Starting phenix.real_space_refine on Tue Nov 21 12:19:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6reu_4857/11_2023/6reu_4857_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6reu_4857/11_2023/6reu_4857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6reu_4857/11_2023/6reu_4857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6reu_4857/11_2023/6reu_4857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6reu_4857/11_2023/6reu_4857_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6reu_4857/11_2023/6reu_4857_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 116 5.16 5 C 21545 2.51 5 N 5796 2.21 5 O 6424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 91": "NH1" <-> "NH2" Residue "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 "P ASP 68": "OD1" <-> "OD2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 123": "OE1" <-> "OE2" 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 GLU 33": "OE1" <-> "OE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 174": "OD1" <-> "OD2" Residue "R PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 196": "OE1" <-> "OE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 83": "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 PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 234": "OE1" <-> "OE2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S ASP 245": "OD1" <-> "OD2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ARG 96": "NH1" <-> "NH2" Residue "T ASP 112": "OD1" <-> "OD2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ASP 172": "OD1" <-> "OD2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T ASP 226": "OD1" <-> "OD2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 384": "OE1" <-> "OE2" 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 GLU 449": "OE1" <-> "OE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 510": "OD1" <-> "OD2" Residue "T GLU 522": "OE1" <-> "OE2" Residue "T ASP 547": "OD1" <-> "OD2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 72": "OE1" <-> "OE2" Residue "U TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 111": "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 GLU 221": "OE1" <-> "OE2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 342": "NH1" <-> "NH2" Residue "U ARG 343": "NH1" <-> "NH2" Residue "U PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 364": "NH1" <-> "NH2" Residue "U PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 449": "OE1" <-> "OE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 467": "OD1" <-> "OD2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U GLU 521": "OE1" <-> "OE2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 360": "NH1" <-> "NH2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V GLU 482": "OE1" <-> "OE2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V GLU 521": "OE1" <-> "OE2" Residue "V GLU 553": "OE1" <-> "OE2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X ASP 49": "OD1" <-> "OD2" Residue "X PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 71": "NH1" <-> "NH2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X ASP 91": "OD1" <-> "OD2" Residue "X ASP 104": "OD1" <-> "OD2" Residue "X ARG 115": "NH1" <-> "NH2" Residue "X ARG 120": "NH1" <-> "NH2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "X TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 258": "NH1" <-> "NH2" Residue "X ASP 279": "OD1" <-> "OD2" Residue "X GLU 296": "OE1" <-> "OE2" Residue "X ASP 317": "OD1" <-> "OD2" 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 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 497": "OE1" <-> "OE2" Residue "X ASP 500": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X GLU 520": "OE1" <-> "OE2" Residue "X GLU 536": "OE1" <-> "OE2" Residue "X GLU 541": "OE1" <-> "OE2" Residue "X GLU 546": "OE1" <-> "OE2" Residue "X GLU 564": "OE1" <-> "OE2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ASP 94": "OD1" <-> "OD2" Residue "Y ARG 98": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y GLU 149": "OE1" <-> "OE2" Residue "Y ASP 168": "OD1" <-> "OD2" Residue "Y ARG 216": "NH1" <-> "NH2" Residue "Y GLU 229": "OE1" <-> "OE2" Residue "Y TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y ARG 401": "NH1" <-> "NH2" Residue "Y ASP 409": "OD1" <-> "OD2" Residue "Y TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 428": "OE1" <-> "OE2" Residue "Y ASP 429": "OD1" <-> "OD2" Residue "Y ARG 435": "NH1" <-> "NH2" Residue "Y ARG 437": "NH1" <-> "NH2" Residue "Y PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 465": "OD1" <-> "OD2" Residue "Y TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 483": "OE1" <-> "OE2" Residue "Y ARG 509": "NH1" <-> "NH2" Residue "Y GLU 519": "OE1" <-> "OE2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 53": "OD1" <-> "OD2" Residue "Z ASP 91": "OD1" <-> "OD2" Residue "Z ASP 104": "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 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 218": "NH1" <-> "NH2" Residue "Z GLU 219": "OE1" <-> "OE2" Residue "Z ARG 225": "NH1" <-> "NH2" Residue "Z GLU 238": "OE1" <-> "OE2" Residue "Z ARG 239": "NH1" <-> "NH2" Residue "Z GLU 296": "OE1" <-> "OE2" Residue "Z TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 483": "OE1" <-> "OE2" Residue "Z TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z GLU 511": "OE1" <-> "OE2" Residue "Z GLU 519": "OE1" <-> "OE2" Residue "Z GLU 541": "OE1" <-> "OE2" Residue "Z ASP 542": "OD1" <-> "OD2" Residue "Z ASP 548": "OD1" <-> "OD2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 33899 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "P" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 895 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3609 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 456} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.22, per 1000 atoms: 0.51 Number of scatterers: 33899 At special positions: 0 Unit cell: (163.08, 137.16, 209.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 13 15.00 Mg 5 11.99 O 6424 8.00 N 5796 7.00 C 21545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.73 Conformation dependent library (CDL) restraints added in 6.1 seconds 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8162 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 29 sheets defined 44.6% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.85 Creating SS restraints... Processing helix chain 'A' and resid 55 through 69 removed outlier: 4.443A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 90 removed outlier: 4.004A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 118 removed outlier: 3.970A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.591A pdb=" N SER B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 116 removed outlier: 5.725A pdb=" N LYS B 97 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL B 100 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU B 104 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 105 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA B 108 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU B 109 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'C' and resid 56 through 65 removed outlier: 4.627A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 89 removed outlier: 3.831A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 116 removed outlier: 3.619A pdb=" N ALA C 96 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LYS C 97 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU C 99 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA C 103 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU C 104 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE C 107 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 109 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU C 111 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 112 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA C 114 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 115 " --> pdb=" O SER C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 123 Processing helix chain 'D' and resid 55 through 91 removed outlier: 4.041A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 95 No H-bonds generated for 'chain 'D' and resid 93 through 95' Processing helix chain 'D' and resid 99 through 125 removed outlier: 4.231A pdb=" N LEU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER D 117 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 69 removed outlier: 4.386A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY E 65 " --> pdb=" O MET E 61 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 90 removed outlier: 3.804A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 126 removed outlier: 3.691A pdb=" N VAL E 100 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 65 removed outlier: 3.514A pdb=" N LYS F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 91 removed outlier: 3.915A pdb=" N GLY F 73 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY F 79 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL F 80 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE F 82 " --> pdb=" O GLY F 79 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU F 85 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY F 88 " --> pdb=" O LEU F 85 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG F 91 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 123 removed outlier: 3.614A pdb=" N ALA F 96 " --> pdb=" O PRO F 93 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU F 99 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL F 100 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU F 104 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE F 107 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA F 108 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU F 111 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER F 117 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU F 118 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU F 119 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU F 123 " --> pdb=" O VAL F 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 66 removed outlier: 3.660A pdb=" N LYS G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 91 removed outlier: 4.201A pdb=" N GLY G 73 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL G 74 " --> pdb=" O LEU G 71 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET G 81 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE G 82 " --> pdb=" O GLY G 79 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU G 85 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY G 88 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA G 89 " --> pdb=" O ILE G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 124 removed outlier: 3.513A pdb=" N ALA G 96 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL G 100 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU G 104 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE G 107 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA G 108 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU G 109 " --> pdb=" O GLY G 106 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU G 111 " --> pdb=" O ALA G 108 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE G 113 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA G 114 " --> pdb=" O GLU G 111 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU G 118 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU G 119 " --> pdb=" O PHE G 116 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE G 122 " --> pdb=" O LEU G 119 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU G 123 " --> pdb=" O VAL G 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 65 removed outlier: 4.148A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 91 removed outlier: 3.652A pdb=" N VAL H 74 " --> pdb=" O LEU H 71 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA H 76 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU H 78 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL H 80 " --> pdb=" O GLY H 77 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU H 85 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY H 88 " --> pdb=" O LEU H 85 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG H 91 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 125 removed outlier: 3.503A pdb=" N VAL H 100 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 91 removed outlier: 3.858A pdb=" N SER I 59 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY I 65 " --> pdb=" O MET I 61 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ALA I 70 " --> pdb=" O CYS I 66 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ALA I 72 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY I 79 " --> pdb=" O GLY I 75 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN I 87 " --> pdb=" O GLY I 83 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 126 removed outlier: 4.524A pdb=" N LYS I 97 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU I 99 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL I 100 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU I 104 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU I 105 " --> pdb=" O TYR I 102 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA I 108 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER I 112 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU I 115 " --> pdb=" O SER I 112 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU I 119 " --> pdb=" O PHE I 116 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE I 122 " --> pdb=" O LEU I 119 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU I 123 " --> pdb=" O VAL I 120 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE I 124 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU I 125 " --> pdb=" O PHE I 122 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE I 126 " --> pdb=" O LEU I 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 91 removed outlier: 3.618A pdb=" N GLY J 63 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS J 66 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU J 85 " --> pdb=" O MET J 81 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 123 removed outlier: 4.102A pdb=" N ALA J 96 " --> pdb=" O PRO J 93 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LYS J 97 " --> pdb=" O ASN J 94 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL J 100 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU J 104 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU J 105 " --> pdb=" O TYR J 102 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE J 107 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR J 110 " --> pdb=" O PHE J 107 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE J 113 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU J 118 " --> pdb=" O LEU J 115 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU J 119 " --> pdb=" O PHE J 116 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL J 121 " --> pdb=" O LEU J 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 64 removed outlier: 4.295A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 83 removed outlier: 4.269A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR P 75 " --> pdb=" O GLN P 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE P 77 " --> pdb=" O GLU P 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 89 No H-bonds generated for 'chain 'P' and resid 86 through 89' Processing helix chain 'P' and resid 100 through 108 removed outlier: 3.712A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 127 removed outlier: 3.585A pdb=" N ALA P 126 " --> pdb=" O PHE P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 146 removed outlier: 3.991A pdb=" N LEU P 134 " --> pdb=" O LEU P 131 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU P 136 " --> pdb=" O ALA P 133 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU P 142 " --> pdb=" O VAL P 139 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU P 144 " --> pdb=" O TYR P 141 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 11 No H-bonds generated for 'chain 'Q' and resid 8 through 11' Processing helix chain 'Q' and resid 16 through 30 removed outlier: 3.729A pdb=" N LEU Q 27 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN Q 29 " --> pdb=" O ASP Q 25 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 40 removed outlier: 3.748A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 53 No H-bonds generated for 'chain 'R' and resid 51 through 53' Processing helix chain 'R' and resid 152 through 154 No H-bonds generated for 'chain 'R' and resid 152 through 154' Processing helix chain 'R' and resid 157 through 167 removed outlier: 4.018A pdb=" N LYS R 161 " --> pdb=" O PRO R 157 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA R 165 " --> pdb=" O LYS R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 192 removed outlier: 3.514A pdb=" N ALA R 179 " --> pdb=" O GLU R 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 69 removed outlier: 3.517A pdb=" N ASN S 52 " --> pdb=" O ARG S 48 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE S 53 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 78 Processing helix chain 'S' and resid 82 through 89 removed outlier: 4.091A pdb=" N VAL S 86 " --> pdb=" O ASP S 83 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG S 87 " --> pdb=" O PRO S 84 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE S 89 " --> pdb=" O VAL S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 130 removed outlier: 3.940A pdb=" N ILE S 119 " --> pdb=" O LEU S 115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR S 120 " --> pdb=" O ASN S 116 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA S 128 " --> pdb=" O ARG S 124 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR S 130 " --> pdb=" O THR S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 149 No H-bonds generated for 'chain 'S' and resid 146 through 149' Processing helix chain 'S' and resid 172 through 182 removed outlier: 3.665A pdb=" N SER S 176 " --> pdb=" O PHE S 172 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU S 177 " --> pdb=" O GLY S 173 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE S 178 " --> pdb=" O GLN S 174 " (cutoff:3.500A) Processing helix chain 'S' and resid 213 through 220 removed outlier: 5.361A pdb=" N LYS S 218 " --> pdb=" O ASP S 214 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLN S 219 " --> pdb=" O LEU S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 227 through 230 No H-bonds generated for 'chain 'S' and resid 227 through 230' Processing helix chain 'S' and resid 239 through 314 removed outlier: 3.754A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR S 256 " --> pdb=" O GLY S 252 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA S 268 " --> pdb=" O CYS S 264 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN S 276 " --> pdb=" O SER S 272 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS S 295 " --> pdb=" O ASP S 291 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA S 298 " --> pdb=" O ARG S 294 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU S 306 " --> pdb=" O THR S 302 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE S 307 " --> pdb=" O GLU S 303 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA S 313 " --> pdb=" O ALA S 309 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU S 314 " --> pdb=" O GLY S 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 207 through 210 No H-bonds generated for 'chain 'T' and resid 207 through 210' Processing helix chain 'T' and resid 231 through 248 removed outlier: 4.037A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLN T 248 " --> pdb=" O ASN T 244 " (cutoff:3.500A) Processing helix chain 'T' and resid 268 through 278 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 296 through 315 Proline residue: T 303 - end of helix removed outlier: 3.669A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 340 removed outlier: 3.551A pdb=" N SER T 338 " --> pdb=" O TYR T 334 " (cutoff:3.500A) Processing helix chain 'T' and resid 347 through 349 No H-bonds generated for 'chain 'T' and resid 347 through 349' Processing helix chain 'T' and resid 352 through 362 removed outlier: 4.083A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG T 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU T 361 " --> pdb=" O HIS T 358 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 401 Processing helix chain 'T' and resid 431 through 434 removed outlier: 3.973A 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 459 removed outlier: 4.483A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL T 442 " --> pdb=" O GLY T 438 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR T 445 " --> pdb=" O GLN T 441 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ALA T 458 " --> pdb=" O ARG T 454 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 471 through 480 Processing helix chain 'T' and resid 482 through 484 No H-bonds generated for 'chain 'T' and resid 482 through 484' Processing helix chain 'T' and resid 494 through 505 removed outlier: 3.616A pdb=" N THR T 498 " --> pdb=" O ILE T 494 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL T 499 " --> pdb=" O GLU T 495 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL T 501 " --> pdb=" O GLN T 497 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 518 through 521 No H-bonds generated for 'chain 'T' and resid 518 through 521' Processing helix chain 'T' and resid 523 through 526 No H-bonds generated for 'chain 'T' and resid 523 through 526' Processing helix chain 'T' and resid 531 through 539 removed outlier: 3.609A pdb=" N ALA T 538 " --> pdb=" O LYS T 534 " (cutoff:3.500A) Processing helix chain 'T' and resid 547 through 555 Processing helix chain 'U' and resid 42 through 49 Processing helix chain 'U' and resid 59 through 62 No H-bonds generated for 'chain 'U' and resid 59 through 62' Processing helix chain 'U' and resid 65 through 72 Processing helix chain 'U' and resid 74 through 76 No H-bonds generated for 'chain 'U' and resid 74 through 76' Processing helix chain 'U' and resid 192 through 194 No H-bonds generated for 'chain 'U' and resid 192 through 194' Processing helix chain 'U' and resid 207 through 210 No H-bonds generated for 'chain 'U' and resid 207 through 210' Processing helix chain 'U' and resid 231 through 244 Processing helix chain 'U' and resid 266 through 279 removed outlier: 3.682A pdb=" N THR U 279 " --> pdb=" O LEU U 275 " (cutoff:3.500A) Processing helix chain 'U' and resid 281 through 284 Processing helix chain 'U' and resid 296 through 300 Processing helix chain 'U' and resid 302 through 315 removed outlier: 3.804A pdb=" N ALA U 310 " --> pdb=" O GLY U 306 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 removed outlier: 4.066A pdb=" N MET U 337 " --> pdb=" O ALA U 333 " (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 363 removed outlier: 4.254A pdb=" N PHE U 355 " --> pdb=" O GLY U 352 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU U 357 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER U 359 " --> pdb=" O TYR U 356 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG U 360 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU U 361 " --> pdb=" O HIS U 358 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU U 363 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 370 through 372 No H-bonds generated for 'chain 'U' and resid 370 through 372' Processing helix chain 'U' and resid 393 through 401 removed outlier: 3.681A pdb=" N ASN U 397 " --> pdb=" O TYR U 393 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER U 400 " --> pdb=" O THR U 396 " (cutoff:3.500A) Processing helix chain 'U' and resid 437 through 456 removed outlier: 3.504A pdb=" N GLN U 441 " --> pdb=" O PRO U 437 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU U 449 " --> pdb=" O THR U 445 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU U 455 " --> pdb=" O ALA U 451 " (cutoff:3.500A) Processing helix chain 'U' and resid 466 through 468 No H-bonds generated for 'chain 'U' and resid 466 through 468' Processing helix chain 'U' and resid 472 through 483 removed outlier: 3.748A pdb=" N ARG U 479 " --> pdb=" O GLU U 475 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 500 removed outlier: 3.701A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (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 521 through 527 Processing helix chain 'U' and resid 532 through 539 Processing helix chain 'U' and resid 544 through 556 removed outlier: 3.635A pdb=" N ALA U 548 " --> pdb=" O PRO U 544 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA U 552 " --> pdb=" O ALA U 548 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU U 554 " --> pdb=" O LEU U 550 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG U 555 " --> pdb=" O LYS U 551 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 65 removed outlier: 3.852A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 71 through 73 No H-bonds generated for 'chain 'V' and resid 71 through 73' Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 212 removed outlier: 3.566A pdb=" N ALA V 211 " --> pdb=" O LYS V 207 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU V 212 " --> pdb=" O ALA V 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 207 through 212' Processing helix chain 'V' and resid 231 through 247 Processing helix chain 'V' and resid 251 through 253 No H-bonds generated for 'chain 'V' and resid 251 through 253' Processing helix chain 'V' and resid 266 through 278 Processing helix chain 'V' and resid 281 through 284 Processing helix chain 'V' and resid 296 through 315 Proline residue: V 303 - end of helix removed outlier: 3.870A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG V 314 " --> pdb=" O ALA V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 339 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 362 removed outlier: 4.164A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU V 361 " --> pdb=" O HIS V 358 " (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 395 through 399 removed outlier: 3.528A pdb=" N ILE V 399 " --> pdb=" O ALA V 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 395 through 399' Processing helix chain 'V' and resid 410 through 413 No H-bonds generated for 'chain 'V' and resid 410 through 413' Processing helix chain 'V' and resid 439 through 452 removed outlier: 4.715A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU V 446 " --> pdb=" O VAL V 442 " (cutoff:3.500A) Processing helix chain 'V' and resid 471 through 483 removed outlier: 4.416A pdb=" N ARG V 479 " --> pdb=" O GLU V 475 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU V 482 " --> pdb=" O ALA V 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 494 through 505 removed outlier: 4.093A pdb=" N VAL V 499 " --> pdb=" O GLU V 495 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA V 500 " --> pdb=" O ARG V 496 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR V 505 " --> pdb=" O VAL V 501 " (cutoff:3.500A) Processing helix chain 'V' and resid 517 through 527 removed outlier: 3.968A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 531 through 539 removed outlier: 3.598A pdb=" N LYS V 537 " --> pdb=" O PHE V 533 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA V 538 " --> pdb=" O LYS V 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 544 through 555 removed outlier: 3.994A pdb=" N ALA V 548 " --> pdb=" O PRO V 544 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG V 555 " --> pdb=" O LYS V 551 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 117 No H-bonds generated for 'chain 'X' and resid 115 through 117' Processing helix chain 'X' and resid 167 through 170 No H-bonds generated for 'chain 'X' and resid 167 through 170' Processing helix chain 'X' and resid 190 through 200 removed outlier: 3.555A pdb=" N GLU X 195 " --> pdb=" O VAL X 191 " (cutoff:3.500A) Processing helix chain 'X' and resid 218 through 228 removed outlier: 3.911A pdb=" N LEU X 223 " --> pdb=" O GLU X 219 " (cutoff:3.500A) Processing helix chain 'X' and resid 239 through 241 No H-bonds generated for 'chain 'X' and resid 239 through 241' Processing helix chain 'X' and resid 261 through 274 removed outlier: 3.730A pdb=" N VAL X 268 " --> pdb=" O THR X 264 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA X 269 " --> pdb=" O GLY X 265 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP X 274 " --> pdb=" O GLU X 270 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 298 removed outlier: 4.146A pdb=" N VAL X 297 " --> pdb=" O ALA X 293 " (cutoff:3.500A) Processing helix chain 'X' and resid 314 through 323 Processing helix chain 'X' and resid 349 through 352 No H-bonds generated for 'chain 'X' and resid 349 through 352' Processing helix chain 'X' and resid 355 through 357 No H-bonds generated for 'chain 'X' and resid 355 through 357' Processing helix chain 'X' and resid 366 through 370 Processing helix chain 'X' and resid 394 through 414 removed outlier: 4.255A pdb=" N VAL X 399 " --> pdb=" O GLU X 395 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA X 400 " --> pdb=" O HIS X 396 " (cutoff:3.500A) Processing helix chain 'X' and resid 416 through 420 removed outlier: 3.841A pdb=" N LEU X 420 " --> pdb=" O ILE X 417 " (cutoff:3.500A) Processing helix chain 'X' and resid 434 through 439 Processing helix chain 'X' and resid 451 through 454 No H-bonds generated for 'chain 'X' and resid 451 through 454' Processing helix chain 'X' and resid 464 through 475 removed outlier: 3.988A pdb=" N SER X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY X 469 " --> pdb=" O ASP X 465 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL X 473 " --> pdb=" O GLY X 469 " (cutoff:3.500A) Processing helix chain 'X' and resid 484 through 486 No H-bonds generated for 'chain 'X' and resid 484 through 486' Processing helix chain 'X' and resid 492 through 507 removed outlier: 3.743A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS X 501 " --> pdb=" O GLU X 497 " (cutoff:3.500A) Processing helix chain 'X' and resid 531 through 533 No H-bonds generated for 'chain 'X' and resid 531 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 202 Processing helix chain 'Y' and resid 217 through 229 removed outlier: 3.654A pdb=" N GLU Y 226 " --> pdb=" O ASP Y 222 " (cutoff:3.500A) Processing helix chain 'Y' and resid 236 through 241 removed outlier: 4.535A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 258 No H-bonds generated for 'chain 'Y' and resid 255 through 258' Processing helix chain 'Y' and resid 261 through 274 removed outlier: 3.903A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 300 removed outlier: 3.569A pdb=" N ALA Y 299 " --> pdb=" O SER Y 295 " (cutoff:3.500A) Processing helix chain 'Y' and resid 314 through 324 removed outlier: 3.875A pdb=" N LEU Y 321 " --> pdb=" O ASP Y 317 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG Y 324 " --> pdb=" O GLY Y 320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 342 through 344 No H-bonds generated for 'chain 'Y' and resid 342 through 344' Processing helix chain 'Y' and resid 349 through 356 removed outlier: 3.532A pdb=" N THR Y 353 " --> pdb=" O PRO Y 349 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 371 removed outlier: 3.660A pdb=" N LEU Y 371 " --> pdb=" O SER Y 367 " (cutoff:3.500A) Processing helix chain 'Y' and resid 393 through 417 removed outlier: 3.753A pdb=" N TYR Y 397 " --> pdb=" O GLY Y 393 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR Y 410 " --> pdb=" O VAL Y 406 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS Y 411 " --> pdb=" O LEU Y 407 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) Processing helix chain 'Y' and resid 428 through 442 removed outlier: 4.337A pdb=" N THR Y 432 " --> pdb=" O GLU Y 428 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL Y 433 " --> pdb=" O ASP Y 429 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS Y 438 " --> pdb=" O ALA Y 434 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG Y 441 " --> pdb=" O ARG Y 437 " (cutoff:3.500A) Processing helix chain 'Y' and resid 464 through 475 removed outlier: 3.529A pdb=" N GLY Y 472 " --> pdb=" O SER Y 468 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 483 through 486 Processing helix chain 'Y' and resid 496 through 508 removed outlier: 3.622A pdb=" N ASP Y 505 " --> pdb=" O LYS Y 501 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE Y 506 " --> pdb=" O MET Y 502 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ALA Y 507 " --> pdb=" O ALA Y 503 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N SER Y 508 " --> pdb=" O LYS Y 504 " (cutoff:3.500A) Processing helix chain 'Y' and resid 519 through 522 No H-bonds generated for 'chain 'Y' and resid 519 through 522' Processing helix chain 'Y' and resid 527 through 530 No H-bonds generated for 'chain 'Y' and resid 527 through 530' Processing helix chain 'Y' and resid 546 through 554 removed outlier: 3.558A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA Y 553 " --> pdb=" O PHE Y 549 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU Y 554 " --> pdb=" O LYS Y 550 " (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 167 through 170 No H-bonds generated for 'chain 'Z' and resid 167 through 170' Processing helix chain 'Z' and resid 191 through 203 removed outlier: 3.530A pdb=" N ILE Z 197 " --> pdb=" O ILE Z 193 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LYS Z 202 " --> pdb=" O ASN Z 198 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA Z 203 " --> pdb=" O ASN Z 199 " (cutoff:3.500A) Processing helix chain 'Z' and resid 217 through 229 removed outlier: 3.647A pdb=" N LEU Z 223 " --> pdb=" O GLU Z 219 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE Z 228 " --> pdb=" O TYR Z 224 " (cutoff:3.500A) Processing helix chain 'Z' and resid 256 through 273 removed outlier: 4.887A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 297 removed outlier: 3.819A pdb=" N ASN Z 294 " --> pdb=" O THR Z 291 " (cutoff:3.500A) Processing helix chain 'Z' and resid 312 through 324 removed outlier: 4.140A pdb=" N ALA Z 315 " --> pdb=" O PRO Z 312 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR Z 316 " --> pdb=" O THR Z 313 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP Z 317 " --> pdb=" O LEU Z 314 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU Z 318 " --> pdb=" O ALA Z 315 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN Z 322 " --> pdb=" O GLY Z 319 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLU Z 323 " --> pdb=" O GLY Z 320 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG Z 324 " --> pdb=" O LEU Z 321 " (cutoff:3.500A) Processing helix chain 'Z' and resid 349 through 352 No H-bonds generated for 'chain 'Z' and resid 349 through 352' Processing helix chain 'Z' and resid 368 through 371 Processing helix chain 'Z' and resid 394 through 412 removed outlier: 3.970A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) Processing helix chain 'Z' and resid 414 through 420 removed outlier: 3.893A pdb=" N ILE Z 419 " --> pdb=" O ASP Z 415 " (cutoff:3.500A) Processing helix chain 'Z' and resid 430 through 442 removed outlier: 3.635A pdb=" N ALA Z 434 " --> pdb=" O LYS Z 430 " (cutoff:3.500A) Processing helix chain 'Z' and resid 450 through 454 removed outlier: 4.139A pdb=" N THR Z 454 " --> pdb=" O GLU Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 463 through 475 removed outlier: 4.070A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU Z 474 " --> pdb=" O PHE Z 470 " (cutoff:3.500A) Processing helix chain 'Z' and resid 483 through 486 removed outlier: 3.739A pdb=" N PHE Z 486 " --> pdb=" O GLU Z 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 483 through 486' Processing helix chain 'Z' and resid 494 through 507 removed outlier: 3.873A pdb=" N LYS Z 498 " --> pdb=" O GLU Z 494 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA Z 499 " --> pdb=" O VAL Z 495 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA Z 503 " --> pdb=" O ALA Z 499 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'R' and resid 72 through 75 removed outlier: 6.913A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE R 144 " --> pdb=" O TYR R 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'R' and resid 96 through 100 removed outlier: 3.506A pdb=" N VAL R 89 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU R 125 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'S' and resid 100 through 102 removed outlier: 6.309A pdb=" N SER S 189 " --> pdb=" O VAL S 101 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA S 208 " --> pdb=" O ILE S 192 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE S 194 " --> pdb=" O THR S 206 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 139 through 142 removed outlier: 3.708A pdb=" N GLN S 159 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA S 161 " --> pdb=" O SER S 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'T' and resid 145 through 150 removed outlier: 3.694A pdb=" N THR T 147 " --> pdb=" O LEU T 108 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU T 108 " --> pdb=" O THR T 147 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TYR T 98 " --> pdb=" O VAL T 87 " (cutoff:3.500A) removed outlier: 5.196A 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 223 through 225 Processing sheet with id= H, first strand: chain 'T' and resid 288 through 290 removed outlier: 3.621A pdb=" N VAL T 288 " --> pdb=" O TYR T 259 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE T 380 " --> pdb=" O TYR T 324 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'U' and resid 85 through 91 removed outlier: 3.506A pdb=" N ARG U 86 " --> pdb=" O TYR U 98 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'U' and resid 152 through 155 removed outlier: 4.094A pdb=" N VAL U 153 " --> pdb=" O SER U 183 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER U 183 " --> pdb=" O VAL U 153 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'U' and resid 404 through 408 removed outlier: 7.963A pdb=" N GLU U 221 " --> pdb=" O LEU U 377 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ALA U 379 " --> pdb=" O GLU U 221 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE U 223 " --> pdb=" O ALA U 379 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N GLY U 225 " --> pdb=" O PRO U 381 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE U 383 " --> pdb=" O GLY U 225 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL U 262 " --> pdb=" O ASP U 325 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'V' and resid 143 through 145 removed outlier: 3.633A pdb=" N GLY V 85 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL V 90 " --> pdb=" O ILE V 94 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE V 94 " --> pdb=" O VAL V 90 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL V 130 " --> pdb=" O MET V 118 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'V' and resid 152 through 155 removed outlier: 3.685A pdb=" N SER V 183 " --> pdb=" O VAL V 153 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'V' and resid 404 through 408 Processing sheet with id= O, first strand: chain 'V' and resid 285 through 290 removed outlier: 9.172A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N PHE V 380 " --> pdb=" O TYR V 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'X' and resid 84 through 86 removed outlier: 6.029A pdb=" N ARG X 51 " --> pdb=" O VAL X 40 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL X 40 " --> pdb=" O ARG X 51 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'X' and resid 73 through 75 removed outlier: 3.510A pdb=" N GLU X 64 " --> pdb=" O VAL X 103 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'X' and resid 110 through 112 removed outlier: 3.585A pdb=" N VAL X 111 " --> pdb=" O TRP X 141 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'X' and resid 179 through 181 removed outlier: 6.816A pdb=" N ALA X 360 " --> pdb=" O GLY X 180 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'X' and resid 244 through 249 removed outlier: 6.998A pdb=" N SER X 208 " --> pdb=" O THR X 245 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N VAL X 247 " --> pdb=" O SER X 208 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE X 210 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLY X 249 " --> pdb=" O PHE X 210 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY X 212 " --> pdb=" O GLY X 249 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE X 207 " --> pdb=" O ASP X 279 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU X 281 " --> pdb=" O PHE X 207 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER X 332 " --> pdb=" O VAL X 280 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LEU X 282 " --> pdb=" O SER X 332 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR X 334 " --> pdb=" O LEU X 282 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL X 284 " --> pdb=" O THR X 334 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL X 336 " --> pdb=" O VAL X 284 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= V, first strand: chain 'Y' and resid 38 through 44 removed outlier: 6.361A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN Y 78 " --> pdb=" O ARG Y 86 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Y' and resid 110 through 113 removed outlier: 3.703A pdb=" N TRP Y 141 " --> pdb=" O VAL Y 111 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL Y 113 " --> pdb=" O ASP Y 139 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP Y 139 " --> pdb=" O VAL Y 113 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Y' and resid 360 through 362 removed outlier: 8.390A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL Y 284 " --> pdb=" O VAL Y 336 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA Y 338 " --> pdb=" O VAL Y 284 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Z' and resid 39 through 44 removed outlier: 6.474A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL Z 50 " --> pdb=" O VAL Z 85 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN Z 78 " --> pdb=" O ARG Z 86 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id= AA, first strand: chain 'Z' and resid 179 through 182 removed outlier: 6.717A pdb=" N ALA Z 360 " --> pdb=" O GLY Z 180 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE Z 182 " --> pdb=" O ALA Z 360 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR Z 362 " --> pdb=" O PHE Z 182 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'Z' and resid 244 through 249 removed outlier: 6.669A pdb=" N SER Z 208 " --> pdb=" O THR Z 245 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N VAL Z 247 " --> pdb=" O SER Z 208 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE Z 210 " --> pdb=" O VAL Z 247 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLY Z 249 " --> pdb=" O PHE Z 210 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY Z 212 " --> pdb=" O GLY Z 249 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU Z 281 " --> pdb=" O VAL Z 209 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA Z 211 " --> pdb=" O LEU Z 281 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE Z 283 " --> pdb=" O ALA Z 211 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL Z 213 " --> pdb=" O PHE Z 283 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASP Z 285 " --> pdb=" O VAL Z 213 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Z' and resid 559 through 561 1146 hydrogen bonds defined for protein. 2898 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: 11.86 Time building geometry restraints manager: 13.73 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: 10445 1.34 - 1.46: 5376 1.46 - 1.58: 18378 1.58 - 1.70: 21 1.70 - 1.82: 200 Bond restraints: 34420 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.37e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.12e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.39e+01 bond pdb=" C5 ATP T1001 " pdb=" C6 ATP T1001 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.29e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.15e+01 ... (remaining 34415 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.48: 904 106.48 - 113.92: 19929 113.92 - 121.36: 17674 121.36 - 128.80: 8030 128.80 - 136.24: 112 Bond angle restraints: 46649 Sorted by residual: angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 119.82 20.05 1.00e+00 1.00e+00 4.02e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 116.87 19.96 1.00e+00 1.00e+00 3.99e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 120.19 19.68 1.00e+00 1.00e+00 3.87e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 121.50 18.37 1.00e+00 1.00e+00 3.37e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 121.00 15.83 1.00e+00 1.00e+00 2.51e+02 ... (remaining 46644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.30: 19752 26.30 - 52.59: 864 52.59 - 78.89: 93 78.89 - 105.18: 24 105.18 - 131.48: 2 Dihedral angle restraints: 20735 sinusoidal: 7975 harmonic: 12760 Sorted by residual: 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 -125.55 -54.45 0 5.00e+00 4.00e-02 1.19e+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 -131.64 -48.36 0 5.00e+00 4.00e-02 9.36e+01 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 -140.03 -39.97 0 5.00e+00 4.00e-02 6.39e+01 ... (remaining 20732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4552 0.073 - 0.147: 864 0.147 - 0.220: 93 0.220 - 0.294: 9 0.294 - 0.367: 2 Chirality restraints: 5520 Sorted by residual: chirality pdb=" CB ILE T 417 " pdb=" CA ILE T 417 " pdb=" CG1 ILE T 417 " pdb=" CG2 ILE T 417 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CB ILE V 542 " pdb=" CA ILE V 542 " pdb=" CG1 ILE V 542 " pdb=" CG2 ILE V 542 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CB VAL T 456 " pdb=" CA VAL T 456 " pdb=" CG1 VAL T 456 " pdb=" CG2 VAL T 456 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 5517 not shown) Planarity restraints: 5999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS P 148 " 0.031 2.00e-02 2.50e+03 6.38e-02 4.07e+01 pdb=" C HIS P 148 " -0.110 2.00e-02 2.50e+03 pdb=" O HIS P 148 " 0.042 2.00e-02 2.50e+03 pdb=" N LYS P 149 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA Z 350 " -0.058 5.00e-02 4.00e+02 8.81e-02 1.24e+01 pdb=" N PRO Z 351 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO Z 351 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO Z 351 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 83 " 0.050 5.00e-02 4.00e+02 7.48e-02 8.95e+00 pdb=" N PRO S 84 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO S 84 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO S 84 " 0.042 5.00e-02 4.00e+02 ... (remaining 5996 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 41 2.32 - 2.97: 15944 2.97 - 3.61: 51969 3.61 - 4.26: 81630 4.26 - 4.90: 130765 Nonbonded interactions: 280349 Sorted by model distance: nonbonded pdb=" OG1 THR X 190 " pdb="MG MG X 602 " model vdw 1.681 2.170 nonbonded pdb=" O3B ADP X 601 " pdb="MG MG X 602 " model vdw 1.956 2.170 nonbonded pdb=" O3G ATP U1001 " pdb="MG MG U1002 " model vdw 2.012 2.170 nonbonded pdb=" O LYS X 498 " pdb=" CG MET X 502 " model vdw 2.034 3.440 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.066 2.170 ... (remaining 280344 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 36 through 556) selection = chain 'Y' selection = (chain 'Z' and resid 36 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 26.790 Check model and map are aligned: 0.540 Set scattering table: 0.300 Process input model: 85.250 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0290 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 34420 Z= 0.421 Angle : 0.987 20.046 46649 Z= 0.576 Chirality : 0.058 0.367 5520 Planarity : 0.007 0.088 5999 Dihedral : 15.071 131.480 12573 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.74 % Favored : 94.13 % Rotamer: Outliers : 0.42 % Allowed : 8.42 % Favored : 91.16 % 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: -4.88 (0.09), residues: 4462 helix: -4.07 (0.06), residues: 1933 sheet: -2.33 (0.20), residues: 526 loop : -2.44 (0.12), residues: 2003 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 495 time to evaluate : 3.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 507 average time/residue: 0.5015 time to fit residues: 402.2011 Evaluate side-chains 249 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 245 time to evaluate : 3.687 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3069 time to fit residues: 7.8123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 10.0000 chunk 335 optimal weight: 2.9990 chunk 185 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 chunk 346 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 210 optimal weight: 0.9990 chunk 257 optimal weight: 7.9990 chunk 401 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 87 ASN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN I 92 ASN P 52 GLN Q 43 GLN R 53 ASN R 73 ASN R 83 GLN S 52 ASN ** T 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 241 HIS T 358 HIS T 386 GLN T 405 GLN T 422 ASN ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 461 GLN T 527 GLN U 83 HIS U 140 GLN ** U 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 241 HIS U 242 GLN U 264 GLN U 319 HIS U 358 HIS U 441 GLN U 549 HIS V 123 GLN ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 244 ASN V 422 ASN ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 79 HIS ** X 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 294 ASN X 390 ASN ** X 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 79 HIS ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 198 ASN Y 199 ASN Y 278 GLN ** Y 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 199 ASN Z 294 ASN ** Z 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 388 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0786 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 34420 Z= 0.229 Angle : 0.687 10.350 46649 Z= 0.353 Chirality : 0.046 0.283 5520 Planarity : 0.006 0.064 5999 Dihedral : 6.582 103.707 4826 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.17 % Favored : 95.70 % Rotamer: Outliers : 0.08 % Allowed : 5.81 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.11), residues: 4462 helix: -2.55 (0.09), residues: 1989 sheet: -1.42 (0.22), residues: 495 loop : -1.95 (0.13), residues: 1978 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 307 time to evaluate : 3.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 310 average time/residue: 0.4676 time to fit residues: 238.2511 Evaluate side-chains 212 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.494 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 223 optimal weight: 4.9990 chunk 124 optimal weight: 30.0000 chunk 334 optimal weight: 0.2980 chunk 273 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 402 optimal weight: 6.9990 chunk 434 optimal weight: 5.9990 chunk 358 optimal weight: 2.9990 chunk 398 optimal weight: 5.9990 chunk 137 optimal weight: 0.3980 chunk 322 optimal weight: 20.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN E 87 ASN G 92 ASN P 140 ASN S 257 ASN ** T 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 435 GLN T 486 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 228 GLN U 330 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 179 ASN V 242 GLN V 253 GLN V 264 GLN ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 386 GLN ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 157 GLN ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 ASN X 286 ASN ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 294 ASN ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 388 ASN Y 440 GLN Z 144 HIS Z 221 ASN ** Z 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1047 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34420 Z= 0.221 Angle : 0.662 12.514 46649 Z= 0.337 Chirality : 0.045 0.218 5520 Planarity : 0.005 0.062 5999 Dihedral : 6.057 77.839 4826 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.00 % Favored : 94.87 % Rotamer: Outliers : 0.14 % Allowed : 5.16 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.12), residues: 4462 helix: -1.83 (0.10), residues: 2019 sheet: -1.05 (0.24), residues: 477 loop : -1.69 (0.13), residues: 1966 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 280 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 284 average time/residue: 0.4654 time to fit residues: 218.7161 Evaluate side-chains 214 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 3.882 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 397 optimal weight: 7.9990 chunk 302 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 270 optimal weight: 1.9990 chunk 403 optimal weight: 7.9990 chunk 427 optimal weight: 6.9990 chunk 210 optimal weight: 7.9990 chunk 382 optimal weight: 4.9990 chunk 115 optimal weight: 30.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 ASN Q 74 ASN S 116 ASN S 195 ASN ** S 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 196 GLN T 486 GLN U 123 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 228 GLN U 278 GLN U 299 GLN ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 461 GLN V 139 HIS ** V 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 278 GLN ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 422 ASN ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 471 GLN X 79 HIS X 221 ASN Y 83 ASN ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 286 ASN ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 357 HIS ** Y 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 174 GLN ** Z 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1499 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 34420 Z= 0.283 Angle : 0.761 11.180 46649 Z= 0.389 Chirality : 0.048 0.309 5520 Planarity : 0.006 0.066 5999 Dihedral : 6.335 62.665 4826 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.74 % Favored : 94.13 % Rotamer: Outliers : 0.20 % Allowed : 6.17 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.52 (0.12), residues: 4462 helix: -1.75 (0.10), residues: 2025 sheet: -0.84 (0.25), residues: 472 loop : -1.64 (0.14), residues: 1965 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 283 time to evaluate : 5.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 289 average time/residue: 0.4789 time to fit residues: 231.6466 Evaluate side-chains 209 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 207 time to evaluate : 3.501 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3444 time to fit residues: 6.2494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 355 optimal weight: 8.9990 chunk 242 optimal weight: 0.0370 chunk 6 optimal weight: 7.9990 chunk 318 optimal weight: 0.3980 chunk 176 optimal weight: 7.9990 chunk 364 optimal weight: 10.0000 chunk 295 optimal weight: 0.0770 chunk 0 optimal weight: 30.0000 chunk 218 optimal weight: 1.9990 chunk 383 optimal weight: 0.0370 chunk 107 optimal weight: 5.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN S 185 HIS ** T 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 441 GLN T 486 GLN T 529 ASN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 264 GLN U 278 GLN ** U 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 140 GLN V 169 GLN ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 278 GLN ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 ASN X 132 GLN X 157 GLN ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 ASN Y 357 HIS Z 157 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1277 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34420 Z= 0.168 Angle : 0.597 11.538 46649 Z= 0.302 Chirality : 0.043 0.250 5520 Planarity : 0.004 0.072 5999 Dihedral : 5.713 62.155 4826 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.44 % Favored : 95.43 % Rotamer: Outliers : 0.03 % Allowed : 2.33 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.00 (0.12), residues: 4462 helix: -1.22 (0.11), residues: 2018 sheet: -0.73 (0.24), residues: 480 loop : -1.45 (0.14), residues: 1964 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 266 time to evaluate : 3.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 267 average time/residue: 0.4677 time to fit residues: 208.2694 Evaluate side-chains 203 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 3.611 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 143 optimal weight: 0.9980 chunk 384 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 250 optimal weight: 8.9990 chunk 105 optimal weight: 0.1980 chunk 427 optimal weight: 10.0000 chunk 355 optimal weight: 0.9980 chunk 198 optimal weight: 5.9990 chunk 35 optimal weight: 0.0670 chunk 141 optimal weight: 8.9990 chunk 224 optimal weight: 5.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 94 ASN I 87 ASN ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 ASN S 219 GLN T 441 GLN T 486 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 264 GLN U 278 GLN U 299 GLN ** U 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 ASN X 448 GLN Y 221 ASN ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 68 HIS Z 79 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1249 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 34420 Z= 0.152 Angle : 0.569 9.873 46649 Z= 0.285 Chirality : 0.042 0.192 5520 Planarity : 0.004 0.049 5999 Dihedral : 5.409 62.306 4826 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.05 % Rotamer: Outliers : 0.06 % Allowed : 1.91 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.70 (0.12), residues: 4462 helix: -0.95 (0.11), residues: 2022 sheet: -0.63 (0.24), residues: 483 loop : -1.31 (0.14), residues: 1957 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 257 time to evaluate : 3.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 259 average time/residue: 0.4572 time to fit residues: 199.1121 Evaluate side-chains 204 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 3.489 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 412 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 243 optimal weight: 4.9990 chunk 312 optimal weight: 0.9990 chunk 241 optimal weight: 9.9990 chunk 359 optimal weight: 6.9990 chunk 238 optimal weight: 0.7980 chunk 426 optimal weight: 0.0030 chunk 266 optimal weight: 0.4980 chunk 259 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 87 ASN ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 441 GLN T 486 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN U 461 GLN V 140 GLN ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 336 GLN ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 78 GLN ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 ASN ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 448 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1261 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 34420 Z= 0.144 Angle : 0.555 9.319 46649 Z= 0.278 Chirality : 0.042 0.203 5520 Planarity : 0.004 0.046 5999 Dihedral : 5.232 63.004 4826 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.10 % Favored : 95.76 % Rotamer: Outliers : 0.03 % Allowed : 1.35 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.49 (0.12), residues: 4462 helix: -0.77 (0.11), residues: 2019 sheet: -0.58 (0.25), residues: 463 loop : -1.19 (0.14), residues: 1980 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 3.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 252 average time/residue: 0.4671 time to fit residues: 201.0421 Evaluate side-chains 198 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 3.487 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 263 optimal weight: 0.6980 chunk 170 optimal weight: 6.9990 chunk 254 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 270 optimal weight: 8.9990 chunk 290 optimal weight: 7.9990 chunk 210 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 334 optimal weight: 0.6980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 HIS S 276 ASN T 358 HIS T 441 GLN T 486 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN V 104 GLN V 126 HIS V 169 GLN V 179 ASN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 299 GLN ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 79 HIS ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 ASN ** X 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1573 moved from start: 0.6485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 34420 Z= 0.209 Angle : 0.662 9.165 46649 Z= 0.333 Chirality : 0.045 0.295 5520 Planarity : 0.005 0.047 5999 Dihedral : 5.647 69.453 4826 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.85 % Favored : 94.02 % Rotamer: Outliers : 0.03 % Allowed : 1.12 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.65 (0.12), residues: 4462 helix: -0.91 (0.11), residues: 1997 sheet: -0.66 (0.25), residues: 453 loop : -1.25 (0.14), residues: 2012 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 260 time to evaluate : 3.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 261 average time/residue: 0.4630 time to fit residues: 206.3678 Evaluate side-chains 198 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 3.494 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 387 optimal weight: 4.9990 chunk 408 optimal weight: 0.2980 chunk 372 optimal weight: 3.9990 chunk 396 optimal weight: 20.0000 chunk 238 optimal weight: 10.0000 chunk 172 optimal weight: 0.4980 chunk 311 optimal weight: 20.0000 chunk 121 optimal weight: 0.0000 chunk 358 optimal weight: 0.8980 chunk 375 optimal weight: 5.9990 chunk 395 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 441 GLN ** T 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 486 GLN U 140 GLN ** U 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN U 461 GLN V 169 GLN ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 336 GLN ** V 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 ASN X 322 GLN X 337 GLN ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 78 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1458 moved from start: 0.6558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 34420 Z= 0.153 Angle : 0.581 10.876 46649 Z= 0.292 Chirality : 0.043 0.330 5520 Planarity : 0.004 0.062 5999 Dihedral : 5.399 68.490 4826 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.57 % Favored : 95.29 % Rotamer: Outliers : 0.08 % Allowed : 0.50 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.48 (0.12), residues: 4462 helix: -0.72 (0.11), residues: 2000 sheet: -0.59 (0.25), residues: 452 loop : -1.21 (0.14), residues: 2010 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 245 time to evaluate : 3.369 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 248 average time/residue: 0.4246 time to fit residues: 180.6008 Evaluate side-chains 195 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 3.563 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 260 optimal weight: 0.9990 chunk 419 optimal weight: 4.9990 chunk 256 optimal weight: 8.9990 chunk 199 optimal weight: 20.0000 chunk 291 optimal weight: 20.0000 chunk 440 optimal weight: 0.6980 chunk 405 optimal weight: 0.0050 chunk 350 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 270 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 267 HIS T 358 HIS T 441 GLN ** T 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 486 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 336 GLN V 358 HIS ** V 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 ASN ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 311 GLN Z 78 GLN Z 79 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1519 moved from start: 0.6809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34420 Z= 0.164 Angle : 0.596 10.429 46649 Z= 0.297 Chirality : 0.044 0.328 5520 Planarity : 0.004 0.054 5999 Dihedral : 5.365 70.691 4826 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.38 % Favored : 94.49 % Rotamer: Outliers : 0.06 % Allowed : 0.39 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.38 (0.13), residues: 4462 helix: -0.66 (0.12), residues: 1992 sheet: -0.57 (0.25), residues: 447 loop : -1.13 (0.14), residues: 2023 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 246 time to evaluate : 3.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 248 average time/residue: 0.4740 time to fit residues: 201.1868 Evaluate side-chains 195 residues out of total 3566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 4.074 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 278 optimal weight: 8.9990 chunk 373 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 323 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 351 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 chunk 360 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 358 HIS T 441 GLN T 452 GLN T 486 GLN U 140 GLN ** U 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 278 GLN V 358 HIS ** X 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 ASN Y 78 GLN ** Y 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 221 ASN ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN Z 78 GLN Z 83 ASN ** Z 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 388 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.224625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.217409 restraints weight = 104193.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.217935 restraints weight = 83501.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.218387 restraints weight = 71739.867| |-----------------------------------------------------------------------------| r_work (final): 0.4901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1887 moved from start: 0.7699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 34420 Z= 0.258 Angle : 0.731 14.035 46649 Z= 0.370 Chirality : 0.048 0.334 5520 Planarity : 0.005 0.052 5999 Dihedral : 6.088 78.289 4826 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.84 % Favored : 93.03 % Rotamer: Outliers : 0.06 % Allowed : 0.45 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.86 (0.12), residues: 4462 helix: -1.08 (0.11), residues: 1980 sheet: -0.75 (0.24), residues: 446 loop : -1.39 (0.14), residues: 2036 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6149.59 seconds wall clock time: 114 minutes 53.25 seconds (6893.25 seconds total)