Starting phenix.real_space_refine on Fri Mar 22 14:57:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdm_4823/03_2024/6rdm_4823_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdm_4823/03_2024/6rdm_4823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdm_4823/03_2024/6rdm_4823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdm_4823/03_2024/6rdm_4823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdm_4823/03_2024/6rdm_4823_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdm_4823/03_2024/6rdm_4823_updated.pdb" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 116 5.16 5 C 21541 2.51 5 N 5795 2.21 5 O 6421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 111": "OE1" <-> "OE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 73": "OE1" <-> "OE2" Residue "P PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 86": "OE1" <-> "OE2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 25": "OD1" <-> "OD2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S GLU 154": "OE1" <-> "OE2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 181": "OE1" <-> "OE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 232": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ASP 142": "OD1" <-> "OD2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 294": "OD1" <-> "OD2" Residue "T TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 325": "OD1" <-> "OD2" Residue "T ASP 326": "OD1" <-> "OD2" Residue "T ASP 403": "OD1" <-> "OD2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 429": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 112": "OD1" <-> "OD2" Residue "U ASP 135": "OD1" <-> "OD2" Residue "U TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ASP 165": "OD1" <-> "OD2" 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 TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U ASP 326": "OD1" <-> "OD2" Residue "U ARG 342": "NH1" <-> "NH2" Residue "U ARG 343": "NH1" <-> "NH2" Residue "U ARG 364": "NH1" <-> "NH2" Residue "U PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 409": "OE1" <-> "OE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U GLU 482": "OE1" <-> "OE2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U ARG 513": "NH1" <-> "NH2" 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 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 142": "OD1" <-> "OD2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V ASP 210": "OD1" <-> "OD2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V ASP 237": "OD1" <-> "OD2" Residue "V TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 266": "NH1" <-> "NH2" Residue "V PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ARG 335": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "V ARG 347": "NH1" <-> "NH2" Residue "V ARG 360": "NH1" <-> "NH2" Residue "V PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 429": "NH1" <-> "NH2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V GLU 455": "OE1" <-> "OE2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 465": "OD1" <-> "OD2" Residue "V ARG 476": "NH1" <-> "NH2" 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 522": "OE1" <-> "OE2" Residue "V GLU 553": "OE1" <-> "OE2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X ASP 36": "OD1" <-> "OD2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X GLU 146": "OE1" <-> "OE2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 168": "OD1" <-> "OD2" Residue "X PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 218": "NH1" <-> "NH2" Residue "X GLU 219": "OE1" <-> "OE2" Residue "X ARG 225": "NH1" <-> "NH2" Residue "X ARG 239": "NH1" <-> "NH2" Residue "X GLU 296": "OE1" <-> "OE2" Residue "X TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 378": "OD1" <-> "OD2" Residue "X ASP 381": "OD1" <-> "OD2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 401": "NH1" <-> "NH2" Residue "X GLU 424": "OE1" <-> "OE2" Residue "X ASP 480": "OD1" <-> "OD2" Residue "X PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 491": "OD1" <-> "OD2" Residue "X GLU 494": "OE1" <-> "OE2" Residue "X GLU 497": "OE1" <-> "OE2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X GLU 533": "OE1" <-> "OE2" Residue "X GLU 536": "OE1" <-> "OE2" Residue "X GLU 546": "OE1" <-> "OE2" Residue "X GLU 552": "OE1" <-> "OE2" Residue "Y TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y ASP 82": "OD1" <-> "OD2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ASP 91": "OD1" <-> "OD2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y ARG 145": "NH1" <-> "NH2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 366": "NH1" <-> "NH2" Residue "Y TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y ASP 409": "OD1" <-> "OD2" Residue "Y PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 511": "OE1" <-> "OE2" Residue "Y GLU 519": "OE1" <-> "OE2" Residue "Y ASP 523": "OD1" <-> "OD2" Residue "Y GLU 533": "OE1" <-> "OE2" Residue "Y GLU 546": "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 ARG 71": "NH1" <-> "NH2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "Z ARG 98": "NH1" <-> "NH2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z ASP 130": "OD1" <-> "OD2" Residue "Z GLU 156": "OE1" <-> "OE2" Residue "Z PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 216": "NH1" <-> "NH2" Residue "Z ASP 222": "OD1" <-> "OD2" Residue "Z ARG 258": "NH1" <-> "NH2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z ARG 289": "NH1" <-> "NH2" Residue "Z GLU 323": "OE1" <-> "OE2" Residue "Z ASP 348": "OD1" <-> "OD2" Residue "Z PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 415": "OD1" <-> "OD2" Residue "Z GLU 427": "OE1" <-> "OE2" Residue "Z ARG 435": "NH1" <-> "NH2" Residue "Z ARG 437": "NH1" <-> "NH2" Residue "Z PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 465": "OD1" <-> "OD2" Residue "Z ASP 480": "OD1" <-> "OD2" Residue "Z GLU 497": "OE1" <-> "OE2" Residue "Z ASP 500": "OD1" <-> "OD2" Residue "Z ASP 505": "OD1" <-> "OD2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z ASP 523": "OD1" <-> "OD2" Residue "Z GLU 536": "OE1" <-> "OE2" Residue "Z GLU 541": "OE1" <-> "OE2" Residue "Z ASP 543": "OD1" <-> "OD2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 552": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33891 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: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} 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: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} 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: "Y" 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: 18.27, per 1000 atoms: 0.54 Number of scatterers: 33891 At special positions: 0 Unit cell: (162.162, 134.784, 209.547, 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 6421 8.00 N 5795 7.00 C 21541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.15 Conformation dependent library (CDL) restraints added in 6.2 seconds 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 171 helices and 27 sheets defined 46.3% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.09 Creating SS restraints... Processing helix chain 'A' and resid 55 through 67 removed outlier: 4.185A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 91 removed outlier: 3.866A pdb=" N GLY A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 98 through 125 removed outlier: 3.603A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 4.007A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 99 through 126 removed outlier: 3.959A pdb=" N LEU B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 89 removed outlier: 4.724A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 99 through 125 removed outlier: 3.809A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 91 removed outlier: 4.063A pdb=" N LYS D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 126 removed outlier: 4.523A pdb=" N VAL D 100 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU D 104 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 115 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE D 124 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE D 126 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 89 removed outlier: 4.032A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 98 through 125 removed outlier: 3.627A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 91 removed outlier: 3.706A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 118 removed outlier: 4.564A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL F 100 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU F 104 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 108 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU F 111 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 126 removed outlier: 4.040A pdb=" N LEU F 125 " --> pdb=" O VAL F 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 91 removed outlier: 4.317A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 95 No H-bonds generated for 'chain 'G' and resid 93 through 95' Processing helix chain 'G' and resid 98 through 126 removed outlier: 3.621A pdb=" N LEU G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA G 114 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU G 125 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE G 126 " --> pdb=" O PHE G 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 69 removed outlier: 4.301A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 91 removed outlier: 3.965A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 125 removed outlier: 5.564A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN H 98 " --> pdb=" O ILE H 95 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA H 108 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU H 119 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL H 121 " --> pdb=" O LEU H 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 65 removed outlier: 3.707A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 91 removed outlier: 3.964A pdb=" N LEU I 85 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG I 91 " --> pdb=" O GLY I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 95 No H-bonds generated for 'chain 'I' and resid 93 through 95' Processing helix chain 'I' and resid 98 through 126 removed outlier: 4.276A pdb=" N SER I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU I 125 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 89 removed outlier: 4.060A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 108 removed outlier: 3.522A pdb=" N ALA J 96 " --> pdb=" O PRO J 93 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LYS J 97 " --> pdb=" O ASN J 94 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU J 104 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA J 108 " --> pdb=" O LEU J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 125 Processing helix chain 'P' and resid 51 through 62 removed outlier: 3.526A pdb=" N GLN P 59 " --> pdb=" O THR P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 78 removed outlier: 3.877A pdb=" N PHE P 77 " --> pdb=" O GLU P 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 83 No H-bonds generated for 'chain 'P' and resid 80 through 83' Processing helix chain 'P' and resid 89 through 92 No H-bonds generated for 'chain 'P' and resid 89 through 92' Processing helix chain 'P' and resid 98 through 108 removed outlier: 3.535A pdb=" N THR P 102 " --> pdb=" O THR P 98 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 118 through 127 removed outlier: 3.527A pdb=" N PHE P 122 " --> pdb=" O THR P 118 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA P 126 " --> pdb=" O PHE P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 146 removed outlier: 4.226A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL P 137 " --> pdb=" O LEU P 134 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU P 143 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU P 146 " --> pdb=" O GLU P 143 " (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: 3.939A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 41 removed outlier: 4.620A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA Q 41 " --> pdb=" O ALA Q 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 37 Processing helix chain 'R' and resid 51 through 54 Processing helix chain 'R' and resid 159 through 167 removed outlier: 3.895A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 195 Processing helix chain 'S' and resid 40 through 78 removed outlier: 3.713A pdb=" N LYS S 44 " --> pdb=" O ASN S 40 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 88 Processing helix chain 'S' and resid 115 through 130 Processing helix chain 'S' and resid 147 through 153 removed outlier: 4.048A pdb=" N THR S 151 " --> pdb=" O ARG S 147 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ARG S 152 " --> pdb=" O SER S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 184 Processing helix chain 'S' and resid 217 through 220 No H-bonds generated for 'chain 'S' and resid 217 through 220' Processing helix chain 'S' and resid 239 through 311 removed outlier: 3.588A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP S 245 " --> pdb=" O ASP S 241 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER S 277 " --> pdb=" O ALA S 273 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR S 278 " --> pdb=" O MET S 274 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE S 307 " --> pdb=" O GLU S 303 " (cutoff:3.500A) Processing helix chain 'T' and resid 207 through 212 removed outlier: 3.667A pdb=" N ALA T 211 " --> pdb=" O LYS T 207 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 207 through 212' Processing helix chain 'T' and resid 231 through 245 removed outlier: 3.535A pdb=" N ALA T 235 " --> pdb=" O LYS T 231 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN T 244 " --> pdb=" O ILE T 240 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 279 Processing helix chain 'T' and resid 281 through 284 Processing helix chain 'T' and resid 296 through 315 Proline residue: T 303 - end of helix removed outlier: 3.721A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 340 removed outlier: 4.137A pdb=" N VAL T 332 " --> pdb=" O LYS T 329 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN T 336 " --> pdb=" O ALA T 333 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET T 337 " --> pdb=" O TYR T 334 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER T 338 " --> pdb=" O ARG T 335 " (cutoff:3.500A) Processing helix chain 'T' and resid 352 through 364 removed outlier: 4.148A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER T 359 " --> pdb=" O TYR T 356 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG T 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU T 362 " --> pdb=" O SER T 359 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU T 363 " --> pdb=" O ARG T 360 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 401 removed outlier: 3.539A pdb=" N ASN T 397 " --> pdb=" O TYR T 393 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL T 398 " --> pdb=" O ILE T 394 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER T 400 " --> pdb=" O THR T 396 " (cutoff:3.500A) Processing helix chain 'T' and resid 431 through 434 removed outlier: 4.185A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 431 through 434' Processing helix chain 'T' and resid 437 through 440 No H-bonds generated for 'chain 'T' and resid 437 through 440' Processing helix chain 'T' and resid 444 through 452 removed outlier: 3.521A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) Processing helix chain 'T' and resid 454 through 462 removed outlier: 3.681A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE T 462 " --> pdb=" O ALA T 458 " (cutoff:3.500A) Processing helix chain 'T' and resid 470 through 483 removed outlier: 3.583A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU T 480 " --> pdb=" O ARG T 476 " (cutoff:3.500A) Processing helix chain 'T' and resid 495 through 505 removed outlier: 3.772A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 514 through 520 removed outlier: 3.978A pdb=" N ILE T 517 " --> pdb=" O VAL T 514 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N VAL T 518 " --> pdb=" O GLN T 515 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA T 520 " --> pdb=" O ILE T 517 " (cutoff:3.500A) 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: 3.622A pdb=" N LEU T 536 " --> pdb=" O VAL T 532 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA T 538 " --> pdb=" O LYS T 534 " (cutoff:3.500A) Processing helix chain 'T' and resid 544 through 555 removed outlier: 3.763A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS T 551 " --> pdb=" O ASP T 547 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU T 553 " --> pdb=" O HIS T 549 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG T 555 " --> pdb=" O LYS T 551 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 49 removed outlier: 3.924A pdb=" N ARG U 49 " --> pdb=" O ASP U 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 46 through 49' Processing helix chain 'U' and resid 59 through 63 Processing helix chain 'U' and resid 67 through 70 No H-bonds generated for 'chain 'U' and resid 67 through 70' Processing helix chain 'U' and resid 135 through 137 No H-bonds generated for 'chain 'U' and resid 135 through 137' Processing helix chain 'U' and resid 157 through 159 No H-bonds generated for 'chain 'U' and resid 157 through 159' Processing helix chain 'U' and resid 207 through 212 Processing helix chain 'U' and resid 231 through 248 removed outlier: 3.999A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLN U 248 " --> pdb=" O ASN U 244 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 278 Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 296 through 315 Proline residue: U 303 - end of helix removed outlier: 3.725A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 341 removed outlier: 3.666A pdb=" N LEU U 341 " --> pdb=" O MET U 337 " (cutoff:3.500A) Processing helix chain 'U' and resid 354 through 362 removed outlier: 3.698A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (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 399 Processing helix chain 'U' and resid 410 through 414 Processing helix chain 'U' and resid 437 through 459 removed outlier: 3.619A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) Processing helix chain 'U' and resid 471 through 484 removed outlier: 3.800A pdb=" N GLU U 482 " --> pdb=" O ALA U 478 " (cutoff:3.500A) Processing helix chain 'U' and resid 495 through 505 removed outlier: 4.035A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 517 through 527 removed outlier: 3.752A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 538 removed outlier: 4.248A pdb=" N LYS U 534 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 544 through 553 Processing helix chain 'V' and resid 45 through 48 Processing helix chain 'V' and resid 59 through 69 removed outlier: 3.717A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Proline residue: V 68 - end of helix Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 212 Processing helix chain 'V' and resid 231 through 246 Processing helix chain 'V' and resid 251 through 253 No H-bonds generated for 'chain 'V' and resid 251 through 253' Processing helix chain 'V' and resid 266 through 279 Processing helix chain 'V' and resid 281 through 283 No H-bonds generated for 'chain 'V' and resid 281 through 283' Processing helix chain 'V' and resid 296 through 315 Proline residue: V 303 - end of helix removed outlier: 3.829A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 340 Processing helix chain 'V' and resid 354 through 364 removed outlier: 4.595A pdb=" N ARG V 364 " --> pdb=" O ARG V 360 " (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 386 through 388 No H-bonds generated for 'chain 'V' and resid 386 through 388' Processing helix chain 'V' and resid 393 through 401 Processing helix chain 'V' and resid 411 through 414 No H-bonds generated for 'chain 'V' and resid 411 through 414' Processing helix chain 'V' and resid 431 through 434 removed outlier: 3.713A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 431 through 434' Processing helix chain 'V' and resid 440 through 455 removed outlier: 5.392A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU V 448 " --> pdb=" O GLY V 444 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 481 Processing helix chain 'V' and resid 494 through 506 Processing helix chain 'V' and resid 514 through 516 No H-bonds generated for 'chain 'V' and resid 514 through 516' Processing helix chain 'V' and resid 518 through 525 removed outlier: 4.246A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA V 523 " --> pdb=" O ALA V 519 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE V 525 " --> pdb=" O GLU V 521 " (cutoff:3.500A) Processing helix chain 'V' and resid 531 through 539 removed outlier: 3.519A pdb=" N ILE V 535 " --> pdb=" O ALA V 531 " (cutoff:3.500A) Processing helix chain 'V' and resid 544 through 555 removed outlier: 3.649A pdb=" N LYS V 551 " --> pdb=" O ASP V 547 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG V 555 " --> pdb=" O LYS V 551 " (cutoff:3.500A) Processing helix chain 'X' and resid 165 through 169 Processing helix chain 'X' and resid 189 through 203 removed outlier: 4.681A pdb=" N LYS X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA X 203 " --> pdb=" O ASN X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 227 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 255 through 258 No H-bonds generated for 'chain 'X' and resid 255 through 258' Processing helix chain 'X' and resid 262 through 274 removed outlier: 3.810A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 288 through 297 Processing helix chain 'X' and resid 314 through 324 removed outlier: 4.277A pdb=" N ARG X 324 " --> pdb=" O GLY X 320 " (cutoff:3.500A) 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 354 through 357 Processing helix chain 'X' and resid 366 through 371 removed outlier: 3.532A pdb=" N LEU X 371 " --> pdb=" O SER X 367 " (cutoff:3.500A) Processing helix chain 'X' and resid 389 through 420 removed outlier: 7.294A pdb=" N ALA X 394 " --> pdb=" O ASN X 390 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N GLU X 395 " --> pdb=" O VAL X 391 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N HIS X 396 " --> pdb=" O ILE X 392 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) Processing helix chain 'X' and resid 422 through 424 No H-bonds generated for 'chain 'X' and resid 422 through 424' Processing helix chain 'X' and resid 427 through 442 Processing helix chain 'X' and resid 451 through 454 No H-bonds generated for 'chain 'X' and resid 451 through 454' Processing helix chain 'X' and resid 463 through 475 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: 3.532A pdb=" N ALA X 507 " --> pdb=" O ALA X 503 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 533 removed outlier: 4.736A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLU X 533 " --> pdb=" O LYS X 529 " (cutoff:3.500A) Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 165 through 169 Processing helix chain 'Y' and resid 189 through 200 Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 4.714A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 274 removed outlier: 4.325A pdb=" N ARG Y 260 " --> pdb=" O GLY Y 256 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL Y 261 " --> pdb=" O ALA Y 257 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 297 removed outlier: 3.535A pdb=" N GLN Y 292 " --> pdb=" O ARG Y 289 " (cutoff:3.500A) Processing helix chain 'Y' and resid 314 through 324 removed outlier: 4.505A pdb=" N ARG Y 324 " --> pdb=" O GLY Y 320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 349 through 356 removed outlier: 3.860A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 370 Processing helix chain 'Y' and resid 389 through 392 No H-bonds generated for 'chain 'Y' and resid 389 through 392' Processing helix chain 'Y' and resid 394 through 420 removed outlier: 4.196A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA Y 418 " --> pdb=" O GLN Y 414 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 429 through 442 Processing helix chain 'Y' and resid 463 through 475 removed outlier: 3.642A pdb=" N THR Y 475 " --> pdb=" O GLN Y 471 " (cutoff:3.500A) Processing helix chain 'Y' and resid 483 through 485 No H-bonds generated for 'chain 'Y' and resid 483 through 485' Processing helix chain 'Y' and resid 492 through 508 removed outlier: 3.641A pdb=" N ASP Y 500 " --> pdb=" O LYS Y 496 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS Y 501 " --> pdb=" O GLU Y 497 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA Y 507 " --> pdb=" O ALA Y 503 " (cutoff:3.500A) Processing helix chain 'Y' and resid 510 through 512 No H-bonds generated for 'chain 'Y' and resid 510 through 512' Processing helix chain 'Y' and resid 527 through 532 Processing helix chain 'Y' and resid 545 through 554 removed outlier: 4.145A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 117 No H-bonds generated for 'chain 'Z' and resid 115 through 117' Processing helix chain 'Z' and resid 150 through 152 No H-bonds generated for 'chain 'Z' and resid 150 through 152' Processing helix chain 'Z' and resid 165 through 169 Processing helix chain 'Z' and resid 189 through 203 Processing helix chain 'Z' and resid 217 through 229 Processing helix chain 'Z' and resid 239 through 241 No H-bonds generated for 'chain 'Z' and resid 239 through 241' Processing helix chain 'Z' and resid 255 through 258 No H-bonds generated for 'chain 'Z' and resid 255 through 258' Processing helix chain 'Z' and resid 261 through 274 removed outlier: 3.530A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 300 Processing helix chain 'Z' and resid 314 through 322 removed outlier: 3.871A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 349 through 357 removed outlier: 3.823A pdb=" N ALA Z 356 " --> pdb=" O ALA Z 352 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N HIS Z 357 " --> pdb=" O THR Z 353 " (cutoff:3.500A) Processing helix chain 'Z' and resid 366 through 370 Processing helix chain 'Z' and resid 394 through 417 removed outlier: 4.153A pdb=" N LEU Z 413 " --> pdb=" O ASP Z 409 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN Z 414 " --> pdb=" O TYR Z 410 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) Processing helix chain 'Z' and resid 427 through 442 removed outlier: 3.711A pdb=" N THR Z 432 " --> pdb=" O GLU Z 428 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS Z 438 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) Processing helix chain 'Z' and resid 448 through 450 No H-bonds generated for 'chain 'Z' and resid 448 through 450' Processing helix chain 'Z' and resid 463 through 475 removed outlier: 3.542A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) Processing helix chain 'Z' and resid 495 through 510 removed outlier: 3.867A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER Z 508 " --> pdb=" O LYS Z 504 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG Z 509 " --> pdb=" O ASP Z 505 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LYS Z 510 " --> pdb=" O ILE Z 506 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 533 Processing sheet with id= A, first strand: chain 'Q' and resid 45 through 49 Processing sheet with id= B, first strand: chain 'R' and resid 96 through 100 removed outlier: 3.569A pdb=" N VAL R 90 " --> pdb=" O GLU R 117 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU R 117 " --> pdb=" O VAL R 90 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'R' and resid 107 through 111 removed outlier: 3.953A pdb=" N GLY R 132 " --> pdb=" O LEU R 111 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE R 135 " --> pdb=" O ASP R 143 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 158 through 162 removed outlier: 8.149A pdb=" N VAL S 139 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ALA S 161 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER S 141 " --> pdb=" O ALA S 161 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N SER S 189 " --> pdb=" O VAL S 101 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N VAL S 103 " --> pdb=" O SER S 189 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN S 191 " --> pdb=" O VAL S 103 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL S 105 " --> pdb=" O GLN S 191 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU S 193 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE S 194 " --> pdb=" O THR S 206 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS S 204 " --> pdb=" O LYS S 196 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'T' and resid 86 through 91 removed outlier: 6.738A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN T 121 " --> pdb=" O GLY T 128 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'T' and resid 152 through 155 Processing sheet with id= G, first strand: chain 'T' and resid 404 through 407 removed outlier: 3.879A pdb=" N LEU T 222 " --> pdb=" O GLY T 404 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'T' and resid 285 through 290 removed outlier: 9.123A pdb=" N ILE T 286 " --> pdb=" O VAL T 255 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N CYS T 257 " --> pdb=" O ILE T 286 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N VAL T 288 " --> pdb=" O CYS T 257 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR T 259 " --> pdb=" O VAL T 288 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ALA T 290 " --> pdb=" O TYR T 259 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ALA T 261 " --> pdb=" O ALA T 290 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N SER T 376 " --> pdb=" O GLY T 320 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ILE T 322 " --> pdb=" O SER T 376 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE T 380 " --> pdb=" O TYR T 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.687A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'U' and resid 109 through 111 Processing sheet with id= K, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= L, first strand: chain 'U' and resid 405 through 408 removed outlier: 6.783A pdb=" N LEU U 222 " --> pdb=" O ILE U 406 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU U 408 " --> pdb=" O LEU U 222 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE U 224 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'U' and resid 285 through 290 removed outlier: 8.976A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE U 380 " --> pdb=" O TYR U 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'V' and resid 84 through 86 removed outlier: 3.672A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET V 118 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU V 120 " --> pdb=" O GLY V 128 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY V 128 " --> pdb=" O LEU V 120 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU V 122 " --> pdb=" O HIS V 126 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N HIS V 126 " --> pdb=" O LEU V 122 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TYR V 98 " --> pdb=" O VAL V 87 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL V 87 " --> pdb=" O TYR V 98 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= P, first strand: chain 'V' and resid 404 through 408 removed outlier: 3.803A pdb=" N LEU V 222 " --> pdb=" O GLY V 404 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'V' and resid 285 through 290 removed outlier: 8.960A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N PHE V 380 " --> pdb=" O TYR V 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'X' and resid 37 through 39 removed outlier: 6.646A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ARG X 51 " --> pdb=" O VAL X 40 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL X 40 " --> pdb=" O ARG X 51 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'X' and resid 110 through 113 Processing sheet with id= T, first strand: chain 'X' and resid 360 through 363 removed outlier: 7.520A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N GLY X 183 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL X 339 " --> pdb=" O GLY X 183 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= V, first strand: chain 'Y' and resid 39 through 44 removed outlier: 6.405A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Y' and resid 360 through 362 removed outlier: 7.419A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL Y 280 " --> pdb=" O THR Y 334 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL Y 336 " --> pdb=" O VAL Y 280 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU Y 282 " --> pdb=" O VAL Y 336 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA Y 338 " --> pdb=" O LEU Y 282 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL Y 284 " --> pdb=" O ALA Y 338 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE Y 207 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N PHE Y 283 " --> pdb=" O PHE Y 207 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA Y 211 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Z' and resid 38 through 44 removed outlier: 6.614A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id= Z, first strand: chain 'Z' and resid 360 through 363 removed outlier: 8.549A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL Z 284 " --> pdb=" O VAL Z 336 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Z' and resid 559 through 561 1368 hydrogen bonds defined for protein. 3666 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.09 Time building geometry restraints manager: 15.06 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: 10561 1.34 - 1.46: 5168 1.46 - 1.57: 18462 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34412 Sorted by residual: bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.25e+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 6.03e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.67e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.62e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.49e+01 ... (remaining 34407 not shown) Histogram of bond angle deviations from ideal: 99.01 - 106.45: 907 106.45 - 113.89: 19925 113.89 - 121.34: 17603 121.34 - 128.78: 8083 128.78 - 136.22: 120 Bond angle restraints: 46638 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 117.27 22.60 1.00e+00 1.00e+00 5.11e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 119.24 20.63 1.00e+00 1.00e+00 4.26e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 121.83 18.04 1.00e+00 1.00e+00 3.25e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 121.12 15.71 1.00e+00 1.00e+00 2.47e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 121.30 15.53 1.00e+00 1.00e+00 2.41e+02 ... (remaining 46633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 18856 17.88 - 35.75: 1577 35.75 - 53.63: 304 53.63 - 71.51: 55 71.51 - 89.38: 31 Dihedral angle restraints: 20823 sinusoidal: 8066 harmonic: 12757 Sorted by residual: dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual -180.00 -124.11 -55.89 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual 180.00 -126.22 -53.78 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" CA GLU V 348 " pdb=" C GLU V 348 " pdb=" N ALA V 349 " pdb=" CA ALA V 349 " ideal model delta harmonic sigma weight residual 180.00 126.83 53.17 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 20820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4893 0.090 - 0.179: 598 0.179 - 0.269: 25 0.269 - 0.358: 2 0.358 - 0.448: 1 Chirality restraints: 5519 Sorted by residual: chirality pdb=" CB ILE U 67 " pdb=" CA ILE U 67 " pdb=" CG1 ILE U 67 " pdb=" CG2 ILE U 67 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CB ILE B 95 " pdb=" CA ILE B 95 " pdb=" CG1 ILE B 95 " pdb=" CG2 ILE B 95 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CB VAL R 90 " pdb=" CA VAL R 90 " pdb=" CG1 VAL R 90 " pdb=" CG2 VAL R 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 5516 not shown) Planarity restraints: 5997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.030 2.00e-02 2.50e+03 5.90e-02 3.48e+01 pdb=" C ALA Z 503 " -0.102 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET X 502 " -0.027 2.00e-02 2.50e+03 5.21e-02 2.71e+01 pdb=" C MET X 502 " 0.090 2.00e-02 2.50e+03 pdb=" O MET X 502 " -0.034 2.00e-02 2.50e+03 pdb=" N ALA X 503 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA X 350 " -0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO X 351 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO X 351 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO X 351 " -0.045 5.00e-02 4.00e+02 ... (remaining 5994 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 615 2.66 - 3.22: 30979 3.22 - 3.78: 54784 3.78 - 4.34: 76464 4.34 - 4.90: 124024 Nonbonded interactions: 286866 Sorted by model distance: nonbonded pdb=" O3B ADP Y 601 " pdb="MG MG Y 602 " model vdw 2.103 2.170 nonbonded pdb=" O2B ATP V1001 " pdb="MG MG V1002 " model vdw 2.104 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.115 2.170 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.117 2.170 nonbonded pdb=" O2B ATP U1001 " pdb="MG MG U1002 " model vdw 2.118 2.170 ... (remaining 286861 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 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.910 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: 0.040 Extract box with map and model: 25.820 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 90.310 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 : 0.007 0.082 34412 Z= 0.430 Angle : 0.936 22.601 46638 Z= 0.553 Chirality : 0.057 0.448 5519 Planarity : 0.007 0.079 5997 Dihedral : 14.280 89.381 12663 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.77 % Favored : 94.98 % Rotamer: Outliers : 0.59 % Allowed : 7.58 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.14 % 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: -4.38 (0.10), residues: 4461 helix: -3.36 (0.07), residues: 2145 sheet: -2.06 (0.21), residues: 507 loop : -2.33 (0.12), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP Z 141 HIS 0.013 0.002 HIS S 250 PHE 0.027 0.002 PHE U 53 TYR 0.032 0.002 TYR X 340 ARG 0.007 0.001 ARG T 479 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 761 time to evaluate : 4.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 LEU cc_start: 0.6709 (mt) cc_final: 0.6466 (pp) REVERT: D 118 LEU cc_start: 0.5855 (mt) cc_final: 0.5616 (mt) REVERT: E 119 LEU cc_start: 0.6643 (mp) cc_final: 0.6153 (pp) REVERT: F 105 LEU cc_start: 0.6639 (tt) cc_final: 0.5359 (mm) REVERT: G 94 ASN cc_start: 0.6813 (m-40) cc_final: 0.6432 (t0) REVERT: G 126 PHE cc_start: 0.6317 (m-80) cc_final: 0.6114 (m-10) REVERT: H 68 THR cc_start: 0.7159 (p) cc_final: 0.6952 (t) REVERT: H 95 ILE cc_start: 0.7718 (mm) cc_final: 0.7499 (mm) REVERT: J 123 LEU cc_start: 0.4761 (tp) cc_final: 0.4519 (tp) REVERT: P 118 THR cc_start: 0.8204 (t) cc_final: 0.7419 (t) REVERT: P 122 PHE cc_start: 0.8390 (m-10) cc_final: 0.8173 (m-10) REVERT: P 145 MET cc_start: 0.7851 (mmm) cc_final: 0.7650 (mmm) REVERT: Q 71 LYS cc_start: 0.6500 (mttp) cc_final: 0.5439 (ttpp) REVERT: R 143 ASP cc_start: 0.6598 (p0) cc_final: 0.6173 (p0) REVERT: R 145 CYS cc_start: 0.7804 (m) cc_final: 0.7551 (m) REVERT: R 175 GLU cc_start: 0.6414 (pt0) cc_final: 0.5805 (pm20) REVERT: S 41 GLN cc_start: 0.6903 (mm-40) cc_final: 0.6500 (pp30) REVERT: S 181 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6374 (mm-30) REVERT: S 275 GLU cc_start: 0.7599 (tp30) cc_final: 0.7190 (tt0) REVERT: S 291 ASP cc_start: 0.7993 (t70) cc_final: 0.7724 (t0) REVERT: T 135 ASP cc_start: 0.8042 (p0) cc_final: 0.7757 (p0) REVERT: T 139 HIS cc_start: 0.7582 (m90) cc_final: 0.6914 (m170) REVERT: T 179 ASN cc_start: 0.8374 (m110) cc_final: 0.8172 (m110) REVERT: T 324 TYR cc_start: 0.9254 (m-80) cc_final: 0.8775 (m-80) REVERT: T 551 LYS cc_start: 0.7239 (ptpt) cc_final: 0.6535 (ptmt) REVERT: U 304 TYR cc_start: 0.8806 (m-80) cc_final: 0.7657 (m-80) REVERT: U 337 MET cc_start: 0.8054 (ttp) cc_final: 0.7650 (ttt) REVERT: U 550 LEU cc_start: 0.8213 (tp) cc_final: 0.7986 (tt) REVERT: V 79 PRO cc_start: 0.7497 (Cg_endo) cc_final: 0.7182 (Cg_exo) REVERT: V 307 CYS cc_start: 0.7884 (t) cc_final: 0.7428 (t) REVERT: X 529 LYS cc_start: 0.8345 (mtpt) cc_final: 0.8040 (mtmt) REVERT: Y 175 ARG cc_start: 0.8103 (ttm-80) cc_final: 0.7773 (ttt180) REVERT: Y 195 GLU cc_start: 0.6820 (tm-30) cc_final: 0.5974 (tm-30) REVERT: Y 260 ARG cc_start: 0.8403 (mmt-90) cc_final: 0.8138 (mmt90) REVERT: Z 82 ASP cc_start: 0.7776 (t70) cc_final: 0.7529 (t0) REVERT: Z 131 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7338 (tm-30) REVERT: Z 491 ASP cc_start: 0.7009 (m-30) cc_final: 0.6591 (m-30) REVERT: Z 493 LYS cc_start: 0.8346 (mmtt) cc_final: 0.7900 (tttm) outliers start: 21 outliers final: 4 residues processed: 775 average time/residue: 0.5030 time to fit residues: 611.2865 Evaluate side-chains 471 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 467 time to evaluate : 3.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 489 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 0.9990 chunk 335 optimal weight: 0.7980 chunk 185 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 346 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 210 optimal weight: 3.9990 chunk 257 optimal weight: 0.8980 chunk 401 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 94 ASN ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN P 83 GLN P 148 HIS R 66 HIS R 73 ASN R 85 GLN ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN S 174 GLN S 186 ASN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 250 HIS S 257 ASN S 262 ASN S 293 ASN T 139 HIS T 152 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN T 386 GLN T 549 HIS U 134 ASN U 242 GLN U 248 GLN ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 139 HIS V 149 GLN V 152 ASN V 196 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS V 244 ASN V 278 GLN V 497 GLN X 199 ASN X 322 GLN X 337 GLN X 408 GLN X 414 GLN X 471 GLN Y 174 GLN ** Y 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 221 ASN Z 42 GLN ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 144 HIS Z 153 GLN Z 199 ASN Z 241 ASN ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 278 GLN Z 286 ASN Z 322 GLN Z 337 GLN Z 404 GLN Z 471 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34412 Z= 0.183 Angle : 0.598 13.198 46638 Z= 0.309 Chirality : 0.043 0.205 5519 Planarity : 0.005 0.063 5997 Dihedral : 6.853 86.654 4924 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.79 % Favored : 95.99 % Rotamer: Outliers : 2.27 % Allowed : 13.78 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.14 % 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: -2.83 (0.11), residues: 4461 helix: -1.85 (0.10), residues: 2153 sheet: -1.64 (0.22), residues: 489 loop : -1.77 (0.13), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP X 141 HIS 0.004 0.001 HIS S 237 PHE 0.024 0.001 PHE D 107 TYR 0.018 0.001 TYR Q 16 ARG 0.006 0.000 ARG X 385 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 544 time to evaluate : 4.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 119 LEU cc_start: 0.6339 (mp) cc_final: 0.5866 (pp) REVERT: F 105 LEU cc_start: 0.6705 (tt) cc_final: 0.5718 (mm) REVERT: F 109 LEU cc_start: 0.8147 (tp) cc_final: 0.7321 (tt) REVERT: G 61 MET cc_start: 0.6539 (mmm) cc_final: 0.6023 (mmm) REVERT: G 94 ASN cc_start: 0.7058 (m110) cc_final: 0.6594 (t0) REVERT: H 95 ILE cc_start: 0.7960 (mm) cc_final: 0.7714 (mm) REVERT: J 97 LYS cc_start: 0.6839 (tptt) cc_final: 0.6115 (mmpt) REVERT: P 75 TYR cc_start: 0.8651 (m-80) cc_final: 0.7850 (m-80) REVERT: Q 66 GLU cc_start: 0.5042 (mp0) cc_final: 0.4732 (mp0) REVERT: Q 71 LYS cc_start: 0.6469 (mttp) cc_final: 0.5541 (ttpp) REVERT: R 143 ASP cc_start: 0.6698 (p0) cc_final: 0.6391 (p0) REVERT: R 175 GLU cc_start: 0.6335 (pt0) cc_final: 0.6091 (pm20) REVERT: S 41 GLN cc_start: 0.7175 (mm-40) cc_final: 0.6497 (pp30) REVERT: S 68 MET cc_start: 0.7253 (ttp) cc_final: 0.7008 (ttt) REVERT: S 204 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8243 (pttt) REVERT: S 291 ASP cc_start: 0.7965 (t70) cc_final: 0.7700 (t0) REVERT: T 135 ASP cc_start: 0.8040 (p0) cc_final: 0.7781 (p0) REVERT: T 139 HIS cc_start: 0.7725 (m-70) cc_final: 0.7048 (m170) REVERT: T 179 ASN cc_start: 0.8419 (m110) cc_final: 0.8219 (m110) REVERT: T 324 TYR cc_start: 0.9178 (m-80) cc_final: 0.8875 (m-80) REVERT: T 551 LYS cc_start: 0.7079 (ptpt) cc_final: 0.6541 (ptmm) REVERT: U 304 TYR cc_start: 0.8751 (m-80) cc_final: 0.7603 (m-80) REVERT: U 337 MET cc_start: 0.8092 (ttp) cc_final: 0.7723 (ttt) REVERT: U 482 GLU cc_start: 0.7218 (mt-10) cc_final: 0.7002 (mt-10) REVERT: U 550 LEU cc_start: 0.8372 (tp) cc_final: 0.8022 (tt) REVERT: V 213 VAL cc_start: 0.9235 (OUTLIER) cc_final: 0.9007 (m) REVERT: V 307 CYS cc_start: 0.7959 (t) cc_final: 0.7613 (t) REVERT: X 194 MET cc_start: 0.7987 (tpp) cc_final: 0.7774 (tpp) REVERT: X 195 GLU cc_start: 0.7015 (tp30) cc_final: 0.6431 (tp30) REVERT: Y 175 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7774 (ttt180) REVERT: Y 194 MET cc_start: 0.8482 (tpp) cc_final: 0.8243 (mmm) REVERT: Y 195 GLU cc_start: 0.6875 (tm-30) cc_final: 0.6174 (tm-30) REVERT: Y 385 ARG cc_start: 0.7467 (tpp80) cc_final: 0.6947 (ttm-80) REVERT: Y 502 MET cc_start: 0.7114 (mpp) cc_final: 0.6628 (ptm) REVERT: Z 49 ASP cc_start: 0.7576 (m-30) cc_final: 0.7355 (m-30) REVERT: Z 52 PHE cc_start: 0.8537 (m-80) cc_final: 0.8287 (m-80) REVERT: Z 80 MET cc_start: 0.7950 (mmm) cc_final: 0.7742 (mmm) REVERT: Z 82 ASP cc_start: 0.7812 (t70) cc_final: 0.7594 (t0) REVERT: Z 131 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7473 (tm-30) REVERT: Z 493 LYS cc_start: 0.8342 (mmtt) cc_final: 0.7926 (tttm) outliers start: 81 outliers final: 39 residues processed: 596 average time/residue: 0.4395 time to fit residues: 431.2726 Evaluate side-chains 486 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 445 time to evaluate : 3.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 361 THR Chi-restraints excluded: chain X residue 368 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 537 VAL Chi-restraints excluded: chain X residue 572 LYS Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 129 VAL Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 286 ASN Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 439 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 223 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 334 optimal weight: 4.9990 chunk 273 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 402 optimal weight: 0.0770 chunk 434 optimal weight: 0.0870 chunk 358 optimal weight: 0.9980 chunk 398 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 322 optimal weight: 2.9990 overall best weight: 0.8118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 98 GLN R 85 GLN S 77 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 152 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 405 GLN ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 139 HIS ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34412 Z= 0.175 Angle : 0.582 14.094 46638 Z= 0.292 Chirality : 0.043 0.200 5519 Planarity : 0.004 0.052 5997 Dihedral : 6.567 88.027 4924 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.90 % Favored : 95.90 % Rotamer: Outliers : 2.33 % Allowed : 16.02 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.16 (0.12), residues: 4461 helix: -1.23 (0.11), residues: 2142 sheet: -1.49 (0.22), residues: 511 loop : -1.46 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 73 HIS 0.005 0.001 HIS V 126 PHE 0.026 0.001 PHE X 207 TYR 0.023 0.001 TYR T 502 ARG 0.005 0.000 ARG V 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 503 time to evaluate : 3.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 60 LYS cc_start: 0.7319 (ptmt) cc_final: 0.6553 (pptt) REVERT: F 105 LEU cc_start: 0.6668 (tt) cc_final: 0.5810 (mm) REVERT: F 109 LEU cc_start: 0.8126 (tp) cc_final: 0.7281 (tt) REVERT: G 61 MET cc_start: 0.6461 (mmm) cc_final: 0.6150 (mmm) REVERT: G 94 ASN cc_start: 0.6834 (m110) cc_final: 0.6490 (t0) REVERT: J 97 LYS cc_start: 0.6569 (tptt) cc_final: 0.5999 (mmpt) REVERT: P 72 ASP cc_start: 0.7003 (m-30) cc_final: 0.6702 (m-30) REVERT: P 75 TYR cc_start: 0.8430 (m-80) cc_final: 0.7721 (m-80) REVERT: Q 71 LYS cc_start: 0.6552 (mttp) cc_final: 0.5616 (ttpp) REVERT: R 143 ASP cc_start: 0.6798 (p0) cc_final: 0.6483 (p0) REVERT: S 41 GLN cc_start: 0.7167 (mm-40) cc_final: 0.6555 (pp30) REVERT: S 204 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8135 (pttt) REVERT: S 271 MET cc_start: 0.7622 (ttp) cc_final: 0.7309 (ttt) REVERT: S 291 ASP cc_start: 0.7971 (t70) cc_final: 0.7729 (t0) REVERT: T 135 ASP cc_start: 0.8027 (p0) cc_final: 0.7822 (p0) REVERT: T 139 HIS cc_start: 0.7679 (m-70) cc_final: 0.6972 (m170) REVERT: T 324 TYR cc_start: 0.9148 (m-80) cc_final: 0.8891 (m-80) REVERT: U 304 TYR cc_start: 0.8764 (m-80) cc_final: 0.7558 (m-80) REVERT: U 337 MET cc_start: 0.8082 (ttp) cc_final: 0.7758 (ttt) REVERT: U 550 LEU cc_start: 0.8371 (tp) cc_final: 0.8044 (tt) REVERT: V 307 CYS cc_start: 0.7952 (t) cc_final: 0.7627 (t) REVERT: Y 175 ARG cc_start: 0.8042 (ttm-80) cc_final: 0.7721 (ttt180) REVERT: Y 195 GLU cc_start: 0.6944 (tm-30) cc_final: 0.6099 (tm-30) REVERT: Y 385 ARG cc_start: 0.7410 (tpp80) cc_final: 0.6820 (ttm-80) REVERT: Y 502 MET cc_start: 0.6975 (mpp) cc_final: 0.6465 (ptm) REVERT: Z 49 ASP cc_start: 0.7614 (m-30) cc_final: 0.7320 (m-30) REVERT: Z 82 ASP cc_start: 0.7705 (t70) cc_final: 0.7447 (t0) REVERT: Z 86 ARG cc_start: 0.8657 (ttt90) cc_final: 0.8147 (ttm170) REVERT: Z 131 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7544 (tm-30) REVERT: Z 493 LYS cc_start: 0.8360 (mmtt) cc_final: 0.7973 (tttm) outliers start: 83 outliers final: 52 residues processed: 560 average time/residue: 0.4342 time to fit residues: 400.7535 Evaluate side-chains 499 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 446 time to evaluate : 3.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 208 SER Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 361 THR Chi-restraints excluded: chain X residue 368 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 420 LEU Chi-restraints excluded: chain X residue 537 VAL Chi-restraints excluded: chain X residue 572 LYS Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 129 VAL Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 368 ILE Chi-restraints excluded: chain Z residue 383 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 397 optimal weight: 5.9990 chunk 302 optimal weight: 0.8980 chunk 208 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 191 optimal weight: 0.0000 chunk 270 optimal weight: 5.9990 chunk 403 optimal weight: 0.0870 chunk 427 optimal weight: 6.9990 chunk 210 optimal weight: 0.6980 chunk 382 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 overall best weight: 0.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 188 GLN T 152 ASN T 179 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 140 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 242 GLN X 322 GLN X 337 GLN ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 34412 Z= 0.151 Angle : 0.563 12.035 46638 Z= 0.282 Chirality : 0.042 0.199 5519 Planarity : 0.004 0.046 5997 Dihedral : 6.281 87.175 4924 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.97 % Favored : 95.90 % Rotamer: Outliers : 2.58 % Allowed : 16.84 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.67 (0.12), residues: 4461 helix: -0.77 (0.11), residues: 2119 sheet: -1.26 (0.22), residues: 518 loop : -1.29 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 73 HIS 0.006 0.001 HIS S 250 PHE 0.025 0.001 PHE D 107 TYR 0.032 0.001 TYR H 102 ARG 0.008 0.000 ARG Y 437 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 505 time to evaluate : 3.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6850 (tmm) cc_final: 0.6559 (tmm) REVERT: B 81 MET cc_start: 0.6389 (tpp) cc_final: 0.5984 (tpp) REVERT: C 105 LEU cc_start: 0.7043 (tt) cc_final: 0.6559 (tp) REVERT: D 98 GLN cc_start: 0.7346 (mt0) cc_final: 0.7071 (mt0) REVERT: F 60 LYS cc_start: 0.7367 (ptmt) cc_final: 0.6765 (pptt) REVERT: F 105 LEU cc_start: 0.6615 (tt) cc_final: 0.5782 (mm) REVERT: F 109 LEU cc_start: 0.7981 (tp) cc_final: 0.7144 (tt) REVERT: G 66 CYS cc_start: 0.7752 (m) cc_final: 0.7414 (t) REVERT: G 94 ASN cc_start: 0.6854 (m110) cc_final: 0.6533 (t0) REVERT: I 105 LEU cc_start: 0.5178 (OUTLIER) cc_final: 0.4974 (mt) REVERT: J 111 GLU cc_start: 0.5627 (tp30) cc_final: 0.4538 (pp20) REVERT: P 75 TYR cc_start: 0.8279 (m-80) cc_final: 0.7416 (m-80) REVERT: Q 48 ARG cc_start: 0.7282 (ptt90) cc_final: 0.6861 (ptt-90) REVERT: Q 71 LYS cc_start: 0.6591 (mttp) cc_final: 0.5606 (ttpp) REVERT: R 143 ASP cc_start: 0.6713 (OUTLIER) cc_final: 0.6401 (p0) REVERT: S 41 GLN cc_start: 0.7177 (mm-40) cc_final: 0.6574 (pp30) REVERT: S 271 MET cc_start: 0.7539 (ttp) cc_final: 0.7233 (ttt) REVERT: S 274 MET cc_start: 0.7443 (mmp) cc_final: 0.7111 (mmp) REVERT: T 121 ASN cc_start: 0.8310 (p0) cc_final: 0.8075 (p0) REVERT: T 139 HIS cc_start: 0.7644 (m-70) cc_final: 0.6909 (m170) REVERT: T 324 TYR cc_start: 0.9111 (m-80) cc_final: 0.8882 (m-80) REVERT: U 304 TYR cc_start: 0.8777 (m-80) cc_final: 0.7517 (m-80) REVERT: U 337 MET cc_start: 0.8025 (ttp) cc_final: 0.7659 (ttt) REVERT: U 502 TYR cc_start: 0.7126 (t80) cc_final: 0.6913 (t80) REVERT: U 550 LEU cc_start: 0.8411 (tp) cc_final: 0.8058 (tt) REVERT: V 307 CYS cc_start: 0.7943 (t) cc_final: 0.7622 (t) REVERT: X 153 GLN cc_start: 0.7096 (mm-40) cc_final: 0.6878 (mm-40) REVERT: Y 175 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.7621 (ttt180) REVERT: Y 385 ARG cc_start: 0.7391 (tpp80) cc_final: 0.6910 (ttm-80) REVERT: Y 502 MET cc_start: 0.6888 (mpp) cc_final: 0.6449 (ptm) REVERT: Y 541 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6795 (tp30) REVERT: Z 49 ASP cc_start: 0.7541 (m-30) cc_final: 0.7267 (m-30) REVERT: Z 82 ASP cc_start: 0.7715 (t70) cc_final: 0.7430 (t0) REVERT: Z 86 ARG cc_start: 0.8478 (ttt90) cc_final: 0.8235 (ttm170) REVERT: Z 448 GLN cc_start: 0.7544 (tm-30) cc_final: 0.7296 (tm-30) REVERT: Z 493 LYS cc_start: 0.8364 (mmtt) cc_final: 0.7968 (tttm) outliers start: 92 outliers final: 62 residues processed: 564 average time/residue: 0.4331 time to fit residues: 405.7705 Evaluate side-chains 512 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 448 time to evaluate : 3.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 175 GLU Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain T residue 152 ASN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 208 SER Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 368 ILE Chi-restraints excluded: chain X residue 420 LEU Chi-restraints excluded: chain X residue 537 VAL Chi-restraints excluded: chain X residue 572 LYS Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 295 SER Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 368 ILE Chi-restraints excluded: chain Z residue 383 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 355 optimal weight: 0.8980 chunk 242 optimal weight: 0.0000 chunk 6 optimal weight: 4.9990 chunk 318 optimal weight: 0.7980 chunk 176 optimal weight: 0.5980 chunk 364 optimal weight: 5.9990 chunk 295 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 218 optimal weight: 7.9990 chunk 383 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN D 94 ASN R 73 ASN T 179 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 337 GLN Y 204 HIS ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 250 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 34412 Z= 0.145 Angle : 0.557 13.678 46638 Z= 0.275 Chirality : 0.042 0.201 5519 Planarity : 0.004 0.045 5997 Dihedral : 6.077 83.886 4923 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.83 % Favored : 96.03 % Rotamer: Outliers : 2.55 % Allowed : 17.56 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.33 (0.12), residues: 4461 helix: -0.46 (0.11), residues: 2117 sheet: -1.14 (0.22), residues: 532 loop : -1.13 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 73 HIS 0.007 0.001 HIS S 250 PHE 0.029 0.001 PHE D 107 TYR 0.022 0.001 TYR G 102 ARG 0.007 0.000 ARG P 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 495 time to evaluate : 4.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6753 (tmm) cc_final: 0.6452 (tmm) REVERT: B 69 ILE cc_start: 0.7617 (mt) cc_final: 0.7222 (mt) REVERT: B 81 MET cc_start: 0.6450 (tpp) cc_final: 0.6246 (tpp) REVERT: B 98 GLN cc_start: 0.4765 (mm-40) cc_final: 0.4535 (tp40) REVERT: C 105 LEU cc_start: 0.7206 (tt) cc_final: 0.6686 (tp) REVERT: D 98 GLN cc_start: 0.7196 (mt0) cc_final: 0.6941 (mt0) REVERT: F 60 LYS cc_start: 0.7344 (ptmt) cc_final: 0.6717 (pptt) REVERT: F 105 LEU cc_start: 0.6388 (tt) cc_final: 0.5581 (mm) REVERT: F 109 LEU cc_start: 0.7926 (tp) cc_final: 0.7159 (tt) REVERT: G 61 MET cc_start: 0.6000 (OUTLIER) cc_final: 0.4965 (mmm) REVERT: G 94 ASN cc_start: 0.6800 (m110) cc_final: 0.6522 (t0) REVERT: G 126 PHE cc_start: 0.6488 (m-80) cc_final: 0.6169 (m-10) REVERT: I 105 LEU cc_start: 0.5333 (OUTLIER) cc_final: 0.5120 (mt) REVERT: J 111 GLU cc_start: 0.5517 (tp30) cc_final: 0.4419 (pp20) REVERT: P 140 ASN cc_start: 0.8345 (m-40) cc_final: 0.8070 (m-40) REVERT: Q 42 ARG cc_start: 0.6341 (ptp90) cc_final: 0.6027 (ptp90) REVERT: Q 71 LYS cc_start: 0.6637 (mttp) cc_final: 0.5578 (ttpp) REVERT: R 143 ASP cc_start: 0.6657 (OUTLIER) cc_final: 0.6339 (p0) REVERT: S 41 GLN cc_start: 0.7147 (mm-40) cc_final: 0.6583 (pp30) REVERT: S 204 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.7975 (pttt) REVERT: S 271 MET cc_start: 0.7419 (ttp) cc_final: 0.7158 (ttt) REVERT: T 139 HIS cc_start: 0.7665 (m-70) cc_final: 0.6950 (m170) REVERT: T 324 TYR cc_start: 0.9105 (m-80) cc_final: 0.8869 (m-80) REVERT: T 391 SER cc_start: 0.8714 (m) cc_final: 0.8228 (p) REVERT: U 304 TYR cc_start: 0.8771 (m-80) cc_final: 0.7511 (m-80) REVERT: U 483 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6440 (tpp) REVERT: U 550 LEU cc_start: 0.8395 (tp) cc_final: 0.8036 (tt) REVERT: V 307 CYS cc_start: 0.7893 (t) cc_final: 0.7418 (t) REVERT: X 346 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9094 (mt) REVERT: Y 175 ARG cc_start: 0.7998 (ttm-80) cc_final: 0.7657 (ttt180) REVERT: Y 411 LYS cc_start: 0.7678 (ttmt) cc_final: 0.7340 (tppt) REVERT: Y 502 MET cc_start: 0.6859 (mpp) cc_final: 0.6486 (ptm) REVERT: Z 448 GLN cc_start: 0.7596 (tm-30) cc_final: 0.7348 (tm-30) outliers start: 91 outliers final: 64 residues processed: 553 average time/residue: 0.4372 time to fit residues: 398.7677 Evaluate side-chains 511 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 441 time to evaluate : 3.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 175 GLU Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain T residue 122 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 522 GLU Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 208 SER Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 346 LEU Chi-restraints excluded: chain X residue 361 THR Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 420 LEU Chi-restraints excluded: chain X residue 537 VAL Chi-restraints excluded: chain X residue 572 LYS Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 295 SER Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 404 GLN 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: 0.5980 chunk 84 optimal weight: 8.9990 chunk 250 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 427 optimal weight: 4.9990 chunk 355 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 224 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN R 73 ASN T 179 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 549 HIS ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 199 ASN Y 398 ASN ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34412 Z= 0.182 Angle : 0.575 12.860 46638 Z= 0.284 Chirality : 0.043 0.214 5519 Planarity : 0.004 0.046 5997 Dihedral : 6.029 87.225 4923 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.92 % Favored : 95.97 % Rotamer: Outliers : 2.67 % Allowed : 18.10 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.09 (0.13), residues: 4461 helix: -0.27 (0.11), residues: 2129 sheet: -0.98 (0.23), residues: 526 loop : -1.03 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 73 HIS 0.007 0.001 HIS S 250 PHE 0.030 0.001 PHE D 107 TYR 0.023 0.001 TYR U 502 ARG 0.006 0.000 ARG P 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 465 time to evaluate : 4.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 LEU cc_start: 0.7220 (tt) cc_final: 0.6769 (tp) REVERT: D 56 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6486 (mp) REVERT: D 98 GLN cc_start: 0.7250 (mt0) cc_final: 0.6977 (mt0) REVERT: F 60 LYS cc_start: 0.7408 (ptmt) cc_final: 0.6638 (pptt) REVERT: F 105 LEU cc_start: 0.6427 (tt) cc_final: 0.5529 (mm) REVERT: G 61 MET cc_start: 0.5950 (OUTLIER) cc_final: 0.5074 (mmm) REVERT: G 94 ASN cc_start: 0.6808 (m110) cc_final: 0.6564 (t0) REVERT: G 126 PHE cc_start: 0.6592 (m-80) cc_final: 0.6259 (m-10) REVERT: I 105 LEU cc_start: 0.5350 (OUTLIER) cc_final: 0.5123 (mt) REVERT: J 111 GLU cc_start: 0.5269 (tp30) cc_final: 0.4306 (pp20) REVERT: P 75 TYR cc_start: 0.8426 (m-80) cc_final: 0.7692 (m-80) REVERT: P 134 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8240 (tt) REVERT: P 140 ASN cc_start: 0.8365 (m-40) cc_final: 0.8089 (m-40) REVERT: Q 42 ARG cc_start: 0.6386 (ptp90) cc_final: 0.6166 (ptp90) REVERT: Q 48 ARG cc_start: 0.7054 (ptt90) cc_final: 0.6834 (ptt-90) REVERT: Q 71 LYS cc_start: 0.6681 (mttp) cc_final: 0.5586 (ttpp) REVERT: R 143 ASP cc_start: 0.6663 (OUTLIER) cc_final: 0.6330 (p0) REVERT: S 41 GLN cc_start: 0.7191 (mm-40) cc_final: 0.6608 (pp30) REVERT: S 204 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7867 (pttt) REVERT: S 271 MET cc_start: 0.7484 (ttp) cc_final: 0.7167 (ttt) REVERT: T 139 HIS cc_start: 0.7708 (m-70) cc_final: 0.6952 (m170) REVERT: T 277 THR cc_start: 0.8235 (p) cc_final: 0.8017 (p) REVERT: T 324 TYR cc_start: 0.9123 (m-80) cc_final: 0.8872 (m-80) REVERT: T 391 SER cc_start: 0.8764 (m) cc_final: 0.8322 (p) REVERT: U 304 TYR cc_start: 0.8793 (m-80) cc_final: 0.7518 (m-80) REVERT: U 483 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.6676 (tpp) REVERT: U 502 TYR cc_start: 0.7166 (t80) cc_final: 0.6693 (t80) REVERT: U 550 LEU cc_start: 0.8424 (tp) cc_final: 0.8081 (tt) REVERT: V 307 CYS cc_start: 0.7878 (t) cc_final: 0.7422 (t) REVERT: Y 175 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7672 (ttt180) REVERT: Y 250 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7934 (mm-40) REVERT: Y 385 ARG cc_start: 0.7076 (tpp80) cc_final: 0.6569 (ttm-80) REVERT: Y 411 LYS cc_start: 0.7675 (ttmt) cc_final: 0.7399 (tppt) REVERT: Y 502 MET cc_start: 0.6821 (mpp) cc_final: 0.6401 (ptm) REVERT: Z 49 ASP cc_start: 0.7611 (m-30) cc_final: 0.7332 (m-30) REVERT: Z 484 MET cc_start: 0.7664 (mmm) cc_final: 0.7183 (mmm) outliers start: 95 outliers final: 67 residues processed: 527 average time/residue: 0.4240 time to fit residues: 373.2465 Evaluate side-chains 520 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 446 time to evaluate : 4.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 522 GLU Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain U residue 492 ILE Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 208 SER Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 361 THR Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 420 LEU Chi-restraints excluded: chain X residue 537 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 295 SER Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 368 ILE Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 404 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 412 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 243 optimal weight: 3.9990 chunk 312 optimal weight: 1.9990 chunk 241 optimal weight: 6.9990 chunk 359 optimal weight: 0.4980 chunk 238 optimal weight: 5.9990 chunk 426 optimal weight: 0.2980 chunk 266 optimal weight: 0.0070 chunk 259 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN H 98 GLN R 73 ASN T 152 ASN T 179 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 358 HIS ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 68 HIS ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34412 Z= 0.163 Angle : 0.564 12.710 46638 Z= 0.278 Chirality : 0.042 0.184 5519 Planarity : 0.004 0.044 5997 Dihedral : 5.921 88.792 4923 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.90 % Favored : 96.01 % Rotamer: Outliers : 2.64 % Allowed : 18.80 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.13), residues: 4461 helix: -0.14 (0.12), residues: 2129 sheet: -0.92 (0.23), residues: 530 loop : -0.93 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 73 HIS 0.007 0.001 HIS S 250 PHE 0.031 0.001 PHE A 107 TYR 0.017 0.001 TYR Q 16 ARG 0.005 0.000 ARG P 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 472 time to evaluate : 3.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6814 (tmm) cc_final: 0.6170 (tmm) REVERT: B 81 MET cc_start: 0.6077 (OUTLIER) cc_final: 0.5800 (tpp) REVERT: C 105 LEU cc_start: 0.7275 (tt) cc_final: 0.6756 (tp) REVERT: D 56 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6425 (mp) REVERT: D 98 GLN cc_start: 0.7036 (mt0) cc_final: 0.6759 (mt0) REVERT: E 56 LEU cc_start: 0.5807 (tt) cc_final: 0.5478 (mt) REVERT: F 60 LYS cc_start: 0.7326 (ptmt) cc_final: 0.6484 (pptt) REVERT: F 105 LEU cc_start: 0.6390 (tt) cc_final: 0.5573 (mm) REVERT: G 61 MET cc_start: 0.6030 (OUTLIER) cc_final: 0.5094 (mmm) REVERT: G 94 ASN cc_start: 0.6823 (m110) cc_final: 0.6581 (t0) REVERT: G 126 PHE cc_start: 0.6618 (m-80) cc_final: 0.6274 (m-10) REVERT: I 105 LEU cc_start: 0.5506 (OUTLIER) cc_final: 0.5305 (mt) REVERT: J 111 GLU cc_start: 0.5407 (tp30) cc_final: 0.4397 (pp20) REVERT: P 64 GLU cc_start: 0.7950 (mp0) cc_final: 0.7609 (mp0) REVERT: P 75 TYR cc_start: 0.8428 (m-80) cc_final: 0.7808 (m-80) REVERT: P 134 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8300 (tt) REVERT: P 140 ASN cc_start: 0.8388 (m-40) cc_final: 0.8097 (m-40) REVERT: Q 42 ARG cc_start: 0.6399 (ptp90) cc_final: 0.6115 (ptp90) REVERT: Q 71 LYS cc_start: 0.6677 (mttp) cc_final: 0.5562 (ttpp) REVERT: R 143 ASP cc_start: 0.6648 (OUTLIER) cc_final: 0.6333 (p0) REVERT: S 41 GLN cc_start: 0.7146 (mm-40) cc_final: 0.6598 (pp30) REVERT: S 204 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.7862 (pttt) REVERT: T 139 HIS cc_start: 0.7721 (m-70) cc_final: 0.6954 (m170) REVERT: T 324 TYR cc_start: 0.9108 (m-80) cc_final: 0.8858 (m-80) REVERT: T 391 SER cc_start: 0.8727 (m) cc_final: 0.8304 (p) REVERT: U 304 TYR cc_start: 0.8769 (m-80) cc_final: 0.7517 (m-80) REVERT: U 483 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.6651 (tpp) REVERT: U 541 LYS cc_start: 0.8210 (ptmt) cc_final: 0.7768 (ptpt) REVERT: V 307 CYS cc_start: 0.7883 (t) cc_final: 0.7414 (t) REVERT: V 482 GLU cc_start: 0.8267 (tp30) cc_final: 0.8038 (tp30) REVERT: Y 75 GLU cc_start: 0.7251 (tt0) cc_final: 0.6977 (tt0) REVERT: Y 175 ARG cc_start: 0.8019 (ttm-80) cc_final: 0.7685 (ttt180) REVERT: Y 250 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7903 (mm-40) REVERT: Y 411 LYS cc_start: 0.7666 (ttmt) cc_final: 0.7385 (tppt) REVERT: Y 502 MET cc_start: 0.6791 (mpp) cc_final: 0.6371 (ptm) REVERT: Z 49 ASP cc_start: 0.7584 (m-30) cc_final: 0.7368 (m-30) outliers start: 94 outliers final: 69 residues processed: 532 average time/residue: 0.4263 time to fit residues: 376.9699 Evaluate side-chains 525 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 448 time to evaluate : 3.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain T residue 152 ASN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 362 LEU Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain U residue 492 ILE Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 208 SER Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 361 THR Chi-restraints excluded: chain X residue 380 LEU Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 420 LEU Chi-restraints excluded: chain X residue 537 VAL Chi-restraints excluded: chain X residue 572 LYS Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 295 SER Chi-restraints excluded: chain Z residue 321 LEU Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 368 ILE Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 404 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 263 optimal weight: 0.8980 chunk 170 optimal weight: 10.0000 chunk 254 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 270 optimal weight: 4.9990 chunk 290 optimal weight: 1.9990 chunk 210 optimal weight: 0.0770 chunk 39 optimal weight: 0.5980 chunk 334 optimal weight: 0.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 77 GLN S 297 GLN T 179 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 34412 Z= 0.161 Angle : 0.570 12.896 46638 Z= 0.281 Chirality : 0.042 0.186 5519 Planarity : 0.004 0.052 5997 Dihedral : 5.843 83.965 4923 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.94 % Rotamer: Outliers : 2.55 % Allowed : 19.28 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.13), residues: 4461 helix: -0.02 (0.12), residues: 2121 sheet: -0.87 (0.23), residues: 530 loop : -0.89 (0.15), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 73 HIS 0.007 0.001 HIS S 250 PHE 0.047 0.001 PHE A 107 TYR 0.023 0.001 TYR U 502 ARG 0.008 0.000 ARG U 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 475 time to evaluate : 4.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6384 (mp) REVERT: D 61 MET cc_start: 0.6658 (OUTLIER) cc_final: 0.6435 (ptp) REVERT: D 98 GLN cc_start: 0.7035 (mt0) cc_final: 0.6768 (mt0) REVERT: E 56 LEU cc_start: 0.5791 (tt) cc_final: 0.5468 (mt) REVERT: F 60 LYS cc_start: 0.7033 (ptmt) cc_final: 0.6287 (pptt) REVERT: F 81 MET cc_start: 0.7143 (mmm) cc_final: 0.6820 (mmt) REVERT: G 61 MET cc_start: 0.6011 (OUTLIER) cc_final: 0.5054 (mmm) REVERT: G 94 ASN cc_start: 0.6796 (m110) cc_final: 0.6574 (t0) REVERT: G 126 PHE cc_start: 0.6630 (m-80) cc_final: 0.6281 (m-10) REVERT: J 111 GLU cc_start: 0.5355 (tp30) cc_final: 0.4220 (pp20) REVERT: P 64 GLU cc_start: 0.7955 (mp0) cc_final: 0.7703 (mp0) REVERT: P 134 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8329 (tt) REVERT: P 140 ASN cc_start: 0.8369 (m-40) cc_final: 0.8071 (m-40) REVERT: Q 42 ARG cc_start: 0.6354 (ptp90) cc_final: 0.6106 (ptp90) REVERT: Q 71 LYS cc_start: 0.6689 (mttp) cc_final: 0.5523 (ttpp) REVERT: R 143 ASP cc_start: 0.6715 (OUTLIER) cc_final: 0.6361 (p0) REVERT: S 41 GLN cc_start: 0.7124 (mm-40) cc_final: 0.6584 (pp30) REVERT: S 204 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.7827 (pttt) REVERT: S 274 MET cc_start: 0.7396 (mmp) cc_final: 0.7161 (mmp) REVERT: T 139 HIS cc_start: 0.7728 (m-70) cc_final: 0.6981 (m170) REVERT: T 324 TYR cc_start: 0.9102 (m-80) cc_final: 0.8857 (m-80) REVERT: T 391 SER cc_start: 0.8731 (m) cc_final: 0.8325 (p) REVERT: T 482 GLU cc_start: 0.8082 (tp30) cc_final: 0.7857 (tp30) REVERT: U 304 TYR cc_start: 0.8759 (m-80) cc_final: 0.7484 (m-80) REVERT: U 483 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.6620 (tpp) REVERT: U 541 LYS cc_start: 0.8130 (ptmt) cc_final: 0.7724 (ptpt) REVERT: V 307 CYS cc_start: 0.7868 (t) cc_final: 0.7405 (t) REVERT: Y 75 GLU cc_start: 0.7259 (tt0) cc_final: 0.6999 (tt0) REVERT: Y 175 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7773 (ttt180) REVERT: Y 411 LYS cc_start: 0.7656 (ttmt) cc_final: 0.7345 (tppt) REVERT: Y 502 MET cc_start: 0.6833 (mpp) cc_final: 0.6400 (ptm) REVERT: Z 49 ASP cc_start: 0.7587 (m-30) cc_final: 0.7375 (m-30) outliers start: 91 outliers final: 72 residues processed: 534 average time/residue: 0.4409 time to fit residues: 393.0783 Evaluate side-chains 529 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 450 time to evaluate : 4.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 152 ASN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 362 LEU Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain U residue 492 ILE Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 208 SER Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 361 THR Chi-restraints excluded: chain X residue 380 LEU Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 420 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 537 VAL Chi-restraints excluded: chain X residue 572 LYS Chi-restraints excluded: chain Y residue 82 ASP Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 295 SER Chi-restraints excluded: chain Z residue 321 LEU Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 404 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 387 optimal weight: 5.9990 chunk 408 optimal weight: 6.9990 chunk 372 optimal weight: 0.2980 chunk 396 optimal weight: 0.9990 chunk 238 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 311 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 358 optimal weight: 2.9990 chunk 375 optimal weight: 1.9990 chunk 395 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 179 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34412 Z= 0.185 Angle : 0.589 13.409 46638 Z= 0.288 Chirality : 0.043 0.188 5519 Planarity : 0.004 0.044 5997 Dihedral : 5.848 77.307 4923 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.63 % Rotamer: Outliers : 2.41 % Allowed : 19.81 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), residues: 4461 helix: -0.00 (0.12), residues: 2127 sheet: -0.86 (0.23), residues: 530 loop : -0.86 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 73 HIS 0.007 0.001 HIS S 250 PHE 0.026 0.001 PHE D 107 TYR 0.016 0.001 TYR G 102 ARG 0.008 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 451 time to evaluate : 3.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6685 (tmm) cc_final: 0.6128 (tmm) REVERT: D 56 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.6491 (mp) REVERT: D 98 GLN cc_start: 0.6958 (mt0) cc_final: 0.6657 (mt0) REVERT: E 56 LEU cc_start: 0.5863 (tt) cc_final: 0.5560 (mt) REVERT: F 60 LYS cc_start: 0.7073 (ptmt) cc_final: 0.6240 (pptt) REVERT: G 61 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.5049 (mmm) REVERT: G 94 ASN cc_start: 0.6817 (m110) cc_final: 0.6592 (t0) REVERT: G 126 PHE cc_start: 0.6685 (m-80) cc_final: 0.6334 (m-10) REVERT: J 111 GLU cc_start: 0.5162 (tp30) cc_final: 0.4108 (pp20) REVERT: P 64 GLU cc_start: 0.7982 (mp0) cc_final: 0.7754 (mp0) REVERT: P 134 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8350 (tt) REVERT: P 140 ASN cc_start: 0.8399 (m-40) cc_final: 0.8091 (m-40) REVERT: Q 71 LYS cc_start: 0.6709 (mttp) cc_final: 0.5543 (ttpp) REVERT: S 41 GLN cc_start: 0.7099 (mm-40) cc_final: 0.6579 (pp30) REVERT: S 204 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.7882 (pttt) REVERT: S 274 MET cc_start: 0.7514 (mmp) cc_final: 0.7242 (mmp) REVERT: T 139 HIS cc_start: 0.7738 (m-70) cc_final: 0.6983 (m170) REVERT: T 324 TYR cc_start: 0.9109 (m-80) cc_final: 0.8858 (m-80) REVERT: T 391 SER cc_start: 0.8752 (m) cc_final: 0.8347 (p) REVERT: T 482 GLU cc_start: 0.8116 (tp30) cc_final: 0.7900 (tp30) REVERT: U 304 TYR cc_start: 0.8777 (m-80) cc_final: 0.7583 (m-80) REVERT: U 483 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.6631 (tpp) REVERT: U 515 GLN cc_start: 0.6824 (tm-30) cc_final: 0.6474 (tm-30) REVERT: U 541 LYS cc_start: 0.8136 (ptmt) cc_final: 0.7706 (ptpt) REVERT: V 307 CYS cc_start: 0.7878 (t) cc_final: 0.7434 (t) REVERT: Y 75 GLU cc_start: 0.7262 (tt0) cc_final: 0.7006 (tt0) REVERT: Y 411 LYS cc_start: 0.7650 (ttmt) cc_final: 0.7343 (tppt) REVERT: Y 502 MET cc_start: 0.6844 (mpp) cc_final: 0.6343 (ptm) REVERT: Z 49 ASP cc_start: 0.7620 (m-30) cc_final: 0.7396 (m-30) outliers start: 86 outliers final: 72 residues processed: 505 average time/residue: 0.4276 time to fit residues: 360.9861 Evaluate side-chains 514 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 437 time to evaluate : 3.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 362 LEU Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain U residue 492 ILE Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 208 SER Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 361 THR Chi-restraints excluded: chain X residue 380 LEU Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 420 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 537 VAL Chi-restraints excluded: chain Y residue 82 ASP Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 409 ASP Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 295 SER Chi-restraints excluded: chain Z residue 321 LEU Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 404 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 260 optimal weight: 1.9990 chunk 419 optimal weight: 0.8980 chunk 256 optimal weight: 0.7980 chunk 199 optimal weight: 2.9990 chunk 291 optimal weight: 0.5980 chunk 440 optimal weight: 6.9990 chunk 405 optimal weight: 0.0770 chunk 350 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 270 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 ASN T 179 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 253 GLN ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 199 ASN ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 34412 Z= 0.157 Angle : 0.581 13.737 46638 Z= 0.282 Chirality : 0.042 0.188 5519 Planarity : 0.004 0.044 5997 Dihedral : 5.708 74.338 4923 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.15 % Favored : 95.79 % Rotamer: Outliers : 2.08 % Allowed : 20.12 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.13), residues: 4461 helix: 0.07 (0.12), residues: 2130 sheet: -0.78 (0.23), residues: 533 loop : -0.80 (0.15), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 73 HIS 0.007 0.001 HIS S 250 PHE 0.040 0.001 PHE A 107 TYR 0.031 0.001 TYR U 502 ARG 0.007 0.000 ARG U 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 463 time to evaluate : 4.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6781 (tmm) cc_final: 0.6218 (tmm) REVERT: D 56 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6107 (mt) REVERT: D 98 GLN cc_start: 0.6882 (mt0) cc_final: 0.6405 (tp-100) REVERT: E 56 LEU cc_start: 0.5854 (tt) cc_final: 0.5208 (mt) REVERT: F 60 LYS cc_start: 0.7101 (ptmt) cc_final: 0.6249 (pptt) REVERT: G 61 MET cc_start: 0.5959 (OUTLIER) cc_final: 0.4911 (mmm) REVERT: G 94 ASN cc_start: 0.6782 (m110) cc_final: 0.6567 (t0) REVERT: G 126 PHE cc_start: 0.6929 (m-80) cc_final: 0.6609 (m-10) REVERT: I 55 VAL cc_start: 0.5849 (t) cc_final: 0.5629 (p) REVERT: J 111 GLU cc_start: 0.5098 (tp30) cc_final: 0.4054 (pp20) REVERT: P 134 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8367 (tt) REVERT: P 140 ASN cc_start: 0.8435 (m-40) cc_final: 0.8084 (m110) REVERT: Q 16 TYR cc_start: 0.6777 (t80) cc_final: 0.6470 (t80) REVERT: Q 71 LYS cc_start: 0.6664 (mttp) cc_final: 0.5551 (ttpp) REVERT: S 41 GLN cc_start: 0.7077 (mm-40) cc_final: 0.6564 (pp30) REVERT: S 204 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.7850 (pttt) REVERT: T 139 HIS cc_start: 0.7724 (m-70) cc_final: 0.6974 (m170) REVERT: T 324 TYR cc_start: 0.9079 (m-80) cc_final: 0.8834 (m-80) REVERT: T 391 SER cc_start: 0.8733 (m) cc_final: 0.8343 (p) REVERT: U 304 TYR cc_start: 0.8749 (m-80) cc_final: 0.7564 (m-80) REVERT: U 483 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.6430 (tpp) REVERT: U 515 GLN cc_start: 0.6795 (tm-30) cc_final: 0.6468 (tm-30) REVERT: U 541 LYS cc_start: 0.8092 (ptmt) cc_final: 0.7671 (ptpt) REVERT: V 307 CYS cc_start: 0.7809 (t) cc_final: 0.7393 (t) REVERT: V 482 GLU cc_start: 0.8213 (tp30) cc_final: 0.8012 (tp30) REVERT: X 529 LYS cc_start: 0.8558 (tmtt) cc_final: 0.7765 (tptp) REVERT: Y 75 GLU cc_start: 0.7253 (tt0) cc_final: 0.6994 (tt0) REVERT: Y 411 LYS cc_start: 0.7629 (ttmt) cc_final: 0.7304 (tppt) REVERT: Y 502 MET cc_start: 0.6644 (mpp) cc_final: 0.6376 (ptm) REVERT: Z 49 ASP cc_start: 0.7589 (m-30) cc_final: 0.7360 (m-30) REVERT: Z 484 MET cc_start: 0.7588 (mmm) cc_final: 0.7142 (mmm) outliers start: 74 outliers final: 63 residues processed: 510 average time/residue: 0.4285 time to fit residues: 362.2347 Evaluate side-chains 517 residues out of total 3565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 449 time to evaluate : 3.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 362 LEU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain U residue 492 ILE Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 208 SER Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 361 THR Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 420 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 537 VAL Chi-restraints excluded: chain Y residue 82 ASP Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 295 SER Chi-restraints excluded: chain Z residue 321 LEU Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 404 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 278 optimal weight: 1.9990 chunk 373 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 323 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 351 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 360 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 179 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.135874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109193 restraints weight = 63481.647| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.92 r_work: 0.3306 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34412 Z= 0.214 Angle : 0.605 13.811 46638 Z= 0.297 Chirality : 0.043 0.188 5519 Planarity : 0.004 0.044 5997 Dihedral : 5.836 75.310 4923 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.51 % Favored : 95.38 % Rotamer: Outliers : 2.02 % Allowed : 20.34 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 4461 helix: 0.11 (0.12), residues: 2119 sheet: -0.78 (0.23), residues: 528 loop : -0.84 (0.15), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 73 HIS 0.007 0.001 HIS S 250 PHE 0.027 0.001 PHE D 107 TYR 0.030 0.001 TYR Q 16 ARG 0.008 0.000 ARG V 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8942.36 seconds wall clock time: 161 minutes 50.80 seconds (9710.80 seconds total)