Starting phenix.real_space_refine on Sat Mar 16 20:41:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5z_13211/03_2024/7p5z_13211_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5z_13211/03_2024/7p5z_13211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5z_13211/03_2024/7p5z_13211.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5z_13211/03_2024/7p5z_13211.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5z_13211/03_2024/7p5z_13211_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5z_13211/03_2024/7p5z_13211_trim_updated.pdb" } resolution = 3.3 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= 0.001 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: 8 Type Number sf(0) Gaussians Zn 11 6.06 5 P 128 5.49 5 Mg 10 5.21 5 S 302 5.16 5 C 42037 2.51 5 N 11762 2.21 5 O 13151 1.98 5 H 66786 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 GLU 240": "OE1" <-> "OE2" Residue "2 TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 ASP 299": "OD1" <-> "OD2" Residue "2 TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 ASP 416": "OD1" <-> "OD2" Residue "2 ASP 495": "OD1" <-> "OD2" Residue "2 PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 ASP 610": "OD1" <-> "OD2" Residue "2 ASP 678": "OD1" <-> "OD2" Residue "2 GLU 693": "OE1" <-> "OE2" Residue "3 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 GLU 183": "OE1" <-> "OE2" Residue "3 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 GLU 260": "OE1" <-> "OE2" Residue "3 GLU 263": "OE1" <-> "OE2" Residue "3 TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 GLU 394": "OE1" <-> "OE2" Residue "3 PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 ASP 476": "OD1" <-> "OD2" Residue "3 PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 GLU 665": "OE1" <-> "OE2" Residue "4 PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 GLU 267": "OE1" <-> "OE2" Residue "4 PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 GLU 806": "OE1" <-> "OE2" Residue "4 ASP 835": "OD1" <-> "OD2" Residue "5 TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 ASP 21": "OD1" <-> "OD2" Residue "5 ASP 22": "OD1" <-> "OD2" Residue "5 PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 ASP 81": "OD1" <-> "OD2" Residue "5 GLU 91": "OE1" <-> "OE2" Residue "5 ASP 150": "OD1" <-> "OD2" Residue "5 PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 ASP 252": "OD1" <-> "OD2" Residue "5 GLU 368": "OE1" <-> "OE2" Residue "5 ASP 409": "OD1" <-> "OD2" Residue "5 PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 GLU 642": "OE1" <-> "OE2" Residue "6 ASP 105": "OD1" <-> "OD2" Residue "6 TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 GLU 162": "OE1" <-> "OE2" Residue "6 PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 TYR 597": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 PHE 709": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 GLU 749": "OE1" <-> "OE2" Residue "6 TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 GLU 808": "OE1" <-> "OE2" Residue "7 PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 ASP 81": "OD1" <-> "OD2" Residue "7 GLU 91": "OE1" <-> "OE2" Residue "7 GLU 164": "OE1" <-> "OE2" Residue "7 PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 GLU 421": "OE1" <-> "OE2" Residue "7 ASP 453": "OD1" <-> "OD2" Residue "7 ASP 500": "OD1" <-> "OD2" Residue "7 GLU 525": "OE1" <-> "OE2" Residue "7 TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 ASP 602": "OD1" <-> "OD2" Residue "7 ASP 609": "OD1" <-> "OD2" Residue "7 GLU 614": "OE1" <-> "OE2" Residue "7 TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 ASP 670": "OD1" <-> "OD2" Residue "7 GLU 714": "OE1" <-> "OE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A GLU 425": "OE1" <-> "OE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 610": "OD1" <-> "OD2" Residue "A GLU 622": "OE1" <-> "OE2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "B ASP 18": "OD1" <-> "OD2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 213": "OD1" <-> "OD2" Residue "B TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B ASP 235": "OD1" <-> "OD2" Residue "B ASP 361": "OD1" <-> "OD2" Residue "B PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 491": "OE1" <-> "OE2" Residue "B ASP 537": "OD1" <-> "OD2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C GLU 295": "OE1" <-> "OE2" Residue "C PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 378": "OE1" <-> "OE2" Residue "C TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 534": "OE1" <-> "OE2" Residue "C PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 569": "OD1" <-> "OD2" Residue "C ASP 635": "OD1" <-> "OD2" Residue "C PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 745": "OE1" <-> "OE2" Residue "C GLU 788": "OE1" <-> "OE2" Residue "C TYR 836": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D ASP 252": "OD1" <-> "OD2" Residue "D ASP 383": "OD1" <-> "OD2" Residue "D GLU 465": "OE1" <-> "OE2" Residue "D TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 620": "OE1" <-> "OE2" Residue "D GLU 637": "OE1" <-> "OE2" Residue "D PHE 684": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 363": "OE1" <-> "OE2" Residue "E GLU 401": "OE1" <-> "OE2" Residue "E PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 645": "OD1" <-> "OD2" Residue "E GLU 657": "OE1" <-> "OE2" Residue "E PHE 709": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 739": "OD1" <-> "OD2" Residue "E GLU 749": "OE1" <-> "OE2" Residue "E TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 801": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 151": "OE1" <-> "OE2" Residue "F GLU 164": "OE1" <-> "OE2" Residue "F ASP 187": "OD1" <-> "OD2" Residue "F TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 233": "OD1" <-> "OD2" Residue "F GLU 256": "OE1" <-> "OE2" Residue "F ASP 263": "OD1" <-> "OD2" Residue "F GLU 268": "OE1" <-> "OE2" Residue "F PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "F GLU 288": "OE1" <-> "OE2" Residue "F TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 377": "OE1" <-> "OE2" Residue "F ASP 396": "OD1" <-> "OD2" Residue "F ASP 500": "OD1" <-> "OD2" Residue "F GLU 531": "OE1" <-> "OE2" Residue "F GLU 614": "OE1" <-> "OE2" Residue "F GLU 634": "OE1" <-> "OE2" Residue "F ASP 670": "OD1" <-> "OD2" Residue "F ASP 706": "OD1" <-> "OD2" Residue "F GLU 715": "OE1" <-> "OE2" Residue "1 PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 GLU 451": "OE1" <-> "OE2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "G PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 282": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 134187 Number of models: 1 Model: "" Number of chains: 29 Chain: "2" Number of atoms: 9918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 9918 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 25, 'TRANS': 597} Chain breaks: 2 Chain: "3" Number of atoms: 9381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 9381 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 24, 'TRANS': 570} Chain breaks: 3 Chain: "4" Number of atoms: 10697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 10697 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 27, 'TRANS': 648} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "5" Number of atoms: 10253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 10253 Classifications: {'peptide': 652} Link IDs: {'PTRANS': 28, 'TRANS': 623} Chain breaks: 3 Chain: "6" Number of atoms: 9681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 9681 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 22, 'TRANS': 586} Chain breaks: 5 Chain: "7" Number of atoms: 10935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 10935 Classifications: {'peptide': 689} Link IDs: {'PTRANS': 30, 'TRANS': 658} Chain breaks: 2 Chain: "A" Number of atoms: 9915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 9915 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 25, 'TRANS': 597} Chain breaks: 2 Chain: "B" Number of atoms: 9381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 9381 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 24, 'TRANS': 570} Chain breaks: 3 Chain: "C" Number of atoms: 10452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 10452 Classifications: {'peptide': 654} Link IDs: {'PTRANS': 24, 'TRANS': 629} Chain breaks: 3 Chain: "D" Number of atoms: 10251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 10251 Classifications: {'peptide': 652} Link IDs: {'PTRANS': 28, 'TRANS': 623} Chain breaks: 3 Chain: "E" Number of atoms: 9681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 9681 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 22, 'TRANS': 586} Chain breaks: 5 Chain: "F" Number of atoms: 10935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 10935 Classifications: {'peptide': 689} Link IDs: {'PTRANS': 30, 'TRANS': 658} Chain breaks: 2 Chain: "1" Number of atoms: 5459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5459 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 13, 'TRANS': 322} Chain breaks: 2 Chain: "G" Number of atoms: 3585 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 3576 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 8, 'TRANS': 204} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 213, 3576 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 8, 'TRANS': 204} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 3608 Chain: "X" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1682 Classifications: {'DNA': 53} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 52} Chain: "Y" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1682 Classifications: {'DNA': 53} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 52} Chain: "2" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" 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: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 2, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 2, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2578 SG CYS 2 341 118.067 147.800 84.287 1.00119.94 S ATOM 2629 SG CYS 2 344 117.178 151.334 84.786 1.00123.90 S ATOM 2933 SG CYS 2 364 116.448 148.846 87.605 1.00129.40 S ATOM 2971 SG CYS 2 367 114.611 149.104 84.203 1.00135.65 S ATOM 22148 SG CYS 4 349 113.717 100.797 102.839 1.00125.04 S ATOM 22188 SG CYS 4 352 112.726 98.955 105.875 1.00135.26 S ATOM 22476 SG CYS 4 371 111.547 97.823 102.626 1.00137.96 S ATOM 22556 SG CYS 4 376 110.166 100.975 104.129 1.00142.63 S ATOM 32576 SG CYS 5 183 114.285 137.982 61.588 1.00 91.77 S ATOM 32624 SG CYS 5 186 111.229 139.468 60.426 1.00 96.15 S ATOM 32889 SG CYS 5 211 112.512 140.635 63.502 1.00100.03 S ATOM 33242 SG CYS 5 236 111.074 137.195 63.243 1.00104.56 S ATOM 42596 SG CYS 6 311 113.977 121.357 102.448 1.00148.89 S ATOM 42635 SG CYS 6 314 111.614 122.446 104.908 1.00154.24 S ATOM 42939 SG CYS 6 333 112.332 118.860 105.105 1.00156.72 S ATOM 43002 SG CYS 6 338 110.309 120.500 102.327 1.00170.22 S ATOM 53562 SG CYS 7 262 112.010 89.625 76.605 1.00101.45 S ATOM 53601 SG CYS 7 265 109.736 88.414 74.079 1.00101.19 S ATOM 53894 SG CYS 7 284 111.223 91.858 73.852 1.00 99.48 S ATOM 53959 SG CYS 7 289 108.567 90.995 76.323 1.00104.98 S ATOM 63441 SG CYS A 341 108.359 111.577 84.589 1.00120.12 S ATOM 63492 SG CYS A 344 109.401 108.127 85.110 1.00122.66 S ATOM 63796 SG CYS A 364 110.129 110.717 87.847 1.00122.16 S ATOM 63834 SG CYS A 367 111.930 110.453 84.450 1.00128.21 S ATOM 82765 SG CYS C 349 112.631 158.896 102.715 1.00128.90 S ATOM 82805 SG CYS C 352 113.761 160.896 105.603 1.00137.05 S ATOM 83093 SG CYS C 371 114.780 161.812 102.229 1.00135.36 S ATOM 83173 SG CYS C 376 116.267 158.799 103.871 1.00141.22 S ATOM 93193 SG CYS D 183 112.257 121.143 61.587 1.00 89.97 S ATOM 93241 SG CYS D 186 115.371 119.650 60.450 1.00 93.02 S ATOM 93506 SG CYS D 211 114.079 118.581 63.547 1.00 97.72 S ATOM 93859 SG CYS D 236 115.495 121.965 63.193 1.00103.43 S ATOM A02H7 SG CYS E 311 112.453 138.324 102.468 1.00151.19 S ATOM A02IA SG CYS E 314 114.639 137.132 105.191 1.00156.37 S ATOM A02QQ SG CYS E 333 114.210 140.838 105.019 1.00158.33 S ATOM A02SH SG CYS E 338 116.111 138.878 102.364 1.00173.09 S ATOM A0AXT SG CYS F 262 114.493 169.621 76.085 1.00103.32 S ATOM A0AYW SG CYS F 265 116.864 170.831 73.596 1.00102.13 S ATOM A0B71 SG CYS F 284 115.337 167.413 73.325 1.00103.69 S ATOM A0B8U SG CYS F 289 117.900 168.126 75.926 1.00105.18 S ATOM A0N30 SG CYS G 661 126.637 43.790 83.627 1.00217.24 S ATOM A0N43 SG CYS G 664 130.512 43.334 83.274 1.00210.92 S Time building chain proxies: 44.05, per 1000 atoms: 0.33 Number of scatterers: 134187 At special positions: 0 Unit cell: (226.8, 222.48, 170.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 11 29.99 S 302 16.00 P 128 15.00 Mg 10 11.99 O 13151 8.00 N 11762 7.00 C 42037 6.00 H 66786 1.00 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: 80.62 Conformation dependent library (CDL) restraints added in 11.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 903 " pdb="ZN ZN 2 903 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 2 903 " - pdb=" SG CYS 2 367 " pdb="ZN ZN 2 903 " - pdb=" SG CYS 2 341 " pdb="ZN ZN 2 903 " - pdb=" SG CYS 2 364 " pdb=" ZN 41002 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 371 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 376 " pdb=" ZN 5 803 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 186 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 211 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 183 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 236 " pdb=" ZN 61101 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 311 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 333 " pdb=" ZN 7 904 " pdb="ZN ZN 7 904 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 7 904 " - pdb=" SG CYS 7 262 " pdb="ZN ZN 7 904 " - pdb=" SG CYS 7 289 " pdb="ZN ZN 7 904 " - pdb=" SG CYS 7 284 " pdb=" ZN A 903 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 344 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 367 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 341 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 364 " pdb=" ZN C1002 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 352 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 371 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 349 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 376 " pdb=" ZN D 803 " pdb="ZN ZN D 803 " - pdb=" SG CYS D 186 " pdb="ZN ZN D 803 " - pdb=" SG CYS D 211 " pdb="ZN ZN D 803 " - pdb=" SG CYS D 236 " pdb="ZN ZN D 803 " - pdb=" SG CYS D 183 " pdb=" ZN E1101 " pdb="ZN ZN E1101 " - pdb=" SG CYS E 314 " pdb="ZN ZN E1101 " - pdb=" SG CYS E 338 " pdb="ZN ZN E1101 " - pdb=" SG CYS E 311 " pdb="ZN ZN E1101 " - pdb=" SG CYS E 333 " pdb=" ZN F 904 " pdb="ZN ZN F 904 " - pdb=" SG CYS F 262 " pdb="ZN ZN F 904 " - pdb=" SG CYS F 265 " pdb="ZN ZN F 904 " - pdb=" SG CYS F 284 " pdb="ZN ZN F 904 " - pdb=" SG CYS F 289 " pdb=" ZN G 801 " pdb="ZN ZN G 801 " - pdb=" NE2 HIS G 674 " pdb="ZN ZN G 801 " - pdb=" ND1 HIS G 680 " pdb="ZN ZN G 801 " - pdb=" SG CYS G 664 " pdb="ZN ZN G 801 " - pdb=" SG CYS G 661 " Number of angles added : 61 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15608 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 287 helices and 83 sheets defined 45.1% alpha, 14.1% beta 49 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 78.53 Creating SS restraints... Processing helix chain '2' and resid 193 through 200 removed outlier: 3.765A pdb=" N GLN 2 200 " --> pdb=" O GLU 2 196 " (cutoff:3.500A) Processing helix chain '2' and resid 201 through 217 Processing helix chain '2' and resid 225 through 238 Processing helix chain '2' and resid 245 through 253 Processing helix chain '2' and resid 254 through 263 Processing helix chain '2' and resid 265 through 283 removed outlier: 4.181A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE 2 270 " --> pdb=" O GLU 2 266 " (cutoff:3.500A) Processing helix chain '2' and resid 477 through 491 removed outlier: 3.539A pdb=" N ASP 2 490 " --> pdb=" O LYS 2 486 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ARG 2 491 " --> pdb=" O ILE 2 487 " (cutoff:3.500A) Processing helix chain '2' and resid 492 through 501 removed outlier: 3.664A pdb=" N SER 2 500 " --> pdb=" O LYS 2 496 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET 2 501 " --> pdb=" O ILE 2 497 " (cutoff:3.500A) Processing helix chain '2' and resid 508 through 521 Processing helix chain '2' and resid 548 through 560 Processing helix chain '2' and resid 594 through 600 removed outlier: 3.706A pdb=" N ASP 2 600 " --> pdb=" O LEU 2 596 " (cutoff:3.500A) Processing helix chain '2' and resid 613 through 626 Processing helix chain '2' and resid 662 through 668 removed outlier: 3.696A pdb=" N VAL 2 667 " --> pdb=" O LEU 2 663 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N SER 2 668 " --> pdb=" O ALA 2 664 " (cutoff:3.500A) Processing helix chain '2' and resid 670 through 677 removed outlier: 4.117A pdb=" N ARG 2 676 " --> pdb=" O PRO 2 672 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE 2 677 " --> pdb=" O ILE 2 673 " (cutoff:3.500A) Processing helix chain '2' and resid 688 through 707 Processing helix chain '2' and resid 759 through 774 removed outlier: 3.892A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) Processing helix chain '2' and resid 782 through 801 Processing helix chain '2' and resid 806 through 825 removed outlier: 3.996A pdb=" N LEU 2 810 " --> pdb=" O THR 2 806 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG 2 824 " --> pdb=" O PHE 2 820 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU 2 825 " --> pdb=" O ALA 2 821 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 849 removed outlier: 3.541A pdb=" N ALA 2 848 " --> pdb=" O SER 2 844 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLN 2 849 " --> pdb=" O PHE 2 845 " (cutoff:3.500A) Processing helix chain '2' and resid 850 through 862 removed outlier: 3.651A pdb=" N ARG 2 859 " --> pdb=" O ARG 2 855 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER 2 860 " --> pdb=" O GLN 2 856 " (cutoff:3.500A) Processing helix chain '2' and resid 184 through 190 removed outlier: 5.685A pdb=" N SER 2 187 " --> pdb=" O GLU 2 184 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASN 2 188 " --> pdb=" O SER 2 185 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LYS 2 190 " --> pdb=" O SER 2 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 200 removed outlier: 3.808A pdb=" N GLN A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 217 Processing helix chain 'A' and resid 225 through 238 Processing helix chain 'A' and resid 245 through 253 Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 265 through 283 removed outlier: 3.889A pdb=" N LYS A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 removed outlier: 3.641A pdb=" N GLU A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ARG A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.783A pdb=" N SER A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET A 501 " --> pdb=" O ILE A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 548 through 560 Processing helix chain 'A' and resid 594 through 600 removed outlier: 3.866A pdb=" N ASP A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 626 Processing helix chain 'A' and resid 662 through 668 removed outlier: 3.691A pdb=" N VAL A 667 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N SER A 668 " --> pdb=" O ALA A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 677 removed outlier: 4.079A pdb=" N ARG A 676 " --> pdb=" O PRO A 672 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE A 677 " --> pdb=" O ILE A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 707 Processing helix chain 'A' and resid 759 through 774 removed outlier: 3.722A pdb=" N LYS A 765 " --> pdb=" O GLU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 801 Processing helix chain 'A' and resid 806 through 825 removed outlier: 3.904A pdb=" N LEU A 810 " --> pdb=" O THR A 806 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A 824 " --> pdb=" O PHE A 820 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 849 removed outlier: 3.716A pdb=" N ALA A 848 " --> pdb=" O SER A 844 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN A 849 " --> pdb=" O PHE A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 862 removed outlier: 3.716A pdb=" N ARG A 859 " --> pdb=" O ARG A 855 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 860 " --> pdb=" O GLN A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 190 removed outlier: 5.536A pdb=" N SER A 187 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN A 188 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS A 190 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 36 removed outlier: 4.371A pdb=" N THR 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) Processing helix chain '3' and resid 37 through 53 removed outlier: 3.852A pdb=" N ALA 3 53 " --> pdb=" O ASN 3 49 " (cutoff:3.500A) Processing helix chain '3' and resid 99 through 107 Processing helix chain '3' and resid 108 through 117 Processing helix chain '3' and resid 118 through 137 Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 343 through 356 removed outlier: 3.893A pdb=" N LYS 3 355 " --> pdb=" O ASN 3 351 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS 3 356 " --> pdb=" O LYS 3 352 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 367 removed outlier: 3.662A pdb=" N LEU 3 367 " --> pdb=" O LEU 3 363 " (cutoff:3.500A) Processing helix chain '3' and resid 374 through 387 Processing helix chain '3' and resid 414 through 426 Processing helix chain '3' and resid 439 through 444 removed outlier: 3.930A pdb=" N THR 3 443 " --> pdb=" O GLY 3 439 " (cutoff:3.500A) Processing helix chain '3' and resid 460 through 466 Processing helix chain '3' and resid 479 through 492 removed outlier: 3.872A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL 3 489 " --> pdb=" O ALA 3 485 " (cutoff:3.500A) Processing helix chain '3' and resid 528 through 534 removed outlier: 3.560A pdb=" N ASN 3 532 " --> pdb=" O ASP 3 528 " (cutoff:3.500A) Processing helix chain '3' and resid 536 through 544 removed outlier: 3.599A pdb=" N ARG 3 542 " --> pdb=" O SER 3 538 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE 3 543 " --> pdb=" O LEU 3 539 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP 3 544 " --> pdb=" O LEU 3 540 " (cutoff:3.500A) Processing helix chain '3' and resid 554 through 570 removed outlier: 3.639A pdb=" N ARG 3 570 " --> pdb=" O LEU 3 566 " (cutoff:3.500A) Processing helix chain '3' and resid 652 through 666 Processing helix chain '3' and resid 672 through 689 Processing helix chain '3' and resid 698 through 717 removed outlier: 3.933A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 Processing helix chain 'B' and resid 18 through 36 removed outlier: 4.542A pdb=" N THR B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 53 Processing helix chain 'B' and resid 99 through 107 Processing helix chain 'B' and resid 108 through 117 Processing helix chain 'B' and resid 118 through 137 Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 343 through 356 removed outlier: 3.798A pdb=" N LYS B 355 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS B 356 " --> pdb=" O LYS B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 367 removed outlier: 3.500A pdb=" N LEU B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 387 Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 439 through 444 removed outlier: 3.937A pdb=" N THR B 443 " --> pdb=" O GLY B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 466 Processing helix chain 'B' and resid 479 through 492 removed outlier: 3.864A pdb=" N ALA B 485 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 534 removed outlier: 3.600A pdb=" N ASN B 532 " --> pdb=" O ASP B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 544 removed outlier: 3.652A pdb=" N PHE B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ASP B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 570 removed outlier: 3.732A pdb=" N ARG B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 666 Processing helix chain 'B' and resid 672 through 689 Processing helix chain 'B' and resid 698 through 717 removed outlier: 3.950A pdb=" N LEU B 702 " --> pdb=" O THR B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 738 Processing helix chain '4' and resid 161 through 169 Proline residue: 4 169 - end of helix Processing helix chain '4' and resid 186 through 201 removed outlier: 3.856A pdb=" N PHE 4 201 " --> pdb=" O PHE 4 197 " (cutoff:3.500A) Processing helix chain '4' and resid 224 through 237 removed outlier: 3.729A pdb=" N LYS 4 228 " --> pdb=" O LEU 4 224 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN 4 229 " --> pdb=" O TYR 4 225 " (cutoff:3.500A) Processing helix chain '4' and resid 244 through 252 removed outlier: 4.307A pdb=" N LEU 4 248 " --> pdb=" O ASP 4 244 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU 4 249 " --> pdb=" O ALA 4 245 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA 4 250 " --> pdb=" O ARG 4 246 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR 4 251 " --> pdb=" O ASN 4 247 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LYS 4 252 " --> pdb=" O LEU 4 248 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 244 through 252' Processing helix chain '4' and resid 254 through 264 removed outlier: 4.483A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 288 removed outlier: 3.898A pdb=" N SER 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN 4 287 " --> pdb=" O LEU 4 283 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN 4 288 " --> pdb=" O ILE 4 284 " (cutoff:3.500A) Processing helix chain '4' and resid 293 through 299 Processing helix chain '4' and resid 477 through 482 removed outlier: 4.172A pdb=" N ILE 4 481 " --> pdb=" O ASP 4 477 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU 4 482 " --> pdb=" O THR 4 478 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 477 through 482' Processing helix chain '4' and resid 483 through 492 Processing helix chain '4' and resid 502 through 515 removed outlier: 3.665A pdb=" N ARG 4 515 " --> pdb=" O GLU 4 511 " (cutoff:3.500A) Processing helix chain '4' and resid 517 through 528 removed outlier: 5.612A pdb=" N ALA 4 527 " --> pdb=" O ALA 4 523 " (cutoff:3.500A) Proline residue: 4 528 - end of helix Processing helix chain '4' and resid 533 through 546 Processing helix chain '4' and resid 573 through 585 removed outlier: 4.452A pdb=" N ILE 4 577 " --> pdb=" O SER 4 573 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU 4 578 " --> pdb=" O LYS 4 574 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN 4 579 " --> pdb=" O SER 4 575 " (cutoff:3.500A) Processing helix chain '4' and resid 597 through 603 Processing helix chain '4' and resid 619 through 625 removed outlier: 3.583A pdb=" N ASP 4 625 " --> pdb=" O LEU 4 621 " (cutoff:3.500A) Processing helix chain '4' and resid 638 through 651 removed outlier: 4.205A pdb=" N VAL 4 644 " --> pdb=" O SER 4 640 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU 4 645 " --> pdb=" O THR 4 641 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N HIS 4 646 " --> pdb=" O ARG 4 642 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLU 4 647 " --> pdb=" O SER 4 643 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 693 removed outlier: 5.247A pdb=" N ASP 4 693 " --> pdb=" O THR 4 689 " (cutoff:3.500A) Processing helix chain '4' and resid 695 through 702 removed outlier: 3.537A pdb=" N LEU 4 699 " --> pdb=" O PRO 4 695 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER 4 700 " --> pdb=" O PRO 4 696 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG 4 701 " --> pdb=" O PRO 4 697 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE 4 702 " --> pdb=" O LEU 4 698 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 695 through 702' Processing helix chain '4' and resid 713 through 730 removed outlier: 3.965A pdb=" N LEU 4 727 " --> pdb=" O HIS 4 723 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR 4 728 " --> pdb=" O LEU 4 724 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU 4 729 " --> pdb=" O THR 4 725 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLU 4 730 " --> pdb=" O ASN 4 726 " (cutoff:3.500A) Processing helix chain '4' and resid 743 through 757 Processing helix chain '4' and resid 763 through 782 removed outlier: 3.634A pdb=" N GLU 4 769 " --> pdb=" O ALA 4 765 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLY 4 781 " --> pdb=" O MET 4 777 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP 4 782 " --> pdb=" O ARG 4 778 " (cutoff:3.500A) Processing helix chain '4' and resid 794 through 813 removed outlier: 3.684A pdb=" N LEU 4 798 " --> pdb=" O THR 4 794 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LYS 4 812 " --> pdb=" O HIS 4 808 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU 4 813 " --> pdb=" O ALA 4 809 " (cutoff:3.500A) Processing helix chain '4' and resid 818 through 834 removed outlier: 3.771A pdb=" N ILE 4 833 " --> pdb=" O ILE 4 829 " (cutoff:3.500A) Processing helix chain '4' and resid 846 through 851 removed outlier: 3.654A pdb=" N VAL 4 850 " --> pdb=" O ASP 4 846 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLN 4 851 " --> pdb=" O MET 4 847 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 846 through 851' Processing helix chain '5' and resid 23 through 37 Processing helix chain '5' and resid 44 through 57 Processing helix chain '5' and resid 64 through 72 removed outlier: 3.598A pdb=" N LEU 5 68 " --> pdb=" O ASN 5 64 " (cutoff:3.500A) Processing helix chain '5' and resid 73 through 82 Processing helix chain '5' and resid 84 through 108 Proline residue: 5 88 - end of helix removed outlier: 3.531A pdb=" N ALA 5 107 " --> pdb=" O ILE 5 103 " (cutoff:3.500A) Processing helix chain '5' and resid 212 through 217 removed outlier: 4.590A pdb=" N SER 5 217 " --> pdb=" O SER 5 213 " (cutoff:3.500A) Processing helix chain '5' and resid 219 through 228 removed outlier: 3.599A pdb=" N ASN 5 223 " --> pdb=" O SER 5 219 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU 5 224 " --> pdb=" O SER 5 220 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE 5 227 " --> pdb=" O ASN 5 223 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLY 5 228 " --> pdb=" O GLU 5 224 " (cutoff:3.500A) Processing helix chain '5' and resid 350 through 364 removed outlier: 3.507A pdb=" N ASN 5 363 " --> pdb=" O GLN 5 359 " (cutoff:3.500A) Proline residue: 5 364 - end of helix Processing helix chain '5' and resid 365 through 376 removed outlier: 5.558A pdb=" N ALA 5 375 " --> pdb=" O THR 5 371 " (cutoff:3.500A) Proline residue: 5 376 - end of helix Processing helix chain '5' and resid 381 through 394 Processing helix chain '5' and resid 421 through 433 removed outlier: 3.843A pdb=" N LEU 5 425 " --> pdb=" O ALA 5 421 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU 5 426 " --> pdb=" O LYS 5 422 " (cutoff:3.500A) Processing helix chain '5' and resid 467 through 473 removed outlier: 4.438A pdb=" N ASP 5 473 " --> pdb=" O MET 5 469 " (cutoff:3.500A) Processing helix chain '5' and resid 486 through 499 removed outlier: 3.841A pdb=" N GLU 5 498 " --> pdb=" O HIS 5 494 " (cutoff:3.500A) Processing helix chain '5' and resid 535 through 541 removed outlier: 5.222A pdb=" N ASP 5 541 " --> pdb=" O GLY 5 537 " (cutoff:3.500A) Processing helix chain '5' and resid 543 through 550 removed outlier: 4.447A pdb=" N LEU 5 547 " --> pdb=" O GLN 5 543 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER 5 548 " --> pdb=" O THR 5 544 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG 5 549 " --> pdb=" O THR 5 545 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE 5 550 " --> pdb=" O ILE 5 546 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 543 through 550' Processing helix chain '5' and resid 561 through 578 Processing helix chain '5' and resid 579 through 592 removed outlier: 4.943A pdb=" N GLN 5 584 " --> pdb=" O ALA 5 580 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ASN 5 585 " --> pdb=" O ASN 5 581 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLN 5 587 " --> pdb=" O MET 5 583 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASN 5 590 " --> pdb=" O GLN 5 586 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLY 5 591 " --> pdb=" O GLN 5 587 " (cutoff:3.500A) Processing helix chain '5' and resid 595 through 610 Processing helix chain '5' and resid 615 through 641 removed outlier: 4.393A pdb=" N THR 5 641 " --> pdb=" O GLU 5 637 " (cutoff:3.500A) Processing helix chain '5' and resid 649 through 668 removed outlier: 3.742A pdb=" N LEU 5 653 " --> pdb=" O THR 5 649 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU 5 666 " --> pdb=" O SER 5 662 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU 5 668 " --> pdb=" O ALA 5 664 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 688 removed outlier: 3.683A pdb=" N GLU 5 679 " --> pdb=" O ARG 5 675 " (cutoff:3.500A) Processing helix chain '5' and resid 690 through 695 removed outlier: 4.977A pdb=" N GLN 5 694 " --> pdb=" O ASP 5 690 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASP 5 695 " --> pdb=" O ALA 5 691 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 690 through 695' Processing helix chain 'D' and resid 23 through 37 Processing helix chain 'D' and resid 44 through 57 Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.645A pdb=" N LEU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 82 Processing helix chain 'D' and resid 84 through 108 Proline residue: D 88 - end of helix removed outlier: 3.565A pdb=" N ARG D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 217 removed outlier: 4.534A pdb=" N SER D 217 " --> pdb=" O SER D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 228 removed outlier: 3.642A pdb=" N ASN D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE D 227 " --> pdb=" O ASN D 223 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLY D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 364 Proline residue: D 364 - end of helix Processing helix chain 'D' and resid 365 through 376 removed outlier: 5.614A pdb=" N ALA D 375 " --> pdb=" O THR D 371 " (cutoff:3.500A) Proline residue: D 376 - end of helix Processing helix chain 'D' and resid 381 through 394 Processing helix chain 'D' and resid 421 through 433 removed outlier: 3.858A pdb=" N LEU D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU D 426 " --> pdb=" O LYS D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 473 removed outlier: 4.289A pdb=" N ASP D 473 " --> pdb=" O MET D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 499 removed outlier: 3.888A pdb=" N GLU D 498 " --> pdb=" O HIS D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 541 removed outlier: 5.309A pdb=" N ASP D 541 " --> pdb=" O GLY D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 550 removed outlier: 4.750A pdb=" N LEU D 547 " --> pdb=" O GLN D 543 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER D 548 " --> pdb=" O THR D 544 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG D 549 " --> pdb=" O THR D 545 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE D 550 " --> pdb=" O ILE D 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 543 through 550' Processing helix chain 'D' and resid 561 through 578 Processing helix chain 'D' and resid 579 through 592 removed outlier: 5.006A pdb=" N GLN D 584 " --> pdb=" O ALA D 580 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ASN D 585 " --> pdb=" O ASN D 581 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLN D 587 " --> pdb=" O MET D 583 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN D 590 " --> pdb=" O GLN D 586 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY D 591 " --> pdb=" O GLN D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 610 Processing helix chain 'D' and resid 615 through 641 removed outlier: 4.188A pdb=" N THR D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 668 removed outlier: 3.739A pdb=" N LEU D 653 " --> pdb=" O THR D 649 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU D 667 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU D 668 " --> pdb=" O ALA D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 688 removed outlier: 3.673A pdb=" N GLU D 679 " --> pdb=" O ARG D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 695 removed outlier: 4.833A pdb=" N GLN D 694 " --> pdb=" O ASP D 690 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASP D 695 " --> pdb=" O ALA D 691 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 690 through 695' Processing helix chain '6' and resid 105 through 122 Processing helix chain '6' and resid 134 through 147 removed outlier: 3.528A pdb=" N ALA 6 138 " --> pdb=" O LYS 6 134 " (cutoff:3.500A) Processing helix chain '6' and resid 154 through 161 removed outlier: 5.201A pdb=" N ARG 6 161 " --> pdb=" O HIS 6 157 " (cutoff:3.500A) Processing helix chain '6' and resid 164 through 173 Processing helix chain '6' and resid 174 through 193 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 347 through 352 removed outlier: 4.174A pdb=" N SER 6 351 " --> pdb=" O ASN 6 347 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG 6 352 " --> pdb=" O VAL 6 348 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 347 through 352' Processing helix chain '6' and resid 511 through 522 removed outlier: 4.145A pdb=" N GLU 6 515 " --> pdb=" O ASP 6 511 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP 6 522 " --> pdb=" O GLU 6 518 " (cutoff:3.500A) Processing helix chain '6' and resid 524 through 533 removed outlier: 3.521A pdb=" N ILE 6 533 " --> pdb=" O LEU 6 529 " (cutoff:3.500A) Processing helix chain '6' and resid 540 through 553 removed outlier: 4.268A pdb=" N LEU 6 549 " --> pdb=" O LYS 6 545 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU 6 552 " --> pdb=" O LEU 6 548 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLY 6 553 " --> pdb=" O LEU 6 549 " (cutoff:3.500A) Processing helix chain '6' and resid 580 through 592 removed outlier: 4.518A pdb=" N PHE 6 584 " --> pdb=" O SER 6 580 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 604 through 610 removed outlier: 4.221A pdb=" N THR 6 609 " --> pdb=" O ALA 6 605 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA 6 610 " --> pdb=" O ALA 6 606 " (cutoff:3.500A) Processing helix chain '6' and resid 626 through 632 removed outlier: 4.671A pdb=" N ALA 6 631 " --> pdb=" O ALA 6 627 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP 6 632 " --> pdb=" O LEU 6 628 " (cutoff:3.500A) Processing helix chain '6' and resid 645 through 658 Processing helix chain '6' and resid 694 through 699 Processing helix chain '6' and resid 702 through 710 removed outlier: 4.307A pdb=" N ARG 6 708 " --> pdb=" O PRO 6 704 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE 6 709 " --> pdb=" O ILE 6 705 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ASP 6 710 " --> pdb=" O MET 6 706 " (cutoff:3.500A) Processing helix chain '6' and resid 720 through 737 Processing helix chain '6' and resid 747 through 761 removed outlier: 4.413A pdb=" N THR 6 760 " --> pdb=" O LYS 6 756 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N PHE 6 761 " --> pdb=" O TYR 6 757 " (cutoff:3.500A) Processing helix chain '6' and resid 766 through 785 removed outlier: 3.917A pdb=" N SER 6 771 " --> pdb=" O LYS 6 767 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR 6 772 " --> pdb=" O GLU 6 768 " (cutoff:3.500A) Processing helix chain '6' and resid 796 through 815 removed outlier: 3.574A pdb=" N LEU 6 800 " --> pdb=" O THR 6 796 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 835 removed outlier: 4.014A pdb=" N ILE 6 835 " --> pdb=" O LEU 6 831 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 122 Processing helix chain 'E' and resid 134 through 147 removed outlier: 3.849A pdb=" N ALA E 138 " --> pdb=" O LYS E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 removed outlier: 3.535A pdb=" N LEU E 158 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER E 159 " --> pdb=" O TYR E 155 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET E 160 " --> pdb=" O GLN E 156 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ARG E 161 " --> pdb=" O HIS E 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 154 through 161' Processing helix chain 'E' and resid 164 through 173 Processing helix chain 'E' and resid 174 through 193 Proline residue: E 179 - end of helix Processing helix chain 'E' and resid 347 through 352 removed outlier: 4.262A pdb=" N SER E 351 " --> pdb=" O ASN E 347 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG E 352 " --> pdb=" O VAL E 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 347 through 352' Processing helix chain 'E' and resid 511 through 522 removed outlier: 4.364A pdb=" N GLU E 515 " --> pdb=" O ASP E 511 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP E 522 " --> pdb=" O GLU E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 533 removed outlier: 3.515A pdb=" N ILE E 533 " --> pdb=" O LEU E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 553 removed outlier: 4.288A pdb=" N LEU E 549 " --> pdb=" O LYS E 545 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLY E 553 " --> pdb=" O LEU E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 592 removed outlier: 4.259A pdb=" N PHE E 584 " --> pdb=" O SER E 580 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU E 585 " --> pdb=" O LYS E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 610 removed outlier: 4.147A pdb=" N THR E 609 " --> pdb=" O ALA E 605 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA E 610 " --> pdb=" O ALA E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 632 removed outlier: 4.586A pdb=" N ALA E 631 " --> pdb=" O ALA E 627 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP E 632 " --> pdb=" O LEU E 628 " (cutoff:3.500A) Processing helix chain 'E' and resid 645 through 658 Processing helix chain 'E' and resid 694 through 699 Processing helix chain 'E' and resid 702 through 710 removed outlier: 3.808A pdb=" N ARG E 708 " --> pdb=" O PRO E 704 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE E 709 " --> pdb=" O ILE E 705 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ASP E 710 " --> pdb=" O MET E 706 " (cutoff:3.500A) Processing helix chain 'E' and resid 720 through 737 Processing helix chain 'E' and resid 747 through 761 removed outlier: 4.514A pdb=" N THR E 760 " --> pdb=" O LYS E 756 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N PHE E 761 " --> pdb=" O TYR E 757 " (cutoff:3.500A) Processing helix chain 'E' and resid 766 through 785 removed outlier: 3.970A pdb=" N SER E 771 " --> pdb=" O LYS E 767 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR E 772 " --> pdb=" O GLU E 768 " (cutoff:3.500A) Processing helix chain 'E' and resid 796 through 815 removed outlier: 3.653A pdb=" N LEU E 800 " --> pdb=" O THR E 796 " (cutoff:3.500A) Processing helix chain 'E' and resid 820 through 835 removed outlier: 4.016A pdb=" N ILE E 835 " --> pdb=" O LEU E 831 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 27 Processing helix chain '7' and resid 61 through 73 Processing helix chain '7' and resid 81 through 96 removed outlier: 3.565A pdb=" N ILE 7 85 " --> pdb=" O ASP 7 81 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN 7 95 " --> pdb=" O GLU 7 91 " (cutoff:3.500A) Processing helix chain '7' and resid 101 through 110 Processing helix chain '7' and resid 111 through 125 removed outlier: 5.165A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU 7 116 " --> pdb=" O HIS 7 112 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN 7 124 " --> pdb=" O ALA 7 120 " (cutoff:3.500A) Processing helix chain '7' and resid 137 through 165 removed outlier: 4.007A pdb=" N ASN 7 165 " --> pdb=" O ILE 7 161 " (cutoff:3.500A) Processing helix chain '7' and resid 178 through 189 Processing helix chain '7' and resid 193 through 198 removed outlier: 3.650A pdb=" N THR 7 197 " --> pdb=" O PRO 7 193 " (cutoff:3.500A) Processing helix chain '7' and resid 208 through 216 Processing helix chain '7' and resid 226 through 231 removed outlier: 5.640A pdb=" N LYS 7 231 " --> pdb=" O VAL 7 227 " (cutoff:3.500A) Processing helix chain '7' and resid 286 through 293 removed outlier: 4.939A pdb=" N GLN 7 293 " --> pdb=" O CYS 7 289 " (cutoff:3.500A) Processing helix chain '7' and resid 301 through 306 removed outlier: 3.631A pdb=" N SER 7 305 " --> pdb=" O SER 7 301 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LYS 7 306 " --> pdb=" O THR 7 302 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 301 through 306' Processing helix chain '7' and resid 363 through 368 removed outlier: 3.845A pdb=" N LYS 7 367 " --> pdb=" O PHE 7 363 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ALA 7 368 " --> pdb=" O LYS 7 364 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 363 through 368' Processing helix chain '7' and resid 394 through 408 removed outlier: 3.674A pdb=" N ARG 7 400 " --> pdb=" O ASP 7 396 " (cutoff:3.500A) Processing helix chain '7' and resid 409 through 418 removed outlier: 3.605A pdb=" N SER 7 417 " --> pdb=" O ARG 7 413 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE 7 418 " --> pdb=" O LEU 7 414 " (cutoff:3.500A) Processing helix chain '7' and resid 425 through 438 removed outlier: 3.708A pdb=" N LYS 7 429 " --> pdb=" O ASN 7 425 " (cutoff:3.500A) Processing helix chain '7' and resid 465 through 478 Proline residue: 7 478 - end of helix Processing helix chain '7' and resid 490 through 495 removed outlier: 4.463A pdb=" N THR 7 494 " --> pdb=" O GLY 7 490 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA 7 495 " --> pdb=" O VAL 7 491 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 490 through 495' Processing helix chain '7' and resid 511 through 517 Processing helix chain '7' and resid 530 through 543 Processing helix chain '7' and resid 579 through 585 removed outlier: 3.635A pdb=" N ILE 7 584 " --> pdb=" O PRO 7 580 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASN 7 585 " --> pdb=" O LEU 7 581 " (cutoff:3.500A) Processing helix chain '7' and resid 587 through 594 removed outlier: 3.884A pdb=" N PHE 7 594 " --> pdb=" O LEU 7 590 " (cutoff:3.500A) Processing helix chain '7' and resid 605 through 623 removed outlier: 3.805A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN 7 623 " --> pdb=" O VAL 7 619 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 648 removed outlier: 3.832A pdb=" N THR 7 647 " --> pdb=" O ALA 7 643 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS 7 648 " --> pdb=" O TYR 7 644 " (cutoff:3.500A) Processing helix chain '7' and resid 653 through 675 removed outlier: 3.809A pdb=" N LYS 7 672 " --> pdb=" O ARG 7 668 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG 7 673 " --> pdb=" O GLN 7 669 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU 7 674 " --> pdb=" O ASP 7 670 " (cutoff:3.500A) Processing helix chain '7' and resid 685 through 704 removed outlier: 3.609A pdb=" N LEU 7 689 " --> pdb=" O THR 7 685 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 729 removed outlier: 3.665A pdb=" N VAL 7 713 " --> pdb=" O ASP 7 709 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS 7 724 " --> pdb=" O VAL 7 720 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU 7 725 " --> pdb=" O ARG 7 721 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER 7 726 " --> pdb=" O VAL 7 722 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU 7 727 " --> pdb=" O SER 7 723 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N TYR 7 728 " --> pdb=" O LYS 7 724 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN 7 729 " --> pdb=" O GLU 7 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 27 removed outlier: 3.597A pdb=" N LEU F 17 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 73 Processing helix chain 'F' and resid 81 through 96 removed outlier: 3.737A pdb=" N ILE F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN F 95 " --> pdb=" O GLU F 91 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY F 96 " --> pdb=" O LYS F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 110 Processing helix chain 'F' and resid 111 through 125 removed outlier: 5.147A pdb=" N GLU F 115 " --> pdb=" O ASN F 111 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU F 116 " --> pdb=" O HIS F 112 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 165 removed outlier: 3.736A pdb=" N GLU F 164 " --> pdb=" O GLU F 160 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN F 165 " --> pdb=" O ILE F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 189 removed outlier: 3.523A pdb=" N THR F 189 " --> pdb=" O VAL F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 198 removed outlier: 3.668A pdb=" N THR F 197 " --> pdb=" O PRO F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 216 Processing helix chain 'F' and resid 226 through 231 removed outlier: 3.577A pdb=" N ILE F 230 " --> pdb=" O SER F 226 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LYS F 231 " --> pdb=" O VAL F 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 226 through 231' Processing helix chain 'F' and resid 286 through 293 removed outlier: 5.184A pdb=" N GLN F 293 " --> pdb=" O CYS F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.668A pdb=" N SER F 305 " --> pdb=" O SER F 301 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LYS F 306 " --> pdb=" O THR F 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 301 through 306' Processing helix chain 'F' and resid 363 through 368 removed outlier: 3.853A pdb=" N LYS F 367 " --> pdb=" O PHE F 363 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ALA F 368 " --> pdb=" O LYS F 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 363 through 368' Processing helix chain 'F' and resid 394 through 408 removed outlier: 3.617A pdb=" N ARG F 400 " --> pdb=" O ASP F 396 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY F 408 " --> pdb=" O LEU F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 418 removed outlier: 3.631A pdb=" N SER F 417 " --> pdb=" O ARG F 413 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE F 418 " --> pdb=" O LEU F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 438 Processing helix chain 'F' and resid 465 through 478 Proline residue: F 478 - end of helix Processing helix chain 'F' and resid 490 through 495 removed outlier: 4.489A pdb=" N THR F 494 " --> pdb=" O GLY F 490 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA F 495 " --> pdb=" O VAL F 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 490 through 495' Processing helix chain 'F' and resid 511 through 517 Processing helix chain 'F' and resid 530 through 543 Processing helix chain 'F' and resid 579 through 585 removed outlier: 3.555A pdb=" N ILE F 584 " --> pdb=" O PRO F 580 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ASN F 585 " --> pdb=" O LEU F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 587 through 594 removed outlier: 3.940A pdb=" N PHE F 594 " --> pdb=" O LEU F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 623 removed outlier: 3.813A pdb=" N GLU F 610 " --> pdb=" O ARG F 606 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS F 611 " --> pdb=" O ASP F 607 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN F 623 " --> pdb=" O VAL F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 648 removed outlier: 3.747A pdb=" N THR F 647 " --> pdb=" O ALA F 643 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS F 648 " --> pdb=" O TYR F 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 675 removed outlier: 3.689A pdb=" N LYS F 672 " --> pdb=" O ARG F 668 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG F 673 " --> pdb=" O GLN F 669 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU F 674 " --> pdb=" O ASP F 670 " (cutoff:3.500A) Processing helix chain 'F' and resid 685 through 704 removed outlier: 3.615A pdb=" N LEU F 689 " --> pdb=" O THR F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 709 through 729 removed outlier: 3.726A pdb=" N VAL F 713 " --> pdb=" O ASP F 709 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS F 724 " --> pdb=" O VAL F 720 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU F 725 " --> pdb=" O ARG F 721 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N SER F 726 " --> pdb=" O VAL F 722 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU F 727 " --> pdb=" O SER F 723 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR F 728 " --> pdb=" O LYS F 724 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN F 729 " --> pdb=" O GLU F 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 201 removed outlier: 3.860A pdb=" N PHE C 201 " --> pdb=" O PHE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 237 removed outlier: 4.105A pdb=" N LYS C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 removed outlier: 4.064A pdb=" N LEU C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR C 251 " --> pdb=" O ASN C 247 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LYS C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 244 through 252' Processing helix chain 'C' and resid 254 through 264 removed outlier: 4.328A pdb=" N HIS C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 288 removed outlier: 3.766A pdb=" N SER C 270 " --> pdb=" O GLN C 266 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN C 287 " --> pdb=" O LEU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 477 through 482 removed outlier: 4.160A pdb=" N ILE C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU C 482 " --> pdb=" O THR C 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 477 through 482' Processing helix chain 'C' and resid 483 through 492 Processing helix chain 'C' and resid 502 through 515 removed outlier: 3.745A pdb=" N ARG C 515 " --> pdb=" O GLU C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 528 removed outlier: 5.586A pdb=" N ALA C 527 " --> pdb=" O ALA C 523 " (cutoff:3.500A) Proline residue: C 528 - end of helix Processing helix chain 'C' and resid 533 through 546 Processing helix chain 'C' and resid 573 through 585 removed outlier: 4.483A pdb=" N ILE C 577 " --> pdb=" O SER C 573 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 603 Processing helix chain 'C' and resid 619 through 625 removed outlier: 3.840A pdb=" N ASP C 625 " --> pdb=" O LEU C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 651 removed outlier: 4.269A pdb=" N VAL C 644 " --> pdb=" O SER C 640 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU C 645 " --> pdb=" O THR C 641 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS C 646 " --> pdb=" O ARG C 642 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU C 647 " --> pdb=" O SER C 643 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL C 648 " --> pdb=" O VAL C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 693 removed outlier: 5.589A pdb=" N ASP C 693 " --> pdb=" O THR C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 702 removed outlier: 3.617A pdb=" N LEU C 699 " --> pdb=" O PRO C 695 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER C 700 " --> pdb=" O PRO C 696 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG C 701 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE C 702 " --> pdb=" O LEU C 698 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 695 through 702' Processing helix chain 'C' and resid 713 through 730 removed outlier: 3.951A pdb=" N LEU C 727 " --> pdb=" O HIS C 723 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR C 728 " --> pdb=" O LEU C 724 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU C 729 " --> pdb=" O THR C 725 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLU C 730 " --> pdb=" O ASN C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 757 Processing helix chain 'C' and resid 763 through 782 removed outlier: 3.669A pdb=" N GLU C 769 " --> pdb=" O ALA C 765 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N GLY C 781 " --> pdb=" O MET C 777 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP C 782 " --> pdb=" O ARG C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 813 removed outlier: 3.896A pdb=" N LEU C 798 " --> pdb=" O THR C 794 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS C 812 " --> pdb=" O HIS C 808 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU C 813 " --> pdb=" O ALA C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 834 removed outlier: 3.673A pdb=" N ILE C 833 " --> pdb=" O ILE C 829 " (cutoff:3.500A) Processing helix chain '1' and resid 16 through 27 removed outlier: 3.969A pdb=" N ILE 1 20 " --> pdb=" O LYS 1 16 " (cutoff:3.500A) Proline residue: 1 27 - end of helix Processing helix chain '1' and resid 28 through 33 Processing helix chain '1' and resid 57 through 62 Processing helix chain '1' and resid 83 through 97 removed outlier: 3.528A pdb=" N TYR 1 95 " --> pdb=" O LEU 1 91 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET 1 97 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) Processing helix chain '1' and resid 127 through 133 removed outlier: 4.458A pdb=" N PHE 1 131 " --> pdb=" O GLU 1 127 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR 1 132 " --> pdb=" O PHE 1 128 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARG 1 133 " --> pdb=" O ARG 1 129 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 127 through 133' Processing helix chain '1' and resid 136 through 158 removed outlier: 3.615A pdb=" N ILE 1 140 " --> pdb=" O PRO 1 136 " (cutoff:3.500A) Processing helix chain '1' and resid 165 through 170 removed outlier: 3.831A pdb=" N PHE 1 169 " --> pdb=" O LYS 1 165 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU 1 170 " --> pdb=" O PRO 1 166 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 165 through 170' Processing helix chain '1' and resid 254 through 264 removed outlier: 3.820A pdb=" N GLY 1 258 " --> pdb=" O ASN 1 254 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP 1 260 " --> pdb=" O VAL 1 256 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LEU 1 261 " --> pdb=" O ASN 1 257 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS 1 263 " --> pdb=" O VAL 1 259 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLY 1 264 " --> pdb=" O ASP 1 260 " (cutoff:3.500A) Processing helix chain '1' and resid 286 through 292 Processing helix chain '1' and resid 299 through 315 removed outlier: 3.543A pdb=" N GLY 1 314 " --> pdb=" O LEU 1 310 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ARG 1 315 " --> pdb=" O SER 1 311 " (cutoff:3.500A) Processing helix chain '1' and resid 324 through 336 Processing helix chain '1' and resid 337 through 349 removed outlier: 3.740A pdb=" N GLY 1 349 " --> pdb=" O ALA 1 345 " (cutoff:3.500A) Processing helix chain '1' and resid 442 through 449 removed outlier: 4.280A pdb=" N CYS 1 449 " --> pdb=" O VAL 1 445 " (cutoff:3.500A) Processing helix chain '1' and resid 459 through 466 removed outlier: 4.065A pdb=" N THR 1 466 " --> pdb=" O ASP 1 462 " (cutoff:3.500A) Processing helix chain '1' and resid 269 through 275 Processing helix chain 'G' and resid 105 through 123 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 181 through 186 removed outlier: 4.209A pdb=" N LEU G 185 " --> pdb=" O ASN G 181 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS G 186 " --> pdb=" O ILE G 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 181 through 186' Processing helix chain 'G' and resid 189 through 198 Processing helix chain 'G' and resid 203 through 215 Processing helix chain 'G' and resid 670 through 678 removed outlier: 3.618A pdb=" N HIS G 674 " --> pdb=" O SER G 670 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL G 676 " --> pdb=" O GLU G 672 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER G 677 " --> pdb=" O GLN G 673 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLU G 678 " --> pdb=" O HIS G 674 " (cutoff:3.500A) Processing helix chain 'G' and resid 679 through 687 removed outlier: 3.516A pdb=" N GLU G 685 " --> pdb=" O LEU G 681 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASP G 687 " --> pdb=" O PHE G 683 " (cutoff:3.500A) Processing helix chain 'G' and resid 690 through 699 removed outlier: 3.619A pdb=" N ASP G 694 " --> pdb=" O PHE G 690 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN G 699 " --> pdb=" O SER G 695 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '2' and resid 240 through 244 Processing sheet with id= 2, first strand: chain '2' and resid 318 through 322 removed outlier: 6.405A pdb=" N GLU 2 423 " --> pdb=" O ARG 2 459 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '2' and resid 330 through 335 removed outlier: 5.935A pdb=" N ARG 2 404 " --> pdb=" O GLU 2 392 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU 2 411 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '2' and resid 346 through 351 removed outlier: 4.340A pdb=" N SER 2 346 " --> pdb=" O CYS 2 341 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE 2 339 " --> pdb=" O LEU 2 348 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL 2 337 " --> pdb=" O PRO 2 350 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LYS 2 338 " --> pdb=" O ASN 2 376 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '2' and resid 538 through 543 Processing sheet with id= 6, first strand: chain '2' and resid 562 through 567 removed outlier: 5.941A pdb=" N ARG 2 562 " --> pdb=" O LYS 2 601 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY 2 602 " --> pdb=" O ARG 2 643 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '2' and resid 578 through 582 Processing sheet with id= 8, first strand: chain 'A' and resid 240 through 244 Processing sheet with id= 9, first strand: chain 'A' and resid 318 through 322 removed outlier: 6.736A pdb=" N GLU A 423 " --> pdb=" O ARG A 459 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 330 through 335 removed outlier: 5.885A pdb=" N ARG A 404 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU A 411 " --> pdb=" O ALA A 453 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 346 through 351 removed outlier: 4.145A pdb=" N SER A 346 " --> pdb=" O CYS A 341 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 339 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL A 337 " --> pdb=" O PRO A 350 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LYS A 338 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 374 " --> pdb=" O ASN A 340 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 538 through 543 Processing sheet with id= 13, first strand: chain 'A' and resid 562 through 567 removed outlier: 5.917A pdb=" N ARG A 562 " --> pdb=" O LYS A 601 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY A 602 " --> pdb=" O ARG A 643 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 578 through 582 Processing sheet with id= 15, first strand: chain '3' and resid 94 through 98 Processing sheet with id= 16, first strand: chain '3' and resid 164 through 167 removed outlier: 5.961A pdb=" N HIS 3 164 " --> pdb=" O LEU 3 179 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU 3 183 " --> pdb=" O LEU 3 166 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ARG 3 291 " --> pdb=" O LEU 3 329 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '3' and resid 192 through 197 removed outlier: 6.780A pdb=" N THR 3 249 " --> pdb=" O ILE 3 197 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '3' and resid 207 through 213 removed outlier: 3.710A pdb=" N ARG 3 208 " --> pdb=" O ALA 3 203 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL 3 200 " --> pdb=" O GLU 3 244 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '3' and resid 428 through 433 removed outlier: 6.357A pdb=" N LEU 3 428 " --> pdb=" O ARG 3 467 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY 3 468 " --> pdb=" O ARG 3 509 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE 3 403 " --> pdb=" O CYS 3 510 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL 3 512 " --> pdb=" O ILE 3 403 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 94 through 98 Processing sheet with id= 21, first strand: chain 'B' and resid 164 through 167 removed outlier: 6.080A pdb=" N HIS B 164 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 183 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG B 291 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.842A pdb=" N THR B 249 " --> pdb=" O ILE B 197 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 207 through 213 removed outlier: 3.737A pdb=" N ARG B 208 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL B 200 " --> pdb=" O GLU B 244 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 428 through 433 removed outlier: 6.353A pdb=" N LEU B 428 " --> pdb=" O ARG B 467 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY B 468 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE B 403 " --> pdb=" O CYS B 510 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 512 " --> pdb=" O ILE B 403 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain '4' and resid 239 through 243 Processing sheet with id= 26, first strand: chain '4' and resid 324 through 329 removed outlier: 3.999A pdb=" N LYS 4 324 " --> pdb=" O PHE 4 439 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR 4 436 " --> pdb=" O VAL 4 464 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N TYR 4 420 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL 4 396 " --> pdb=" O THR 4 336 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain '4' and resid 344 through 350 removed outlier: 4.109A pdb=" N HIS 4 354 " --> pdb=" O CYS 4 349 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain '4' and resid 587 through 592 removed outlier: 3.568A pdb=" N VAL 4 589 " --> pdb=" O VAL 4 628 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE 4 562 " --> pdb=" O SER 4 669 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE 4 671 " --> pdb=" O ILE 4 562 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY 4 568 " --> pdb=" O ALA 4 675 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU 4 704 " --> pdb=" O ASN 4 563 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU 4 565 " --> pdb=" O LEU 4 704 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain '4' and resid 604 through 608 removed outlier: 3.843A pdb=" N GLN 4 613 " --> pdb=" O ASP 4 608 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain '4' and resid 652 through 658 removed outlier: 5.441A pdb=" N GLN 4 652 " --> pdb=" O ALA 4 667 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '4' and resid 338 through 343 No H-bonds generated for sheet with id= 31 Processing sheet with id= 32, first strand: chain '4' and resid 433 through 436 Processing sheet with id= 33, first strand: chain '5' and resid 60 through 63 Processing sheet with id= 34, first strand: chain '5' and resid 159 through 164 Processing sheet with id= 35, first strand: chain '5' and resid 172 through 177 removed outlier: 6.036A pdb=" N ASP 5 279 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain '5' and resid 187 through 193 removed outlier: 3.973A pdb=" N HIS 5 188 " --> pdb=" O CYS 5 183 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N SER 5 180 " --> pdb=" O ILE 5 244 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain '5' and resid 435 through 440 removed outlier: 5.913A pdb=" N ILE 5 435 " --> pdb=" O GLY 5 474 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY 5 475 " --> pdb=" O ARG 5 516 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE 5 410 " --> pdb=" O THR 5 517 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL 5 519 " --> pdb=" O ILE 5 410 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain '5' and resid 452 through 455 No H-bonds generated for sheet with id= 38 Processing sheet with id= 39, first strand: chain 'D' and resid 60 through 63 Processing sheet with id= 40, first strand: chain 'D' and resid 159 through 164 Processing sheet with id= 41, first strand: chain 'D' and resid 172 through 177 removed outlier: 5.992A pdb=" N ASP D 279 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'D' and resid 187 through 193 removed outlier: 4.061A pdb=" N HIS D 188 " --> pdb=" O CYS D 183 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER D 180 " --> pdb=" O ILE D 244 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'D' and resid 435 through 440 removed outlier: 6.060A pdb=" N ILE D 435 " --> pdb=" O GLY D 474 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY D 475 " --> pdb=" O ARG D 516 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE D 410 " --> pdb=" O THR D 517 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL D 519 " --> pdb=" O ILE D 410 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'D' and resid 452 through 455 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain '6' and resid 149 through 153 Processing sheet with id= 46, first strand: chain '6' and resid 287 through 291 Processing sheet with id= 47, first strand: chain '6' and resid 308 through 311 removed outlier: 4.741A pdb=" N ALA 6 316 " --> pdb=" O CYS 6 311 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '6' and resid 356 through 363 removed outlier: 5.837A pdb=" N ARG 6 375 " --> pdb=" O GLU 6 363 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '6' and resid 417 through 420 Processing sheet with id= 50, first strand: chain '6' and resid 571 through 575 Processing sheet with id= 51, first strand: chain '6' and resid 594 through 599 removed outlier: 3.655A pdb=" N VAL 6 596 " --> pdb=" O ILE 6 635 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain '6' and resid 611 through 614 Processing sheet with id= 53, first strand: chain '6' and resid 659 through 663 removed outlier: 5.750A pdb=" N GLN 6 659 " --> pdb=" O ALA 6 674 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'E' and resid 149 through 153 Processing sheet with id= 55, first strand: chain 'E' and resid 287 through 291 Processing sheet with id= 56, first strand: chain 'E' and resid 308 through 311 removed outlier: 4.769A pdb=" N ALA E 316 " --> pdb=" O CYS E 311 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'E' and resid 356 through 363 removed outlier: 6.128A pdb=" N ARG E 375 " --> pdb=" O GLU E 363 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'E' and resid 417 through 420 Processing sheet with id= 59, first strand: chain 'E' and resid 571 through 575 Processing sheet with id= 60, first strand: chain 'E' and resid 594 through 599 Processing sheet with id= 61, first strand: chain 'E' and resid 611 through 614 Processing sheet with id= 62, first strand: chain 'E' and resid 659 through 663 removed outlier: 5.716A pdb=" N GLN E 659 " --> pdb=" O ALA E 674 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain '7' and resid 76 through 80 Processing sheet with id= 64, first strand: chain '7' and resid 237 through 241 removed outlier: 3.893A pdb=" N GLN 7 237 " --> pdb=" O PHE 7 355 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR 7 352 " --> pdb=" O GLN 7 379 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N THR 7 374 " --> pdb=" O SER 7 330 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ASN 7 332 " --> pdb=" O THR 7 374 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASN 7 336 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ARG 7 329 " --> pdb=" O GLU 7 317 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ALA 7 309 " --> pdb=" O GLY 7 337 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain '7' and resid 257 through 263 removed outlier: 3.501A pdb=" N TYR 7 267 " --> pdb=" O CYS 7 262 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain '7' and resid 479 through 484 removed outlier: 4.061A pdb=" N ILE 7 520 " --> pdb=" O ARG 7 479 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '7' and resid 544 through 549 removed outlier: 5.258A pdb=" N GLN 7 544 " --> pdb=" O ALA 7 559 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'F' and resid 76 through 80 Processing sheet with id= 69, first strand: chain 'F' and resid 237 through 241 removed outlier: 4.014A pdb=" N GLN F 237 " --> pdb=" O PHE F 355 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR F 352 " --> pdb=" O GLN F 379 " (cutoff:3.500A) removed outlier: 9.809A pdb=" N THR F 374 " --> pdb=" O SER F 330 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ASN F 332 " --> pdb=" O THR F 374 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASN F 336 " --> pdb=" O ALA F 378 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG F 329 " --> pdb=" O GLU F 317 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ALA F 309 " --> pdb=" O GLY F 337 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'F' and resid 257 through 263 removed outlier: 3.555A pdb=" N TYR F 267 " --> pdb=" O CYS F 262 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'F' and resid 479 through 484 removed outlier: 3.853A pdb=" N ILE F 520 " --> pdb=" O ARG F 479 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'F' and resid 544 through 549 removed outlier: 5.362A pdb=" N GLN F 544 " --> pdb=" O ALA F 559 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'C' and resid 239 through 243 Processing sheet with id= 74, first strand: chain 'C' and resid 324 through 329 removed outlier: 4.012A pdb=" N LYS C 324 " --> pdb=" O PHE C 439 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR C 436 " --> pdb=" O VAL C 464 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N TYR C 420 " --> pdb=" O VAL C 463 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'C' and resid 344 through 350 removed outlier: 4.318A pdb=" N HIS C 354 " --> pdb=" O CYS C 349 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'C' and resid 587 through 592 removed outlier: 5.555A pdb=" N ARG C 587 " --> pdb=" O GLY C 626 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 589 " --> pdb=" O VAL C 628 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY C 627 " --> pdb=" O ARG C 668 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE C 562 " --> pdb=" O SER C 669 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE C 671 " --> pdb=" O ILE C 562 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 704 " --> pdb=" O ASN C 563 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'C' and resid 604 through 607 Processing sheet with id= 78, first strand: chain 'C' and resid 837 through 840 removed outlier: 6.417A pdb=" N ALA C 837 " --> pdb=" O ASP C 846 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS C 844 " --> pdb=" O ASP C 839 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'C' and resid 433 through 436 Processing sheet with id= 80, first strand: chain '1' and resid 45 through 51 removed outlier: 6.188A pdb=" N TYR 1 72 " --> pdb=" O TYR 1 122 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL 1 116 " --> pdb=" O ILE 1 78 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP 1 108 " --> pdb=" O VAL 1 119 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'G' and resid 160 through 163 removed outlier: 6.089A pdb=" N PHE G 128 " --> pdb=" O THR G 163 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'G' and resid 265 through 269 removed outlier: 3.728A pdb=" N VAL G 266 " --> pdb=" O THR G 280 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'G' and resid 659 through 662 2792 hydrogen bonds defined for protein. 8292 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 124 hydrogen bonds 244 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 52.91 Time building geometry restraints manager: 85.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 66709 1.03 - 1.23: 109 1.23 - 1.42: 28012 1.42 - 1.62: 40184 1.62 - 1.82: 485 Bond restraints: 135499 Sorted by residual: bond pdb=" N HIS A 707 " pdb=" CA HIS A 707 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.39e-02 5.18e+03 4.72e+00 bond pdb=" N HIS 2 707 " pdb=" CA HIS 2 707 " ideal model delta sigma weight residual 1.455 1.483 -0.028 1.39e-02 5.18e+03 3.99e+00 bond pdb=" C SER A 706 " pdb=" N HIS A 707 " ideal model delta sigma weight residual 1.327 1.357 -0.030 1.61e-02 3.86e+03 3.42e+00 bond pdb=" C SER 2 706 " pdb=" N HIS 2 707 " ideal model delta sigma weight residual 1.327 1.357 -0.029 1.61e-02 3.86e+03 3.33e+00 bond pdb=" C LEU 1 313 " pdb=" N GLY 1 314 " ideal model delta sigma weight residual 1.331 1.353 -0.022 1.46e-02 4.69e+03 2.29e+00 ... (remaining 135494 not shown) Histogram of bond angle deviations from ideal: 79.74 - 91.68: 4 91.68 - 103.62: 909 103.62 - 115.56: 175899 115.56 - 127.51: 67817 127.51 - 139.45: 679 Bond angle restraints: 245308 Sorted by residual: angle pdb=" NZ LYS A 587 " pdb=" CE LYS A 587 " pdb=" HE2 LYS A 587 " ideal model delta sigma weight residual 108.00 79.74 28.26 3.00e+00 1.11e-01 8.88e+01 angle pdb=" NZ LYS A 587 " pdb=" CE LYS A 587 " pdb=" HE3 LYS A 587 " ideal model delta sigma weight residual 108.00 79.81 28.19 3.00e+00 1.11e-01 8.83e+01 angle pdb=" CD LYS A 587 " pdb=" CE LYS A 587 " pdb=" HE3 LYS A 587 " ideal model delta sigma weight residual 109.00 81.85 27.15 3.00e+00 1.11e-01 8.19e+01 angle pdb=" CD LYS A 587 " pdb=" CE LYS A 587 " pdb=" HE2 LYS A 587 " ideal model delta sigma weight residual 109.00 81.97 27.03 3.00e+00 1.11e-01 8.12e+01 angle pdb=" CD LYS A 587 " pdb=" CE LYS A 587 " pdb=" NZ LYS A 587 " ideal model delta sigma weight residual 111.90 136.67 -24.77 3.20e+00 9.77e-02 5.99e+01 ... (remaining 245303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 61093 35.82 - 71.64: 1737 71.64 - 107.46: 105 107.46 - 143.27: 6 143.27 - 179.09: 6 Dihedral angle restraints: 62947 sinusoidal: 35733 harmonic: 27214 Sorted by residual: dihedral pdb=" O1B ADP C1001 " pdb=" O3A ADP C1001 " pdb=" PB ADP C1001 " pdb=" PA ADP C1001 " ideal model delta sinusoidal sigma weight residual 300.00 120.90 179.09 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP 41001 " pdb=" O3A ADP 41001 " pdb=" PB ADP 41001 " pdb=" PA ADP 41001 " ideal model delta sinusoidal sigma weight residual -60.00 105.11 -165.11 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5' ADP F 902 " pdb=" O5' ADP F 902 " pdb=" PA ADP F 902 " pdb=" O2A ADP F 902 " ideal model delta sinusoidal sigma weight residual 300.00 150.50 149.50 1 2.00e+01 2.50e-03 4.47e+01 ... (remaining 62944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 9247 0.057 - 0.115: 1324 0.115 - 0.172: 201 0.172 - 0.229: 0 0.229 - 0.286: 6 Chirality restraints: 10778 Sorted by residual: chirality pdb=" C3' ATP 2 901 " pdb=" C2' ATP 2 901 " pdb=" C4' ATP 2 901 " pdb=" O3' ATP 2 901 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C3' ATP A 901 " pdb=" C2' ATP A 901 " pdb=" C4' ATP A 901 " pdb=" O3' ATP A 901 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C2' ATP 2 901 " pdb=" C1' ATP 2 901 " pdb=" C3' ATP 2 901 " pdb=" O2' ATP 2 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 10775 not shown) Planarity restraints: 19535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU 1 313 " 0.024 2.00e-02 2.50e+03 4.77e-02 2.27e+01 pdb=" C LEU 1 313 " -0.082 2.00e-02 2.50e+03 pdb=" O LEU 1 313 " 0.031 2.00e-02 2.50e+03 pdb=" N GLY 1 314 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER 2 706 " 0.023 2.00e-02 2.50e+03 4.51e-02 2.03e+01 pdb=" C SER 2 706 " -0.078 2.00e-02 2.50e+03 pdb=" O SER 2 706 " 0.029 2.00e-02 2.50e+03 pdb=" N HIS 2 707 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 706 " 0.023 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C SER A 706 " -0.077 2.00e-02 2.50e+03 pdb=" O SER A 706 " 0.029 2.00e-02 2.50e+03 pdb=" N HIS A 707 " 0.026 2.00e-02 2.50e+03 ... (remaining 19532 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 2676 2.10 - 2.72: 230360 2.72 - 3.35: 372337 3.35 - 3.97: 465509 3.97 - 4.60: 733679 Nonbonded interactions: 1804561 Sorted by model distance: nonbonded pdb=" O3B ADP D 801 " pdb="MG MG D 802 " model vdw 1.475 2.050 nonbonded pdb=" O3B ADP 5 801 " pdb="MG MG 5 802 " model vdw 1.505 2.050 nonbonded pdb=" OE1 GLN 6 323 " pdb=" H THR 6 328 " model vdw 1.507 1.850 nonbonded pdb=" OG SER 7 723 " pdb=" HZ2 LYS 7 724 " model vdw 1.514 1.850 nonbonded pdb=" O PRO 2 394 " pdb="HD21 ASN 6 673 " model vdw 1.536 1.850 ... (remaining 1804556 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 '2' and (resid 183 through 223 or (resid 224 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name H \ G3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21)) o \ r (resid 225 and (name N or name CA or name C or name O or name CB or name OG or \ name H or name HA or name HB2 or name HB3)) or resid 226 through 436 or (resid \ 437 and (name N or name CA or name C or name O or name CB or name CG or name OD1 \ or name ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resi \ d 438 through 864 or resid 901 through 903)) selection = chain 'A' } ncs_group { reference = chain '3' selection = chain 'B' } ncs_group { reference = (chain '4' and ((resid 177 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 178 through 852 or resid 1001 through 1002)) selection = chain 'C' } ncs_group { reference = (chain '5' and (resid 2 through 459 or (resid 460 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH21 or name HH22)) or resid 461 thr \ ough 699 or resid 801 through 803)) selection = chain 'D' } ncs_group { reference = chain '6' selection = chain 'E' } ncs_group { reference = chain '7' selection = chain 'F' } ncs_group { reference = (chain 'X' and (resid 1 through 25 or resid 29 through 53)) selection = (chain 'Y' and (resid -53 through -29 or resid -25 through -1)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.910 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: 1.410 Extract box with map and model: 26.790 Check model and map are aligned: 1.490 Set scattering table: 0.920 Process input model: 420.230 Find NCS groups from input model: 6.290 Set up NCS constraints: 0.870 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: 0.020 Load rotamer database and sin/cos tables:2.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 466.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 : 0.003 0.050 68713 Z= 0.171 Angle : 0.584 24.771 93397 Z= 0.324 Chirality : 0.042 0.286 10778 Planarity : 0.004 0.079 11622 Dihedral : 15.550 179.093 26369 Min Nonbonded Distance : 1.475 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.73 % Favored : 96.20 % Rotamer: Outliers : 0.03 % Allowed : 0.25 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.09), residues: 8108 helix: 1.56 (0.09), residues: 3147 sheet: -0.27 (0.13), residues: 1545 loop : -0.81 (0.11), residues: 3416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D 343 HIS 0.019 0.001 HIS 7 538 PHE 0.017 0.001 PHE 1 450 TYR 0.018 0.001 TYR G 263 ARG 0.015 0.000 ARG F 593 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 550 is missing expected H atoms. Skipping. Residue SER 416 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue THR 160 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue SER 550 is missing expected H atoms. Skipping. Residue SER 416 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Evaluate side-chains 1768 residues out of total 7267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1766 time to evaluate : 8.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 266 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8354 (mm-30) REVERT: 2 387 ARG cc_start: 0.8087 (ttp-170) cc_final: 0.7886 (mtm-85) REVERT: 3 710 THR cc_start: 0.9379 (m) cc_final: 0.9031 (p) REVERT: 4 188 GLN cc_start: 0.8138 (tp40) cc_final: 0.7795 (tp-100) REVERT: 4 497 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7392 (mm-30) REVERT: 5 5 ARG cc_start: 0.8240 (ttp-110) cc_final: 0.7802 (ttp80) REVERT: 5 279 ASP cc_start: 0.8714 (p0) cc_final: 0.8283 (p0) REVERT: 5 409 ASP cc_start: 0.8517 (m-30) cc_final: 0.7989 (m-30) REVERT: 5 518 SER cc_start: 0.9224 (m) cc_final: 0.8685 (m) REVERT: 6 587 TYR cc_start: 0.8694 (t80) cc_final: 0.7904 (t80) REVERT: 6 649 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8703 (mt0) REVERT: 6 707 SER cc_start: 0.9266 (m) cc_final: 0.9024 (m) REVERT: 7 283 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7836 (mm-30) REVERT: A 359 ILE cc_start: 0.8861 (mm) cc_final: 0.8650 (mm) REVERT: A 407 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7331 (mm-30) REVERT: A 423 GLU cc_start: 0.8282 (tm-30) cc_final: 0.8056 (tm-30) REVERT: A 592 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7265 (mt-10) REVERT: B 234 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8274 (mm-30) REVERT: B 334 THR cc_start: 0.8977 (m) cc_final: 0.8628 (p) REVERT: B 448 THR cc_start: 0.8364 (p) cc_final: 0.8113 (p) REVERT: B 456 ARG cc_start: 0.7115 (ptp90) cc_final: 0.6851 (ptp90) REVERT: B 476 ASP cc_start: 0.8870 (p0) cc_final: 0.8360 (p0) REVERT: B 483 ARG cc_start: 0.8621 (mtm180) cc_final: 0.8420 (mtm-85) REVERT: B 505 THR cc_start: 0.9122 (m) cc_final: 0.8921 (p) REVERT: C 297 GLU cc_start: 0.8847 (tt0) cc_final: 0.8111 (tp30) REVERT: C 579 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8170 (mm-40) REVERT: C 580 TYR cc_start: 0.8575 (t80) cc_final: 0.8283 (t80) REVERT: C 710 ASP cc_start: 0.8144 (t0) cc_final: 0.7880 (t0) REVERT: D 531 ASP cc_start: 0.8306 (t70) cc_final: 0.7927 (t70) REVERT: D 688 THR cc_start: 0.8935 (m) cc_final: 0.8713 (m) REVERT: E 146 TYR cc_start: 0.7778 (m-80) cc_final: 0.7403 (m-80) REVERT: E 191 LYS cc_start: 0.8812 (mtmt) cc_final: 0.8448 (mttp) REVERT: E 305 TYR cc_start: 0.8659 (t80) cc_final: 0.8256 (t80) REVERT: E 406 ASP cc_start: 0.8355 (t0) cc_final: 0.7906 (t0) REVERT: E 623 ILE cc_start: 0.9135 (mp) cc_final: 0.8878 (tp) REVERT: F 344 SER cc_start: 0.8998 (p) cc_final: 0.8344 (p) REVERT: F 361 THR cc_start: 0.9102 (t) cc_final: 0.8655 (t) REVERT: F 515 LEU cc_start: 0.9576 (tp) cc_final: 0.9361 (tt) REVERT: F 582 ASP cc_start: 0.9414 (m-30) cc_final: 0.9042 (m-30) REVERT: F 602 ASP cc_start: 0.8185 (t0) cc_final: 0.7736 (t0) REVERT: 1 86 ARG cc_start: 0.9155 (ttt-90) cc_final: 0.8825 (tpt-90) REVERT: 1 90 GLU cc_start: 0.8119 (tt0) cc_final: 0.7501 (mm-30) REVERT: 1 133 ARG cc_start: 0.3978 (ptp-170) cc_final: 0.3454 (ptm160) REVERT: 1 143 TYR cc_start: 0.7266 (t80) cc_final: 0.6923 (t80) REVERT: 1 319 MET cc_start: 0.7267 (mpp) cc_final: 0.6825 (mmt) REVERT: 1 331 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8629 (mm-30) REVERT: G 117 LYS cc_start: 0.4632 (tmmt) cc_final: 0.4422 (tmmt) REVERT: G 118 LYS cc_start: 0.1122 (tmtt) cc_final: 0.0761 (tptt) REVERT: G 195 LYS cc_start: 0.6675 (tmtt) cc_final: 0.6468 (ttpt) REVERT: G 263 TYR cc_start: 0.9355 (m-80) cc_final: 0.8886 (m-80) REVERT: G 293 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7237 (tp30) outliers start: 2 outliers final: 0 residues processed: 1768 average time/residue: 1.6720 time to fit residues: 4855.4784 Evaluate side-chains 1426 residues out of total 7267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1426 time to evaluate : 7.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 695 optimal weight: 5.9990 chunk 624 optimal weight: 6.9990 chunk 346 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 421 optimal weight: 4.9990 chunk 333 optimal weight: 3.9990 chunk 645 optimal weight: 4.9990 chunk 249 optimal weight: 4.9990 chunk 392 optimal weight: 0.6980 chunk 480 optimal weight: 7.9990 chunk 748 optimal weight: 0.3980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 282 HIS 4 613 GLN 5 381 ASN 5 543 GLN ** 6 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN C 666 ASN ** D 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 291 GLN F 455 ASN F 669 GLN 1 155 HIS 1 252 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 68713 Z= 0.253 Angle : 0.571 24.856 93397 Z= 0.301 Chirality : 0.042 0.175 10778 Planarity : 0.004 0.079 11622 Dihedral : 12.848 170.322 10273 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 1.12 % Allowed : 8.48 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.09), residues: 8108 helix: 1.48 (0.09), residues: 3165 sheet: -0.38 (0.13), residues: 1611 loop : -0.85 (0.11), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 343 HIS 0.007 0.001 HIS 7 538 PHE 0.024 0.001 PHE G 683 TYR 0.016 0.001 TYR G 198 ARG 0.009 0.000 ARG 4 451 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 550 is missing expected H atoms. Skipping. Residue SER 416 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue THR 160 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue SER 550 is missing expected H atoms. Skipping. Residue SER 416 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Evaluate side-chains 1521 residues out of total 7267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1440 time to evaluate : 8.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 266 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8280 (mm-30) REVERT: 2 374 ARG cc_start: 0.7824 (ttm110) cc_final: 0.7621 (ttm170) REVERT: 3 691 ASN cc_start: 0.8093 (t0) cc_final: 0.7724 (t0) REVERT: 3 710 THR cc_start: 0.9384 (m) cc_final: 0.9035 (p) REVERT: 4 410 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8090 (tm130) REVERT: 4 497 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7404 (mm-30) REVERT: 4 534 GLU cc_start: 0.7308 (pm20) cc_final: 0.6893 (pm20) REVERT: 5 5 ARG cc_start: 0.8190 (ttp-110) cc_final: 0.7928 (ttp80) REVERT: 5 154 GLU cc_start: 0.8136 (mp0) cc_final: 0.7619 (mp0) REVERT: 5 279 ASP cc_start: 0.8786 (p0) cc_final: 0.8429 (p0) REVERT: 5 409 ASP cc_start: 0.8593 (m-30) cc_final: 0.8222 (m-30) REVERT: 5 410 ILE cc_start: 0.8569 (mt) cc_final: 0.8272 (mm) REVERT: 5 518 SER cc_start: 0.9188 (m) cc_final: 0.8645 (m) REVERT: 6 587 TYR cc_start: 0.8695 (t80) cc_final: 0.7842 (t80) REVERT: 6 649 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8733 (mt0) REVERT: 6 654 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8240 (tm-30) REVERT: 6 707 SER cc_start: 0.9301 (m) cc_final: 0.9057 (m) REVERT: 7 149 ARG cc_start: 0.8231 (tpt170) cc_final: 0.8027 (tpt90) REVERT: A 359 ILE cc_start: 0.8965 (mm) cc_final: 0.8478 (mm) REVERT: A 368 LYS cc_start: 0.9170 (mmmt) cc_final: 0.8922 (mmmt) REVERT: A 423 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8003 (tm-30) REVERT: B 234 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8302 (mm-30) REVERT: B 334 THR cc_start: 0.8982 (m) cc_final: 0.8635 (p) REVERT: B 435 ARG cc_start: 0.8585 (mmm160) cc_final: 0.8370 (mmm160) REVERT: B 456 ARG cc_start: 0.7382 (ptp90) cc_final: 0.7138 (ptp90) REVERT: B 505 THR cc_start: 0.9126 (m) cc_final: 0.8874 (p) REVERT: C 297 GLU cc_start: 0.8869 (tt0) cc_final: 0.8142 (tp30) REVERT: C 710 ASP cc_start: 0.8191 (t0) cc_final: 0.7956 (t0) REVERT: D 91 GLU cc_start: 0.8479 (tt0) cc_final: 0.8265 (tt0) REVERT: D 269 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6939 (mm-30) REVERT: D 417 ASP cc_start: 0.8346 (t0) cc_final: 0.8146 (t0) REVERT: D 688 THR cc_start: 0.8959 (m) cc_final: 0.8748 (m) REVERT: E 146 TYR cc_start: 0.7883 (m-80) cc_final: 0.7550 (m-80) REVERT: E 191 LYS cc_start: 0.8824 (mtmt) cc_final: 0.8444 (mttt) REVERT: E 305 TYR cc_start: 0.8643 (t80) cc_final: 0.8268 (t80) REVERT: E 406 ASP cc_start: 0.8395 (t0) cc_final: 0.7956 (t0) REVERT: E 623 ILE cc_start: 0.9147 (mp) cc_final: 0.8893 (tp) REVERT: F 515 LEU cc_start: 0.9557 (tp) cc_final: 0.9352 (tt) REVERT: F 602 ASP cc_start: 0.8060 (t0) cc_final: 0.7762 (t0) REVERT: 1 86 ARG cc_start: 0.9141 (ttt-90) cc_final: 0.8814 (tpt-90) REVERT: 1 90 GLU cc_start: 0.8125 (tt0) cc_final: 0.7523 (mm-30) REVERT: 1 319 MET cc_start: 0.7149 (mpp) cc_final: 0.6800 (mmt) REVERT: 1 327 ASP cc_start: 0.9079 (t0) cc_final: 0.8356 (t0) REVERT: 1 331 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8638 (mm-30) REVERT: G 118 LYS cc_start: 0.0783 (tmtt) cc_final: 0.0377 (mmtp) REVERT: G 195 LYS cc_start: 0.7074 (tmtt) cc_final: 0.6874 (ttpt) outliers start: 81 outliers final: 62 residues processed: 1469 average time/residue: 1.6165 time to fit residues: 3914.2632 Evaluate side-chains 1431 residues out of total 7267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1368 time to evaluate : 7.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 282 HIS Chi-restraints excluded: chain 2 residue 504 SER Chi-restraints excluded: chain 2 residue 620 ILE Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 2 residue 797 SER Chi-restraints excluded: chain 2 residue 812 SER Chi-restraints excluded: chain 3 residue 412 SER Chi-restraints excluded: chain 3 residue 482 ASP Chi-restraints excluded: chain 3 residue 539 LEU Chi-restraints excluded: chain 3 residue 569 HIS Chi-restraints excluded: chain 4 residue 162 ASP Chi-restraints excluded: chain 4 residue 242 ASN Chi-restraints excluded: chain 4 residue 410 GLN Chi-restraints excluded: chain 4 residue 553 THR Chi-restraints excluded: chain 4 residue 576 GLN Chi-restraints excluded: chain 5 residue 220 SER Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 258 LEU Chi-restraints excluded: chain 5 residue 439 THR Chi-restraints excluded: chain 5 residue 483 ASP Chi-restraints excluded: chain 5 residue 510 THR Chi-restraints excluded: chain 5 residue 546 ILE Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 599 SER Chi-restraints excluded: chain 6 residue 603 SER Chi-restraints excluded: chain 6 residue 650 VAL Chi-restraints excluded: chain 6 residue 677 SER Chi-restraints excluded: chain 7 residue 373 GLU Chi-restraints excluded: chain 7 residue 619 VAL Chi-restraints excluded: chain 7 residue 660 VAL Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain E residue 395 CYS Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain F residue 118 CYS Chi-restraints excluded: chain F residue 244 ILE Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain 1 residue 21 GLN Chi-restraints excluded: chain 1 residue 147 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 415 optimal weight: 3.9990 chunk 232 optimal weight: 0.9990 chunk 622 optimal weight: 3.9990 chunk 509 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 749 optimal weight: 3.9990 chunk 809 optimal weight: 5.9990 chunk 667 optimal weight: 6.9990 chunk 743 optimal weight: 0.7980 chunk 255 optimal weight: 5.9990 chunk 601 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 238 ASN 2 665 GLN 3 492 GLN ** 6 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 68713 Z= 0.253 Angle : 0.553 25.191 93397 Z= 0.291 Chirality : 0.042 0.160 10778 Planarity : 0.004 0.078 11622 Dihedral : 12.870 165.261 10273 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.51 % Rotamer: Outliers : 1.50 % Allowed : 9.60 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.09), residues: 8108 helix: 1.50 (0.09), residues: 3158 sheet: -0.44 (0.12), residues: 1619 loop : -0.89 (0.11), residues: 3331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 343 HIS 0.015 0.001 HIS 2 282 PHE 0.018 0.001 PHE B 421 TYR 0.021 0.001 TYR E 450 ARG 0.010 0.000 ARG 4 451 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 550 is missing expected H atoms. Skipping. Residue SER 416 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue THR 160 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue SER 550 is missing expected H atoms. Skipping. Residue SER 416 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Evaluate side-chains 1491 residues out of total 7267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1382 time to evaluate : 7.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 266 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8203 (mm-30) REVERT: 2 343 LYS cc_start: 0.8354 (mppt) cc_final: 0.8045 (mptt) REVERT: 3 477 LYS cc_start: 0.9264 (mptt) cc_final: 0.8981 (mptt) REVERT: 3 691 ASN cc_start: 0.8149 (t0) cc_final: 0.7692 (t0) REVERT: 3 710 THR cc_start: 0.9389 (m) cc_final: 0.9035 (p) REVERT: 4 410 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8045 (tm130) REVERT: 4 497 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7373 (mm-30) REVERT: 5 5 ARG cc_start: 0.8264 (ttp-110) cc_final: 0.7847 (ttp80) REVERT: 5 154 GLU cc_start: 0.8144 (mp0) cc_final: 0.7592 (mp0) REVERT: 5 410 ILE cc_start: 0.8563 (mt) cc_final: 0.8328 (mm) REVERT: 5 637 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8314 (mm-30) REVERT: 5 690 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8237 (t0) REVERT: 6 586 LYS cc_start: 0.9224 (mmmt) cc_final: 0.8978 (mmmt) REVERT: 6 587 TYR cc_start: 0.8678 (t80) cc_final: 0.7830 (t80) REVERT: 6 649 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8781 (mt0) REVERT: 6 654 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8246 (tm-30) REVERT: 6 707 SER cc_start: 0.9323 (m) cc_final: 0.9085 (m) REVERT: 7 283 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7544 (mm-30) REVERT: 7 539 GLU cc_start: 0.8527 (tt0) cc_final: 0.8314 (tt0) REVERT: 7 543 GLN cc_start: 0.8400 (pt0) cc_final: 0.8149 (pt0) REVERT: A 368 LYS cc_start: 0.9165 (mmmt) cc_final: 0.8893 (mmmt) REVERT: A 387 ARG cc_start: 0.8436 (ttm110) cc_final: 0.8203 (ttp80) REVERT: B 234 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8222 (mp0) REVERT: B 264 MET cc_start: 0.8492 (mmm) cc_final: 0.7967 (mmm) REVERT: B 334 THR cc_start: 0.8991 (m) cc_final: 0.8625 (p) REVERT: B 456 ARG cc_start: 0.7598 (ptp90) cc_final: 0.7248 (ptp90) REVERT: B 505 THR cc_start: 0.9127 (m) cc_final: 0.8856 (p) REVERT: C 297 GLU cc_start: 0.8884 (tt0) cc_final: 0.8155 (tp30) REVERT: C 690 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8688 (mm-30) REVERT: C 710 ASP cc_start: 0.8216 (t0) cc_final: 0.7948 (t0) REVERT: D 417 ASP cc_start: 0.8376 (t0) cc_final: 0.8168 (t0) REVERT: D 688 THR cc_start: 0.8977 (m) cc_final: 0.8777 (m) REVERT: E 146 TYR cc_start: 0.7890 (m-80) cc_final: 0.7553 (m-80) REVERT: E 191 LYS cc_start: 0.8842 (mtmt) cc_final: 0.8450 (mttt) REVERT: E 305 TYR cc_start: 0.8641 (t80) cc_final: 0.8271 (t80) REVERT: E 406 ASP cc_start: 0.8403 (t0) cc_final: 0.7956 (t0) REVERT: E 623 ILE cc_start: 0.9158 (mp) cc_final: 0.8881 (tp) REVERT: F 515 LEU cc_start: 0.9567 (tp) cc_final: 0.9356 (tt) REVERT: F 602 ASP cc_start: 0.8145 (t0) cc_final: 0.7849 (t0) REVERT: 1 86 ARG cc_start: 0.9134 (ttt-90) cc_final: 0.8806 (tpt-90) REVERT: 1 90 GLU cc_start: 0.8066 (tt0) cc_final: 0.7485 (mm-30) REVERT: 1 319 MET cc_start: 0.6999 (mpp) cc_final: 0.6632 (mmt) REVERT: 1 327 ASP cc_start: 0.9076 (t0) cc_final: 0.8382 (t0) REVERT: 1 331 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8662 (mm-30) REVERT: G 118 LYS cc_start: 0.0708 (tmtt) cc_final: 0.0293 (mmtp) REVERT: G 195 LYS cc_start: 0.7127 (tmtt) cc_final: 0.6915 (ttpt) REVERT: G 667 LYS cc_start: 0.9312 (mmtm) cc_final: 0.8672 (tptt) outliers start: 109 outliers final: 85 residues processed: 1427 average time/residue: 1.6037 time to fit residues: 3757.2818 Evaluate side-chains 1425 residues out of total 7267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1338 time to evaluate : 8.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 504 SER Chi-restraints excluded: chain 2 residue 797 SER Chi-restraints excluded: chain 2 residue 812 SER Chi-restraints excluded: chain 3 residue 97 ILE Chi-restraints excluded: chain 3 residue 227 THR Chi-restraints excluded: chain 3 residue 341 MET Chi-restraints excluded: chain 3 residue 412 SER Chi-restraints excluded: chain 3 residue 482 ASP Chi-restraints excluded: chain 3 residue 539 LEU Chi-restraints excluded: chain 3 residue 552 ASP Chi-restraints excluded: chain 3 residue 566 LEU Chi-restraints excluded: chain 3 residue 569 HIS Chi-restraints excluded: chain 4 residue 242 ASN Chi-restraints excluded: chain 4 residue 410 GLN Chi-restraints excluded: chain 4 residue 414 SER Chi-restraints excluded: chain 4 residue 561 ASP Chi-restraints excluded: chain 4 residue 576 GLN Chi-restraints excluded: chain 4 residue 640 SER Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 258 LEU Chi-restraints excluded: chain 5 residue 439 THR Chi-restraints excluded: chain 5 residue 510 THR Chi-restraints excluded: chain 5 residue 511 THR Chi-restraints excluded: chain 5 residue 573 ILE Chi-restraints excluded: chain 5 residue 690 ASP Chi-restraints excluded: chain 6 residue 279 ILE Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 599 SER Chi-restraints excluded: chain 6 residue 603 SER Chi-restraints excluded: chain 6 residue 645 ASP Chi-restraints excluded: chain 6 residue 650 VAL Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 672 LEU Chi-restraints excluded: chain 6 residue 677 SER Chi-restraints excluded: chain 6 residue 699 LEU Chi-restraints excluded: chain 6 residue 739 ASP Chi-restraints excluded: chain 7 residue 373 GLU Chi-restraints excluded: chain 7 residue 425 ASN Chi-restraints excluded: chain 7 residue 619 VAL Chi-restraints excluded: chain 7 residue 660 VAL Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 395 CYS Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain E residue 559 THR Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain F residue 118 CYS Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 541 MET Chi-restraints excluded: chain F residue 561 THR Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 695 LEU Chi-restraints excluded: chain 1 residue 21 GLN Chi-restraints excluded: chain 1 residue 297 SER Chi-restraints excluded: chain 1 residue 332 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 740 optimal weight: 4.9990 chunk 563 optimal weight: 6.9990 chunk 389 optimal weight: 3.9990 chunk 82 optimal weight: 0.0670 chunk 357 optimal weight: 0.7980 chunk 503 optimal weight: 4.9990 chunk 752 optimal weight: 0.9990 chunk 796 optimal weight: 20.0000 chunk 393 optimal weight: 6.9990 chunk 713 optimal weight: 0.8980 chunk 214 optimal weight: 0.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 454 GLN ** 6 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 GLN ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 291 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 68713 Z= 0.155 Angle : 0.525 25.493 93397 Z= 0.272 Chirality : 0.041 0.169 10778 Planarity : 0.004 0.074 11622 Dihedral : 12.765 172.314 10273 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.75 % Favored : 96.18 % Rotamer: Outliers : 1.23 % Allowed : 10.75 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.09), residues: 8108 helix: 1.75 (0.09), residues: 3177 sheet: -0.29 (0.13), residues: 1591 loop : -0.76 (0.11), residues: 3340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 1 66 HIS 0.007 0.001 HIS 2 282 PHE 0.015 0.001 PHE 1 450 TYR 0.013 0.001 TYR G 198 ARG 0.008 0.000 ARG 4 451 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 550 is missing expected H atoms. Skipping. Residue SER 416 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue THR 160 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue SER 550 is missing expected H atoms. Skipping. Residue SER 416 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Evaluate side-chains 1486 residues out of total 7267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1397 time to evaluate : 8.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 343 LYS cc_start: 0.8383 (mppt) cc_final: 0.8090 (mptt) REVERT: 2 665 GLN cc_start: 0.8750 (mt0) cc_final: 0.8550 (mp10) REVERT: 3 477 LYS cc_start: 0.9191 (mptt) cc_final: 0.8849 (mptt) REVERT: 3 691 ASN cc_start: 0.8165 (t0) cc_final: 0.7654 (t0) REVERT: 3 710 THR cc_start: 0.9363 (m) cc_final: 0.9007 (p) REVERT: 4 410 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.8031 (tm130) REVERT: 4 497 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7409 (mm-30) REVERT: 4 576 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8821 (mm110) REVERT: 4 613 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8408 (mm110) REVERT: 4 647 GLU cc_start: 0.7451 (tt0) cc_final: 0.7162 (tm-30) REVERT: 5 5 ARG cc_start: 0.8232 (ttp-110) cc_final: 0.7688 (ttp80) REVERT: 5 154 GLU cc_start: 0.8127 (mp0) cc_final: 0.7646 (mp0) REVERT: 6 587 TYR cc_start: 0.8700 (t80) cc_final: 0.7978 (t80) REVERT: 6 649 GLN cc_start: 0.8985 (mm-40) cc_final: 0.8734 (mt0) REVERT: 6 654 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8204 (tm-30) REVERT: 6 707 SER cc_start: 0.9298 (m) cc_final: 0.9056 (m) REVERT: 7 283 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7513 (mm-30) REVERT: 7 287 GLU cc_start: 0.7176 (pm20) cc_final: 0.6625 (pm20) REVERT: 7 543 GLN cc_start: 0.8390 (pt0) cc_final: 0.8106 (pt0) REVERT: 7 675 MET cc_start: 0.8454 (tpt) cc_final: 0.8188 (tpp) REVERT: A 387 ARG cc_start: 0.8406 (ttm110) cc_final: 0.8165 (ttp80) REVERT: A 494 ILE cc_start: 0.8879 (mp) cc_final: 0.8324 (mm) REVERT: B 234 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8160 (mp0) REVERT: B 264 MET cc_start: 0.8521 (mmm) cc_final: 0.8104 (mmm) REVERT: B 334 THR cc_start: 0.9016 (m) cc_final: 0.8626 (p) REVERT: B 435 ARG cc_start: 0.8584 (mmm160) cc_final: 0.8303 (mmm-85) REVERT: B 456 ARG cc_start: 0.7541 (ptp90) cc_final: 0.7139 (ptp90) REVERT: B 505 THR cc_start: 0.9058 (m) cc_final: 0.8617 (p) REVERT: C 297 GLU cc_start: 0.8863 (tt0) cc_final: 0.8123 (tp30) REVERT: C 710 ASP cc_start: 0.8206 (t0) cc_final: 0.8002 (t0) REVERT: D 91 GLU cc_start: 0.8496 (tt0) cc_final: 0.8200 (tt0) REVERT: D 417 ASP cc_start: 0.8314 (t0) cc_final: 0.8107 (t0) REVERT: D 688 THR cc_start: 0.8955 (m) cc_final: 0.8742 (m) REVERT: E 146 TYR cc_start: 0.7793 (m-80) cc_final: 0.7426 (m-80) REVERT: E 305 TYR cc_start: 0.8627 (t80) cc_final: 0.8298 (t80) REVERT: E 406 ASP cc_start: 0.8375 (t0) cc_final: 0.7941 (t0) REVERT: E 623 ILE cc_start: 0.9151 (mp) cc_final: 0.8858 (tp) REVERT: F 537 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8868 (mp) REVERT: F 602 ASP cc_start: 0.8100 (t0) cc_final: 0.7795 (t0) REVERT: 1 86 ARG cc_start: 0.9130 (ttt-90) cc_final: 0.8799 (tpt-90) REVERT: 1 90 GLU cc_start: 0.8062 (tt0) cc_final: 0.7472 (mm-30) REVERT: 1 319 MET cc_start: 0.6770 (mpp) cc_final: 0.6337 (mmt) REVERT: 1 327 ASP cc_start: 0.9079 (t0) cc_final: 0.8383 (t0) REVERT: 1 331 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8676 (mm-30) REVERT: 1 338 TRP cc_start: 0.8947 (p-90) cc_final: 0.8676 (p-90) REVERT: 1 352 PHE cc_start: 0.6857 (t80) cc_final: 0.6654 (t80) REVERT: G 118 LYS cc_start: 0.0690 (tmtt) cc_final: 0.0288 (mmtp) outliers start: 89 outliers final: 65 residues processed: 1437 average time/residue: 1.5921 time to fit residues: 3757.0473 Evaluate side-chains 1420 residues out of total 7267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1352 time to evaluate : 7.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 242 LEU Chi-restraints excluded: chain 2 residue 504 SER Chi-restraints excluded: chain 2 residue 620 ILE Chi-restraints excluded: chain 3 residue 227 THR Chi-restraints excluded: chain 3 residue 236 THR Chi-restraints excluded: chain 3 residue 458 GLU Chi-restraints excluded: chain 3 residue 482 ASP Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 552 ASP Chi-restraints excluded: chain 3 residue 566 LEU Chi-restraints excluded: chain 3 residue 569 HIS Chi-restraints excluded: chain 4 residue 162 ASP Chi-restraints excluded: chain 4 residue 410 GLN Chi-restraints excluded: chain 4 residue 576 GLN Chi-restraints excluded: chain 5 residue 220 SER Chi-restraints excluded: chain 5 residue 258 LEU Chi-restraints excluded: chain 5 residue 439 THR Chi-restraints excluded: chain 5 residue 510 THR Chi-restraints excluded: chain 5 residue 573 ILE Chi-restraints excluded: chain 6 residue 279 ILE Chi-restraints excluded: chain 6 residue 355 ASP Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 559 THR Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 599 SER Chi-restraints excluded: chain 6 residue 603 SER Chi-restraints excluded: chain 6 residue 645 ASP Chi-restraints excluded: chain 6 residue 650 VAL Chi-restraints excluded: chain 6 residue 672 LEU Chi-restraints excluded: chain 6 residue 699 LEU Chi-restraints excluded: chain 6 residue 739 ASP Chi-restraints excluded: chain 7 residue 373 GLU Chi-restraints excluded: chain 7 residue 425 ASN Chi-restraints excluded: chain 7 residue 660 VAL Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain E residue 559 THR Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 739 ASP Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 537 ILE Chi-restraints excluded: chain F residue 541 MET Chi-restraints excluded: chain F residue 598 PHE Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 695 LEU Chi-restraints excluded: chain 1 residue 21 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 663 optimal weight: 4.9990 chunk 452 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 593 optimal weight: 0.8980 chunk 328 optimal weight: 1.9990 chunk 679 optimal weight: 4.9990 chunk 550 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 406 optimal weight: 8.9990 chunk 714 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 665 GLN ** 6 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 GLN A 703 HIS ** D 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 68713 Z= 0.294 Angle : 0.553 25.267 93397 Z= 0.291 Chirality : 0.041 0.165 10778 Planarity : 0.004 0.072 11622 Dihedral : 12.785 177.338 10273 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.85 % Favored : 95.08 % Rotamer: Outliers : 1.79 % Allowed : 11.47 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.09), residues: 8108 helix: 1.60 (0.09), residues: 3168 sheet: -0.48 (0.12), residues: 1631 loop : -0.89 (0.11), residues: 3309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 66 HIS 0.007 0.001 HIS C 413 PHE 0.017 0.001 PHE B 421 TYR 0.011 0.001 TYR 1 265 ARG 0.012 0.000 ARG 4 451 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 550 is missing expected H atoms. Skipping. Residue SER 416 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue THR 160 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue SER 550 is missing expected H atoms. Skipping. Residue SER 416 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Evaluate side-chains 1485 residues out of total 7267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1355 time to evaluate : 8.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 665 GLN cc_start: 0.8805 (mt0) cc_final: 0.8504 (mp10) REVERT: 3 477 LYS cc_start: 0.9218 (mptt) cc_final: 0.8822 (mptt) REVERT: 3 691 ASN cc_start: 0.8287 (t0) cc_final: 0.7755 (t0) REVERT: 3 710 THR cc_start: 0.9388 (m) cc_final: 0.9034 (p) REVERT: 4 410 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8062 (tm130) REVERT: 4 576 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8867 (mm110) REVERT: 4 647 GLU cc_start: 0.7453 (tt0) cc_final: 0.7056 (tm-30) REVERT: 5 5 ARG cc_start: 0.8294 (ttp-110) cc_final: 0.7898 (ttp80) REVERT: 5 82 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7961 (mm-30) REVERT: 5 154 GLU cc_start: 0.8157 (mp0) cc_final: 0.7707 (mp0) REVERT: 6 428 LYS cc_start: 0.9193 (mmmm) cc_final: 0.8668 (mmtp) REVERT: 6 569 ILE cc_start: 0.9192 (mt) cc_final: 0.8959 (tt) REVERT: 6 587 TYR cc_start: 0.8773 (t80) cc_final: 0.7944 (t80) REVERT: 6 649 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8845 (mt0) REVERT: 6 654 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8215 (tm-30) REVERT: 6 707 SER cc_start: 0.9349 (m) cc_final: 0.9112 (m) REVERT: 7 543 GLN cc_start: 0.8495 (pt0) cc_final: 0.8210 (pt0) REVERT: 7 675 MET cc_start: 0.8500 (tpt) cc_final: 0.8243 (tpp) REVERT: A 360 ARG cc_start: 0.8151 (mmm-85) cc_final: 0.7912 (mmm-85) REVERT: A 387 ARG cc_start: 0.8454 (ttm170) cc_final: 0.8236 (ttp80) REVERT: A 422 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7590 (mt-10) REVERT: B 234 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8176 (mp0) REVERT: B 264 MET cc_start: 0.8473 (mmm) cc_final: 0.8077 (mmm) REVERT: B 334 THR cc_start: 0.9024 (m) cc_final: 0.8635 (p) REVERT: C 561 ASP cc_start: 0.7817 (m-30) cc_final: 0.7605 (m-30) REVERT: C 690 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8685 (mm-30) REVERT: D 417 ASP cc_start: 0.8417 (t0) cc_final: 0.8211 (t0) REVERT: D 688 THR cc_start: 0.9003 (m) cc_final: 0.8792 (m) REVERT: E 146 TYR cc_start: 0.7940 (m-80) cc_final: 0.7615 (m-80) REVERT: E 305 TYR cc_start: 0.8642 (t80) cc_final: 0.8301 (t80) REVERT: E 406 ASP cc_start: 0.8434 (t0) cc_final: 0.8043 (t0) REVERT: F 537 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8938 (mp) REVERT: F 602 ASP cc_start: 0.8146 (t0) cc_final: 0.7791 (t0) REVERT: 1 86 ARG cc_start: 0.9123 (ttt-90) cc_final: 0.8775 (tpt-90) REVERT: 1 90 GLU cc_start: 0.8070 (tt0) cc_final: 0.7487 (mm-30) REVERT: 1 108 ASP cc_start: 0.6602 (t0) cc_final: 0.6382 (p0) REVERT: 1 319 MET cc_start: 0.6752 (mpp) cc_final: 0.6285 (mmt) REVERT: 1 327 ASP cc_start: 0.9100 (t0) cc_final: 0.8439 (t0) REVERT: 1 331 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8669 (mm-30) REVERT: 1 338 TRP cc_start: 0.8952 (p-90) cc_final: 0.8672 (p-90) REVERT: G 115 ASN cc_start: 0.5242 (m-40) cc_final: 0.4719 (p0) REVERT: G 306 ARG cc_start: 0.4020 (ptt180) cc_final: 0.2616 (ttt180) outliers start: 130 outliers final: 109 residues processed: 1406 average time/residue: 1.5947 time to fit residues: 3676.7978 Evaluate side-chains 1439 residues out of total 7267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1327 time to evaluate : 7.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 242 LEU Chi-restraints excluded: chain 2 residue 450 ILE Chi-restraints excluded: chain 2 residue 504 SER Chi-restraints excluded: chain 2 residue 574 VAL Chi-restraints excluded: chain 2 residue 620 ILE Chi-restraints excluded: chain 2 residue 797 SER Chi-restraints excluded: chain 3 residue 97 ILE Chi-restraints excluded: chain 3 residue 227 THR Chi-restraints excluded: chain 3 residue 341 MET Chi-restraints excluded: chain 3 residue 412 SER Chi-restraints excluded: chain 3 residue 458 GLU Chi-restraints excluded: chain 3 residue 482 ASP Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 3 residue 552 ASP Chi-restraints excluded: chain 3 residue 566 LEU Chi-restraints excluded: chain 3 residue 569 HIS Chi-restraints excluded: chain 4 residue 242 ASN Chi-restraints excluded: chain 4 residue 351 VAL Chi-restraints excluded: chain 4 residue 410 GLN Chi-restraints excluded: chain 4 residue 414 SER Chi-restraints excluded: chain 4 residue 526 ILE Chi-restraints excluded: chain 4 residue 567 CYS Chi-restraints excluded: chain 4 residue 576 GLN Chi-restraints excluded: chain 4 residue 794 THR Chi-restraints excluded: chain 5 residue 220 SER Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 258 LEU Chi-restraints excluded: chain 5 residue 417 ASP Chi-restraints excluded: chain 5 residue 439 THR Chi-restraints excluded: chain 5 residue 510 THR Chi-restraints excluded: chain 5 residue 511 THR Chi-restraints excluded: chain 5 residue 573 ILE Chi-restraints excluded: chain 5 residue 633 LEU Chi-restraints excluded: chain 6 residue 279 ILE Chi-restraints excluded: chain 6 residue 355 ASP Chi-restraints excluded: chain 6 residue 559 THR Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 599 SER Chi-restraints excluded: chain 6 residue 603 SER Chi-restraints excluded: chain 6 residue 645 ASP Chi-restraints excluded: chain 6 residue 650 VAL Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 672 LEU Chi-restraints excluded: chain 6 residue 688 ARG Chi-restraints excluded: chain 6 residue 699 LEU Chi-restraints excluded: chain 6 residue 739 ASP Chi-restraints excluded: chain 7 residue 187 ASP Chi-restraints excluded: chain 7 residue 373 GLU Chi-restraints excluded: chain 7 residue 425 ASN Chi-restraints excluded: chain 7 residue 541 MET Chi-restraints excluded: chain 7 residue 555 THR Chi-restraints excluded: chain 7 residue 640 GLU Chi-restraints excluded: chain 7 residue 660 VAL Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 395 CYS Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain E residue 559 THR Chi-restraints excluded: chain E residue 654 GLU Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 739 ASP Chi-restraints excluded: chain F residue 118 CYS Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 244 ILE Chi-restraints excluded: chain F residue 537 ILE Chi-restraints excluded: chain F residue 541 MET Chi-restraints excluded: chain F residue 561 THR Chi-restraints excluded: chain F residue 598 PHE Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 695 LEU Chi-restraints excluded: chain 1 residue 21 GLN Chi-restraints excluded: chain 1 residue 332 LEU Chi-restraints excluded: chain G residue 290 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 267 optimal weight: 5.9990 chunk 717 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 467 optimal weight: 6.9990 chunk 196 optimal weight: 0.7980 chunk 797 optimal weight: 6.9990 chunk 661 optimal weight: 6.9990 chunk 369 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 263 optimal weight: 3.9990 chunk 418 optimal weight: 8.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 GLN A 703 HIS ** D 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 291 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 68713 Z= 0.275 Angle : 0.554 25.428 93397 Z= 0.292 Chirality : 0.042 0.161 10778 Planarity : 0.004 0.083 11622 Dihedral : 12.770 170.208 10273 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.53 % Favored : 95.40 % Rotamer: Outliers : 2.02 % Allowed : 11.90 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.09), residues: 8108 helix: 1.54 (0.09), residues: 3168 sheet: -0.52 (0.13), residues: 1605 loop : -0.95 (0.11), residues: 3335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 66 HIS 0.008 0.001 HIS C 413 PHE 0.019 0.001 PHE B 421 TYR 0.012 0.001 TYR 1 265 ARG 0.008 0.000 ARG D 187 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 550 is missing expected H atoms. Skipping. Residue SER 416 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue THR 160 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue SER 550 is missing expected H atoms. Skipping. Residue SER 416 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Evaluate side-chains 1479 residues out of total 7267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1332 time to evaluate : 8.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 614 ASP cc_start: 0.8119 (t70) cc_final: 0.7918 (t0) REVERT: 3 490 MET cc_start: 0.8833 (mtt) cc_final: 0.8455 (mtt) REVERT: 3 691 ASN cc_start: 0.8345 (t0) cc_final: 0.7840 (t0) REVERT: 3 710 THR cc_start: 0.9405 (m) cc_final: 0.9056 (p) REVERT: 4 410 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8045 (tm130) REVERT: 4 576 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8873 (mm110) REVERT: 4 647 GLU cc_start: 0.7476 (tt0) cc_final: 0.7094 (tm-30) REVERT: 5 5 ARG cc_start: 0.8328 (ttp-110) cc_final: 0.7902 (ttp80) REVERT: 5 154 GLU cc_start: 0.8135 (mp0) cc_final: 0.7671 (mp0) REVERT: 5 348 MET cc_start: 0.7550 (mmm) cc_final: 0.7336 (mmm) REVERT: 6 174 TYR cc_start: 0.9166 (t80) cc_final: 0.8899 (t80) REVERT: 6 569 ILE cc_start: 0.9189 (mt) cc_final: 0.8955 (tt) REVERT: 6 587 TYR cc_start: 0.8758 (t80) cc_final: 0.8035 (t80) REVERT: 6 654 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8224 (tm-30) REVERT: 6 671 THR cc_start: 0.8996 (m) cc_final: 0.8676 (p) REVERT: 6 707 SER cc_start: 0.9370 (m) cc_final: 0.9138 (m) REVERT: 7 115 GLU cc_start: 0.8282 (tp30) cc_final: 0.7913 (tp30) REVERT: 7 283 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7647 (mm-30) REVERT: 7 543 GLN cc_start: 0.8501 (pt0) cc_final: 0.8191 (pt0) REVERT: 7 675 MET cc_start: 0.8525 (tpt) cc_final: 0.8275 (tpp) REVERT: A 387 ARG cc_start: 0.8416 (ttm170) cc_final: 0.8215 (ttp80) REVERT: A 423 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7180 (tm-30) REVERT: B 234 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8175 (mp0) REVERT: B 264 MET cc_start: 0.8482 (mmm) cc_final: 0.8065 (mmm) REVERT: B 306 MET cc_start: 0.8930 (mmm) cc_final: 0.8706 (mtp) REVERT: B 334 THR cc_start: 0.9024 (m) cc_final: 0.8634 (p) REVERT: B 435 ARG cc_start: 0.8588 (mmm160) cc_final: 0.8341 (mmm160) REVERT: C 561 ASP cc_start: 0.7790 (m-30) cc_final: 0.7570 (m-30) REVERT: C 690 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8677 (mm-30) REVERT: D 17 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: D 409 ASP cc_start: 0.8159 (m-30) cc_final: 0.7764 (m-30) REVERT: D 417 ASP cc_start: 0.8423 (t0) cc_final: 0.8220 (t0) REVERT: D 688 THR cc_start: 0.9022 (m) cc_final: 0.8811 (m) REVERT: E 146 TYR cc_start: 0.7928 (m-80) cc_final: 0.7598 (m-80) REVERT: E 305 TYR cc_start: 0.8660 (t80) cc_final: 0.8359 (t80) REVERT: F 537 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8948 (mp) REVERT: F 602 ASP cc_start: 0.8114 (t0) cc_final: 0.7780 (t0) REVERT: 1 86 ARG cc_start: 0.9125 (ttt-90) cc_final: 0.8775 (tpt-90) REVERT: 1 90 GLU cc_start: 0.8117 (tt0) cc_final: 0.7520 (mm-30) REVERT: 1 108 ASP cc_start: 0.6428 (t0) cc_final: 0.6078 (p0) REVERT: 1 319 MET cc_start: 0.6744 (mpp) cc_final: 0.6272 (mmt) REVERT: 1 327 ASP cc_start: 0.9099 (t0) cc_final: 0.8391 (t0) REVERT: 1 331 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8667 (mm-30) REVERT: 1 338 TRP cc_start: 0.8951 (p-90) cc_final: 0.8658 (p-90) REVERT: G 115 ASN cc_start: 0.5256 (m-40) cc_final: 0.4702 (p0) REVERT: G 306 ARG cc_start: 0.3960 (ptt180) cc_final: 0.2530 (ttt180) outliers start: 147 outliers final: 123 residues processed: 1398 average time/residue: 1.5681 time to fit residues: 3590.4830 Evaluate side-chains 1441 residues out of total 7267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1314 time to evaluate : 7.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 242 LEU Chi-restraints excluded: chain 2 residue 450 ILE Chi-restraints excluded: chain 2 residue 504 SER Chi-restraints excluded: chain 2 residue 574 VAL Chi-restraints excluded: chain 2 residue 620 ILE Chi-restraints excluded: chain 2 residue 797 SER Chi-restraints excluded: chain 2 residue 812 SER Chi-restraints excluded: chain 3 residue 97 ILE Chi-restraints excluded: chain 3 residue 227 THR Chi-restraints excluded: chain 3 residue 236 THR Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 341 MET Chi-restraints excluded: chain 3 residue 458 GLU Chi-restraints excluded: chain 3 residue 482 ASP Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 3 residue 552 ASP Chi-restraints excluded: chain 3 residue 566 LEU Chi-restraints excluded: chain 3 residue 569 HIS Chi-restraints excluded: chain 4 residue 242 ASN Chi-restraints excluded: chain 4 residue 351 VAL Chi-restraints excluded: chain 4 residue 410 GLN Chi-restraints excluded: chain 4 residue 414 SER Chi-restraints excluded: chain 4 residue 526 ILE Chi-restraints excluded: chain 4 residue 567 CYS Chi-restraints excluded: chain 4 residue 576 GLN Chi-restraints excluded: chain 4 residue 640 SER Chi-restraints excluded: chain 4 residue 794 THR Chi-restraints excluded: chain 5 residue 220 SER Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 258 LEU Chi-restraints excluded: chain 5 residue 417 ASP Chi-restraints excluded: chain 5 residue 439 THR Chi-restraints excluded: chain 5 residue 510 THR Chi-restraints excluded: chain 5 residue 511 THR Chi-restraints excluded: chain 5 residue 573 ILE Chi-restraints excluded: chain 5 residue 633 LEU Chi-restraints excluded: chain 6 residue 279 ILE Chi-restraints excluded: chain 6 residue 355 ASP Chi-restraints excluded: chain 6 residue 559 THR Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 599 SER Chi-restraints excluded: chain 6 residue 603 SER Chi-restraints excluded: chain 6 residue 645 ASP Chi-restraints excluded: chain 6 residue 650 VAL Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 662 SER Chi-restraints excluded: chain 6 residue 665 LYS Chi-restraints excluded: chain 6 residue 672 LEU Chi-restraints excluded: chain 6 residue 677 SER Chi-restraints excluded: chain 6 residue 688 ARG Chi-restraints excluded: chain 6 residue 699 LEU Chi-restraints excluded: chain 6 residue 739 ASP Chi-restraints excluded: chain 7 residue 187 ASP Chi-restraints excluded: chain 7 residue 373 GLU Chi-restraints excluded: chain 7 residue 425 ASN Chi-restraints excluded: chain 7 residue 541 MET Chi-restraints excluded: chain 7 residue 555 THR Chi-restraints excluded: chain 7 residue 619 VAL Chi-restraints excluded: chain 7 residue 640 GLU Chi-restraints excluded: chain 7 residue 660 VAL Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 395 CYS Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain E residue 559 THR Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 654 GLU Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 739 ASP Chi-restraints excluded: chain F residue 118 CYS Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 244 ILE Chi-restraints excluded: chain F residue 537 ILE Chi-restraints excluded: chain F residue 541 MET Chi-restraints excluded: chain F residue 561 THR Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain F residue 598 PHE Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 695 LEU Chi-restraints excluded: chain 1 residue 21 GLN Chi-restraints excluded: chain 1 residue 297 SER Chi-restraints excluded: chain 1 residue 332 LEU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain G residue 667 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 768 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 454 optimal weight: 1.9990 chunk 582 optimal weight: 2.9990 chunk 451 optimal weight: 4.9990 chunk 671 optimal weight: 10.0000 chunk 445 optimal weight: 0.9980 chunk 794 optimal weight: 2.9990 chunk 497 optimal weight: 6.9990 chunk 484 optimal weight: 5.9990 chunk 366 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 95 GLN 7 291 GLN A 626 GLN ** D 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 291 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 68713 Z= 0.276 Angle : 0.554 25.501 93397 Z= 0.291 Chirality : 0.042 0.169 10778 Planarity : 0.004 0.104 11622 Dihedral : 12.720 154.102 10273 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.97 % Favored : 94.95 % Rotamer: Outliers : 1.96 % Allowed : 12.46 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.09), residues: 8108 helix: 1.56 (0.09), residues: 3165 sheet: -0.53 (0.13), residues: 1599 loop : -0.99 (0.11), residues: 3344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 112 HIS 0.009 0.001 HIS C 413 PHE 0.019 0.001 PHE B 421 TYR 0.015 0.001 TYR G 269 ARG 0.021 0.000 ARG 4 451 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 550 is missing expected H atoms. Skipping. Residue SER 416 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue THR 160 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue SER 550 is missing expected H atoms. Skipping. Residue SER 416 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Evaluate side-chains 1464 residues out of total 7267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1322 time to evaluate : 8.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 452 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7094 (tm-30) REVERT: 3 490 MET cc_start: 0.8871 (mtt) cc_final: 0.8526 (mtt) REVERT: 3 691 ASN cc_start: 0.8396 (t0) cc_final: 0.7933 (t0) REVERT: 4 410 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8014 (tm130) REVERT: 4 647 GLU cc_start: 0.7520 (tt0) cc_final: 0.7138 (tm-30) REVERT: 5 5 ARG cc_start: 0.8387 (ttp-110) cc_final: 0.7963 (ttp80) REVERT: 5 154 GLU cc_start: 0.8132 (mp0) cc_final: 0.7662 (mp0) REVERT: 6 174 TYR cc_start: 0.9179 (t80) cc_final: 0.8918 (t80) REVERT: 6 569 ILE cc_start: 0.9195 (mt) cc_final: 0.8963 (tt) REVERT: 6 587 TYR cc_start: 0.8769 (t80) cc_final: 0.7994 (t80) REVERT: 6 654 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8312 (tm-30) REVERT: 6 671 THR cc_start: 0.9001 (m) cc_final: 0.8685 (p) REVERT: 6 707 SER cc_start: 0.9405 (m) cc_final: 0.8990 (p) REVERT: 7 101 ASP cc_start: 0.8286 (t70) cc_final: 0.7945 (t0) REVERT: 7 283 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7649 (mm-30) REVERT: 7 543 GLN cc_start: 0.8516 (pt0) cc_final: 0.8228 (pt0) REVERT: 7 675 MET cc_start: 0.8551 (tpt) cc_final: 0.8305 (tpp) REVERT: A 423 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7112 (tm-30) REVERT: B 234 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8167 (mp0) REVERT: B 264 MET cc_start: 0.8497 (mmm) cc_final: 0.8056 (mmm) REVERT: B 306 MET cc_start: 0.8936 (mmm) cc_final: 0.8698 (mtp) REVERT: B 334 THR cc_start: 0.9019 (m) cc_final: 0.8628 (p) REVERT: B 435 ARG cc_start: 0.8583 (mmm160) cc_final: 0.8342 (mmm160) REVERT: B 543 PHE cc_start: 0.8856 (m-80) cc_final: 0.8476 (m-80) REVERT: C 690 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8680 (mm-30) REVERT: D 17 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: D 409 ASP cc_start: 0.8166 (m-30) cc_final: 0.7771 (m-30) REVERT: D 417 ASP cc_start: 0.8436 (t0) cc_final: 0.8231 (t0) REVERT: D 688 THR cc_start: 0.9027 (m) cc_final: 0.8817 (m) REVERT: E 146 TYR cc_start: 0.7937 (m-80) cc_final: 0.7610 (m-80) REVERT: E 305 TYR cc_start: 0.8656 (t80) cc_final: 0.8355 (t80) REVERT: F 427 ASP cc_start: 0.8584 (m-30) cc_final: 0.8215 (m-30) REVERT: F 531 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7657 (tt0) REVERT: F 537 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8934 (mp) REVERT: F 602 ASP cc_start: 0.8073 (t0) cc_final: 0.7729 (t0) REVERT: 1 86 ARG cc_start: 0.9124 (ttt-90) cc_final: 0.8832 (tpt-90) REVERT: 1 90 GLU cc_start: 0.8102 (tt0) cc_final: 0.7568 (mm-30) REVERT: 1 108 ASP cc_start: 0.6376 (t0) cc_final: 0.6002 (p0) REVERT: 1 319 MET cc_start: 0.6733 (mpp) cc_final: 0.6292 (mmt) REVERT: 1 327 ASP cc_start: 0.9073 (t0) cc_final: 0.8345 (t0) REVERT: 1 331 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8690 (mm-30) REVERT: G 115 ASN cc_start: 0.5296 (m-40) cc_final: 0.4730 (p0) outliers start: 142 outliers final: 124 residues processed: 1384 average time/residue: 1.5811 time to fit residues: 3582.2144 Evaluate side-chains 1430 residues out of total 7267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1302 time to evaluate : 8.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 242 LEU Chi-restraints excluded: chain 2 residue 450 ILE Chi-restraints excluded: chain 2 residue 504 SER Chi-restraints excluded: chain 2 residue 515 VAL Chi-restraints excluded: chain 2 residue 574 VAL Chi-restraints excluded: chain 2 residue 620 ILE Chi-restraints excluded: chain 2 residue 797 SER Chi-restraints excluded: chain 2 residue 812 SER Chi-restraints excluded: chain 3 residue 97 ILE Chi-restraints excluded: chain 3 residue 227 THR Chi-restraints excluded: chain 3 residue 236 THR Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 341 MET Chi-restraints excluded: chain 3 residue 458 GLU Chi-restraints excluded: chain 3 residue 482 ASP Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 3 residue 552 ASP Chi-restraints excluded: chain 3 residue 566 LEU Chi-restraints excluded: chain 3 residue 569 HIS Chi-restraints excluded: chain 4 residue 242 ASN Chi-restraints excluded: chain 4 residue 351 VAL Chi-restraints excluded: chain 4 residue 410 GLN Chi-restraints excluded: chain 4 residue 414 SER Chi-restraints excluded: chain 4 residue 526 ILE Chi-restraints excluded: chain 4 residue 567 CYS Chi-restraints excluded: chain 4 residue 576 GLN Chi-restraints excluded: chain 4 residue 794 THR Chi-restraints excluded: chain 5 residue 220 SER Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 258 LEU Chi-restraints excluded: chain 5 residue 417 ASP Chi-restraints excluded: chain 5 residue 439 THR Chi-restraints excluded: chain 5 residue 510 THR Chi-restraints excluded: chain 5 residue 511 THR Chi-restraints excluded: chain 5 residue 573 ILE Chi-restraints excluded: chain 5 residue 633 LEU Chi-restraints excluded: chain 6 residue 279 ILE Chi-restraints excluded: chain 6 residue 355 ASP Chi-restraints excluded: chain 6 residue 559 THR Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 599 SER Chi-restraints excluded: chain 6 residue 603 SER Chi-restraints excluded: chain 6 residue 645 ASP Chi-restraints excluded: chain 6 residue 650 VAL Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 661 ILE Chi-restraints excluded: chain 6 residue 665 LYS Chi-restraints excluded: chain 6 residue 672 LEU Chi-restraints excluded: chain 6 residue 677 SER Chi-restraints excluded: chain 6 residue 699 LEU Chi-restraints excluded: chain 6 residue 739 ASP Chi-restraints excluded: chain 7 residue 187 ASP Chi-restraints excluded: chain 7 residue 373 GLU Chi-restraints excluded: chain 7 residue 425 ASN Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 541 MET Chi-restraints excluded: chain 7 residue 555 THR Chi-restraints excluded: chain 7 residue 619 VAL Chi-restraints excluded: chain 7 residue 640 GLU Chi-restraints excluded: chain 7 residue 660 VAL Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 395 CYS Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain E residue 559 THR Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 739 ASP Chi-restraints excluded: chain F residue 118 CYS Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 244 ILE Chi-restraints excluded: chain F residue 531 GLU Chi-restraints excluded: chain F residue 537 ILE Chi-restraints excluded: chain F residue 541 MET Chi-restraints excluded: chain F residue 561 THR Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain F residue 598 PHE Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 695 LEU Chi-restraints excluded: chain 1 residue 21 GLN Chi-restraints excluded: chain 1 residue 94 LEU Chi-restraints excluded: chain 1 residue 297 SER Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 290 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 491 optimal weight: 0.9980 chunk 317 optimal weight: 0.4980 chunk 474 optimal weight: 4.9990 chunk 239 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 504 optimal weight: 4.9990 chunk 541 optimal weight: 0.9990 chunk 392 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 624 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 454 ASN ** 6 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 GLN ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 291 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 68713 Z= 0.156 Angle : 0.531 25.883 93397 Z= 0.274 Chirality : 0.041 0.177 10778 Planarity : 0.004 0.076 11622 Dihedral : 12.553 155.563 10273 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 1.56 % Allowed : 13.26 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.09), residues: 8108 helix: 1.85 (0.09), residues: 3163 sheet: -0.41 (0.13), residues: 1575 loop : -0.76 (0.11), residues: 3370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 66 HIS 0.008 0.001 HIS F 538 PHE 0.015 0.001 PHE B 421 TYR 0.013 0.001 TYR G 269 ARG 0.011 0.000 ARG 3 224 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 550 is missing expected H atoms. Skipping. Residue SER 416 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue THR 160 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue SER 550 is missing expected H atoms. Skipping. Residue SER 416 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Evaluate side-chains 1482 residues out of total 7267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1369 time to evaluate : 8.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 275 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7647 (m-30) REVERT: 3 490 MET cc_start: 0.8837 (mtt) cc_final: 0.8493 (mtt) REVERT: 3 691 ASN cc_start: 0.8385 (t0) cc_final: 0.7919 (t0) REVERT: 3 710 THR cc_start: 0.9364 (m) cc_final: 0.8997 (p) REVERT: 4 410 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7940 (tm130) REVERT: 4 576 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8842 (mm110) REVERT: 4 647 GLU cc_start: 0.7510 (tt0) cc_final: 0.7127 (tm-30) REVERT: 5 5 ARG cc_start: 0.8372 (ttp-110) cc_final: 0.7900 (ttp80) REVERT: 5 154 GLU cc_start: 0.8123 (mp0) cc_final: 0.7642 (mp0) REVERT: 6 587 TYR cc_start: 0.8703 (t80) cc_final: 0.8073 (t80) REVERT: 6 654 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8203 (tm-30) REVERT: 6 671 THR cc_start: 0.8959 (m) cc_final: 0.8678 (p) REVERT: 6 707 SER cc_start: 0.9426 (m) cc_final: 0.9062 (p) REVERT: 7 101 ASP cc_start: 0.8237 (t70) cc_final: 0.7958 (t70) REVERT: 7 283 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7610 (mm-30) REVERT: 7 543 GLN cc_start: 0.8403 (pt0) cc_final: 0.8061 (pt0) REVERT: 7 675 MET cc_start: 0.8521 (tpt) cc_final: 0.8282 (tpp) REVERT: A 422 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7625 (mt-10) REVERT: A 423 GLU cc_start: 0.7366 (tm-30) cc_final: 0.7119 (tm-30) REVERT: B 234 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8086 (mp0) REVERT: B 264 MET cc_start: 0.8479 (mmm) cc_final: 0.8069 (mmm) REVERT: B 306 MET cc_start: 0.8935 (mmm) cc_final: 0.8686 (mtp) REVERT: B 334 THR cc_start: 0.8996 (m) cc_final: 0.8595 (p) REVERT: B 435 ARG cc_start: 0.8558 (mmm160) cc_final: 0.8339 (mmm160) REVERT: B 543 PHE cc_start: 0.8826 (m-80) cc_final: 0.8425 (m-80) REVERT: B 689 ASP cc_start: 0.7920 (m-30) cc_final: 0.7464 (t0) REVERT: C 690 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8651 (mm-30) REVERT: C 757 HIS cc_start: 0.8545 (OUTLIER) cc_final: 0.8344 (m170) REVERT: D 409 ASP cc_start: 0.8161 (m-30) cc_final: 0.7771 (m-30) REVERT: D 417 ASP cc_start: 0.8388 (t0) cc_final: 0.8170 (t0) REVERT: D 688 THR cc_start: 0.8989 (m) cc_final: 0.8772 (m) REVERT: E 146 TYR cc_start: 0.7805 (m-80) cc_final: 0.7457 (m-80) REVERT: E 305 TYR cc_start: 0.8628 (t80) cc_final: 0.8321 (t80) REVERT: F 427 ASP cc_start: 0.8518 (m-30) cc_final: 0.8138 (m-30) REVERT: F 537 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8875 (mp) REVERT: F 602 ASP cc_start: 0.8057 (t0) cc_final: 0.7725 (t0) REVERT: 1 86 ARG cc_start: 0.9122 (ttt-90) cc_final: 0.8798 (tpt-90) REVERT: 1 90 GLU cc_start: 0.8062 (tt0) cc_final: 0.7539 (mm-30) REVERT: 1 108 ASP cc_start: 0.6311 (t0) cc_final: 0.5930 (p0) REVERT: 1 319 MET cc_start: 0.6641 (mpp) cc_final: 0.6235 (mmt) REVERT: 1 327 ASP cc_start: 0.9117 (t0) cc_final: 0.8422 (t0) REVERT: 1 338 TRP cc_start: 0.8938 (p-90) cc_final: 0.8650 (p-90) REVERT: G 115 ASN cc_start: 0.5297 (m-40) cc_final: 0.4738 (p0) REVERT: G 306 ARG cc_start: 0.3951 (ptt180) cc_final: 0.2539 (ttt180) REVERT: G 667 LYS cc_start: 0.9393 (mmtm) cc_final: 0.8759 (tptt) outliers start: 113 outliers final: 90 residues processed: 1419 average time/residue: 1.5671 time to fit residues: 3650.3115 Evaluate side-chains 1420 residues out of total 7267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1325 time to evaluate : 7.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 477 THR Chi-restraints excluded: chain 2 residue 504 SER Chi-restraints excluded: chain 2 residue 515 VAL Chi-restraints excluded: chain 2 residue 620 ILE Chi-restraints excluded: chain 2 residue 797 SER Chi-restraints excluded: chain 3 residue 97 ILE Chi-restraints excluded: chain 3 residue 227 THR Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 341 MET Chi-restraints excluded: chain 3 residue 412 SER Chi-restraints excluded: chain 3 residue 458 GLU Chi-restraints excluded: chain 3 residue 482 ASP Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 552 ASP Chi-restraints excluded: chain 3 residue 566 LEU Chi-restraints excluded: chain 3 residue 569 HIS Chi-restraints excluded: chain 4 residue 242 ASN Chi-restraints excluded: chain 4 residue 410 GLN Chi-restraints excluded: chain 4 residue 414 SER Chi-restraints excluded: chain 4 residue 526 ILE Chi-restraints excluded: chain 4 residue 576 GLN Chi-restraints excluded: chain 4 residue 794 THR Chi-restraints excluded: chain 5 residue 220 SER Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 258 LEU Chi-restraints excluded: chain 5 residue 417 ASP Chi-restraints excluded: chain 5 residue 439 THR Chi-restraints excluded: chain 5 residue 510 THR Chi-restraints excluded: chain 5 residue 511 THR Chi-restraints excluded: chain 5 residue 573 ILE Chi-restraints excluded: chain 6 residue 279 ILE Chi-restraints excluded: chain 6 residue 559 THR Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 599 SER Chi-restraints excluded: chain 6 residue 603 SER Chi-restraints excluded: chain 6 residue 645 ASP Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 672 LEU Chi-restraints excluded: chain 6 residue 699 LEU Chi-restraints excluded: chain 6 residue 739 ASP Chi-restraints excluded: chain 7 residue 187 ASP Chi-restraints excluded: chain 7 residue 373 GLU Chi-restraints excluded: chain 7 residue 425 ASN Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 757 HIS Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 559 THR Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 648 ASP Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 739 ASP Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 537 ILE Chi-restraints excluded: chain F residue 541 MET Chi-restraints excluded: chain F residue 561 THR Chi-restraints excluded: chain F residue 598 PHE Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 695 LEU Chi-restraints excluded: chain 1 residue 21 GLN Chi-restraints excluded: chain 1 residue 94 LEU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 290 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 722 optimal weight: 3.9990 chunk 760 optimal weight: 8.9990 chunk 694 optimal weight: 0.6980 chunk 740 optimal weight: 4.9990 chunk 445 optimal weight: 3.9990 chunk 322 optimal weight: 0.0970 chunk 581 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 668 optimal weight: 4.9990 chunk 699 optimal weight: 0.7980 chunk 737 optimal weight: 5.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 291 GLN ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 291 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 68713 Z= 0.196 Angle : 0.537 25.738 93397 Z= 0.278 Chirality : 0.041 0.161 10778 Planarity : 0.004 0.120 11622 Dihedral : 12.481 155.536 10273 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.32 % Favored : 95.61 % Rotamer: Outliers : 1.47 % Allowed : 13.60 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.09), residues: 8108 helix: 1.85 (0.09), residues: 3162 sheet: -0.44 (0.13), residues: 1579 loop : -0.76 (0.11), residues: 3367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 112 HIS 0.007 0.001 HIS 7 538 PHE 0.016 0.001 PHE B 421 TYR 0.012 0.001 TYR G 660 ARG 0.021 0.000 ARG 4 451 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 550 is missing expected H atoms. Skipping. Residue SER 416 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue THR 160 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue SER 550 is missing expected H atoms. Skipping. Residue SER 416 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Evaluate side-chains 1444 residues out of total 7267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1337 time to evaluate : 8.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 275 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7640 (m-30) REVERT: 3 490 MET cc_start: 0.8846 (mtt) cc_final: 0.8575 (mtt) REVERT: 3 691 ASN cc_start: 0.8420 (t0) cc_final: 0.8086 (t0) REVERT: 3 710 THR cc_start: 0.9366 (m) cc_final: 0.8996 (p) REVERT: 4 410 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7957 (tm130) REVERT: 4 576 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8853 (mm110) REVERT: 4 647 GLU cc_start: 0.7523 (tt0) cc_final: 0.7137 (tm-30) REVERT: 5 5 ARG cc_start: 0.8356 (ttp-110) cc_final: 0.7875 (ttp80) REVERT: 5 154 GLU cc_start: 0.8117 (mp0) cc_final: 0.7628 (mp0) REVERT: 6 569 ILE cc_start: 0.9180 (mt) cc_final: 0.8888 (tt) REVERT: 6 587 TYR cc_start: 0.8754 (t80) cc_final: 0.8112 (t80) REVERT: 6 654 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8309 (tm-30) REVERT: 6 671 THR cc_start: 0.8981 (m) cc_final: 0.8689 (p) REVERT: 6 707 SER cc_start: 0.9400 (m) cc_final: 0.9065 (p) REVERT: 7 101 ASP cc_start: 0.8226 (t70) cc_final: 0.7898 (t70) REVERT: 7 115 GLU cc_start: 0.8283 (tp30) cc_final: 0.7905 (tp30) REVERT: 7 283 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7622 (mm-30) REVERT: 7 543 GLN cc_start: 0.8413 (pt0) cc_final: 0.8091 (pt0) REVERT: 7 675 MET cc_start: 0.8522 (tpt) cc_final: 0.8269 (tpp) REVERT: A 422 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7627 (mt-10) REVERT: A 423 GLU cc_start: 0.7372 (tm-30) cc_final: 0.7144 (tm-30) REVERT: B 234 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8053 (mp0) REVERT: B 264 MET cc_start: 0.8479 (mmm) cc_final: 0.8064 (mmm) REVERT: B 306 MET cc_start: 0.8944 (mmm) cc_final: 0.8682 (mtp) REVERT: B 334 THR cc_start: 0.8996 (m) cc_final: 0.8588 (p) REVERT: B 435 ARG cc_start: 0.8577 (mmm160) cc_final: 0.8352 (mmm160) REVERT: B 689 ASP cc_start: 0.7939 (m-30) cc_final: 0.7470 (t0) REVERT: C 690 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8679 (mm-30) REVERT: D 409 ASP cc_start: 0.8174 (m-30) cc_final: 0.7750 (m-30) REVERT: D 417 ASP cc_start: 0.8405 (t0) cc_final: 0.8186 (t0) REVERT: D 688 THR cc_start: 0.8981 (m) cc_final: 0.8759 (m) REVERT: E 146 TYR cc_start: 0.7849 (m-80) cc_final: 0.7498 (m-80) REVERT: E 305 TYR cc_start: 0.8629 (t80) cc_final: 0.8319 (t80) REVERT: F 427 ASP cc_start: 0.8538 (m-30) cc_final: 0.8169 (m-30) REVERT: F 537 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8934 (mp) REVERT: F 602 ASP cc_start: 0.8069 (t0) cc_final: 0.7699 (t0) REVERT: 1 86 ARG cc_start: 0.9123 (ttt-90) cc_final: 0.8768 (tpt-90) REVERT: 1 90 GLU cc_start: 0.8053 (tt0) cc_final: 0.7470 (mm-30) REVERT: 1 108 ASP cc_start: 0.6452 (t0) cc_final: 0.5990 (p0) REVERT: 1 319 MET cc_start: 0.6726 (mpp) cc_final: 0.6426 (mmt) REVERT: 1 338 TRP cc_start: 0.8945 (p-90) cc_final: 0.8661 (p-90) REVERT: G 115 ASN cc_start: 0.5309 (m-40) cc_final: 0.4746 (p0) outliers start: 107 outliers final: 98 residues processed: 1381 average time/residue: 1.5435 time to fit residues: 3486.7081 Evaluate side-chains 1428 residues out of total 7267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1326 time to evaluate : 7.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 450 ILE Chi-restraints excluded: chain 2 residue 477 THR Chi-restraints excluded: chain 2 residue 504 SER Chi-restraints excluded: chain 2 residue 515 VAL Chi-restraints excluded: chain 2 residue 620 ILE Chi-restraints excluded: chain 2 residue 781 MET Chi-restraints excluded: chain 2 residue 797 SER Chi-restraints excluded: chain 3 residue 227 THR Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 341 MET Chi-restraints excluded: chain 3 residue 482 ASP Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 552 ASP Chi-restraints excluded: chain 3 residue 566 LEU Chi-restraints excluded: chain 3 residue 569 HIS Chi-restraints excluded: chain 4 residue 242 ASN Chi-restraints excluded: chain 4 residue 410 GLN Chi-restraints excluded: chain 4 residue 414 SER Chi-restraints excluded: chain 4 residue 526 ILE Chi-restraints excluded: chain 4 residue 576 GLN Chi-restraints excluded: chain 4 residue 794 THR Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 258 LEU Chi-restraints excluded: chain 5 residue 417 ASP Chi-restraints excluded: chain 5 residue 439 THR Chi-restraints excluded: chain 5 residue 481 GLU Chi-restraints excluded: chain 5 residue 510 THR Chi-restraints excluded: chain 5 residue 511 THR Chi-restraints excluded: chain 5 residue 573 ILE Chi-restraints excluded: chain 6 residue 279 ILE Chi-restraints excluded: chain 6 residue 355 ASP Chi-restraints excluded: chain 6 residue 378 ASP Chi-restraints excluded: chain 6 residue 559 THR Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 599 SER Chi-restraints excluded: chain 6 residue 603 SER Chi-restraints excluded: chain 6 residue 645 ASP Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 661 ILE Chi-restraints excluded: chain 6 residue 665 LYS Chi-restraints excluded: chain 6 residue 672 LEU Chi-restraints excluded: chain 6 residue 677 SER Chi-restraints excluded: chain 6 residue 699 LEU Chi-restraints excluded: chain 6 residue 739 ASP Chi-restraints excluded: chain 7 residue 373 GLU Chi-restraints excluded: chain 7 residue 425 ASN Chi-restraints excluded: chain 7 residue 555 THR Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 395 CYS Chi-restraints excluded: chain E residue 559 THR Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 648 ASP Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 739 ASP Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 537 ILE Chi-restraints excluded: chain F residue 541 MET Chi-restraints excluded: chain F residue 561 THR Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain F residue 598 PHE Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 695 LEU Chi-restraints excluded: chain 1 residue 21 GLN Chi-restraints excluded: chain 1 residue 94 LEU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 290 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 485 optimal weight: 2.9990 chunk 782 optimal weight: 3.9990 chunk 477 optimal weight: 4.9990 chunk 371 optimal weight: 2.9990 chunk 544 optimal weight: 5.9990 chunk 820 optimal weight: 8.9990 chunk 755 optimal weight: 3.9990 chunk 653 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 504 optimal weight: 4.9990 chunk 400 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 411 ASN ** 6 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 GLN ** D 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 291 GLN F 538 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 68713 Z= 0.319 Angle : 0.578 25.491 93397 Z= 0.303 Chirality : 0.042 0.184 10778 Planarity : 0.004 0.104 11622 Dihedral : 12.512 155.654 10273 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.05 % Favored : 94.88 % Rotamer: Outliers : 1.61 % Allowed : 13.59 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.09), residues: 8108 helix: 1.57 (0.09), residues: 3166 sheet: -0.54 (0.13), residues: 1593 loop : -0.97 (0.11), residues: 3349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 112 HIS 0.008 0.001 HIS C 413 PHE 0.019 0.001 PHE B 421 TYR 0.013 0.001 TYR 1 265 ARG 0.021 0.001 ARG 4 451 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16216 Ramachandran restraints generated. 8108 Oldfield, 0 Emsley, 8108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 550 is missing expected H atoms. Skipping. Residue SER 416 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue THR 160 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue SER 550 is missing expected H atoms. Skipping. Residue SER 416 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Evaluate side-chains 1425 residues out of total 7267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1308 time to evaluate : 8.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 452 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7166 (tm-30) REVERT: 2 504 SER cc_start: 0.8877 (OUTLIER) cc_final: 0.8519 (p) REVERT: 3 490 MET cc_start: 0.8856 (mtt) cc_final: 0.8604 (mtt) REVERT: 3 691 ASN cc_start: 0.8463 (t0) cc_final: 0.8179 (t0) REVERT: 4 410 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7966 (tm130) REVERT: 4 647 GLU cc_start: 0.7525 (tt0) cc_final: 0.7131 (tm-30) REVERT: 5 5 ARG cc_start: 0.8395 (ttp-110) cc_final: 0.7949 (ttp80) REVERT: 5 154 GLU cc_start: 0.8121 (mp0) cc_final: 0.7635 (mp0) REVERT: 6 174 TYR cc_start: 0.9214 (t80) cc_final: 0.8957 (t80) REVERT: 6 569 ILE cc_start: 0.9216 (mt) cc_final: 0.8988 (tt) REVERT: 6 587 TYR cc_start: 0.8834 (t80) cc_final: 0.8100 (t80) REVERT: 6 654 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8323 (tm-30) REVERT: 6 671 THR cc_start: 0.9056 (m) cc_final: 0.8784 (p) REVERT: 6 707 SER cc_start: 0.9405 (m) cc_final: 0.9146 (p) REVERT: 7 101 ASP cc_start: 0.8286 (t70) cc_final: 0.7922 (t0) REVERT: 7 115 GLU cc_start: 0.8336 (tp30) cc_final: 0.7937 (tp30) REVERT: 7 543 GLN cc_start: 0.8481 (pt0) cc_final: 0.8146 (pt0) REVERT: 7 675 MET cc_start: 0.8567 (tpt) cc_final: 0.8323 (tpp) REVERT: A 423 GLU cc_start: 0.7331 (tm-30) cc_final: 0.7108 (tm-30) REVERT: B 234 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8072 (mp0) REVERT: B 264 MET cc_start: 0.8441 (mmm) cc_final: 0.8022 (mmm) REVERT: B 306 MET cc_start: 0.8968 (mmm) cc_final: 0.8685 (mtp) REVERT: B 334 THR cc_start: 0.9020 (m) cc_final: 0.8609 (p) REVERT: B 435 ARG cc_start: 0.8615 (mmm160) cc_final: 0.8365 (mmm160) REVERT: C 690 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8686 (mm-30) REVERT: D 409 ASP cc_start: 0.8140 (m-30) cc_final: 0.7750 (m-30) REVERT: D 417 ASP cc_start: 0.8448 (t0) cc_final: 0.8241 (t0) REVERT: D 688 THR cc_start: 0.9011 (m) cc_final: 0.8796 (m) REVERT: E 121 ASP cc_start: 0.7960 (m-30) cc_final: 0.7579 (m-30) REVERT: E 146 TYR cc_start: 0.7936 (m-80) cc_final: 0.7615 (m-80) REVERT: E 305 TYR cc_start: 0.8645 (t80) cc_final: 0.8331 (t80) REVERT: F 427 ASP cc_start: 0.8599 (m-30) cc_final: 0.8236 (m-30) REVERT: F 449 LYS cc_start: 0.9005 (tptt) cc_final: 0.8773 (tppt) REVERT: F 598 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.7930 (t80) REVERT: F 602 ASP cc_start: 0.7990 (t0) cc_final: 0.7609 (t0) REVERT: 1 86 ARG cc_start: 0.9133 (ttt-90) cc_final: 0.8823 (tpt-90) REVERT: 1 90 GLU cc_start: 0.8030 (tt0) cc_final: 0.7520 (mm-30) REVERT: 1 108 ASP cc_start: 0.6344 (t0) cc_final: 0.5829 (p0) REVERT: 1 319 MET cc_start: 0.6569 (mpp) cc_final: 0.6271 (mmt) REVERT: 1 338 TRP cc_start: 0.8939 (p-90) cc_final: 0.8641 (p-90) REVERT: G 115 ASN cc_start: 0.5081 (m-40) cc_final: 0.4554 (p0) outliers start: 117 outliers final: 110 residues processed: 1357 average time/residue: 1.5853 time to fit residues: 3520.2390 Evaluate side-chains 1412 residues out of total 7267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1299 time to evaluate : 7.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 450 ILE Chi-restraints excluded: chain 2 residue 477 THR Chi-restraints excluded: chain 2 residue 504 SER Chi-restraints excluded: chain 2 residue 574 VAL Chi-restraints excluded: chain 2 residue 620 ILE Chi-restraints excluded: chain 2 residue 781 MET Chi-restraints excluded: chain 2 residue 797 SER Chi-restraints excluded: chain 2 residue 812 SER Chi-restraints excluded: chain 3 residue 227 THR Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 341 MET Chi-restraints excluded: chain 3 residue 412 SER Chi-restraints excluded: chain 3 residue 482 ASP Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 552 ASP Chi-restraints excluded: chain 3 residue 566 LEU Chi-restraints excluded: chain 3 residue 569 HIS Chi-restraints excluded: chain 4 residue 242 ASN Chi-restraints excluded: chain 4 residue 410 GLN Chi-restraints excluded: chain 4 residue 414 SER Chi-restraints excluded: chain 4 residue 526 ILE Chi-restraints excluded: chain 4 residue 576 GLN Chi-restraints excluded: chain 4 residue 794 THR Chi-restraints excluded: chain 5 residue 220 SER Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 258 LEU Chi-restraints excluded: chain 5 residue 417 ASP Chi-restraints excluded: chain 5 residue 439 THR Chi-restraints excluded: chain 5 residue 481 GLU Chi-restraints excluded: chain 5 residue 510 THR Chi-restraints excluded: chain 5 residue 511 THR Chi-restraints excluded: chain 5 residue 573 ILE Chi-restraints excluded: chain 5 residue 633 LEU Chi-restraints excluded: chain 6 residue 279 ILE Chi-restraints excluded: chain 6 residue 355 ASP Chi-restraints excluded: chain 6 residue 378 ASP Chi-restraints excluded: chain 6 residue 559 THR Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 599 SER Chi-restraints excluded: chain 6 residue 603 SER Chi-restraints excluded: chain 6 residue 645 ASP Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 661 ILE Chi-restraints excluded: chain 6 residue 665 LYS Chi-restraints excluded: chain 6 residue 672 LEU Chi-restraints excluded: chain 6 residue 677 SER Chi-restraints excluded: chain 6 residue 699 LEU Chi-restraints excluded: chain 6 residue 739 ASP Chi-restraints excluded: chain 7 residue 373 GLU Chi-restraints excluded: chain 7 residue 425 ASN Chi-restraints excluded: chain 7 residue 555 THR Chi-restraints excluded: chain 7 residue 640 GLU Chi-restraints excluded: chain 7 residue 660 VAL Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 395 CYS Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain E residue 559 THR Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 648 ASP Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 739 ASP Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 541 MET Chi-restraints excluded: chain F residue 561 THR Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain F residue 598 PHE Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 695 LEU Chi-restraints excluded: chain 1 residue 21 GLN Chi-restraints excluded: chain 1 residue 91 LEU Chi-restraints excluded: chain 1 residue 94 LEU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 290 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 519 optimal weight: 3.9990 chunk 696 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 602 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 654 optimal weight: 4.9990 chunk 274 optimal weight: 3.9990 chunk 672 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 437 ASN ** 6 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 ASN ** D 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 538 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.132120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.100054 restraints weight = 411117.989| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.47 r_work: 0.3145 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 68713 Z= 0.194 Angle : 0.546 25.749 93397 Z= 0.282 Chirality : 0.041 0.172 10778 Planarity : 0.004 0.126 11622 Dihedral : 12.470 157.039 10273 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.28 % Favored : 95.66 % Rotamer: Outliers : 1.47 % Allowed : 13.80 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.09), residues: 8108 helix: 1.78 (0.09), residues: 3148 sheet: -0.47 (0.13), residues: 1559 loop : -0.85 (0.11), residues: 3401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 112 HIS 0.009 0.001 HIS 6 653 PHE 0.017 0.001 PHE G 690 TYR 0.012 0.001 TYR 7 88 ARG 0.023 0.000 ARG 4 451 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 49760.97 seconds wall clock time: 849 minutes 38.14 seconds (50978.14 seconds total)