Starting phenix.real_space_refine on Thu Feb 22 10:22:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re4_4841/02_2024/6re4_4841_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re4_4841/02_2024/6re4_4841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re4_4841/02_2024/6re4_4841.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re4_4841/02_2024/6re4_4841.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re4_4841/02_2024/6re4_4841_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re4_4841/02_2024/6re4_4841_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 116 5.16 5 C 21526 2.51 5 N 5790 2.21 5 O 6413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 111": "OE1" <-> "OE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 64": "OE1" <-> "OE2" Residue "P ASP 68": "OD1" <-> "OD2" Residue "P GLU 79": "OE1" <-> "OE2" Residue "P PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 142": "OE1" <-> "OE2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 25": "OD1" <-> "OD2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 64": "OE1" <-> "OE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 148": "OE1" <-> "OE2" Residue "R ASP 174": "OD1" <-> "OD2" Residue "R PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 177": "OE1" <-> "OE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 83": "OD1" <-> "OD2" Residue "S TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 133": "OE1" <-> "OE2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 214": "OD1" <-> "OD2" Residue "S ASP 222": "OD1" <-> "OD2" Residue "S TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S ASP 291": "OD1" <-> "OD2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ASP 125": "OD1" <-> "OD2" 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 ASP 237": "OD1" <-> "OD2" Residue "T TYR 256": "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 325": "OD1" <-> "OD2" Residue "T ASP 353": "OD1" <-> "OD2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 418": "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 PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 510": "OD1" <-> "OD2" Residue "T GLU 522": "OE1" <-> "OE2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ASP 41": "OD1" <-> "OD2" Residue "U ASP 46": "OD1" <-> "OD2" 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 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U ARG 342": "NH1" <-> "NH2" Residue "U ARG 343": "NH1" <-> "NH2" Residue "U ARG 364": "NH1" <-> "NH2" Residue "U GLU 371": "OE1" <-> "OE2" Residue "U PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 465": "OD1" <-> "OD2" 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 135": "OD1" <-> "OD2" 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 TYR 256": "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 PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ASP 326": "OD1" <-> "OD2" Residue "V ARG 335": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "V ARG 347": "NH1" <-> "NH2" Residue "V ARG 360": "NH1" <-> "NH2" Residue "V ASP 389": "OD1" <-> "OD2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 429": "NH1" <-> "NH2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X ARG 71": "NH1" <-> "NH2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X ASP 104": "OD1" <-> "OD2" Residue "X ARG 120": "NH1" <-> "NH2" Residue "X ASP 130": "OD1" <-> "OD2" Residue "X GLU 131": "OE1" <-> "OE2" Residue "X PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "X GLU 229": "OE1" <-> "OE2" Residue "X ARG 258": "NH1" <-> "NH2" Residue "X GLU 270": "OE1" <-> "OE2" Residue "X GLU 323": "OE1" <-> "OE2" Residue "X PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 359": "OD1" <-> "OD2" Residue "X ASP 378": "OD1" <-> "OD2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X ARG 401": "NH1" <-> "NH2" Residue "X TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 429": "OD1" <-> "OD2" Residue "X ARG 435": "NH1" <-> "NH2" Residue "X ARG 437": "NH1" <-> "NH2" Residue "X PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 505": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X ASP 513": "OD1" <-> "OD2" Residue "X GLU 519": "OE1" <-> "OE2" Residue "X ASP 523": "OD1" <-> "OD2" Residue "X GLU 541": "OE1" <-> "OE2" Residue "X PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 36": "OD1" <-> "OD2" Residue "Y TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y ASP 82": "OD1" <-> "OD2" Residue "Y ASP 136": "OD1" <-> "OD2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 156": "OE1" <-> "OE2" Residue "Y ASP 168": "OD1" <-> "OD2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 218": "NH1" <-> "NH2" Residue "Y ARG 225": "NH1" <-> "NH2" Residue "Y ARG 239": "NH1" <-> "NH2" Residue "Y TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 296": "OE1" <-> "OE2" Residue "Y TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 401": "NH1" <-> "NH2" Residue "Y ASP 429": "OD1" <-> "OD2" Residue "Y PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 479": "OD1" <-> "OD2" Residue "Y GLU 494": "OE1" <-> "OE2" Residue "Y ASP 500": "OD1" <-> "OD2" Residue "Y ASP 505": "OD1" <-> "OD2" Residue "Y ARG 509": "NH1" <-> "NH2" Residue "Y GLU 533": "OE1" <-> "OE2" Residue "Y GLU 540": "OE1" <-> "OE2" Residue "Y GLU 541": "OE1" <-> "OE2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z ASP 82": "OD1" <-> "OD2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "Z ARG 115": "NH1" <-> "NH2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z GLU 127": "OE1" <-> "OE2" Residue "Z ARG 145": "NH1" <-> "NH2" Residue "Z PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 258": "NH1" <-> "NH2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 317": "OD1" <-> "OD2" Residue "Z ASP 345": "OD1" <-> "OD2" Residue "Z ARG 366": "NH1" <-> "NH2" Residue "Z TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 378": "OD1" <-> "OD2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z GLU 451": "OE1" <-> "OE2" Residue "Z PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 513": "OD1" <-> "OD2" Residue "Z GLU 520": "OE1" <-> "OE2" Residue "Z ASP 523": "OD1" <-> "OD2" Residue "Z ASP 528": "OD1" <-> "OD2" Residue "Z ASP 542": "OD1" <-> "OD2" Residue "Z ASP 548": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33863 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: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 3961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3961 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" 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: "Y" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3952 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 497} Chain: "Z" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "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: "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} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.61, per 1000 atoms: 0.52 Number of scatterers: 33863 At special positions: 0 Unit cell: (164.268, 129.519, 207.441, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 13 15.00 Mg 5 11.99 O 6413 8.00 N 5790 7.00 C 21526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.40 Conformation dependent library (CDL) restraints added in 6.5 seconds 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8150 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 162 helices and 28 sheets defined 46.0% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.86 Creating SS restraints... Processing helix chain 'A' and resid 55 through 91 removed outlier: 3.542A pdb=" N CYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 125 removed outlier: 3.682A pdb=" N ALA A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LYS A 97 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL A 100 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU A 104 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 105 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 107 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 111 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 112 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 115 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU A 118 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 119 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 125 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.644A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 125 removed outlier: 3.553A pdb=" N ALA B 96 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LYS B 97 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 106 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU B 111 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU B 115 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 119 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU B 125 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 65 removed outlier: 4.001A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 91 removed outlier: 3.652A pdb=" N GLY C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY C 77 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 85 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG C 91 " --> pdb=" O GLY C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 125 removed outlier: 3.508A pdb=" N ALA C 96 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LYS C 97 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER C 112 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU C 119 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 125 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 91 removed outlier: 4.385A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 125 removed outlier: 3.545A pdb=" N ALA D 96 " --> pdb=" O PRO D 93 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS D 97 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL D 100 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR D 110 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 91 removed outlier: 4.520A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 126 removed outlier: 3.552A pdb=" N ALA E 96 " --> pdb=" O PRO E 93 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LYS E 97 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL E 100 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR E 110 " --> pdb=" O PHE E 107 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER E 112 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU E 119 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE E 124 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU E 125 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE E 126 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 91 removed outlier: 4.341A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 126 removed outlier: 3.526A pdb=" N ALA F 96 " --> pdb=" O PRO F 93 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL F 100 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU F 111 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE F 124 " --> pdb=" O VAL F 121 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE F 126 " --> pdb=" O LEU F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 89 removed outlier: 3.932A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 125 removed outlier: 3.502A pdb=" N ALA G 96 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL G 100 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU G 104 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR G 110 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU G 111 " --> pdb=" O ALA G 108 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER G 112 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU G 118 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU G 125 " --> pdb=" O PHE G 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 67 removed outlier: 4.286A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA H 64 " --> pdb=" O LYS H 60 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY H 65 " --> pdb=" O MET H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 91 removed outlier: 3.679A pdb=" N ARG H 91 " --> pdb=" O ASN H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 126 removed outlier: 5.146A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL H 100 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE H 107 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE H 113 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU H 125 " --> pdb=" O PHE H 122 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE H 126 " --> pdb=" O LEU H 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 67 removed outlier: 4.278A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 91 removed outlier: 3.503A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 124 removed outlier: 3.933A pdb=" N ALA I 96 " --> pdb=" O PRO I 93 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LYS I 97 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL I 100 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER I 112 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE I 124 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 91 removed outlier: 3.667A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 125 removed outlier: 3.612A pdb=" N VAL J 100 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY J 101 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 63 removed outlier: 3.921A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 83 removed outlier: 3.610A pdb=" N PHE P 77 " --> pdb=" O GLU P 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 92 removed outlier: 4.435A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 108 removed outlier: 3.579A pdb=" N THR P 102 " --> pdb=" O THR P 98 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER P 106 " --> pdb=" O THR P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 118 through 128 removed outlier: 3.871A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 148 removed outlier: 3.853A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU P 142 " --> pdb=" O VAL P 139 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU P 143 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU P 144 " --> pdb=" O TYR P 141 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA P 147 " --> pdb=" O LEU P 144 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 12 No H-bonds generated for 'chain 'Q' and resid 10 through 12' Processing helix chain 'Q' and resid 16 through 30 removed outlier: 3.739A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 39 removed outlier: 3.686A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 43 No H-bonds generated for 'chain 'Q' and resid 41 through 43' Processing helix chain 'R' and resid 30 through 38 removed outlier: 3.667A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 53 No H-bonds generated for 'chain 'R' and resid 51 through 53' Processing helix chain 'R' and resid 152 through 154 No H-bonds generated for 'chain 'R' and resid 152 through 154' Processing helix chain 'R' and resid 159 through 169 removed outlier: 4.189A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 193 removed outlier: 3.614A pdb=" N ALA R 190 " --> pdb=" O GLU R 186 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 78 removed outlier: 3.523A pdb=" N LYS S 55 " --> pdb=" O LYS S 51 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN S 70 " --> pdb=" O SER S 66 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 88 Processing helix chain 'S' and resid 116 through 130 Processing helix chain 'S' and resid 144 through 150 removed outlier: 3.819A pdb=" N GLN S 149 " --> pdb=" O LYS S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 182 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 273 removed outlier: 3.744A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 312 Processing helix chain 'T' and resid 135 through 137 No H-bonds generated for 'chain 'T' and resid 135 through 137' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 207 through 212 removed outlier: 3.509A pdb=" N ALA T 211 " --> pdb=" O LYS T 207 " (cutoff:3.500A) Processing helix chain 'T' and resid 231 through 247 removed outlier: 3.606A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 251 through 253 No H-bonds generated for 'chain 'T' and resid 251 through 253' Processing helix chain 'T' and resid 266 through 279 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 296 through 315 Proline residue: T 303 - end of helix removed outlier: 3.630A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 328 through 340 removed outlier: 3.663A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA T 333 " --> pdb=" O LYS T 329 " (cutoff:3.500A) Processing helix chain 'T' and resid 347 through 349 No H-bonds generated for 'chain 'T' and resid 347 through 349' Processing helix chain 'T' and resid 354 through 362 removed outlier: 3.834A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 399 Processing helix chain 'T' and resid 411 through 414 No H-bonds generated for 'chain 'T' and resid 411 through 414' Processing helix chain 'T' and resid 432 through 434 No H-bonds generated for 'chain 'T' and resid 432 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 446 through 456 Processing helix chain 'T' and resid 460 through 462 No H-bonds generated for 'chain 'T' and resid 460 through 462' Processing helix chain 'T' and resid 470 through 483 removed outlier: 3.814A pdb=" N GLU T 475 " --> pdb=" O GLN T 471 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 505 removed outlier: 4.012A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 514 through 527 removed outlier: 3.888A pdb=" N ILE T 517 " --> pdb=" O VAL T 514 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL T 518 " --> pdb=" O GLN T 515 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU T 521 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU T 522 " --> pdb=" O ALA T 519 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL T 524 " --> pdb=" O GLU T 521 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE T 525 " --> pdb=" O GLU T 522 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER T 526 " --> pdb=" O ALA T 523 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN T 527 " --> pdb=" O VAL T 524 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 539 removed outlier: 3.615A pdb=" N LYS T 534 " --> pdb=" O PRO T 530 " (cutoff:3.500A) Processing helix chain 'T' and resid 544 through 555 removed outlier: 3.860A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA T 552 " --> pdb=" O ALA T 548 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 49 No H-bonds generated for 'chain 'U' and resid 47 through 49' Processing helix chain 'U' and resid 59 through 64 removed outlier: 3.974A pdb=" N SER U 63 " --> pdb=" O ILE U 59 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 59 through 64' Processing helix chain 'U' and resid 66 through 71 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 207 through 212 Processing helix chain 'U' and resid 231 through 248 removed outlier: 3.945A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLN U 248 " --> pdb=" O ASN U 244 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 279 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 314 Proline residue: U 303 - end of helix removed outlier: 3.670A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG U 314 " --> pdb=" O ALA U 310 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 removed outlier: 3.807A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 347 through 349 No H-bonds generated for 'chain 'U' and resid 347 through 349' Processing helix chain 'U' and resid 354 through 364 removed outlier: 5.000A pdb=" N ARG U 364 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 393 through 401 Processing helix chain 'U' and resid 410 through 413 No H-bonds generated for 'chain 'U' and resid 410 through 413' Processing helix chain 'U' and resid 437 through 456 removed outlier: 4.074A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU U 455 " --> pdb=" O ALA U 451 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 484 removed outlier: 3.535A pdb=" N GLU U 482 " --> pdb=" O ALA U 478 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 505 Processing helix chain 'U' and resid 517 through 526 removed outlier: 4.095A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 531 through 539 removed outlier: 3.710A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 544 through 553 Processing helix chain 'V' and resid 46 through 48 No H-bonds generated for 'chain 'V' and resid 46 through 48' Processing helix chain 'V' and resid 58 through 66 removed outlier: 3.994A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 210 No H-bonds generated for 'chain 'V' and resid 207 through 210' Processing helix chain 'V' and resid 231 through 246 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: 3.727A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 340 Processing helix chain 'V' and resid 347 through 349 No H-bonds generated for 'chain 'V' and resid 347 through 349' Processing helix chain 'V' and resid 352 through 364 removed outlier: 4.347A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU V 363 " --> pdb=" O ARG V 360 " (cutoff:3.500A) Processing helix chain 'V' and resid 393 through 401 Processing helix chain 'V' and resid 431 through 434 removed outlier: 3.953A 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 439 through 456 removed outlier: 3.713A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 483 Processing helix chain 'V' and resid 494 through 505 removed outlier: 3.663A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) 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 520 through 527 Processing helix chain 'V' and resid 531 through 539 removed outlier: 3.802A pdb=" N ILE V 535 " --> pdb=" O ALA V 531 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA V 538 " --> pdb=" O LYS V 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 549 through 553 Processing helix chain 'X' and resid 115 through 117 No H-bonds generated for 'chain 'X' and resid 115 through 117' Processing helix chain 'X' and resid 165 through 170 Processing helix chain 'X' and resid 189 through 203 Processing helix chain 'X' and resid 217 through 230 Processing helix chain 'X' and resid 236 through 241 removed outlier: 4.939A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 255 through 258 No H-bonds generated for 'chain 'X' and resid 255 through 258' Processing helix chain 'X' and resid 261 through 274 removed outlier: 3.556A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 300 Processing helix chain 'X' and resid 314 through 324 removed outlier: 4.468A pdb=" N ARG X 324 " --> pdb=" O GLY X 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 342 through 344 No H-bonds generated for 'chain 'X' and resid 342 through 344' Processing helix chain 'X' and resid 349 through 354 Processing helix chain 'X' and resid 366 through 369 No H-bonds generated for 'chain 'X' and resid 366 through 369' Processing helix chain 'X' and resid 394 through 412 Processing helix chain 'X' and resid 427 through 442 Processing helix chain 'X' and resid 450 through 454 removed outlier: 3.510A pdb=" N PHE X 453 " --> pdb=" O ALA X 450 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR X 454 " --> pdb=" O GLU X 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 450 through 454' Processing helix chain 'X' and resid 463 through 474 removed outlier: 3.715A pdb=" N SER X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) Processing helix chain 'X' and resid 492 through 500 removed outlier: 3.910A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 532 Processing helix chain 'Y' and resid 150 through 152 No H-bonds generated for 'chain 'Y' and resid 150 through 152' Processing helix chain 'Y' and resid 165 through 170 Processing helix chain 'Y' and resid 191 through 203 removed outlier: 4.268A pdb=" N LYS Y 202 " --> pdb=" O ASN Y 198 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA Y 203 " --> pdb=" O ASN Y 199 " (cutoff:3.500A) Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 3.617A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 258 No H-bonds generated for 'chain 'Y' and resid 255 through 258' Processing helix chain 'Y' and resid 261 through 274 removed outlier: 3.747A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 297 removed outlier: 3.523A pdb=" N GLN Y 292 " --> pdb=" O ARG Y 289 " (cutoff:3.500A) Processing helix chain 'Y' and resid 314 through 324 removed outlier: 4.302A pdb=" N ARG Y 324 " --> pdb=" O GLY Y 320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 342 through 344 No H-bonds generated for 'chain 'Y' and resid 342 through 344' Processing helix chain 'Y' and resid 349 through 357 removed outlier: 4.577A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N HIS Y 357 " --> pdb=" O THR Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 370 Processing helix chain 'Y' and resid 395 through 419 removed outlier: 3.557A pdb=" N LEU Y 413 " --> pdb=" O ASP Y 409 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN Y 414 " --> pdb=" O TYR Y 410 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) Processing helix chain 'Y' and resid 422 through 424 No H-bonds generated for 'chain 'Y' and resid 422 through 424' Processing helix chain 'Y' and resid 427 through 443 removed outlier: 3.584A pdb=" N ALA Y 434 " --> pdb=" O LYS Y 430 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG Y 441 " --> pdb=" O ARG Y 437 " (cutoff:3.500A) Processing helix chain 'Y' and resid 463 through 475 Processing helix chain 'Y' and resid 492 through 503 removed outlier: 4.100A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) Processing helix chain 'Y' and resid 527 through 531 Processing helix chain 'Y' and resid 545 through 549 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 165 through 170 Processing helix chain 'Z' and resid 189 through 199 Processing helix chain 'Z' and resid 217 through 228 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 3.531A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 274 removed outlier: 3.601A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 288 through 298 removed outlier: 3.712A pdb=" N VAL Z 297 " --> pdb=" O ALA Z 293 " (cutoff:3.500A) Processing helix chain 'Z' and resid 314 through 324 removed outlier: 4.532A pdb=" N ARG Z 324 " --> pdb=" O GLY Z 320 " (cutoff:3.500A) Processing helix chain 'Z' and resid 342 through 344 No H-bonds generated for 'chain 'Z' and resid 342 through 344' Processing helix chain 'Z' and resid 349 through 353 Processing helix chain 'Z' and resid 366 through 369 No H-bonds generated for 'chain 'Z' and resid 366 through 369' Processing helix chain 'Z' and resid 394 through 417 removed outlier: 3.993A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) Processing helix chain 'Z' and resid 430 through 443 removed outlier: 3.695A pdb=" N LYS Z 438 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) Processing helix chain 'Z' and resid 463 through 475 Processing helix chain 'Z' and resid 492 through 505 removed outlier: 4.043A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS Z 501 " --> pdb=" O GLU Z 497 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 533 removed outlier: 3.900A pdb=" N VAL Z 531 " --> pdb=" O LEU Z 527 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'Q' and resid 45 through 50 removed outlier: 3.602A pdb=" N PHE Q 47 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'R' and resid 72 through 75 removed outlier: 6.883A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE R 144 " --> pdb=" O TYR R 75 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'R' and resid 96 through 100 removed outlier: 3.838A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 203 through 211 removed outlier: 5.082A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA S 161 " --> pdb=" O SER S 141 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'T' and resid 87 through 91 removed outlier: 6.490A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'T' and resid 152 through 155 Processing sheet with id= G, first strand: chain 'T' and resid 404 through 408 removed outlier: 3.881A 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: 8.770A pdb=" N ILE T 286 " --> pdb=" O VAL T 255 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N CYS T 257 " --> pdb=" O ILE T 286 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL T 288 " --> pdb=" O CYS T 257 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR T 259 " --> pdb=" O VAL T 288 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA T 290 " --> pdb=" O TYR T 259 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA T 261 " --> pdb=" O ALA T 290 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SER T 376 " --> pdb=" O GLY T 320 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE T 322 " --> pdb=" O SER T 376 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) removed outlier: 6.698A 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: 6.667A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= K, first strand: chain 'U' and resid 163 through 165 removed outlier: 8.246A pdb=" N THR U 164 " --> pdb=" O THR U 285 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N MET U 287 " --> pdb=" O THR U 164 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE U 380 " --> pdb=" O TYR U 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'U' and resid 405 through 408 removed outlier: 6.432A pdb=" N LEU U 222 " --> pdb=" O ILE U 406 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU U 408 " --> pdb=" O LEU U 222 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE U 224 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'U' and resid 107 through 111 removed outlier: 4.585A pdb=" N GLN U 149 " --> pdb=" O LEU U 108 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N CYS U 110 " --> pdb=" O THR U 147 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR U 147 " --> pdb=" O CYS U 110 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'V' and resid 143 through 145 removed outlier: 6.505A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLN V 149 " --> pdb=" O LEU V 108 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N CYS V 110 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR V 147 " --> pdb=" O CYS V 110 " (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 407 Processing sheet with id= Q, first strand: chain 'V' and resid 285 through 290 removed outlier: 8.914A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'X' and resid 38 through 44 removed outlier: 6.339A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (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: 8.519A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL X 213 " --> pdb=" O ASP X 285 " (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 37 through 39 removed outlier: 6.553A pdb=" N ARG Y 86 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N HIS Y 79 " --> pdb=" O THR Y 84 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR Y 84 " --> pdb=" O HIS Y 79 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ARG Y 51 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL Y 40 " --> pdb=" O ARG Y 51 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Y' and resid 110 through 113 Processing sheet with id= X, first strand: chain 'Y' and resid 360 through 363 removed outlier: 7.380A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N GLY Y 183 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL Y 339 " --> pdb=" O GLY Y 183 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE Y 207 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N PHE Y 283 " --> pdb=" O PHE Y 207 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ALA Y 211 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Z' and resid 38 through 44 removed outlier: 6.469A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Z' and resid 110 through 113 removed outlier: 3.708A pdb=" N ASP Z 139 " --> pdb=" O VAL Z 113 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Z' and resid 360 through 363 removed outlier: 7.345A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLY Z 183 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL Z 339 " --> pdb=" O GLY Z 183 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU Z 282 " --> pdb=" O THR Z 334 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR Z 245 " --> pdb=" O PHE Z 210 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLY Z 212 " --> pdb=" O THR Z 245 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL Z 247 " --> pdb=" O GLY Z 212 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Z' and resid 559 through 561 1400 hydrogen bonds defined for protein. 3405 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: 12.05 Time building geometry restraints manager: 14.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5776 1.31 - 1.44: 8165 1.44 - 1.56: 20222 1.56 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34384 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.94e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.83e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.82e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.470 -0.061 1.00e-02 1.00e+04 3.77e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.42e+01 ... (remaining 34379 not shown) Histogram of bond angle deviations from ideal: 95.50 - 103.69: 470 103.69 - 111.88: 16202 111.88 - 120.07: 15887 120.07 - 128.26: 13877 128.26 - 136.45: 162 Bond angle restraints: 46598 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 120.44 19.43 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " 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 136.83 120.35 16.48 1.00e+00 1.00e+00 2.72e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 123.56 16.31 1.00e+00 1.00e+00 2.66e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 120.55 16.28 1.00e+00 1.00e+00 2.65e+02 ... (remaining 46593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.08: 20200 31.08 - 62.17: 553 62.17 - 93.25: 48 93.25 - 124.33: 0 124.33 - 155.42: 2 Dihedral angle restraints: 20803 sinusoidal: 8060 harmonic: 12743 Sorted by residual: dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -128.54 -51.46 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual 180.00 -130.64 -49.36 0 5.00e+00 4.00e-02 9.74e+01 dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -132.37 -47.63 0 5.00e+00 4.00e-02 9.07e+01 ... (remaining 20800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3995 0.066 - 0.132: 1296 0.132 - 0.198: 197 0.198 - 0.264: 20 0.264 - 0.330: 5 Chirality restraints: 5513 Sorted by residual: chirality pdb=" CB VAL T 180 " pdb=" CA VAL T 180 " pdb=" CG1 VAL T 180 " pdb=" CG2 VAL T 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB THR Z 334 " pdb=" CA THR Z 334 " pdb=" OG1 THR Z 334 " pdb=" CG2 THR Z 334 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CG LEU Y 266 " pdb=" CB LEU Y 266 " pdb=" CD1 LEU Y 266 " pdb=" CD2 LEU Y 266 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 5510 not shown) Planarity restraints: 5991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Y 503 " 0.031 2.00e-02 2.50e+03 6.05e-02 3.66e+01 pdb=" C ALA Y 503 " -0.105 2.00e-02 2.50e+03 pdb=" O ALA Y 503 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS Y 504 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 5.97e-02 3.57e+01 pdb=" C ALA Z 503 " -0.103 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=" C THR T 543 " -0.052 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO T 544 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO T 544 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO T 544 " -0.043 5.00e-02 4.00e+02 ... (remaining 5988 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 331 2.58 - 3.16: 27309 3.16 - 3.74: 54292 3.74 - 4.32: 81099 4.32 - 4.90: 131669 Nonbonded interactions: 294700 Sorted by model distance: nonbonded pdb=" O ALA X 499 " pdb=" N ALA X 503 " model vdw 1.994 2.520 nonbonded pdb=" O ASN Z 514 " pdb=" CG2 VAL Z 517 " model vdw 2.031 3.460 nonbonded pdb=" O1G ATP T1001 " pdb="MG MG T1002 " model vdw 2.084 2.170 nonbonded pdb=" CD1 LEU E 78 " pdb=" OE2 GLU E 111 " model vdw 2.179 3.460 nonbonded pdb=" O ALA X 450 " pdb=" OG1 THR X 454 " model vdw 2.240 2.440 ... (remaining 294695 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 562 or resid 1001 through 1002)) selection = (chain 'V' and (resid 85 through 562 or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 552) selection = (chain 'Y' and resid 37 through 552) selection = (chain 'Z' and resid 37 through 552) } 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: 6.110 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: 0.020 Extract box with map and model: 25.290 Check model and map are aligned: 0.490 Set scattering table: 0.330 Process input model: 91.250 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.180 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:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.154 34384 Z= 0.789 Angle : 1.045 19.426 46598 Z= 0.594 Chirality : 0.063 0.330 5513 Planarity : 0.007 0.079 5991 Dihedral : 14.262 155.418 12653 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.69 % Favored : 95.09 % Rotamer: Outliers : 0.34 % Allowed : 6.57 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.10), residues: 4457 helix: -3.02 (0.08), residues: 2120 sheet: -1.43 (0.21), residues: 543 loop : -2.17 (0.13), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP Y 141 HIS 0.011 0.002 HIS T 549 PHE 0.038 0.003 PHE S 249 TYR 0.022 0.003 TYR V 324 ARG 0.011 0.001 ARG X 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 690 time to evaluate : 4.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 VAL cc_start: 0.8049 (t) cc_final: 0.7773 (t) REVERT: H 123 LEU cc_start: 0.7847 (mp) cc_final: 0.7538 (mp) REVERT: P 140 ASN cc_start: 0.8511 (m-40) cc_final: 0.8240 (m110) REVERT: P 149 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7945 (pptt) REVERT: R 31 LYS cc_start: 0.7867 (tmtt) cc_final: 0.7661 (tmtt) REVERT: R 40 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7717 (mtpt) REVERT: S 303 GLU cc_start: 0.7591 (mp0) cc_final: 0.7170 (mm-30) REVERT: U 348 GLU cc_start: 0.7289 (mt-10) cc_final: 0.7048 (mt-10) REVERT: V 311 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7386 (mt-10) REVERT: V 471 GLN cc_start: 0.7636 (tt0) cc_final: 0.7350 (mm-40) REVERT: Z 90 MET cc_start: 0.8852 (mmp) cc_final: 0.8385 (mmt) REVERT: Z 437 ARG cc_start: 0.8447 (mtt-85) cc_final: 0.8193 (mtt-85) REVERT: Z 440 GLN cc_start: 0.8109 (mt0) cc_final: 0.7860 (mt0) outliers start: 12 outliers final: 7 residues processed: 701 average time/residue: 1.4744 time to fit residues: 1238.5437 Evaluate side-chains 446 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 439 time to evaluate : 3.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 372 optimal weight: 0.9990 chunk 334 optimal weight: 10.0000 chunk 185 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 225 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 345 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 chunk 400 optimal weight: 7.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 98 GLN F 98 GLN G 98 GLN P 59 GLN P 66 GLN P 76 GLN Q 46 HIS Q 49 GLN R 38 ASN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN R 137 HIS R 154 GLN R 178 GLN R 181 ASN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 149 GLN S 262 ASN S 267 HIS T 152 ASN T 241 HIS T 264 GLN T 358 HIS T 441 GLN ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 64 GLN U 179 ASN U 242 GLN U 246 ASN U 248 GLN U 264 GLN U 319 HIS U 386 GLN U 539 ASN V 152 ASN V 179 ASN V 241 HIS V 244 ASN V 386 GLN V 452 GLN V 486 GLN V 488 GLN V 497 GLN V 527 GLN X 144 HIS X 199 ASN X 278 GLN X 294 ASN X 414 GLN Y 157 GLN Y 174 GLN Y 199 ASN Y 278 GLN Z 157 GLN Z 174 GLN Z 278 GLN Z 398 ASN Z 408 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34384 Z= 0.202 Angle : 0.577 11.858 46598 Z= 0.299 Chirality : 0.043 0.174 5513 Planarity : 0.005 0.060 5991 Dihedral : 7.223 133.864 4922 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.03 % Favored : 96.81 % Rotamer: Outliers : 3.34 % Allowed : 14.80 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.12), residues: 4457 helix: -1.41 (0.10), residues: 2141 sheet: -1.04 (0.21), residues: 558 loop : -1.57 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 141 HIS 0.004 0.001 HIS T 549 PHE 0.019 0.001 PHE B 107 TYR 0.016 0.001 TYR U 414 ARG 0.007 0.000 ARG Y 385 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 534 time to evaluate : 3.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 60 LYS cc_start: 0.7212 (mtmm) cc_final: 0.6896 (mtmm) REVERT: P 49 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7884 (m) REVERT: P 149 LYS cc_start: 0.8300 (mtmt) cc_final: 0.7996 (pptt) REVERT: Q 43 GLN cc_start: 0.7893 (mt0) cc_final: 0.7645 (mm110) REVERT: R 127 PHE cc_start: 0.8404 (m-80) cc_final: 0.8200 (m-80) REVERT: S 96 ASN cc_start: 0.7358 (m-40) cc_final: 0.7132 (m110) REVERT: U 199 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7142 (mpt180) REVERT: U 348 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7145 (mt-10) REVERT: U 521 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6046 (pp20) REVERT: V 452 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7301 (mp-120) REVERT: V 471 GLN cc_start: 0.7566 (tt0) cc_final: 0.6890 (mm110) REVERT: X 474 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7539 (mt) REVERT: Y 51 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7765 (ttm-80) REVERT: Z 90 MET cc_start: 0.8760 (mmp) cc_final: 0.8357 (mmt) REVERT: Z 440 GLN cc_start: 0.7904 (mt0) cc_final: 0.7564 (mt0) outliers start: 119 outliers final: 45 residues processed: 609 average time/residue: 1.3278 time to fit residues: 987.2056 Evaluate side-chains 490 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 439 time to evaluate : 3.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 66 CYS Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 35 GLU Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 428 SER Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 199 ARG Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 521 GLU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 452 GLN Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 217 THR Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 474 LEU Chi-restraints excluded: chain Z residue 545 LEU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 222 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 333 optimal weight: 0.0770 chunk 272 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 401 optimal weight: 0.6980 chunk 433 optimal weight: 2.9990 chunk 357 optimal weight: 1.9990 chunk 397 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 321 optimal weight: 10.0000 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 92 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 ASN J 92 ASN P 59 GLN P 71 GLN P 76 GLN P 140 ASN Q 43 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN S 149 GLN S 267 HIS T 121 ASN U 179 ASN U 196 GLN U 549 HIS V 488 GLN V 527 GLN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 414 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34384 Z= 0.191 Angle : 0.544 11.202 46598 Z= 0.279 Chirality : 0.042 0.176 5513 Planarity : 0.004 0.054 5991 Dihedral : 6.632 128.522 4920 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.54 % Favored : 96.30 % Rotamer: Outliers : 3.82 % Allowed : 17.41 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.12), residues: 4457 helix: -0.88 (0.11), residues: 2161 sheet: -0.83 (0.22), residues: 564 loop : -1.18 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 37 HIS 0.004 0.001 HIS Z 396 PHE 0.020 0.001 PHE B 107 TYR 0.016 0.001 TYR U 414 ARG 0.006 0.000 ARG Z 441 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 494 time to evaluate : 4.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 111 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6568 (mm-30) REVERT: G 116 PHE cc_start: 0.5540 (OUTLIER) cc_final: 0.4845 (t80) REVERT: G 123 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7464 (mt) REVERT: I 60 LYS cc_start: 0.7275 (mtmm) cc_final: 0.6826 (mtmm) REVERT: J 61 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6339 (mmp) REVERT: P 49 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7748 (m) REVERT: P 66 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.7069 (tp40) REVERT: P 83 GLN cc_start: 0.6400 (OUTLIER) cc_final: 0.5724 (mp10) REVERT: P 149 LYS cc_start: 0.8342 (mtmt) cc_final: 0.7951 (pptt) REVERT: S 96 ASN cc_start: 0.7364 (m-40) cc_final: 0.7108 (m110) REVERT: S 147 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7160 (ppt90) REVERT: S 220 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8232 (mm) REVERT: T 414 TYR cc_start: 0.6683 (t80) cc_final: 0.6448 (t80) REVERT: T 487 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7779 (mtmm) REVERT: U 199 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7005 (mpt180) REVERT: U 348 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7142 (mt-10) REVERT: U 483 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6576 (tpp) REVERT: U 521 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6064 (pp20) REVERT: U 522 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7547 (tp30) REVERT: V 405 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7294 (mp10) REVERT: V 471 GLN cc_start: 0.7494 (tt0) cc_final: 0.7032 (mm110) REVERT: V 549 HIS cc_start: 0.7741 (OUTLIER) cc_final: 0.7449 (m-70) REVERT: X 474 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7543 (mt) REVERT: Y 51 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7825 (ttm-80) REVERT: Y 480 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7320 (p0) REVERT: Z 90 MET cc_start: 0.8749 (mmp) cc_final: 0.8384 (mmt) REVERT: Z 440 GLN cc_start: 0.7955 (mt0) cc_final: 0.7615 (mt0) outliers start: 136 outliers final: 53 residues processed: 577 average time/residue: 1.3112 time to fit residues: 926.2809 Evaluate side-chains 486 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 415 time to evaluate : 4.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 61 MET Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 83 GLN Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 147 ARG Chi-restraints excluded: chain S residue 218 LYS Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 428 SER Chi-restraints excluded: chain T residue 487 LYS Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 521 GLU Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 199 ARG Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 521 GLU Chi-restraints excluded: chain U residue 522 GLU Chi-restraints excluded: chain V residue 52 LYS Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 420 LEU Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 396 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 269 optimal weight: 10.0000 chunk 402 optimal weight: 6.9990 chunk 426 optimal weight: 10.0000 chunk 210 optimal weight: 0.6980 chunk 381 optimal weight: 0.8980 chunk 114 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN J 98 GLN P 76 GLN P 140 ASN Q 43 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 70 ASN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 149 GLN S 267 HIS T 121 ASN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 152 ASN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 452 GLN V 488 GLN V 527 GLN X 241 ASN X 574 ASN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 34384 Z= 0.379 Angle : 0.620 9.295 46598 Z= 0.318 Chirality : 0.046 0.170 5513 Planarity : 0.005 0.050 5991 Dihedral : 6.954 121.906 4920 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.06 % Favored : 95.76 % Rotamer: Outliers : 5.03 % Allowed : 18.23 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.12), residues: 4457 helix: -0.79 (0.11), residues: 2154 sheet: -0.92 (0.22), residues: 570 loop : -1.02 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 37 HIS 0.005 0.001 HIS S 250 PHE 0.028 0.002 PHE G 107 TYR 0.017 0.002 TYR V 324 ARG 0.007 0.001 ARG Y 385 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 443 time to evaluate : 3.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8053 (mp) REVERT: E 95 ILE cc_start: 0.8073 (pt) cc_final: 0.7803 (mm) REVERT: G 123 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7529 (mt) REVERT: I 60 LYS cc_start: 0.7399 (mtmm) cc_final: 0.6902 (mtmm) REVERT: J 60 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6735 (tppp) REVERT: J 61 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.7105 (mmt) REVERT: P 49 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7844 (m) REVERT: P 66 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.7116 (tp40) REVERT: P 83 GLN cc_start: 0.6447 (OUTLIER) cc_final: 0.5289 (mp10) REVERT: P 149 LYS cc_start: 0.8422 (mtmt) cc_final: 0.7855 (pptt) REVERT: Q 43 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7924 (tp40) REVERT: S 96 ASN cc_start: 0.7795 (m-40) cc_final: 0.7406 (m110) REVERT: S 147 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7188 (ppt90) REVERT: S 220 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8254 (mm) REVERT: T 287 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7550 (tpp) REVERT: T 487 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7747 (mtmm) REVERT: U 521 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6145 (pp20) REVERT: U 522 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7603 (tp30) REVERT: V 452 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7309 (mp-120) REVERT: V 471 GLN cc_start: 0.7557 (tt0) cc_final: 0.7169 (mm110) REVERT: V 549 HIS cc_start: 0.7849 (OUTLIER) cc_final: 0.7439 (m-70) REVERT: X 474 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7435 (mm) REVERT: Y 51 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7785 (ttm-80) REVERT: Z 90 MET cc_start: 0.8879 (mmp) cc_final: 0.8347 (mmt) REVERT: Z 395 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: Z 440 GLN cc_start: 0.8086 (mt0) cc_final: 0.7736 (mt0) outliers start: 179 outliers final: 76 residues processed: 555 average time/residue: 1.2984 time to fit residues: 887.4348 Evaluate side-chains 487 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 392 time to evaluate : 4.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 61 MET Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 83 GLN Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 35 GLU Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 147 ARG Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 260 LEU Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 200 GLU Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 428 SER Chi-restraints excluded: chain T residue 430 VAL Chi-restraints excluded: chain T residue 487 LYS Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 521 GLU Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain T residue 546 LEU Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 521 GLU Chi-restraints excluded: chain U residue 522 GLU Chi-restraints excluded: chain U residue 528 VAL Chi-restraints excluded: chain V residue 52 LYS Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 421 LEU Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 452 GLN Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain V residue 559 LEU Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 416 ILE Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 420 LEU Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 546 GLU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 217 THR Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 395 GLU Chi-restraints excluded: chain Z residue 489 VAL Chi-restraints excluded: chain Z residue 545 LEU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 355 optimal weight: 2.9990 chunk 241 optimal weight: 0.8980 chunk 6 optimal weight: 0.0670 chunk 317 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 363 optimal weight: 3.9990 chunk 294 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 chunk 382 optimal weight: 1.9990 chunk 107 optimal weight: 0.0060 overall best weight: 0.4934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 98 GLN P 140 ASN Q 43 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 149 GLN T 441 GLN U 152 ASN ** U 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 405 GLN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 452 GLN V 488 GLN V 527 GLN Z 42 GLN ** Z 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 34384 Z= 0.148 Angle : 0.522 10.550 46598 Z= 0.266 Chirality : 0.041 0.170 5513 Planarity : 0.004 0.044 5991 Dihedral : 6.325 123.372 4920 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.28 % Favored : 96.59 % Rotamer: Outliers : 3.54 % Allowed : 20.36 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.13), residues: 4457 helix: -0.42 (0.11), residues: 2151 sheet: -0.60 (0.22), residues: 566 loop : -0.87 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP U 73 HIS 0.004 0.001 HIS Z 396 PHE 0.012 0.001 PHE J 107 TYR 0.018 0.001 TYR R 54 ARG 0.010 0.000 ARG Y 385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 467 time to evaluate : 4.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 111 GLU cc_start: 0.6041 (OUTLIER) cc_final: 0.5794 (tt0) REVERT: E 95 ILE cc_start: 0.7951 (pt) cc_final: 0.7741 (mm) REVERT: F 123 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6500 (tp) REVERT: G 123 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7589 (mt) REVERT: I 60 LYS cc_start: 0.7366 (mtmm) cc_final: 0.6931 (mtmm) REVERT: I 81 MET cc_start: 0.8351 (ttp) cc_final: 0.8142 (ttm) REVERT: P 49 THR cc_start: 0.7940 (OUTLIER) cc_final: 0.7694 (m) REVERT: P 83 GLN cc_start: 0.6531 (OUTLIER) cc_final: 0.5280 (mp10) REVERT: P 149 LYS cc_start: 0.8426 (mtmt) cc_final: 0.7881 (pptt) REVERT: S 96 ASN cc_start: 0.7539 (m-40) cc_final: 0.7137 (m110) REVERT: S 147 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7073 (ppt90) REVERT: S 220 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8101 (mm) REVERT: T 487 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7782 (mtmm) REVERT: T 543 THR cc_start: 0.7445 (OUTLIER) cc_final: 0.7104 (p) REVERT: U 483 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6787 (tpp) REVERT: U 522 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7559 (tp30) REVERT: V 471 GLN cc_start: 0.7511 (tt0) cc_final: 0.7184 (mm110) REVERT: V 549 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.7602 (m-70) REVERT: X 474 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7580 (mt) REVERT: Y 51 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7783 (ttm-80) REVERT: Y 480 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7359 (p0) REVERT: Z 90 MET cc_start: 0.8755 (mmp) cc_final: 0.8445 (mmt) REVERT: Z 440 GLN cc_start: 0.7952 (mt0) cc_final: 0.7602 (mt0) outliers start: 126 outliers final: 44 residues processed: 553 average time/residue: 1.2989 time to fit residues: 880.8032 Evaluate side-chains 476 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 417 time to evaluate : 3.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 83 GLN Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 147 ARG Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 428 SER Chi-restraints excluded: chain T residue 487 LYS Chi-restraints excluded: chain T residue 521 GLU Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 522 GLU Chi-restraints excluded: chain U residue 528 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 488 MET Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 420 LEU Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 143 optimal weight: 0.8980 chunk 383 optimal weight: 0.0040 chunk 84 optimal weight: 9.9990 chunk 250 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 426 optimal weight: 1.9990 chunk 354 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 224 optimal weight: 0.0980 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 66 GLN P 140 ASN Q 43 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 72 GLN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 149 GLN S 267 HIS ** T 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 452 GLN V 488 GLN V 527 GLN X 250 GLN X 414 GLN Z 157 GLN Z 241 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34384 Z= 0.218 Angle : 0.548 9.826 46598 Z= 0.278 Chirality : 0.043 0.169 5513 Planarity : 0.004 0.049 5991 Dihedral : 6.288 119.135 4920 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.63 % Favored : 96.23 % Rotamer: Outliers : 3.90 % Allowed : 21.06 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.13), residues: 4457 helix: -0.28 (0.11), residues: 2144 sheet: -0.58 (0.22), residues: 562 loop : -0.77 (0.15), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 37 HIS 0.003 0.001 HIS T 139 PHE 0.030 0.001 PHE G 107 TYR 0.025 0.001 TYR V 453 ARG 0.011 0.000 ARG Y 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 427 time to evaluate : 4.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7986 (mp) REVERT: C 116 PHE cc_start: 0.7639 (m-10) cc_final: 0.7396 (m-10) REVERT: G 116 PHE cc_start: 0.5484 (OUTLIER) cc_final: 0.4896 (t80) REVERT: G 123 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7624 (mt) REVERT: I 60 LYS cc_start: 0.7340 (mtmm) cc_final: 0.6942 (mtmm) REVERT: P 49 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.7702 (m) REVERT: P 83 GLN cc_start: 0.6410 (OUTLIER) cc_final: 0.5214 (mp10) REVERT: Q 43 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7618 (tp40) REVERT: S 96 ASN cc_start: 0.7563 (m-40) cc_final: 0.7157 (m110) REVERT: S 147 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.7065 (ppt90) REVERT: S 220 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8153 (mm) REVERT: T 287 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7460 (tpp) REVERT: T 487 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7820 (mtmm) REVERT: U 521 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6196 (pp20) REVERT: U 522 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7539 (tp30) REVERT: V 471 GLN cc_start: 0.7561 (tt0) cc_final: 0.7213 (mm110) REVERT: V 549 HIS cc_start: 0.7916 (OUTLIER) cc_final: 0.7579 (m-70) REVERT: X 474 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7574 (mt) REVERT: Y 51 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7763 (ttm-80) REVERT: Z 90 MET cc_start: 0.8829 (mmp) cc_final: 0.8375 (mmt) REVERT: Z 440 GLN cc_start: 0.7991 (mt0) cc_final: 0.7647 (mt0) outliers start: 139 outliers final: 68 residues processed: 524 average time/residue: 1.2713 time to fit residues: 821.2107 Evaluate side-chains 490 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 407 time to evaluate : 3.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 83 GLN Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 35 GLU Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 147 ARG Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 200 GLU Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 428 SER Chi-restraints excluded: chain T residue 487 LYS Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 517 ILE Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 546 LEU Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 521 GLU Chi-restraints excluded: chain U residue 522 GLU Chi-restraints excluded: chain U residue 528 VAL Chi-restraints excluded: chain V residue 52 LYS Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 421 LEU Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 464 SER Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Y residue 546 GLU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 411 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 243 optimal weight: 2.9990 chunk 311 optimal weight: 0.7980 chunk 241 optimal weight: 2.9990 chunk 359 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 425 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 259 optimal weight: 0.4980 chunk 196 optimal weight: 0.0370 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN P 66 GLN P 140 ASN Q 43 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN S 72 GLN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 149 GLN T 405 GLN T 471 GLN U 152 ASN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 452 GLN V 488 GLN V 527 GLN X 250 GLN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34384 Z= 0.178 Angle : 0.532 10.026 46598 Z= 0.270 Chirality : 0.042 0.165 5513 Planarity : 0.004 0.046 5991 Dihedral : 6.124 118.022 4919 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.28 % Favored : 96.59 % Rotamer: Outliers : 3.71 % Allowed : 21.54 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 4457 helix: -0.13 (0.11), residues: 2145 sheet: -0.49 (0.23), residues: 561 loop : -0.69 (0.15), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 37 HIS 0.003 0.001 HIS Z 396 PHE 0.034 0.001 PHE G 107 TYR 0.019 0.001 TYR V 453 ARG 0.011 0.000 ARG Y 385 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 436 time to evaluate : 3.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 PHE cc_start: 0.7625 (m-10) cc_final: 0.7376 (m-10) REVERT: G 123 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7803 (mt) REVERT: I 60 LYS cc_start: 0.7320 (mtmm) cc_final: 0.6912 (mtmm) REVERT: J 61 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6322 (mmp) REVERT: P 49 THR cc_start: 0.7757 (OUTLIER) cc_final: 0.7480 (m) REVERT: P 83 GLN cc_start: 0.6352 (OUTLIER) cc_final: 0.5129 (mp10) REVERT: Q 25 ASP cc_start: 0.7084 (m-30) cc_final: 0.6590 (m-30) REVERT: Q 32 LYS cc_start: 0.6704 (mttp) cc_final: 0.6491 (mttp) REVERT: S 48 ARG cc_start: 0.7374 (ptm160) cc_final: 0.6934 (mtp-110) REVERT: S 96 ASN cc_start: 0.7507 (m-40) cc_final: 0.7095 (m110) REVERT: S 147 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.7122 (ppt90) REVERT: S 220 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8142 (mm) REVERT: S 259 MET cc_start: 0.8405 (ptm) cc_final: 0.8143 (ttp) REVERT: T 287 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7493 (tpp) REVERT: T 487 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7822 (mtmm) REVERT: T 543 THR cc_start: 0.7350 (OUTLIER) cc_final: 0.7096 (p) REVERT: U 521 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.6168 (pp20) REVERT: U 522 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7532 (tp30) REVERT: V 452 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7220 (mp-120) REVERT: V 471 GLN cc_start: 0.7566 (tt0) cc_final: 0.7232 (mm110) REVERT: V 549 HIS cc_start: 0.7922 (OUTLIER) cc_final: 0.7572 (m-70) REVERT: X 474 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7594 (mt) REVERT: Y 51 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7789 (ttm-80) REVERT: Z 90 MET cc_start: 0.8792 (mmp) cc_final: 0.8404 (mmt) REVERT: Z 440 GLN cc_start: 0.7972 (mt0) cc_final: 0.7641 (mt0) outliers start: 132 outliers final: 73 residues processed: 524 average time/residue: 1.2915 time to fit residues: 832.1937 Evaluate side-chains 501 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 413 time to evaluate : 3.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 61 MET Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 83 GLN Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 35 GLU Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 147 ARG Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 200 GLU Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 409 GLU Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 428 SER Chi-restraints excluded: chain T residue 487 LYS Chi-restraints excluded: chain T residue 517 ILE Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 546 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 455 GLU Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 521 GLU Chi-restraints excluded: chain U residue 522 GLU Chi-restraints excluded: chain U residue 528 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 421 LEU Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 452 GLN Chi-restraints excluded: chain V residue 464 SER Chi-restraints excluded: chain V residue 516 ASP Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 488 MET Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 419 ILE Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Y residue 546 GLU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 262 optimal weight: 0.9980 chunk 169 optimal weight: 0.5980 chunk 253 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 270 optimal weight: 6.9990 chunk 289 optimal weight: 5.9990 chunk 210 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 334 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 GLN P 66 GLN P 140 ASN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN S 149 GLN U 152 ASN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 488 GLN V 527 GLN X 250 GLN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34384 Z= 0.182 Angle : 0.543 13.734 46598 Z= 0.273 Chirality : 0.042 0.232 5513 Planarity : 0.004 0.051 5991 Dihedral : 6.059 116.235 4919 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.50 % Favored : 96.37 % Rotamer: Outliers : 3.54 % Allowed : 21.96 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 4457 helix: -0.05 (0.11), residues: 2141 sheet: -0.46 (0.22), residues: 571 loop : -0.62 (0.16), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 37 HIS 0.003 0.001 HIS Z 396 PHE 0.035 0.001 PHE G 107 TYR 0.021 0.001 TYR T 414 ARG 0.012 0.000 ARG Y 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 434 time to evaluate : 4.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 PHE cc_start: 0.7632 (m-10) cc_final: 0.7407 (m-10) REVERT: F 60 LYS cc_start: 0.6177 (tptp) cc_final: 0.5886 (tptp) REVERT: G 123 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7860 (mt) REVERT: I 60 LYS cc_start: 0.7255 (mtmm) cc_final: 0.6839 (mtmm) REVERT: J 61 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6236 (mmp) REVERT: P 49 THR cc_start: 0.7836 (OUTLIER) cc_final: 0.7567 (m) REVERT: S 48 ARG cc_start: 0.7359 (ptm160) cc_final: 0.6929 (mtp-110) REVERT: S 96 ASN cc_start: 0.7456 (m-40) cc_final: 0.7055 (m110) REVERT: S 147 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.7046 (ppt90) REVERT: S 220 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8121 (mm) REVERT: S 259 MET cc_start: 0.8387 (ptm) cc_final: 0.8083 (ttp) REVERT: S 303 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: T 487 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7820 (mtmm) REVERT: T 543 THR cc_start: 0.7373 (OUTLIER) cc_final: 0.7107 (p) REVERT: U 407 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6839 (m-80) REVERT: U 483 MET cc_start: 0.6909 (tpp) cc_final: 0.6539 (tpp) REVERT: U 521 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6045 (pp20) REVERT: U 522 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7526 (tp30) REVERT: V 452 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.6537 (mt0) REVERT: V 471 GLN cc_start: 0.7587 (tt0) cc_final: 0.7244 (mm110) REVERT: V 549 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.7512 (m-70) REVERT: X 474 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7563 (mt) REVERT: Y 51 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7772 (ttm-80) REVERT: Y 365 SER cc_start: 0.8307 (p) cc_final: 0.8086 (m) REVERT: Z 90 MET cc_start: 0.8792 (mmp) cc_final: 0.8402 (mmt) REVERT: Z 440 GLN cc_start: 0.7973 (mt0) cc_final: 0.7640 (mt0) outliers start: 126 outliers final: 73 residues processed: 515 average time/residue: 1.3299 time to fit residues: 853.1364 Evaluate side-chains 493 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 405 time to evaluate : 4.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 61 MET Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 147 ARG Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 200 GLU Chi-restraints excluded: chain T residue 409 GLU Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 428 SER Chi-restraints excluded: chain T residue 487 LYS Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 546 LEU Chi-restraints excluded: chain U residue 407 PHE Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 521 GLU Chi-restraints excluded: chain U residue 522 GLU Chi-restraints excluded: chain U residue 528 VAL Chi-restraints excluded: chain U residue 549 HIS Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 282 MET Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 421 LEU Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 452 GLN Chi-restraints excluded: chain V residue 464 SER Chi-restraints excluded: chain V residue 516 ASP Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 488 MET Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 279 ASP Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 419 ILE Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Y residue 546 GLU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 386 optimal weight: 6.9990 chunk 407 optimal weight: 0.9990 chunk 371 optimal weight: 4.9990 chunk 396 optimal weight: 0.6980 chunk 238 optimal weight: 4.9990 chunk 172 optimal weight: 0.4980 chunk 311 optimal weight: 2.9990 chunk 121 optimal weight: 0.0040 chunk 357 optimal weight: 0.9990 chunk 374 optimal weight: 3.9990 chunk 394 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN P 66 GLN P 140 ASN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 149 GLN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 179 ASN V 452 GLN V 488 GLN V 527 GLN X 250 GLN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 34384 Z= 0.161 Angle : 0.532 13.097 46598 Z= 0.268 Chirality : 0.042 0.220 5513 Planarity : 0.004 0.053 5991 Dihedral : 5.897 113.752 4919 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.25 % Favored : 96.61 % Rotamer: Outliers : 3.31 % Allowed : 22.47 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.13), residues: 4457 helix: 0.06 (0.11), residues: 2150 sheet: -0.40 (0.22), residues: 572 loop : -0.50 (0.16), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 58 HIS 0.003 0.001 HIS Z 396 PHE 0.030 0.001 PHE G 107 TYR 0.017 0.001 TYR Z 478 ARG 0.014 0.000 ARG Y 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 447 time to evaluate : 3.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 113 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7780 (tt) REVERT: G 123 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8222 (mm) REVERT: I 60 LYS cc_start: 0.7158 (mtmm) cc_final: 0.6735 (mtmm) REVERT: J 61 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6072 (mmp) REVERT: P 49 THR cc_start: 0.7771 (OUTLIER) cc_final: 0.7566 (m) REVERT: R 35 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: S 48 ARG cc_start: 0.7339 (ptm160) cc_final: 0.6940 (mtp-110) REVERT: S 96 ASN cc_start: 0.7345 (m-40) cc_final: 0.6962 (m110) REVERT: S 147 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.7024 (ppt90) REVERT: S 220 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8032 (mm) REVERT: S 259 MET cc_start: 0.8334 (ptm) cc_final: 0.8013 (ttp) REVERT: T 287 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7494 (tpp) REVERT: T 487 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7810 (mtmm) REVERT: T 543 THR cc_start: 0.7150 (OUTLIER) cc_final: 0.6933 (p) REVERT: U 282 MET cc_start: 0.8627 (tpt) cc_final: 0.8118 (mmt) REVERT: U 407 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.6811 (m-80) REVERT: U 522 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7548 (tp30) REVERT: V 471 GLN cc_start: 0.7566 (tt0) cc_final: 0.7264 (mm110) REVERT: V 549 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7544 (m-70) REVERT: X 474 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7561 (mt) REVERT: X 502 MET cc_start: 0.7178 (ttm) cc_final: 0.6335 (mtp) REVERT: Y 51 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7798 (ttm-80) REVERT: Y 365 SER cc_start: 0.8285 (p) cc_final: 0.8045 (m) REVERT: Z 90 MET cc_start: 0.8766 (mmp) cc_final: 0.8390 (mmt) REVERT: Z 440 GLN cc_start: 0.7903 (mt0) cc_final: 0.7606 (mt0) outliers start: 118 outliers final: 64 residues processed: 526 average time/residue: 1.2968 time to fit residues: 835.0213 Evaluate side-chains 482 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 403 time to evaluate : 3.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 61 MET Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 35 GLU Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 147 ARG Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 118 MET Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 409 GLU Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 428 SER Chi-restraints excluded: chain T residue 487 LYS Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 407 PHE Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 522 GLU Chi-restraints excluded: chain U residue 528 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 421 LEU Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 488 MET Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 260 optimal weight: 0.6980 chunk 418 optimal weight: 0.9990 chunk 255 optimal weight: 5.9990 chunk 198 optimal weight: 0.7980 chunk 291 optimal weight: 4.9990 chunk 439 optimal weight: 0.0270 chunk 404 optimal weight: 2.9990 chunk 349 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 270 optimal weight: 1.9990 chunk 214 optimal weight: 0.6980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 66 GLN P 140 ASN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 405 GLN U 152 ASN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 488 GLN V 527 GLN X 132 GLN X 250 GLN Y 471 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 34384 Z= 0.161 Angle : 0.540 12.885 46598 Z= 0.271 Chirality : 0.042 0.226 5513 Planarity : 0.004 0.058 5991 Dihedral : 5.817 109.794 4919 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.43 % Rotamer: Outliers : 2.64 % Allowed : 23.50 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.13), residues: 4457 helix: 0.12 (0.12), residues: 2151 sheet: -0.33 (0.22), residues: 578 loop : -0.50 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 58 HIS 0.003 0.001 HIS Z 396 PHE 0.028 0.001 PHE C 107 TYR 0.024 0.001 TYR T 414 ARG 0.015 0.000 ARG Y 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 433 time to evaluate : 4.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.7916 (t0) cc_final: 0.7494 (t0) REVERT: E 113 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7828 (tt) REVERT: F 60 LYS cc_start: 0.6236 (OUTLIER) cc_final: 0.5968 (tptp) REVERT: G 123 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8381 (mm) REVERT: J 61 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.5924 (mmp) REVERT: J 119 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7216 (tt) REVERT: R 35 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: S 48 ARG cc_start: 0.7324 (ptm160) cc_final: 0.6935 (mtp-110) REVERT: S 96 ASN cc_start: 0.7093 (m-40) cc_final: 0.6706 (m110) REVERT: S 147 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.7020 (ppt90) REVERT: S 220 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8031 (mm) REVERT: S 259 MET cc_start: 0.8337 (ptm) cc_final: 0.7988 (ttp) REVERT: S 303 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: T 287 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7494 (tpp) REVERT: T 487 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7813 (mtmm) REVERT: T 543 THR cc_start: 0.7098 (OUTLIER) cc_final: 0.6860 (p) REVERT: T 549 HIS cc_start: 0.6783 (t70) cc_final: 0.6580 (t70) REVERT: U 407 PHE cc_start: 0.7273 (OUTLIER) cc_final: 0.6809 (m-80) REVERT: U 483 MET cc_start: 0.6645 (tpp) cc_final: 0.6281 (tpp) REVERT: V 67 ILE cc_start: 0.8163 (pp) cc_final: 0.7711 (mp) REVERT: V 471 GLN cc_start: 0.7559 (tt0) cc_final: 0.7247 (mm110) REVERT: V 549 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.7513 (m-70) REVERT: X 474 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7618 (mt) REVERT: X 484 MET cc_start: 0.7761 (tpp) cc_final: 0.7526 (tpp) REVERT: X 502 MET cc_start: 0.7197 (ttm) cc_final: 0.6403 (mtp) REVERT: Y 51 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7810 (ttm-80) REVERT: Y 365 SER cc_start: 0.8272 (p) cc_final: 0.8057 (m) REVERT: Z 90 MET cc_start: 0.8768 (mmp) cc_final: 0.8451 (mmt) REVERT: Z 440 GLN cc_start: 0.7906 (mt0) cc_final: 0.7626 (mt0) outliers start: 94 outliers final: 58 residues processed: 493 average time/residue: 1.3608 time to fit residues: 820.8103 Evaluate side-chains 477 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 403 time to evaluate : 4.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 61 MET Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 35 GLU Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 147 ARG Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 118 MET Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 409 GLU Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 487 LYS Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 407 PHE Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 528 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 421 LEU Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 464 SER Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 488 MET Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 277 optimal weight: 0.9980 chunk 372 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 322 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 350 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 359 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 66 GLN P 140 ASN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 73 ASN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 159 GLN S 267 HIS ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 488 GLN V 527 GLN X 250 GLN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.136358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106450 restraints weight = 50435.534| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.67 r_work: 0.3138 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34384 Z= 0.189 Angle : 0.555 13.582 46598 Z= 0.278 Chirality : 0.043 0.211 5513 Planarity : 0.004 0.059 5991 Dihedral : 5.861 108.780 4919 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.57 % Favored : 96.30 % Rotamer: Outliers : 2.56 % Allowed : 23.84 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 4457 helix: 0.12 (0.12), residues: 2142 sheet: -0.33 (0.22), residues: 575 loop : -0.50 (0.16), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 37 HIS 0.004 0.001 HIS T 549 PHE 0.027 0.001 PHE C 107 TYR 0.015 0.001 TYR E 102 ARG 0.014 0.000 ARG Y 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13986.81 seconds wall clock time: 249 minutes 44.46 seconds (14984.46 seconds total)