Starting phenix.real_space_refine on Thu Feb 22 10:30:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re7_4844/02_2024/6re7_4844_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re7_4844/02_2024/6re7_4844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re7_4844/02_2024/6re7_4844.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re7_4844/02_2024/6re7_4844.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re7_4844/02_2024/6re7_4844_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re7_4844/02_2024/6re7_4844_updated.pdb" } resolution = 3.1 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 "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 72": "OD1" <-> "OD2" Residue "P PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 33": "OE1" <-> "OE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 54": "OD1" <-> "OD2" Residue "Q GLU 64": "OE1" <-> "OE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 35": "OE1" <-> "OE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 117": "OE1" <-> "OE2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "R GLU 148": "OE1" <-> "OE2" Residue "R ASP 153": "OD1" <-> "OD2" Residue "R ASP 174": "OD1" <-> "OD2" Residue "R PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 177": "OE1" <-> "OE2" Residue "R GLU 186": "OE1" <-> "OE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 83": "OD1" <-> "OD2" Residue "S GLU 131": "OE1" <-> "OE2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S GLU 154": "OE1" <-> "OE2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 214": "OD1" <-> "OD2" Residue "S GLU 221": "OE1" <-> "OE2" Residue "S ASP 222": "OD1" <-> "OD2" Residue "S ASP 229": "OD1" <-> "OD2" Residue "S GLU 234": "OE1" <-> "OE2" Residue "S ASP 241": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S GLU 283": "OE1" <-> "OE2" 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 ASP 165": "OD1" <-> "OD2" Residue "T ASP 172": "OD1" <-> "OD2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 237": "OD1" <-> "OD2" Residue "T TYR 256": "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 ASP 403": "OD1" <-> "OD2" Residue "T GLU 409": "OE1" <-> "OE2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 418": "NH1" <-> "NH2" Residue "T ARG 429": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 465": "OD1" <-> "OD2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 547": "OD1" <-> "OD2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ASP 46": "OD1" <-> "OD2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 92": "OD1" <-> "OD2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 125": "OD1" <-> "OD2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U 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 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 409": "OE1" <-> "OE2" Residue "U GLU 411": "OE1" <-> "OE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 449": "OE1" <-> "OE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U GLU 455": "OE1" <-> "OE2" Residue "U PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 475": "OE1" <-> "OE2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U GLU 521": "OE1" <-> "OE2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 74": "OE1" <-> "OE2" Residue "V PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 125": "OD1" <-> "OD2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 135": "OD1" <-> "OD2" Residue "V ASP 142": "OD1" <-> "OD2" Residue "V ASP 165": "OD1" <-> "OD2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V GLU 186": "OE1" <-> "OE2" Residue "V ASP 210": "OD1" <-> "OD2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V ASP 226": "OD1" <-> "OD2" 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 GLU 371": "OE1" <-> "OE2" Residue "V ASP 403": "OD1" <-> "OD2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 429": "NH1" <-> "NH2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V ASP 465": "OD1" <-> "OD2" Residue "V ASP 467": "OD1" <-> "OD2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V ASP 547": "OD1" <-> "OD2" Residue "V GLU 553": "OE1" <-> "OE2" 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 ASP 82": "OD1" <-> "OD2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X ASP 91": "OD1" <-> "OD2" Residue "X ASP 94": "OD1" <-> "OD2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X ASP 104": "OD1" <-> "OD2" Residue "X ARG 120": "NH1" <-> "NH2" Residue "X GLU 131": "OE1" <-> "OE2" Residue "X GLU 149": "OE1" <-> "OE2" Residue "X GLU 152": "OE1" <-> "OE2" Residue "X GLU 195": "OE1" <-> "OE2" Residue "X PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "X ASP 222": "OD1" <-> "OD2" Residue "X GLU 229": "OE1" <-> "OE2" Residue "X GLU 238": "OE1" <-> "OE2" Residue "X ARG 258": "NH1" <-> "NH2" Residue "X GLU 270": "OE1" <-> "OE2" Residue "X PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 285": "OD1" <-> "OD2" Residue "X ASP 317": "OD1" <-> "OD2" Residue "X PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 359": "OD1" <-> "OD2" Residue "X GLU 370": "OE1" <-> "OE2" Residue "X ASP 378": "OD1" <-> "OD2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X GLU 395": "OE1" <-> "OE2" Residue "X ARG 401": "NH1" <-> "NH2" Residue "X TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 435": "NH1" <-> "NH2" Residue "X ARG 437": "NH1" <-> "NH2" Residue "X PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 480": "OD1" <-> "OD2" Residue "X GLU 497": "OE1" <-> "OE2" Residue "X ASP 500": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X ASP 513": "OD1" <-> "OD2" Residue "X GLU 519": "OE1" <-> "OE2" Residue "X GLU 520": "OE1" <-> "OE2" Residue "X ASP 523": "OD1" <-> "OD2" Residue "X ASP 543": "OD1" <-> "OD2" Residue "X ASP 548": "OD1" <-> "OD2" Residue "X PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 552": "OE1" <-> "OE2" Residue "X GLU 557": "OE1" <-> "OE2" Residue "X GLU 564": "OE1" <-> "OE2" Residue "Y ASP 36": "OD1" <-> "OD2" Residue "Y TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y ASP 53": "OD1" <-> "OD2" Residue "Y GLU 146": "OE1" <-> "OE2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 296": "OE1" <-> "OE2" 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 409": "OD1" <-> "OD2" Residue "Y GLU 428": "OE1" <-> "OE2" Residue "Y ASP 429": "OD1" <-> "OD2" Residue "Y PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 479": "OD1" <-> "OD2" Residue "Y ASP 491": "OD1" <-> "OD2" Residue "Y GLU 494": "OE1" <-> "OE2" Residue "Y ARG 509": "NH1" <-> "NH2" Residue "Y GLU 519": "OE1" <-> "OE2" Residue "Y ASP 528": "OD1" <-> "OD2" Residue "Y GLU 533": "OE1" <-> "OE2" Residue "Y GLU 541": "OE1" <-> "OE2" Residue "Y ASP 548": "OD1" <-> "OD2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 36": "OD1" <-> "OD2" 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 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 GLU 195": "OE1" <-> "OE2" Residue "Z GLU 229": "OE1" <-> "OE2" Residue "Z GLU 238": "OE1" <-> "OE2" Residue "Z ARG 258": "NH1" <-> "NH2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 366": "NH1" <-> "NH2" Residue "Z GLU 370": "OE1" <-> "OE2" Residue "Z TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z GLU 424": "OE1" <-> "OE2" Residue "Z GLU 427": "OE1" <-> "OE2" Residue "Z GLU 428": "OE1" <-> "OE2" Residue "Z GLU 451": "OE1" <-> "OE2" Residue "Z PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 462": "OD1" <-> "OD2" Residue "Z PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 479": "OD1" <-> "OD2" Residue "Z ASP 480": "OD1" <-> "OD2" Residue "Z TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 513": "OD1" <-> "OD2" Residue "Z GLU 536": "OE1" <-> "OE2" Residue "Z GLU 540": "OE1" <-> "OE2" Residue "Z GLU 547": "OE1" <-> "OE2" Residue "Z GLU 563": "OE1" <-> "OE2" Residue "Z GLU 564": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 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: 17.50, per 1000 atoms: 0.52 Number of scatterers: 33863 At special positions: 0 Unit cell: (163.215, 130.572, 208.494, 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: 13.24 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: 167 helices and 27 sheets defined 47.8% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.09 Creating SS restraints... Processing helix chain 'A' and resid 56 through 91 removed outlier: 3.521A pdb=" N ALA A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 125 removed outlier: 3.772A pdb=" N ALA A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LYS A 97 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL A 100 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 104 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 105 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 107 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU A 111 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER A 112 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 113 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 119 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU A 125 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.641A pdb=" N LYS B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 125 removed outlier: 5.172A pdb=" N LYS B 97 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B 106 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU B 111 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 113 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 115 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE B 116 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU B 118 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU B 119 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 125 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 91 removed outlier: 3.870A pdb=" N LYS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 125 removed outlier: 5.249A pdb=" N LYS C 97 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR C 110 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER C 112 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 113 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 119 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 122 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 124 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU C 125 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 91 removed outlier: 4.044A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY D 65 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 125 removed outlier: 5.049A pdb=" N LYS D 97 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL D 100 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY D 101 " --> pdb=" O GLN D 98 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU D 104 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU D 111 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU D 119 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 91 removed outlier: 4.148A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA E 64 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 123 removed outlier: 4.958A pdb=" N LYS E 97 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL E 100 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER E 112 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU E 119 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL E 121 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 69 removed outlier: 3.783A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 91 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: 5.117A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL F 100 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU F 111 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU F 115 " --> pdb=" O SER F 112 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU F 119 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU F 125 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE F 126 " --> pdb=" O LEU F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 67 removed outlier: 4.018A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 91 removed outlier: 3.676A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 126 removed outlier: 3.574A pdb=" N ALA G 96 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL G 100 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU G 104 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR G 110 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU G 111 " --> pdb=" O ALA G 108 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER G 112 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU G 125 " --> pdb=" O PHE G 122 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE G 126 " --> pdb=" O LEU G 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 89 removed outlier: 3.800A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA H 64 " --> pdb=" O LYS H 60 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY H 65 " --> pdb=" O MET H 61 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA H 70 " --> pdb=" O CYS H 66 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA H 72 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 125 removed outlier: 5.192A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE H 107 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU H 109 " --> pdb=" O GLY H 106 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU H 125 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 91 removed outlier: 3.801A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ALA I 70 " --> pdb=" O CYS I 66 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LEU I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA I 72 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 125 removed outlier: 3.660A pdb=" N ALA I 96 " --> pdb=" O PRO I 93 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LYS I 97 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL I 100 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER I 112 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU I 125 " --> pdb=" O PHE I 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 91 removed outlier: 4.409A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 125 removed outlier: 3.607A pdb=" N ALA J 96 " --> pdb=" O PRO J 93 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS J 97 " --> pdb=" O ASN J 94 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU J 99 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL J 100 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU J 104 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU J 111 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER J 112 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU J 125 " --> pdb=" O PHE J 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 63 Processing helix chain 'P' and resid 67 through 83 removed outlier: 3.532A pdb=" N GLN P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 92 removed outlier: 3.829A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 108 Processing helix chain 'P' and resid 116 through 127 Processing helix chain 'P' and resid 131 through 148 removed outlier: 3.906A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU P 136 " --> pdb=" O ALA P 133 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 30 removed outlier: 4.061A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 39 removed outlier: 3.701A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 4.214A 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: 3.533A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 54 removed outlier: 3.611A pdb=" N TYR R 54 " --> pdb=" O PRO R 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 51 through 54' Processing helix chain 'R' and resid 152 through 154 No H-bonds generated for 'chain 'R' and resid 152 through 154' Processing helix chain 'R' and resid 159 through 168 removed outlier: 3.883A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 195 removed outlier: 3.942A pdb=" N ALA R 190 " --> pdb=" O GLU R 186 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL R 195 " --> pdb=" O LEU R 191 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 78 removed outlier: 3.745A pdb=" N ARG S 48 " --> pdb=" O LYS S 44 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS S 55 " --> pdb=" O LYS S 51 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.409A 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 118 through 130 removed outlier: 3.503A pdb=" N ALA S 128 " --> pdb=" O ARG S 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 147 No H-bonds generated for 'chain 'S' and resid 144 through 147' Processing helix chain 'S' and resid 150 through 153 No H-bonds generated for 'chain 'S' and resid 150 through 153' Processing helix chain 'S' and resid 172 through 184 Processing helix chain 'S' and resid 213 through 221 removed outlier: 5.375A pdb=" N LYS S 218 " --> pdb=" O ASP S 214 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLN S 219 " --> pdb=" O LEU S 215 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU S 221 " --> pdb=" O GLU S 217 " (cutoff:3.500A) Processing helix chain 'S' and resid 239 through 273 removed outlier: 3.650A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) Processing helix chain 'S' and resid 276 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 Processing helix chain 'T' and resid 231 through 247 removed outlier: 3.900A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 278 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 296 through 315 Proline residue: T 303 - end of helix removed outlier: 4.264A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 341 removed outlier: 3.715A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 347 through 349 No H-bonds generated for 'chain 'T' and resid 347 through 349' Processing helix chain 'T' and resid 352 through 362 removed outlier: 4.311A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR T 356 " --> pdb=" O ASP T 353 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU T 357 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG T 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU T 362 " --> pdb=" O SER T 359 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 399 Processing helix chain 'T' and resid 410 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 442 removed outlier: 3.530A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 444 through 457 Processing helix chain 'T' and resid 470 through 483 removed outlier: 3.652A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 505 removed outlier: 3.562A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 527 removed outlier: 4.361A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 539 Processing helix chain 'T' and resid 546 through 555 Processing helix chain 'U' and resid 46 through 48 No H-bonds generated for 'chain 'U' and resid 46 through 48' Processing helix chain 'U' and resid 59 through 73 removed outlier: 4.275A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix removed outlier: 4.345A pdb=" N TRP U 73 " --> pdb=" O ALA U 69 " (cutoff:3.500A) Processing helix chain 'U' and resid 135 through 137 No H-bonds generated for 'chain 'U' and resid 135 through 137' Processing helix chain 'U' and resid 207 through 211 Processing helix chain 'U' and resid 231 through 246 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 315 Proline residue: U 303 - end of helix removed outlier: 3.880A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 removed outlier: 3.961A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 347 through 349 No H-bonds generated for 'chain 'U' and resid 347 through 349' Processing helix chain 'U' and resid 352 through 364 removed outlier: 4.308A pdb=" N PHE U 355 " --> pdb=" O GLY U 352 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR U 356 " --> pdb=" O ASP U 353 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU U 357 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG U 360 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLU U 363 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 393 through 401 Processing helix chain 'U' and resid 411 through 414 No H-bonds generated for 'chain 'U' and resid 411 through 414' Processing helix chain 'U' and resid 437 through 459 removed outlier: 4.017A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR U 453 " --> pdb=" O GLU U 449 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU U 455 " --> pdb=" O ALA U 451 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL U 456 " --> pdb=" O GLN U 452 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ALA U 458 " --> pdb=" O ARG U 454 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE U 459 " --> pdb=" O GLU U 455 " (cutoff:3.500A) Processing helix chain 'U' and resid 468 through 484 removed outlier: 3.646A pdb=" N TYR U 472 " --> pdb=" O ALA U 468 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 505 removed outlier: 3.622A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 517 through 527 Processing helix chain 'U' and resid 531 through 539 removed outlier: 3.676A 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 44 through 48 removed outlier: 3.602A pdb=" N GLU V 47 " --> pdb=" O ALA V 44 " (cutoff:3.500A) Processing helix chain 'V' and resid 58 through 69 Proline residue: V 68 - end of helix Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 211 Processing helix chain 'V' and resid 231 through 246 removed outlier: 3.697A pdb=" N GLN V 242 " --> pdb=" O ALA V 238 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS V 243 " --> pdb=" O ILE V 239 " (cutoff:3.500A) Processing helix chain 'V' and resid 251 through 253 No H-bonds generated for 'chain 'V' and resid 251 through 253' Processing helix chain 'V' and resid 266 through 279 Processing helix chain 'V' and resid 281 through 284 Processing helix chain 'V' and resid 296 through 315 Proline residue: V 303 - end of helix removed outlier: 3.818A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 339 Processing helix chain 'V' and resid 347 through 349 No H-bonds generated for 'chain 'V' and resid 347 through 349' Processing helix chain 'V' and resid 352 through 364 removed outlier: 4.231A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 4.298A 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 410 through 415 removed outlier: 3.669A pdb=" N LYS V 415 " --> pdb=" O GLU V 411 " (cutoff:3.500A) Processing helix chain 'V' and resid 431 through 434 removed outlier: 3.700A 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: 3.807A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.896A 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: 3.644A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) Processing helix chain 'V' and resid 514 through 527 removed outlier: 4.131A pdb=" N ILE V 517 " --> pdb=" O VAL V 514 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL V 518 " --> pdb=" O GLN V 515 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA V 519 " --> pdb=" O ASP V 516 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU V 521 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 532 through 539 removed outlier: 3.872A 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: 4.648A 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: 3.608A 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 322 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 356 removed outlier: 3.877A pdb=" N ALA X 356 " --> pdb=" O ALA X 352 " (cutoff:3.500A) 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 389 through 392 No H-bonds generated for 'chain 'X' and resid 389 through 392' Processing helix chain 'X' and resid 394 through 412 Processing helix chain 'X' and resid 415 through 419 Processing helix chain 'X' and resid 422 through 424 No H-bonds generated for 'chain 'X' and resid 422 through 424' Processing helix chain 'X' and resid 427 through 443 removed outlier: 3.564A pdb=" N ARG X 441 " --> pdb=" O ARG X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 450 through 452 No H-bonds generated for 'chain 'X' and resid 450 through 452' Processing helix chain 'X' and resid 463 through 475 Processing helix chain 'X' and resid 483 through 486 No H-bonds generated for 'chain 'X' and resid 483 through 486' Processing helix chain 'X' and resid 492 through 506 removed outlier: 4.230A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASP X 505 " --> pdb=" O LYS X 501 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE X 506 " --> pdb=" O MET X 502 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 531 Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 165 through 170 Processing helix chain 'Y' and resid 191 through 200 Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 238 through 241 Processing helix chain 'Y' and resid 255 through 258 No H-bonds generated for 'chain 'Y' and resid 255 through 258' Processing helix chain 'Y' and resid 261 through 274 removed outlier: 3.600A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 288 through 298 Processing helix chain 'Y' and resid 314 through 322 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: 4.451A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS Y 357 " --> pdb=" O THR Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 369 No H-bonds generated for 'chain 'Y' and resid 366 through 369' Processing helix chain 'Y' and resid 389 through 392 No H-bonds generated for 'chain 'Y' and resid 389 through 392' Processing helix chain 'Y' and resid 394 through 419 removed outlier: 3.776A pdb=" N LEU Y 413 " --> pdb=" O ASP Y 409 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN Y 414 " --> pdb=" O TYR Y 410 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 5.685A 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: 3.901A pdb=" N ALA Y 434 " --> pdb=" O LYS Y 430 " (cutoff:3.500A) Processing helix chain 'Y' and resid 463 through 475 removed outlier: 3.517A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 483 through 485 No H-bonds generated for 'chain 'Y' and resid 483 through 485' Processing helix chain 'Y' and resid 492 through 507 removed outlier: 4.027A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE Y 506 " --> pdb=" O MET Y 502 " (cutoff:3.500A) Processing helix chain 'Y' and resid 512 through 514 No H-bonds generated for 'chain 'Y' and resid 512 through 514' Processing helix chain 'Y' and resid 527 through 531 Processing helix chain 'Y' and resid 545 through 549 removed outlier: 3.618A pdb=" N PHE Y 549 " --> pdb=" O LEU Y 545 " (cutoff:3.500A) No H-bonds generated for '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 200 Processing helix chain 'Z' and resid 217 through 229 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 3.987A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 274 removed outlier: 4.874A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 298 removed outlier: 3.579A pdb=" N GLN Z 292 " --> pdb=" O ARG Z 289 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER Z 298 " --> pdb=" O SER Z 295 " (cutoff:3.500A) Processing helix chain 'Z' and resid 314 through 324 removed outlier: 4.576A 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 370 Processing helix chain 'Z' and resid 389 through 417 removed outlier: 7.600A pdb=" N ALA Z 394 " --> pdb=" O ASN Z 390 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N GLU Z 395 " --> pdb=" O VAL Z 391 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N HIS Z 396 " --> pdb=" O ILE Z 392 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR Z 397 " --> pdb=" O GLY Z 393 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) Processing helix chain 'Z' and resid 430 through 442 removed outlier: 3.601A pdb=" N ALA Z 434 " --> pdb=" O LYS Z 430 " (cutoff:3.500A) Processing helix chain 'Z' and resid 463 through 475 Processing helix chain 'Z' and resid 483 through 485 No H-bonds generated for 'chain 'Z' and resid 483 through 485' Processing helix chain 'Z' and resid 492 through 508 removed outlier: 4.012A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS Z 501 " --> pdb=" O GLU Z 497 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 533 removed outlier: 4.192A pdb=" N VAL Z 531 " --> pdb=" O LEU Z 527 " (cutoff:3.500A) removed outlier: 4.243A 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 Processing sheet with id= B, first strand: chain 'R' and resid 72 through 75 removed outlier: 6.745A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.330A 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: 3.538A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.504A 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: 5.111A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA S 161 " --> pdb=" O SER S 141 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'T' and resid 94 through 98 removed outlier: 6.902A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.904A 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: 3.825A pdb=" N LEU T 222 " --> pdb=" O GLY T 404 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'T' and resid 286 through 290 removed outlier: 6.863A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N SER T 376 " --> pdb=" O GLY T 320 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ILE T 322 " --> pdb=" O SER T 376 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.638A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.824A 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 405 through 408 removed outlier: 6.826A pdb=" N LEU U 222 " --> pdb=" O ILE U 406 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU U 408 " --> pdb=" O LEU U 222 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE U 224 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'U' and resid 285 through 290 removed outlier: 8.722A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE U 380 " --> pdb=" O TYR U 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'V' and resid 85 through 89 removed outlier: 6.526A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLN V 149 " --> pdb=" O LEU V 108 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N CYS V 110 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR V 147 " --> pdb=" O CYS V 110 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= O, first strand: chain 'V' and resid 404 through 408 Processing sheet with id= P, first strand: chain 'V' and resid 285 through 290 removed outlier: 8.709A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'X' and resid 38 through 44 removed outlier: 6.385A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'X' and resid 110 through 113 removed outlier: 3.620A pdb=" N ASP X 139 " --> pdb=" O VAL X 113 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'X' and resid 360 through 362 removed outlier: 8.498A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL X 284 " --> pdb=" O VAL X 336 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= U, first strand: chain 'Y' and resid 37 through 39 removed outlier: 6.684A pdb=" N ARG Y 86 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N HIS Y 79 " --> pdb=" O THR Y 84 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR Y 84 " --> pdb=" O HIS Y 79 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ARG Y 51 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL Y 40 " --> pdb=" O ARG Y 51 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'Y' and resid 110 through 113 Processing sheet with id= W, first strand: chain 'Y' and resid 360 through 363 removed outlier: 7.442A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLY Y 183 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL Y 339 " --> pdb=" O GLY Y 183 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE Y 207 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N PHE Y 283 " --> pdb=" O PHE Y 207 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ALA Y 211 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Z' and resid 38 through 44 removed outlier: 6.575A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU Z 72 " --> pdb=" O VAL Z 65 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id= Z, first strand: chain 'Z' and resid 360 through 363 removed outlier: 7.221A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLY Z 183 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL Z 339 " --> pdb=" O GLY Z 183 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Z' and resid 559 through 561 1450 hydrogen bonds defined for protein. 3516 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: 12.79 Time building geometry restraints manager: 14.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8797 1.33 - 1.45: 5813 1.45 - 1.57: 19553 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34384 Sorted by residual: bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.14e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.04e+01 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 4.83e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.470 -0.061 1.00e-02 1.00e+04 3.74e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.45e+01 ... (remaining 34379 not shown) Histogram of bond angle deviations from ideal: 95.69 - 103.75: 466 103.75 - 111.81: 16034 111.81 - 119.87: 14903 119.87 - 127.94: 15011 127.94 - 136.00: 184 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 139.87 120.20 19.67 1.00e+00 1.00e+00 3.87e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 120.53 19.34 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 123.94 15.93 1.00e+00 1.00e+00 2.54e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 121.20 15.63 1.00e+00 1.00e+00 2.44e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 121.89 14.94 1.00e+00 1.00e+00 2.23e+02 ... (remaining 46593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 20347 35.83 - 71.67: 428 71.67 - 107.50: 27 107.50 - 143.33: 0 143.33 - 179.17: 1 Dihedral angle restraints: 20803 sinusoidal: 8060 harmonic: 12743 Sorted by residual: dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -130.24 -49.76 0 5.00e+00 4.00e-02 9.90e+01 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 -135.40 -44.60 0 5.00e+00 4.00e-02 7.96e+01 dihedral pdb=" C5' ADP Z 601 " pdb=" O5' ADP Z 601 " pdb=" PA ADP Z 601 " pdb=" O2A ADP Z 601 " ideal model delta sinusoidal sigma weight residual -60.00 119.17 -179.17 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 20800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4245 0.070 - 0.139: 1139 0.139 - 0.209: 114 0.209 - 0.279: 13 0.279 - 0.349: 2 Chirality restraints: 5513 Sorted by residual: chirality pdb=" CB ILE C 95 " pdb=" CA ILE C 95 " pdb=" CG1 ILE C 95 " pdb=" CG2 ILE C 95 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.04e+00 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 -2.28 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB THR U 378 " pdb=" CA THR U 378 " pdb=" OG1 THR U 378 " pdb=" CG2 THR U 378 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 5510 not shown) Planarity restraints: 5991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Y 503 " 0.032 2.00e-02 2.50e+03 6.27e-02 3.93e+01 pdb=" C ALA Y 503 " -0.108 2.00e-02 2.50e+03 pdb=" O ALA Y 503 " 0.040 2.00e-02 2.50e+03 pdb=" N LYS Y 504 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.030 2.00e-02 2.50e+03 5.79e-02 3.36e+01 pdb=" C ALA Z 503 " -0.100 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.037 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU T 509 " 0.015 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C LEU T 509 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU T 509 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP T 510 " 0.019 2.00e-02 2.50e+03 ... (remaining 5988 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1691 2.71 - 3.26: 33107 3.26 - 3.81: 57734 3.81 - 4.35: 75008 4.35 - 4.90: 125798 Nonbonded interactions: 293338 Sorted by model distance: nonbonded pdb=" O3B ADP Z 601 " pdb="MG MG Z 602 " model vdw 2.164 2.170 nonbonded pdb=" OG1 THR Y 190 " pdb="MG MG Y 602 " model vdw 2.225 2.170 nonbonded pdb=" O3G ATP U1001 " pdb="MG MG U1002 " model vdw 2.226 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.228 2.170 nonbonded pdb=" O LYS Z 515 " pdb=" N VAL Z 517 " model vdw 2.234 2.520 ... (remaining 293333 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: 6.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 26.740 Check model and map are aligned: 0.480 Set scattering table: 0.260 Process input model: 89.240 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 0.011 0.106 34384 Z= 0.692 Angle : 0.975 19.670 46598 Z= 0.569 Chirality : 0.060 0.349 5513 Planarity : 0.007 0.072 5991 Dihedral : 14.722 179.168 12653 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.53 % Favored : 95.24 % Rotamer: Outliers : 0.34 % Allowed : 10.19 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.10), residues: 4457 helix: -2.86 (0.08), residues: 2136 sheet: -1.51 (0.21), residues: 548 loop : -2.27 (0.12), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP Y 141 HIS 0.011 0.002 HIS S 250 PHE 0.034 0.003 PHE S 249 TYR 0.024 0.003 TYR T 324 ARG 0.010 0.001 ARG U 454 *********************** 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 673 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 661 time to evaluate : 3.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ILE cc_start: 0.8502 (tt) cc_final: 0.7959 (tt) REVERT: F 56 LEU cc_start: 0.5977 (tp) cc_final: 0.5442 (mt) REVERT: H 97 LYS cc_start: 0.6939 (mmtt) cc_final: 0.5827 (mtpt) REVERT: J 105 LEU cc_start: 0.7848 (tt) cc_final: 0.7283 (mt) REVERT: P 50 SER cc_start: 0.8787 (t) cc_final: 0.8330 (m) REVERT: P 79 GLU cc_start: 0.7849 (tp30) cc_final: 0.7383 (tp30) REVERT: S 241 ASP cc_start: 0.7557 (m-30) cc_final: 0.6830 (m-30) REVERT: T 101 LYS cc_start: 0.8098 (ttpp) cc_final: 0.7805 (mtpp) REVERT: T 492 ILE cc_start: 0.8795 (mt) cc_final: 0.8573 (mm) REVERT: T 537 LYS cc_start: 0.8522 (tmmt) cc_final: 0.8116 (ttpt) REVERT: U 483 MET cc_start: 0.6709 (tmm) cc_final: 0.6213 (tmm) REVERT: U 550 LEU cc_start: 0.8907 (tp) cc_final: 0.8679 (mt) REVERT: X 90 MET cc_start: 0.9006 (mmt) cc_final: 0.8511 (mmt) REVERT: X 386 MET cc_start: 0.8471 (mmm) cc_final: 0.7869 (mmm) REVERT: Z 195 GLU cc_start: 0.7581 (tp30) cc_final: 0.7337 (tp30) REVERT: Z 248 TYR cc_start: 0.8567 (m-80) cc_final: 0.8070 (m-80) REVERT: Z 448 GLN cc_start: 0.7399 (tm-30) cc_final: 0.6958 (mm-40) REVERT: Z 484 MET cc_start: 0.7384 (mmt) cc_final: 0.6974 (mmt) REVERT: Z 504 LYS cc_start: 0.7049 (mttt) cc_final: 0.6702 (mttt) outliers start: 12 outliers final: 6 residues processed: 670 average time/residue: 0.5261 time to fit residues: 555.1027 Evaluate side-chains 474 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 468 time to evaluate : 3.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 372 optimal weight: 0.8980 chunk 334 optimal weight: 0.0370 chunk 185 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 345 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 210 optimal weight: 0.8980 chunk 257 optimal weight: 0.7980 chunk 400 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN C 87 ASN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN F 98 GLN G 98 GLN I 87 ASN I 94 ASN Q 43 GLN Q 49 GLN R 83 GLN R 85 GLN S 98 ASN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 ASN S 267 HIS T 134 ASN T 241 HIS T 386 GLN T 441 GLN U 149 GLN U 152 ASN U 246 ASN U 248 GLN U 264 GLN U 358 HIS U 386 GLN U 515 GLN U 539 ASN V 61 HIS V 121 ASN V 126 HIS V 134 ASN V 139 HIS V 149 GLN ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 242 GLN V 244 ASN V 264 GLN V 278 GLN V 358 HIS V 486 GLN V 497 GLN X 78 GLN X 278 GLN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 404 GLN X 574 ASN Y 174 GLN Y 199 ASN Y 278 GLN Y 408 GLN Y 414 GLN Z 83 ASN Z 174 GLN Z 204 HIS Z 408 GLN Z 414 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 34384 Z= 0.162 Angle : 0.532 8.362 46598 Z= 0.282 Chirality : 0.042 0.160 5513 Planarity : 0.005 0.057 5991 Dihedral : 6.548 162.204 4918 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.60 % Favored : 97.22 % Rotamer: Outliers : 1.63 % Allowed : 14.29 % Favored : 84.08 % 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: -2.15 (0.12), residues: 4457 helix: -1.20 (0.10), residues: 2164 sheet: -1.15 (0.21), residues: 563 loop : -1.61 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP U 73 HIS 0.007 0.001 HIS T 549 PHE 0.019 0.001 PHE C 107 TYR 0.014 0.001 TYR U 77 ARG 0.004 0.000 ARG X 435 *********************** 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 621 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 563 time to evaluate : 3.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ILE cc_start: 0.8308 (tt) cc_final: 0.8008 (tt) REVERT: C 97 LYS cc_start: 0.8138 (mttp) cc_final: 0.7743 (mmmt) REVERT: C 124 ILE cc_start: 0.7522 (mm) cc_final: 0.7201 (mt) REVERT: F 56 LEU cc_start: 0.6503 (tp) cc_final: 0.6073 (pp) REVERT: F 95 ILE cc_start: 0.8334 (mm) cc_final: 0.7912 (tt) REVERT: H 97 LYS cc_start: 0.6364 (mmtt) cc_final: 0.5840 (mmtp) REVERT: I 118 LEU cc_start: 0.8136 (mt) cc_final: 0.7839 (mt) REVERT: J 123 LEU cc_start: 0.7442 (tp) cc_final: 0.7105 (mt) REVERT: P 79 GLU cc_start: 0.7845 (tp30) cc_final: 0.7643 (tp30) REVERT: P 120 LYS cc_start: 0.8352 (mmpt) cc_final: 0.8040 (mttt) REVERT: Q 25 ASP cc_start: 0.7682 (m-30) cc_final: 0.7420 (m-30) REVERT: R 188 TYR cc_start: 0.6343 (m-10) cc_final: 0.6081 (m-10) REVERT: T 537 LYS cc_start: 0.8505 (tmmt) cc_final: 0.8158 (ttpt) REVERT: U 483 MET cc_start: 0.6788 (tmm) cc_final: 0.6448 (tmm) REVERT: U 550 LEU cc_start: 0.8819 (tp) cc_final: 0.8615 (mt) REVERT: V 283 ARG cc_start: 0.7589 (ptm-80) cc_final: 0.7334 (ttp-170) REVERT: V 547 ASP cc_start: 0.6680 (p0) cc_final: 0.6366 (t0) REVERT: X 374 TYR cc_start: 0.8325 (m-80) cc_final: 0.8024 (m-80) REVERT: X 386 MET cc_start: 0.8187 (mmm) cc_final: 0.7723 (mmm) REVERT: Y 502 MET cc_start: 0.7333 (ptp) cc_final: 0.6965 (ptm) REVERT: Z 193 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8325 (tt) REVERT: Z 248 TYR cc_start: 0.8328 (m-80) cc_final: 0.7859 (m-80) REVERT: Z 310 TYR cc_start: 0.8098 (m-80) cc_final: 0.7775 (m-80) REVERT: Z 448 GLN cc_start: 0.7410 (tm-30) cc_final: 0.7078 (mm-40) REVERT: Z 504 LYS cc_start: 0.6888 (mttt) cc_final: 0.6579 (mttt) REVERT: Z 516 LYS cc_start: 0.3365 (OUTLIER) cc_final: 0.3031 (mmmm) outliers start: 58 outliers final: 39 residues processed: 597 average time/residue: 0.4867 time to fit residues: 465.8107 Evaluate side-chains 531 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 490 time to evaluate : 3.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain R residue 53 ASN Chi-restraints excluded: chain R residue 83 GLN Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain V residue 558 LYS Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 501 LYS Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 278 GLN Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 516 LYS Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 222 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 333 optimal weight: 10.0000 chunk 272 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 401 optimal weight: 3.9990 chunk 433 optimal weight: 6.9990 chunk 357 optimal weight: 4.9990 chunk 397 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 321 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 98 GLN B 92 ASN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN G 98 GLN Q 43 GLN ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 ASN T 134 ASN T 196 GLN U 104 GLN U 152 ASN U 169 GLN U 486 GLN ** U 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN U 549 HIS V 61 HIS ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 34384 Z= 0.383 Angle : 0.613 9.030 46598 Z= 0.320 Chirality : 0.046 0.247 5513 Planarity : 0.005 0.051 5991 Dihedral : 6.602 141.207 4917 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.93 % Favored : 95.92 % Rotamer: Outliers : 2.61 % Allowed : 17.10 % Favored : 80.29 % 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: -1.75 (0.12), residues: 4457 helix: -0.81 (0.11), residues: 2128 sheet: -1.20 (0.21), residues: 587 loop : -1.39 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Y 141 HIS 0.006 0.001 HIS Z 144 PHE 0.021 0.002 PHE P 77 TYR 0.019 0.002 TYR Z 460 ARG 0.006 0.000 ARG X 435 *********************** 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 586 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 493 time to evaluate : 3.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.7802 (ttp) cc_final: 0.7583 (ttm) REVERT: B 92 ASN cc_start: 0.7532 (OUTLIER) cc_final: 0.7299 (t0) REVERT: B 95 ILE cc_start: 0.8555 (tt) cc_final: 0.8213 (tt) REVERT: B 105 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7180 (tp) REVERT: C 97 LYS cc_start: 0.8090 (mttp) cc_final: 0.7805 (mmmt) REVERT: H 97 LYS cc_start: 0.6529 (mmtt) cc_final: 0.5808 (mmtp) REVERT: I 118 LEU cc_start: 0.8156 (mt) cc_final: 0.7936 (mt) REVERT: I 124 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7004 (mt) REVERT: J 56 LEU cc_start: 0.7740 (pt) cc_final: 0.6887 (tp) REVERT: J 123 LEU cc_start: 0.7424 (tp) cc_final: 0.7133 (mt) REVERT: P 79 GLU cc_start: 0.7913 (tp30) cc_final: 0.7705 (tp30) REVERT: R 171 GLN cc_start: 0.7834 (mm110) cc_final: 0.7536 (mp10) REVERT: R 188 TYR cc_start: 0.6456 (m-10) cc_final: 0.6149 (m-10) REVERT: S 159 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7586 (mt0) REVERT: T 475 GLU cc_start: 0.7854 (tp30) cc_final: 0.7575 (tp30) REVERT: T 483 MET cc_start: 0.6687 (tpp) cc_final: 0.6294 (tpt) REVERT: T 537 LYS cc_start: 0.8581 (tmmt) cc_final: 0.8199 (ttpt) REVERT: U 121 ASN cc_start: 0.8426 (p0) cc_final: 0.8185 (p0) REVERT: U 550 LEU cc_start: 0.8889 (tp) cc_final: 0.8678 (mt) REVERT: V 283 ARG cc_start: 0.7756 (ptm-80) cc_final: 0.7490 (ttp-170) REVERT: X 386 MET cc_start: 0.8353 (mmm) cc_final: 0.7796 (mmm) REVERT: Y 66 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: Y 502 MET cc_start: 0.7310 (ptp) cc_final: 0.6969 (ptm) REVERT: Z 248 TYR cc_start: 0.8438 (m-80) cc_final: 0.7910 (m-80) REVERT: Z 448 GLN cc_start: 0.7546 (tm-30) cc_final: 0.7280 (mm-40) REVERT: Z 504 LYS cc_start: 0.6894 (mttt) cc_final: 0.6579 (mttt) REVERT: Z 536 GLU cc_start: 0.6504 (mm-30) cc_final: 0.5867 (mm-30) outliers start: 93 outliers final: 68 residues processed: 553 average time/residue: 0.4745 time to fit residues: 422.3033 Evaluate side-chains 525 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 452 time to evaluate : 3.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 98 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 53 ASN Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain U residue 49 ARG Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 137 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 445 THR Chi-restraints excluded: chain U residue 481 THR Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 306 SER Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 361 THR Chi-restraints excluded: chain X residue 420 LEU Chi-restraints excluded: chain X residue 501 LYS Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 396 optimal weight: 0.9990 chunk 301 optimal weight: 0.6980 chunk 208 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 269 optimal weight: 2.9990 chunk 402 optimal weight: 0.9980 chunk 426 optimal weight: 8.9990 chunk 210 optimal weight: 0.9990 chunk 381 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 ASN R 83 GLN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 ASN U 336 GLN U 486 GLN U 515 GLN U 539 ASN V 61 HIS ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 144 HIS ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 278 GLN Z 294 ASN Z 414 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34384 Z= 0.180 Angle : 0.511 8.542 46598 Z= 0.265 Chirality : 0.042 0.164 5513 Planarity : 0.004 0.050 5991 Dihedral : 6.158 128.713 4917 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.94 % Favored : 96.93 % Rotamer: Outliers : 2.33 % Allowed : 18.42 % Favored : 79.25 % 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: -1.25 (0.12), residues: 4457 helix: -0.37 (0.11), residues: 2130 sheet: -1.03 (0.21), residues: 596 loop : -1.16 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Y 141 HIS 0.004 0.001 HIS V 83 PHE 0.025 0.001 PHE B 107 TYR 0.014 0.001 TYR X 487 ARG 0.009 0.000 ARG U 429 *********************** 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 581 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 498 time to evaluate : 3.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7008 (tp) REVERT: B 119 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6780 (tp) REVERT: F 56 LEU cc_start: 0.6636 (tp) cc_final: 0.6097 (pp) REVERT: H 97 LYS cc_start: 0.6476 (mmtt) cc_final: 0.5564 (ptmt) REVERT: I 118 LEU cc_start: 0.8214 (mt) cc_final: 0.7995 (mt) REVERT: J 105 LEU cc_start: 0.7744 (tp) cc_final: 0.7265 (mt) REVERT: J 123 LEU cc_start: 0.7401 (tp) cc_final: 0.7094 (mt) REVERT: P 120 LYS cc_start: 0.8309 (mmpt) cc_final: 0.7938 (mmmt) REVERT: R 188 TYR cc_start: 0.6477 (m-10) cc_final: 0.5983 (m-10) REVERT: S 241 ASP cc_start: 0.7834 (m-30) cc_final: 0.7508 (m-30) REVERT: T 134 ASN cc_start: 0.7775 (OUTLIER) cc_final: 0.7571 (m110) REVERT: T 537 LYS cc_start: 0.8557 (tmmt) cc_final: 0.8209 (ttpt) REVERT: U 550 LEU cc_start: 0.8847 (tp) cc_final: 0.8632 (mt) REVERT: V 283 ARG cc_start: 0.7729 (ptm-80) cc_final: 0.7455 (ttp-170) REVERT: X 386 MET cc_start: 0.8137 (mmm) cc_final: 0.7656 (mmm) REVERT: Y 502 MET cc_start: 0.7240 (ptp) cc_final: 0.7002 (ptm) REVERT: Z 248 TYR cc_start: 0.8355 (m-80) cc_final: 0.7939 (m-80) REVERT: Z 310 TYR cc_start: 0.8004 (m-80) cc_final: 0.7697 (m-80) REVERT: Z 441 ARG cc_start: 0.8028 (mmt-90) cc_final: 0.7668 (mpt180) REVERT: Z 516 LYS cc_start: 0.3480 (OUTLIER) cc_final: 0.3091 (mmmm) REVERT: Z 536 GLU cc_start: 0.6510 (mm-30) cc_final: 0.5881 (mm-30) outliers start: 83 outliers final: 53 residues processed: 552 average time/residue: 0.4621 time to fit residues: 415.0118 Evaluate side-chains 505 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 448 time to evaluate : 3.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain R residue 53 ASN Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 134 ASN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain U residue 49 ARG Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 249 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain V residue 558 LYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 516 LYS Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 355 optimal weight: 0.7980 chunk 241 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 317 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 363 optimal weight: 0.9980 chunk 294 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 217 optimal weight: 0.0050 chunk 382 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN I 87 ASN ** J 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN R 83 GLN S 174 GLN U 169 GLN U 515 GLN U 539 ASN V 61 HIS ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 42 GLN Z 414 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 34384 Z= 0.159 Angle : 0.500 9.678 46598 Z= 0.257 Chirality : 0.042 0.197 5513 Planarity : 0.004 0.048 5991 Dihedral : 5.928 120.511 4916 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.21 % Favored : 96.66 % Rotamer: Outliers : 2.39 % Allowed : 19.07 % Favored : 78.55 % 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: -0.90 (0.13), residues: 4457 helix: -0.09 (0.11), residues: 2133 sheet: -0.90 (0.21), residues: 596 loop : -0.96 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Y 141 HIS 0.003 0.001 HIS V 83 PHE 0.026 0.001 PHE B 107 TYR 0.010 0.001 TYR T 312 ARG 0.006 0.000 ARG U 429 *********************** 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 571 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 486 time to evaluate : 3.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.6431 (tt0) cc_final: 0.6208 (tt0) REVERT: B 105 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6970 (tp) REVERT: B 119 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6624 (tp) REVERT: H 97 LYS cc_start: 0.6541 (mmtt) cc_final: 0.5645 (ptmt) REVERT: I 118 LEU cc_start: 0.8158 (mt) cc_final: 0.7937 (mt) REVERT: J 105 LEU cc_start: 0.7823 (tp) cc_final: 0.7382 (mt) REVERT: J 123 LEU cc_start: 0.7404 (tp) cc_final: 0.7037 (mt) REVERT: P 52 GLN cc_start: 0.7771 (mt0) cc_final: 0.7421 (mm-40) REVERT: P 65 ASN cc_start: 0.7888 (t0) cc_final: 0.7654 (t0) REVERT: P 120 LYS cc_start: 0.8303 (mmpt) cc_final: 0.7909 (mmmt) REVERT: R 188 TYR cc_start: 0.6420 (m-10) cc_final: 0.5793 (m-10) REVERT: S 217 GLU cc_start: 0.7405 (tp30) cc_final: 0.6967 (tp30) REVERT: T 537 LYS cc_start: 0.8537 (tmmt) cc_final: 0.8195 (ttpt) REVERT: U 282 MET cc_start: 0.8837 (mmt) cc_final: 0.8428 (mmt) REVERT: V 283 ARG cc_start: 0.7729 (ptm-80) cc_final: 0.7467 (ttp-170) REVERT: V 465 ASP cc_start: 0.2303 (OUTLIER) cc_final: 0.1055 (p0) REVERT: X 386 MET cc_start: 0.8106 (mmm) cc_final: 0.7870 (mmm) REVERT: X 484 MET cc_start: 0.7791 (mmt) cc_final: 0.7296 (mmt) REVERT: Y 310 TYR cc_start: 0.8891 (m-80) cc_final: 0.8667 (m-80) REVERT: Z 248 TYR cc_start: 0.8352 (m-80) cc_final: 0.7956 (m-80) REVERT: Z 310 TYR cc_start: 0.7858 (m-80) cc_final: 0.7640 (m-80) REVERT: Z 441 ARG cc_start: 0.8019 (mmt-90) cc_final: 0.7656 (mpt180) REVERT: Z 516 LYS cc_start: 0.3382 (OUTLIER) cc_final: 0.3002 (mmmm) REVERT: Z 536 GLU cc_start: 0.6468 (mm-30) cc_final: 0.5844 (mm-30) outliers start: 85 outliers final: 63 residues processed: 545 average time/residue: 0.4623 time to fit residues: 405.7301 Evaluate side-chains 527 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 460 time to evaluate : 3.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain R residue 53 ASN Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 83 GLN Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain U residue 49 ARG Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 249 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 558 LYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 306 SER Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Y residue 495 VAL Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 467 ILE Chi-restraints excluded: chain Z residue 516 LYS Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 143 optimal weight: 0.9990 chunk 383 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 426 optimal weight: 10.0000 chunk 354 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 224 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 121 ASN U 319 HIS U 486 GLN U 539 ASN V 61 HIS ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 199 ASN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 278 GLN Y 337 GLN Z 414 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34384 Z= 0.252 Angle : 0.542 8.614 46598 Z= 0.280 Chirality : 0.043 0.239 5513 Planarity : 0.004 0.048 5991 Dihedral : 6.042 116.201 4916 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.61 % Favored : 96.23 % Rotamer: Outliers : 2.81 % Allowed : 19.69 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 4457 helix: -0.03 (0.12), residues: 2124 sheet: -0.89 (0.21), residues: 610 loop : -0.87 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP U 73 HIS 0.004 0.001 HIS Z 144 PHE 0.027 0.001 PHE C 107 TYR 0.014 0.001 TYR X 487 ARG 0.010 0.000 ARG U 429 *********************** 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 565 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 465 time to evaluate : 3.729 Fit side-chains revert: symmetry clash REVERT: B 105 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6961 (tp) REVERT: B 119 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6755 (tp) REVERT: C 95 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7807 (tp) REVERT: G 123 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6726 (tt) REVERT: H 97 LYS cc_start: 0.6578 (mmtt) cc_final: 0.5684 (ptmt) REVERT: I 118 LEU cc_start: 0.8144 (mt) cc_final: 0.7940 (mt) REVERT: J 105 LEU cc_start: 0.7954 (tp) cc_final: 0.7484 (mt) REVERT: J 123 LEU cc_start: 0.7213 (tp) cc_final: 0.6831 (mt) REVERT: P 65 ASN cc_start: 0.7838 (t0) cc_final: 0.7547 (t0) REVERT: P 75 TYR cc_start: 0.8325 (m-10) cc_final: 0.7891 (m-10) REVERT: R 153 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7936 (p0) REVERT: R 188 TYR cc_start: 0.6643 (m-10) cc_final: 0.6003 (m-10) REVERT: T 537 LYS cc_start: 0.8580 (tmmt) cc_final: 0.8233 (ttpt) REVERT: U 282 MET cc_start: 0.8918 (mmt) cc_final: 0.8430 (mmt) REVERT: V 283 ARG cc_start: 0.7730 (ptm-80) cc_final: 0.7492 (ttp-170) REVERT: X 90 MET cc_start: 0.9061 (mmt) cc_final: 0.8530 (mmt) REVERT: X 386 MET cc_start: 0.8140 (mmm) cc_final: 0.7835 (mmm) REVERT: Z 248 TYR cc_start: 0.8433 (m-80) cc_final: 0.8009 (m-80) REVERT: Z 310 TYR cc_start: 0.8065 (m-80) cc_final: 0.7766 (m-80) REVERT: Z 441 ARG cc_start: 0.8091 (mmt-90) cc_final: 0.7723 (mpt180) REVERT: Z 516 LYS cc_start: 0.3478 (OUTLIER) cc_final: 0.2870 (mmmm) outliers start: 100 outliers final: 83 residues processed: 527 average time/residue: 0.4686 time to fit residues: 401.8159 Evaluate side-chains 539 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 450 time to evaluate : 3.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 66 CYS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain R residue 53 ASN Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain U residue 49 ARG Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 121 ASN Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 249 VAL Chi-restraints excluded: chain U residue 272 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 481 THR Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 558 LYS Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 306 SER Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 420 LEU Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Y residue 495 VAL Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 355 PHE Chi-restraints excluded: chain Z residue 467 ILE Chi-restraints excluded: chain Z residue 516 LYS Chi-restraints excluded: chain Z residue 554 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 411 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 311 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 359 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 425 optimal weight: 0.7980 chunk 266 optimal weight: 0.9980 chunk 259 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN Q 49 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN U 336 GLN U 486 GLN U 539 ASN V 61 HIS ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 337 GLN Z 414 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34384 Z= 0.201 Angle : 0.519 8.370 46598 Z= 0.267 Chirality : 0.042 0.223 5513 Planarity : 0.004 0.050 5991 Dihedral : 5.918 110.721 4915 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.28 % Favored : 96.59 % Rotamer: Outliers : 3.00 % Allowed : 19.85 % Favored : 77.14 % 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: -0.66 (0.13), residues: 4457 helix: 0.09 (0.12), residues: 2127 sheet: -0.76 (0.21), residues: 598 loop : -0.82 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP U 73 HIS 0.004 0.001 HIS V 83 PHE 0.027 0.001 PHE B 107 TYR 0.011 0.001 TYR U 414 ARG 0.009 0.000 ARG U 429 *********************** 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 572 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 465 time to evaluate : 3.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 105 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7026 (tp) REVERT: B 119 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6781 (tp) REVERT: C 95 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7829 (tp) REVERT: G 123 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6623 (tt) REVERT: H 97 LYS cc_start: 0.6447 (mmtt) cc_final: 0.5641 (ptmt) REVERT: J 95 ILE cc_start: 0.8513 (tp) cc_final: 0.7900 (tp) REVERT: J 105 LEU cc_start: 0.7987 (tp) cc_final: 0.7504 (mt) REVERT: J 123 LEU cc_start: 0.7295 (tp) cc_final: 0.6896 (mt) REVERT: P 65 ASN cc_start: 0.7656 (t0) cc_final: 0.7242 (t0) REVERT: P 120 LYS cc_start: 0.8315 (mmpt) cc_final: 0.7973 (mmmt) REVERT: Q 32 LYS cc_start: 0.5921 (mmmt) cc_final: 0.5535 (mmtm) REVERT: R 153 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7890 (p0) REVERT: R 188 TYR cc_start: 0.6614 (m-10) cc_final: 0.5867 (m-10) REVERT: T 134 ASN cc_start: 0.7728 (OUTLIER) cc_final: 0.7455 (m110) REVERT: T 537 LYS cc_start: 0.8561 (tmmt) cc_final: 0.8218 (ttpt) REVERT: U 282 MET cc_start: 0.8903 (mmt) cc_final: 0.8520 (mmt) REVERT: V 283 ARG cc_start: 0.7730 (ptm-80) cc_final: 0.7487 (ttp-170) REVERT: X 386 MET cc_start: 0.8059 (mmm) cc_final: 0.7823 (mmm) REVERT: Y 66 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6570 (mp0) REVERT: Z 248 TYR cc_start: 0.8406 (m-80) cc_final: 0.7987 (m-80) REVERT: Z 310 TYR cc_start: 0.7956 (m-80) cc_final: 0.7681 (m-80) REVERT: Z 441 ARG cc_start: 0.8042 (mmt-90) cc_final: 0.7676 (mpt180) REVERT: Z 516 LYS cc_start: 0.3362 (OUTLIER) cc_final: 0.2784 (mmmm) REVERT: Z 536 GLU cc_start: 0.6534 (mm-30) cc_final: 0.5846 (mm-30) outliers start: 107 outliers final: 76 residues processed: 532 average time/residue: 0.4662 time to fit residues: 399.6959 Evaluate side-chains 534 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 450 time to evaluate : 3.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 66 CYS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain R residue 53 ASN Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 134 ASN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain U residue 49 ARG Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 185 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 249 VAL Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 445 THR Chi-restraints excluded: chain U residue 481 THR Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 558 LYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 306 SER Chi-restraints excluded: chain X residue 332 SER Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Y residue 495 VAL Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 355 PHE Chi-restraints excluded: chain Z residue 467 ILE Chi-restraints excluded: chain Z residue 516 LYS Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 262 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 253 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 270 optimal weight: 0.9990 chunk 289 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 334 optimal weight: 4.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN G 98 GLN Q 49 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN U 134 ASN U 152 ASN U 336 GLN U 539 ASN V 61 HIS ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 337 GLN Z 414 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34384 Z= 0.189 Angle : 0.516 9.794 46598 Z= 0.265 Chirality : 0.042 0.279 5513 Planarity : 0.004 0.051 5991 Dihedral : 5.828 103.476 4915 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.39 % Favored : 96.48 % Rotamer: Outliers : 3.09 % Allowed : 19.55 % Favored : 77.37 % 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: -0.52 (0.13), residues: 4457 helix: 0.22 (0.12), residues: 2120 sheet: -0.72 (0.21), residues: 600 loop : -0.74 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP R 37 HIS 0.004 0.001 HIS V 83 PHE 0.027 0.001 PHE B 107 TYR 0.017 0.001 TYR T 414 ARG 0.006 0.000 ARG X 435 *********************** 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 587 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 477 time to evaluate : 3.908 Fit side-chains revert: symmetry clash REVERT: B 105 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7070 (tp) REVERT: B 119 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6640 (tp) REVERT: C 95 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7843 (tp) REVERT: D 61 MET cc_start: 0.5787 (mmm) cc_final: 0.5323 (mmm) REVERT: G 56 LEU cc_start: 0.5710 (OUTLIER) cc_final: 0.5507 (tt) REVERT: G 123 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6833 (tt) REVERT: H 97 LYS cc_start: 0.6554 (mmtt) cc_final: 0.5693 (ptmt) REVERT: J 95 ILE cc_start: 0.8411 (tp) cc_final: 0.7911 (tp) REVERT: J 105 LEU cc_start: 0.7966 (tp) cc_final: 0.7538 (mt) REVERT: J 123 LEU cc_start: 0.7346 (tp) cc_final: 0.6922 (mt) REVERT: P 65 ASN cc_start: 0.7705 (t0) cc_final: 0.7364 (t0) REVERT: Q 32 LYS cc_start: 0.5862 (mmmt) cc_final: 0.5620 (mmtm) REVERT: R 153 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7779 (p0) REVERT: R 188 TYR cc_start: 0.6578 (m-10) cc_final: 0.5890 (m-10) REVERT: T 134 ASN cc_start: 0.7721 (OUTLIER) cc_final: 0.7442 (m110) REVERT: T 537 LYS cc_start: 0.8586 (tmmt) cc_final: 0.8236 (ttpt) REVERT: U 282 MET cc_start: 0.8877 (mmt) cc_final: 0.8498 (mmt) REVERT: U 516 ASP cc_start: 0.6828 (OUTLIER) cc_final: 0.6541 (m-30) REVERT: V 283 ARG cc_start: 0.7723 (ptm-80) cc_final: 0.7482 (ttp-170) REVERT: V 465 ASP cc_start: 0.2002 (OUTLIER) cc_final: 0.1068 (p0) REVERT: X 386 MET cc_start: 0.8047 (mmm) cc_final: 0.7829 (mmm) REVERT: Z 248 TYR cc_start: 0.8361 (m-80) cc_final: 0.7985 (m-80) REVERT: Z 310 TYR cc_start: 0.7895 (m-80) cc_final: 0.7657 (m-80) REVERT: Z 441 ARG cc_start: 0.8017 (mmt-90) cc_final: 0.7661 (mpt180) REVERT: Z 516 LYS cc_start: 0.3392 (OUTLIER) cc_final: 0.2788 (mmmm) REVERT: Z 536 GLU cc_start: 0.6524 (mm-30) cc_final: 0.5823 (mm-30) outliers start: 110 outliers final: 81 residues processed: 549 average time/residue: 0.4566 time to fit residues: 406.3948 Evaluate side-chains 547 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 456 time to evaluate : 3.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 66 CYS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain R residue 53 ASN Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 134 ASN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain U residue 49 ARG Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 249 VAL Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 445 THR Chi-restraints excluded: chain U residue 481 THR Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 558 LYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 233 ILE Chi-restraints excluded: chain X residue 306 SER Chi-restraints excluded: chain X residue 332 SER Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Y residue 495 VAL Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 355 PHE Chi-restraints excluded: chain Z residue 467 ILE Chi-restraints excluded: chain Z residue 516 LYS Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 386 optimal weight: 2.9990 chunk 407 optimal weight: 2.9990 chunk 371 optimal weight: 0.7980 chunk 396 optimal weight: 0.9980 chunk 238 optimal weight: 7.9990 chunk 172 optimal weight: 0.6980 chunk 311 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 357 optimal weight: 0.9990 chunk 374 optimal weight: 0.9990 chunk 394 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN F 98 GLN G 98 GLN I 98 GLN Q 49 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN U 336 GLN U 515 GLN U 539 ASN V 61 HIS ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 337 GLN Z 414 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34384 Z= 0.177 Angle : 0.515 8.686 46598 Z= 0.264 Chirality : 0.042 0.224 5513 Planarity : 0.004 0.052 5991 Dihedral : 5.770 97.356 4915 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 2.95 % Allowed : 19.94 % Favored : 77.11 % 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: -0.43 (0.13), residues: 4457 helix: 0.26 (0.12), residues: 2128 sheet: -0.63 (0.21), residues: 598 loop : -0.68 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 37 HIS 0.004 0.001 HIS V 83 PHE 0.031 0.001 PHE D 107 TYR 0.016 0.001 TYR F 102 ARG 0.008 0.000 ARG X 289 *********************** 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 583 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 478 time to evaluate : 3.745 Fit side-chains revert: symmetry clash REVERT: B 105 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7045 (tp) REVERT: B 119 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6552 (tp) REVERT: C 66 CYS cc_start: 0.7352 (m) cc_final: 0.7112 (m) REVERT: C 95 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7856 (tp) REVERT: F 109 LEU cc_start: 0.7971 (mm) cc_final: 0.7763 (mm) REVERT: G 123 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6864 (tt) REVERT: H 97 LYS cc_start: 0.6630 (mmtt) cc_final: 0.5813 (ptmt) REVERT: J 95 ILE cc_start: 0.8217 (tp) cc_final: 0.7962 (tp) REVERT: J 105 LEU cc_start: 0.7972 (tp) cc_final: 0.7579 (mt) REVERT: J 123 LEU cc_start: 0.7328 (tp) cc_final: 0.6900 (mt) REVERT: P 65 ASN cc_start: 0.7695 (t0) cc_final: 0.7347 (t0) REVERT: P 120 LYS cc_start: 0.8279 (mmpt) cc_final: 0.7925 (mmmt) REVERT: R 153 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7722 (p0) REVERT: R 188 TYR cc_start: 0.6607 (m-10) cc_final: 0.5833 (m-10) REVERT: T 134 ASN cc_start: 0.7707 (OUTLIER) cc_final: 0.7435 (m110) REVERT: T 537 LYS cc_start: 0.8577 (tmmt) cc_final: 0.8247 (ttpt) REVERT: V 283 ARG cc_start: 0.7746 (ptm-80) cc_final: 0.7504 (ttp-170) REVERT: V 465 ASP cc_start: 0.2203 (OUTLIER) cc_final: 0.1250 (p0) REVERT: Z 193 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8300 (tt) REVERT: Z 248 TYR cc_start: 0.8371 (m-80) cc_final: 0.8001 (m-80) REVERT: Z 310 TYR cc_start: 0.7819 (m-80) cc_final: 0.7610 (m-80) REVERT: Z 441 ARG cc_start: 0.7988 (mmt-90) cc_final: 0.7644 (mpt180) REVERT: Z 516 LYS cc_start: 0.3350 (OUTLIER) cc_final: 0.2768 (mmmm) REVERT: Z 536 GLU cc_start: 0.6431 (mm-30) cc_final: 0.5750 (mm-30) outliers start: 105 outliers final: 81 residues processed: 545 average time/residue: 0.4731 time to fit residues: 418.9477 Evaluate side-chains 550 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 460 time to evaluate : 3.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 66 CYS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain R residue 53 ASN Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 134 ASN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain U residue 49 ARG Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 249 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 445 THR Chi-restraints excluded: chain U residue 481 THR Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 515 GLN Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 558 LYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 233 ILE Chi-restraints excluded: chain X residue 306 SER Chi-restraints excluded: chain X residue 332 SER Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Y residue 495 VAL Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 355 PHE Chi-restraints excluded: chain Z residue 467 ILE Chi-restraints excluded: chain Z residue 516 LYS Chi-restraints excluded: chain Z residue 554 LEU Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 260 optimal weight: 0.9990 chunk 418 optimal weight: 0.9980 chunk 255 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 291 optimal weight: 3.9990 chunk 439 optimal weight: 4.9990 chunk 404 optimal weight: 0.9990 chunk 349 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 270 optimal weight: 0.4980 chunk 214 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN J 87 ASN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN U 486 GLN U 515 GLN U 539 ASN V 61 HIS ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 337 GLN Z 414 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34384 Z= 0.181 Angle : 0.517 8.456 46598 Z= 0.266 Chirality : 0.042 0.224 5513 Planarity : 0.004 0.053 5991 Dihedral : 5.750 92.277 4915 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 2.75 % Allowed : 20.28 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.13), residues: 4457 helix: 0.31 (0.12), residues: 2132 sheet: -0.61 (0.21), residues: 600 loop : -0.63 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 37 HIS 0.004 0.001 HIS V 83 PHE 0.034 0.001 PHE D 107 TYR 0.017 0.001 TYR X 487 ARG 0.005 0.000 ARG T 513 ********************** 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 567 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 469 time to evaluate : 3.807 Fit side-chains revert: symmetry clash REVERT: B 105 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7030 (tp) REVERT: B 119 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6485 (tp) REVERT: C 66 CYS cc_start: 0.7473 (m) cc_final: 0.7204 (m) REVERT: G 123 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6799 (tt) REVERT: H 97 LYS cc_start: 0.6706 (mmtt) cc_final: 0.5852 (ptmt) REVERT: J 105 LEU cc_start: 0.8001 (tp) cc_final: 0.7652 (mt) REVERT: J 123 LEU cc_start: 0.7381 (tp) cc_final: 0.6942 (mt) REVERT: P 65 ASN cc_start: 0.7691 (t0) cc_final: 0.7363 (t0) REVERT: P 120 LYS cc_start: 0.8281 (mmpt) cc_final: 0.7918 (mmmt) REVERT: R 153 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7699 (p0) REVERT: R 188 TYR cc_start: 0.6623 (m-10) cc_final: 0.5803 (m-10) REVERT: T 134 ASN cc_start: 0.7702 (OUTLIER) cc_final: 0.7436 (m110) REVERT: T 537 LYS cc_start: 0.8580 (tmmt) cc_final: 0.8259 (ttpt) REVERT: U 53 PHE cc_start: 0.6927 (p90) cc_final: 0.6384 (p90) REVERT: V 283 ARG cc_start: 0.7698 (ptm-80) cc_final: 0.7465 (ttp-170) REVERT: V 465 ASP cc_start: 0.2101 (OUTLIER) cc_final: 0.1216 (p0) REVERT: X 435 ARG cc_start: 0.7156 (mtt-85) cc_final: 0.6729 (mtt-85) REVERT: Z 193 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8322 (tt) REVERT: Z 248 TYR cc_start: 0.8377 (m-80) cc_final: 0.8005 (m-80) REVERT: Z 310 TYR cc_start: 0.7775 (m-80) cc_final: 0.7573 (m-80) REVERT: Z 317 ASP cc_start: 0.7084 (m-30) cc_final: 0.6866 (m-30) REVERT: Z 441 ARG cc_start: 0.7980 (mmt-90) cc_final: 0.7640 (mpt180) REVERT: Z 516 LYS cc_start: 0.3224 (OUTLIER) cc_final: 0.2656 (mmmm) REVERT: Z 536 GLU cc_start: 0.6439 (mm-30) cc_final: 0.5756 (mm-30) outliers start: 98 outliers final: 84 residues processed: 537 average time/residue: 0.4626 time to fit residues: 403.4095 Evaluate side-chains 546 residues out of total 3562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 454 time to evaluate : 3.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 66 CYS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 69 LYS Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain R residue 53 ASN Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 134 ASN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain U residue 49 ARG Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 249 VAL Chi-restraints excluded: chain U residue 272 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 445 THR Chi-restraints excluded: chain U residue 481 THR Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 515 GLN Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 558 LYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 233 ILE Chi-restraints excluded: chain X residue 306 SER Chi-restraints excluded: chain X residue 332 SER Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 491 ASP Chi-restraints excluded: chain Y residue 495 VAL Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 355 PHE Chi-restraints excluded: chain Z residue 467 ILE Chi-restraints excluded: chain Z residue 516 LYS Chi-restraints excluded: chain Z residue 554 LEU Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 277 optimal weight: 0.1980 chunk 372 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 322 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 350 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 chunk 359 optimal weight: 0.1980 chunk 44 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN T 435 GLN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 486 GLN U 515 GLN U 539 ASN V 61 HIS ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 336 GLN ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.138275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.110901 restraints weight = 51197.526| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.59 r_work: 0.3196 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 34384 Z= 0.150 Angle : 0.509 10.292 46598 Z= 0.260 Chirality : 0.042 0.210 5513 Planarity : 0.004 0.054 5991 Dihedral : 5.612 88.678 4915 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.21 % Favored : 96.66 % Rotamer: Outliers : 2.47 % Allowed : 20.81 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.13), residues: 4457 helix: 0.42 (0.12), residues: 2121 sheet: -0.54 (0.21), residues: 608 loop : -0.54 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 37 HIS 0.004 0.001 HIS V 83 PHE 0.034 0.001 PHE D 107 TYR 0.010 0.001 TYR T 414 ARG 0.005 0.000 ARG T 513 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8880.06 seconds wall clock time: 161 minutes 38.78 seconds (9698.78 seconds total)