: 88 outliers final: 51 residues processed: 503 average time/residue: 1.3741 time to fit residues: 834.5852 Evaluate side-chains 480 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 419 time to evaluate : 3.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain Q residue 5 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 445 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain U residue 150 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 274 LYS Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 370 GLU Chi-restraints excluded: chain Y residue 405 LYS Chi-restraints excluded: chain Y residue 547 GLU Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 473 VAL Chi-restraints excluded: chain Z residue 480 ASP Chi-restraints excluded: chain Z residue 535 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 388 optimal weight: 0.9980 chunk 409 optimal weight: 2.9990 chunk 373 optimal weight: 0.7980 chunk 397 optimal weight: 4.9990 chunk 408 optimal weight: 0.9980 chunk 239 optimal weight: 0.6980 chunk 173 optimal weight: 0.8980 chunk 312 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 359 optimal weight: 0.9980 chunk 376 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN P 52 GLN P 59 GLN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN T 461 GLN T 497 GLN U 134 ASN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 121 ASN V 134 ASN V 452 GLN Y 83 ASN ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Z 440 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34453 Z= 0.187 Angle : 0.551 9.831 46696 Z= 0.276 Chirality : 0.043 0.199 5527 Planarity : 0.003 0.056 6004 Dihedral : 6.413 101.936 4923 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.67 % Favored : 96.19 % Rotamer: Outliers : 2.49 % Allowed : 20.17 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 4466 helix: -0.13 (0.12), residues: 2118 sheet: -0.61 (0.20), residues: 617 loop : -0.35 (0.16), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 37 HIS 0.005 0.001 HIS V 83 PHE 0.042 0.001 PHE E 107 TYR 0.028 0.001 TYR U 57 ARG 0.013 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 429 time to evaluate : 3.775 Fit side-chains REVERT: B 107 PHE cc_start: 0.7502 (t80) cc_final: 0.7099 (t80) REVERT: B 113 ILE cc_start: 0.8102 (mt) cc_final: 0.7886 (mp) REVERT: D 61 MET cc_start: 0.7082 (mmt) cc_final: 0.6438 (mmt) REVERT: E 61 MET cc_start: 0.8066 (mtm) cc_final: 0.7272 (mtt) REVERT: E 62 VAL cc_start: 0.8772 (p) cc_final: 0.8356 (t) REVERT: G 86 ILE cc_start: 0.8869 (mt) cc_final: 0.8623 (mp) REVERT: I 61 MET cc_start: 0.6021 (mmt) cc_final: 0.5734 (mmt) REVERT: J 102 TYR cc_start: 0.7861 (m-10) cc_final: 0.7613 (m-10) REVERT: P 69 LYS cc_start: 0.7777 (tttm) cc_final: 0.7572 (tptt) REVERT: P 73 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6482 (mt-10) REVERT: P 84 HIS cc_start: 0.7604 (m-70) cc_final: 0.7136 (m170) REVERT: P 145 MET cc_start: 0.8749 (mmm) cc_final: 0.8460 (mmm) REVERT: Q 38 LYS cc_start: 0.7655 (mttp) cc_final: 0.7307 (mmmm) REVERT: Q 52 TYR cc_start: 0.7104 (m-80) cc_final: 0.6684 (m-10) REVERT: S 124 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6467 (ptm-80) REVERT: S 147 ARG cc_start: 0.7534 (tmm-80) cc_final: 0.7240 (tmm-80) REVERT: S 153 ILE cc_start: 0.7559 (tt) cc_final: 0.6979 (pt) REVERT: S 220 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7769 (mm) REVERT: S 234 GLU cc_start: 0.7575 (tt0) cc_final: 0.7028 (tm-30) REVERT: S 275 GLU cc_start: 0.7012 (pp20) cc_final: 0.6750 (pp20) REVERT: T 179 ASN cc_start: 0.8489 (t0) cc_final: 0.7965 (t0) REVERT: T 181 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7535 (ptm160) REVERT: U 46 ASP cc_start: 0.7064 (OUTLIER) cc_final: 0.6555 (m-30) REVERT: U 57 TYR cc_start: 0.7568 (p90) cc_final: 0.7090 (p90) REVERT: U 59 ILE cc_start: 0.7981 (mt) cc_final: 0.7756 (mt) REVERT: U 74 GLU cc_start: 0.7794 (pp20) cc_final: 0.7437 (pm20) REVERT: U 150 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8755 (mm) REVERT: U 496 ARG cc_start: 0.8506 (mtt-85) cc_final: 0.8272 (mtt-85) REVERT: V 274 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8199 (ttpt) REVERT: Y 292 GLN cc_start: 0.8093 (tt0) cc_final: 0.7810 (tt0) REVERT: Y 366 ARG cc_start: 0.7734 (ttm110) cc_final: 0.6799 (ptp-110) REVERT: Y 370 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6255 (mp0) REVERT: Y 405 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8340 (ttpp) REVERT: Y 430 LYS cc_start: 0.6802 (ptpt) cc_final: 0.6356 (mtmm) REVERT: Y 453 PHE cc_start: 0.8067 (p90) cc_final: 0.7760 (p90) REVERT: Y 488 MET cc_start: 0.8324 (mmm) cc_final: 0.8092 (tpt) REVERT: Y 497 GLU cc_start: 0.7086 (mp0) cc_final: 0.6842 (mp0) REVERT: Z 82 ASP cc_start: 0.7824 (t0) cc_final: 0.7415 (t0) REVERT: Z 198 ASN cc_start: 0.8452 (t0) cc_final: 0.8077 (t0) REVERT: Z 480 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7468 (m-30) outliers start: 89 outliers final: 54 residues processed: 491 average time/residue: 1.3638 time to fit residues: 810.2702 Evaluate side-chains 475 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 412 time to evaluate : 4.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 5 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 181 ARG Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 445 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain U residue 150 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 274 LYS Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 559 LEU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 370 GLU Chi-restraints excluded: chain Y residue 405 LYS Chi-restraints excluded: chain Y residue 547 GLU Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 473 VAL Chi-restraints excluded: chain Z residue 480 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 396 optimal weight: 2.9990 chunk 261 optimal weight: 0.5980 chunk 420 optimal weight: 0.0470 chunk 256 optimal weight: 0.2980 chunk 199 optimal weight: 0.0170 chunk 292 optimal weight: 1.9990 chunk 441 optimal weight: 0.0000 chunk 406 optimal weight: 4.9990 chunk 351 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 271 optimal weight: 0.0570 overall best weight: 0.0838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN C 87 ASN G 98 GLN J 98 GLN P 52 GLN P 59 GLN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 461 GLN T 497 GLN U 134 ASN U 241 HIS U 319 HIS U 386 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 121 ASN V 134 ASN V 452 GLN Y 286 ASN Y 471 GLN Z 440 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34453 Z= 0.136 Angle : 0.539 10.787 46696 Z= 0.267 Chirality : 0.041 0.162 5527 Planarity : 0.003 0.056 6004 Dihedral : 5.949 86.979 4923 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.18 % Favored : 96.69 % Rotamer: Outliers : 1.40 % Allowed : 21.38 % Favored : 77.22 % 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: -0.29 (0.13), residues: 4466 helix: 0.11 (0.12), residues: 2112 sheet: -0.51 (0.21), residues: 587 loop : -0.24 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP P 58 HIS 0.006 0.001 HIS V 83 PHE 0.038 0.001 PHE E 107 TYR 0.026 0.001 TYR U 57 ARG 0.013 0.000 ARG V 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 481 time to evaluate : 4.359 Fit side-chains REVERT: A 102 TYR cc_start: 0.7859 (m-80) cc_final: 0.7319 (m-80) REVERT: A 107 PHE cc_start: 0.7938 (t80) cc_final: 0.7619 (t80) REVERT: B 107 PHE cc_start: 0.7477 (t80) cc_final: 0.7115 (t80) REVERT: D 61 MET cc_start: 0.7011 (mmt) cc_final: 0.6505 (mmt) REVERT: D 111 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: E 61 MET cc_start: 0.8032 (mtm) cc_final: 0.7279 (mtt) REVERT: E 62 VAL cc_start: 0.8718 (p) cc_final: 0.8343 (t) REVERT: I 61 MET cc_start: 0.5959 (mmt) cc_final: 0.5707 (mmt) REVERT: J 109 LEU cc_start: 0.8111 (mt) cc_final: 0.7850 (mp) REVERT: P 73 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6500 (mt-10) REVERT: P 84 HIS cc_start: 0.7586 (m-70) cc_final: 0.7257 (m-70) REVERT: P 145 MET cc_start: 0.8695 (mmm) cc_final: 0.8464 (mmm) REVERT: Q 29 ASN cc_start: 0.8061 (m-40) cc_final: 0.7728 (m-40) REVERT: Q 38 LYS cc_start: 0.7577 (mttp) cc_final: 0.7241 (mmmm) REVERT: Q 48 ARG cc_start: 0.8282 (ptt-90) cc_final: 0.8053 (ptt90) REVERT: Q 52 TYR cc_start: 0.7011 (m-80) cc_final: 0.6686 (m-10) REVERT: S 62 MET cc_start: 0.7802 (mmm) cc_final: 0.7496 (mmm) REVERT: S 124 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6320 (ptm-80) REVERT: S 153 ILE cc_start: 0.7372 (tt) cc_final: 0.6908 (pt) REVERT: S 234 GLU cc_start: 0.7598 (tt0) cc_final: 0.7078 (tm-30) REVERT: S 284 MET cc_start: 0.7943 (mtp) cc_final: 0.7638 (mtm) REVERT: T 179 ASN cc_start: 0.8345 (t0) cc_final: 0.7924 (t0) REVERT: T 181 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7575 (ptm160) REVERT: T 445 THR cc_start: 0.8701 (p) cc_final: 0.8383 (t) REVERT: U 46 ASP cc_start: 0.6943 (OUTLIER) cc_final: 0.6502 (m-30) REVERT: U 57 TYR cc_start: 0.7591 (p90) cc_final: 0.7121 (p90) REVERT: U 74 GLU cc_start: 0.7757 (pp20) cc_final: 0.7387 (pm20) REVERT: U 496 ARG cc_start: 0.8462 (mtt-85) cc_final: 0.8166 (mtt-85) REVERT: V 274 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8305 (ttpt) REVERT: Y 292 GLN cc_start: 0.8008 (tt0) cc_final: 0.7747 (tt0) REVERT: Y 366 ARG cc_start: 0.7671 (ttm110) cc_final: 0.7461 (ptp-110) REVERT: Y 430 LYS cc_start: 0.6602 (ptpt) cc_final: 0.6230 (mtmm) REVERT: Y 453 PHE cc_start: 0.7983 (p90) cc_final: 0.7585 (p90) REVERT: Y 497 GLU cc_start: 0.7108 (mp0) cc_final: 0.6842 (mp0) REVERT: Z 82 ASP cc_start: 0.7728 (t0) cc_final: 0.7330 (t0) REVERT: Z 198 ASN cc_start: 0.8324 (t0) cc_final: 0.7992 (t0) REVERT: Z 316 THR cc_start: 0.9015 (m) cc_final: 0.8687 (m) outliers start: 50 outliers final: 21 residues processed: 511 average time/residue: 1.4511 time to fit residues: 897.5344 Evaluate side-chains 456 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 431 time to evaluate : 3.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 274 LYS Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Z residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 215 optimal weight: 0.0270 chunk 279 optimal weight: 4.9990 chunk 374 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 324 optimal weight: 0.3980 chunk 51 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 352 optimal weight: 0.0570 chunk 147 optimal weight: 0.8980 chunk 361 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN G 98 GLN J 98 GLN P 52 GLN P 59 GLN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 461 GLN T 497 GLN U 134 ASN U 149 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN V 452 GLN ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Z 440 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.102531 restraints weight = 47479.091| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.73 r_work: 0.3032 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.175 34453 Z= 0.203 Angle : 0.653 59.193 46696 Z= 0.352 Chirality : 0.043 0.361 5527 Planarity : 0.003 0.056 6004 Dihedral : 5.943 86.853 4923 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.27 % Favored : 96.60 % Rotamer: Outliers : 1.12 % Allowed : 22.53 % Favored : 76.35 % Cbeta Deviations : 0.02 % 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: -0.29 (0.13), residues: 4466 helix: 0.12 (0.12), residues: 2112 sheet: -0.51 (0.21), residues: 587 loop : -0.23 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP P 58 HIS 0.006 0.001 HIS V 83 PHE 0.035 0.001 PHE E 107 TYR 0.025 0.001 TYR U 57 ARG 0.011 0.000 ARG V 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14153.50 seconds wall clock time: 252 minutes 1.64 seconds (15121.64 seconds total)