Starting phenix.real_space_refine on Sun Mar 24 02:15:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kni_22950/03_2024/7kni_22950.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kni_22950/03_2024/7kni_22950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kni_22950/03_2024/7kni_22950.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kni_22950/03_2024/7kni_22950.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kni_22950/03_2024/7kni_22950.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kni_22950/03_2024/7kni_22950.pdb" } resolution = 3.91 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= 0.008 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: 4 Type Number sf(0) Gaussians S 198 5.16 5 C 25249 2.51 5 N 6476 2.21 5 O 7651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 796": "OD1" <-> "OD2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 796": "OD1" <-> "OD2" Residue "C PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 37": "OE1" <-> "OE2" Residue "F ASP 38": "OD1" <-> "OD2" Residue "F ASP 111": "OD1" <-> "OD2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F ASP 157": "OD1" <-> "OD2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 206": "OD1" <-> "OD2" Residue "F TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 213": "OD1" <-> "OD2" Residue "F TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 245": "NH1" <-> "NH2" Residue "F TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 273": "NH1" <-> "NH2" Residue "F PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F ASP 368": "OD1" <-> "OD2" Residue "F TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 402": "OE1" <-> "OE2" Residue "F GLU 406": "OE1" <-> "OE2" Residue "F ASP 427": "OD1" <-> "OD2" Residue "F PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 471": "OD1" <-> "OD2" Residue "F ARG 518": "NH1" <-> "NH2" Residue "F GLU 536": "OE1" <-> "OE2" Residue "F PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 559": "NH1" <-> "NH2" Residue "F GLU 564": "OE1" <-> "OE2" Residue "F TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D ASP 38": "OD1" <-> "OD2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 206": "OD1" <-> "OD2" Residue "D TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 213": "OD1" <-> "OD2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ASP 368": "OD1" <-> "OD2" Residue "D TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "D ASP 427": "OD1" <-> "OD2" Residue "D ASP 431": "OD1" <-> "OD2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "D GLU 536": "OE1" <-> "OE2" Residue "D PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 559": "NH1" <-> "NH2" Residue "D GLU 564": "OE1" <-> "OE2" Residue "D TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 37": "OE1" <-> "OE2" Residue "E ASP 38": "OD1" <-> "OD2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E ASP 111": "OD1" <-> "OD2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 206": "OD1" <-> "OD2" Residue "E TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 213": "OD1" <-> "OD2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E ARG 245": "NH1" <-> "NH2" Residue "E TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 273": "NH1" <-> "NH2" Residue "E PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E ASP 368": "OD1" <-> "OD2" Residue "E TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 402": "OE1" <-> "OE2" Residue "E GLU 406": "OE1" <-> "OE2" Residue "E ASP 427": "OD1" <-> "OD2" Residue "E PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 471": "OD1" <-> "OD2" Residue "E ARG 518": "NH1" <-> "NH2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "E GLU 536": "OE1" <-> "OE2" Residue "E PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 559": "NH1" <-> "NH2" Residue "E GLU 564": "OE1" <-> "OE2" Residue "E TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39574 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8012 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 51, 'TRANS': 978} Chain breaks: 7 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 8012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8012 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 51, 'TRANS': 978} Chain breaks: 7 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 8012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8012 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 51, 'TRANS': 978} Chain breaks: 7 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 19.44, per 1000 atoms: 0.49 Number of scatterers: 39574 At special positions: 0 Unit cell: (168.222, 171.396, 239.108, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 198 16.00 O 7651 8.00 N 6476 7.00 C 25249 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A1134 " " NAG A1303 " - " ASN A1098 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A 61 " " NAG A1311 " - " ASN A 234 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 603 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B1134 " " NAG B1303 " - " ASN B1098 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 61 " " NAG B1310 " - " ASN B 234 " " NAG B1311 " - " ASN B 165 " " NAG B1312 " - " ASN B 343 " " NAG B1313 " - " ASN B 603 " " NAG B1314 " - " ASN B1074 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C1134 " " NAG C1303 " - " ASN C1098 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C 61 " " NAG C1311 " - " ASN C 234 " " NAG C1312 " - " ASN C 165 " " NAG C1313 " - " ASN C 343 " " NAG C1314 " - " ASN C 603 " " NAG D 701 " - " ASN D 322 " " NAG D 702 " - " ASN D 432 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 90 " " NAG D 705 " - " ASN D 53 " " NAG E 701 " - " ASN E 322 " " NAG E 702 " - " ASN E 432 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 90 " " NAG E 705 " - " ASN E 53 " " NAG F 701 " - " ASN F 322 " " NAG F 702 " - " ASN F 432 " " NAG F 703 " - " ASN F 103 " " NAG F 704 " - " ASN F 90 " " NAG F 705 " - " ASN F 53 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN F 546 " " NAG K 1 " - " ASN D 546 " " NAG L 1 " - " ASN E 546 " Time building additional restraints: 14.94 Conformation dependent library (CDL) restraints added in 6.3 seconds 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9186 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 51 sheets defined 38.2% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.660A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.814A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.897A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.391A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 removed outlier: 4.006A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.647A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 946 through 968 removed outlier: 3.923A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN A 953 " --> pdb=" O GLN A 949 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.518A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.858A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1148 removed outlier: 3.859A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.565A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.902A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.563A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.716A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.556A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.523A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.831A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.553A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.328A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 946 through 968 removed outlier: 3.599A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN B 953 " --> pdb=" O GLN B 949 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.984A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.797A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 3.888A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.536A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.006A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.627A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.522A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.582A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.770A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.755A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 4.193A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.533A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.793A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.897A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASN C 953 " --> pdb=" O GLN C 949 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.011A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1148 removed outlier: 3.815A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 51 removed outlier: 3.781A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 80 removed outlier: 3.797A pdb=" N VAL F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR F 78 " --> pdb=" O LYS F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 90 through 101 removed outlier: 3.561A pdb=" N LYS F 94 " --> pdb=" O ASN F 90 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN F 96 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 128 removed outlier: 3.568A pdb=" N LYS F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN F 117 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE F 119 " --> pdb=" O ARG F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 154 removed outlier: 3.976A pdb=" N ASN F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLU F 150 " --> pdb=" O PRO F 146 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE F 151 " --> pdb=" O GLY F 147 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 170 removed outlier: 3.767A pdb=" N TRP F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER F 170 " --> pdb=" O GLU F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.682A pdb=" N GLN F 175 " --> pdb=" O VAL F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 176 through 187 removed outlier: 3.858A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU F 186 " --> pdb=" O GLU F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 194 removed outlier: 3.537A pdb=" N ALA F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 204 removed outlier: 3.775A pdb=" N ARG F 204 " --> pdb=" O GLY F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 245 removed outlier: 4.043A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 300 removed outlier: 3.965A pdb=" N VAL F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP F 299 " --> pdb=" O ASP F 295 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN F 300 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.543A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA F 311 " --> pdb=" O ILE F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 329 removed outlier: 4.489A pdb=" N TRP F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU F 329 " --> pdb=" O GLN F 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 324 through 329' Processing helix chain 'F' and resid 365 through 383 removed outlier: 3.890A pdb=" N HIS F 378 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE F 379 " --> pdb=" O GLU F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 413 removed outlier: 4.076A pdb=" N GLY F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU F 406 " --> pdb=" O GLU F 402 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 422 removed outlier: 3.505A pdb=" N ILE F 421 " --> pdb=" O HIS F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 447 removed outlier: 4.111A pdb=" N PHE F 438 " --> pdb=" O THR F 434 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 466 removed outlier: 4.405A pdb=" N PHE F 452 " --> pdb=" O GLY F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 471 No H-bonds generated for 'chain 'F' and resid 469 through 471' Processing helix chain 'F' and resid 472 through 484 removed outlier: 3.560A pdb=" N LYS F 476 " --> pdb=" O GLN F 472 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU F 479 " --> pdb=" O LYS F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 512 through 523 removed outlier: 4.043A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 533 Processing helix chain 'F' and resid 547 through 559 removed outlier: 4.116A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 572 removed outlier: 3.670A pdb=" N GLU F 571 " --> pdb=" O THR F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 586 removed outlier: 4.143A pdb=" N LEU F 585 " --> pdb=" O VAL F 581 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN F 586 " --> pdb=" O ARG F 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 581 through 586' Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.633A pdb=" N TRP F 594 " --> pdb=" O PRO F 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 51 removed outlier: 3.776A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 removed outlier: 3.843A pdb=" N VAL D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA D 80 " --> pdb=" O GLN D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 91 through 101 removed outlier: 3.709A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 128 removed outlier: 4.594A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 154 removed outlier: 4.340A pdb=" N ASN D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.764A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.637A pdb=" N GLN D 175 " --> pdb=" O VAL D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 176 through 187 removed outlier: 4.505A pdb=" N GLU D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 194 removed outlier: 4.366A pdb=" N ARG D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.643A pdb=" N ARG D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 247 removed outlier: 3.743A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.824A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS D 247 " --> pdb=" O TYR D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.865A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP D 299 " --> pdb=" O ASP D 295 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.504A pdb=" N GLU D 310 " --> pdb=" O ARG D 306 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.616A pdb=" N MET D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY D 377 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 4.123A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.512A pdb=" N ILE D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 447 removed outlier: 4.090A pdb=" N PHE D 438 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.667A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET D 480 " --> pdb=" O LYS D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 523 removed outlier: 4.097A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 533 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.946A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.694A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 586 removed outlier: 3.989A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN D 586 " --> pdb=" O ARG D 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 581 through 586' Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.931A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 51 removed outlier: 3.777A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 82 removed outlier: 4.070A pdb=" N VAL E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR E 78 " --> pdb=" O LYS E 74 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N MET E 82 " --> pdb=" O THR E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 101 removed outlier: 3.722A pdb=" N GLN E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 removed outlier: 4.573A pdb=" N ARG E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 154 removed outlier: 3.881A pdb=" N ASN E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU E 150 " --> pdb=" O PRO E 146 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN E 154 " --> pdb=" O GLU E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 169 removed outlier: 3.705A pdb=" N TRP E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.654A pdb=" N GLN E 175 " --> pdb=" O VAL E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 176 through 187 removed outlier: 3.577A pdb=" N GLU E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU E 186 " --> pdb=" O GLU E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 194 removed outlier: 4.425A pdb=" N ARG E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 204 removed outlier: 3.584A pdb=" N ARG E 204 " --> pdb=" O GLY E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 245 removed outlier: 3.719A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE E 233 " --> pdb=" O THR E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.682A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 293 through 300 removed outlier: 3.856A pdb=" N VAL E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.590A pdb=" N PHE E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU E 310 " --> pdb=" O ARG E 306 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA E 311 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 329 removed outlier: 4.148A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU E 329 " --> pdb=" O GLN E 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 324 through 329' Processing helix chain 'E' and resid 365 through 383 removed outlier: 3.874A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 413 removed outlier: 4.096A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 Processing helix chain 'E' and resid 432 through 447 removed outlier: 4.039A pdb=" N PHE E 438 " --> pdb=" O THR E 434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 removed outlier: 3.594A pdb=" N LYS E 476 " --> pdb=" O GLN E 472 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU E 479 " --> pdb=" O LYS E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 523 removed outlier: 4.038A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 533 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.938A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 removed outlier: 3.674A pdb=" N GLU E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 586 removed outlier: 4.201A pdb=" N LEU E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN E 586 " --> pdb=" O ARG E 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 581 through 586' Processing helix chain 'E' and resid 588 through 599 removed outlier: 3.691A pdb=" N TRP E 594 " --> pdb=" O PRO E 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.806A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.806A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.640A pdb=" N TYR A 279 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 276 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.808A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 7.212A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 356 removed outlier: 4.065A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.773A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.582A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 578 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 642 through 645 removed outlier: 3.677A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 650 " --> pdb=" O PHE A 643 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.333A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 704 removed outlier: 7.243A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 719 removed outlier: 6.484A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 722 through 728 removed outlier: 3.666A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.241A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.534A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 7.975A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.906A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.633A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.955A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 356 removed outlier: 4.027A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.760A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 538 through 542 removed outlier: 3.534A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 642 through 645 removed outlier: 3.577A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 650 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.812A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS B 671 " --> pdb=" O TYR B 695 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 703 through 704 removed outlier: 7.169A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 714 through 728 removed outlier: 6.478A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B1066 " --> pdb=" O SER B 721 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 714 through 728 removed outlier: 6.478A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B1066 " --> pdb=" O SER B 721 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.533A pdb=" N LYS B1086 " --> pdb=" O HIS B1083 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.134A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.066A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 289 " --> pdb=" O LEU C 276 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.623A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.776A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 356 removed outlier: 4.094A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 removed outlier: 3.795A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 538 through 542 removed outlier: 3.607A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 642 through 644 removed outlier: 3.639A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 650 " --> pdb=" O PHE C 643 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.946A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 712 through 719 removed outlier: 6.901A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 722 through 728 removed outlier: 3.546A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.277A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.769A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.601A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'F' and resid 347 through 352 removed outlier: 5.969A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.537A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.527A pdb=" N LEU D 359 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.969A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'E' and resid 347 through 352 removed outlier: 5.964A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1412 hydrogen bonds defined for protein. 3966 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.34 Time building geometry restraints manager: 16.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12551 1.34 - 1.46: 10187 1.46 - 1.59: 17505 1.59 - 1.71: 0 1.71 - 1.84: 291 Bond restraints: 40534 Sorted by residual: bond pdb=" N ASN A1074 " pdb=" CA ASN A1074 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.17e-02 7.31e+03 6.62e+00 bond pdb=" N ASN A 331 " pdb=" CA ASN A 331 " ideal model delta sigma weight residual 1.455 1.486 -0.032 1.26e-02 6.30e+03 6.34e+00 bond pdb=" N ASN B1074 " pdb=" CA ASN B1074 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.27e-02 6.20e+03 6.16e+00 bond pdb=" N ASN C 709 " pdb=" CA ASN C 709 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.35e-02 5.49e+03 5.85e+00 bond pdb=" N ASN C 616 " pdb=" CA ASN C 616 " ideal model delta sigma weight residual 1.456 1.484 -0.029 1.22e-02 6.72e+03 5.56e+00 ... (remaining 40529 not shown) Histogram of bond angle deviations from ideal: 97.18 - 104.57: 654 104.57 - 111.95: 19364 111.95 - 119.33: 13768 119.33 - 126.71: 20732 126.71 - 134.09: 606 Bond angle restraints: 55124 Sorted by residual: angle pdb=" N TYR D 180 " pdb=" CA TYR D 180 " pdb=" C TYR D 180 " ideal model delta sigma weight residual 111.82 117.48 -5.66 1.16e+00 7.43e-01 2.38e+01 angle pdb=" CA MET D 152 " pdb=" CB MET D 152 " pdb=" CG MET D 152 " ideal model delta sigma weight residual 114.10 122.48 -8.38 2.00e+00 2.50e-01 1.76e+01 angle pdb=" N LEU D 179 " pdb=" CA LEU D 179 " pdb=" C LEU D 179 " ideal model delta sigma weight residual 112.45 117.80 -5.35 1.39e+00 5.18e-01 1.48e+01 angle pdb=" CB MET E 579 " pdb=" CG MET E 579 " pdb=" SD MET E 579 " ideal model delta sigma weight residual 112.70 123.75 -11.05 3.00e+00 1.11e-01 1.36e+01 angle pdb=" N TRP D 594 " pdb=" CA TRP D 594 " pdb=" CB TRP D 594 " ideal model delta sigma weight residual 110.16 115.51 -5.35 1.48e+00 4.57e-01 1.31e+01 ... (remaining 55119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 22408 17.96 - 35.91: 2011 35.91 - 53.87: 412 53.87 - 71.83: 96 71.83 - 89.79: 33 Dihedral angle restraints: 24960 sinusoidal: 10707 harmonic: 14253 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -141.53 55.53 1 1.00e+01 1.00e-02 4.17e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -137.56 51.56 1 1.00e+01 1.00e-02 3.63e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -136.79 50.79 1 1.00e+01 1.00e-02 3.53e+01 ... (remaining 24957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 5719 0.084 - 0.168: 528 0.168 - 0.252: 18 0.252 - 0.336: 19 0.336 - 0.421: 2 Chirality restraints: 6286 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.55e+01 chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 6283 not shown) Planarity restraints: 7102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " 0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG A1301 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " 0.089 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " -0.537 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " 0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " -0.339 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG B1301 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " -0.172 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " 0.510 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1301 " 0.293 2.00e-02 2.50e+03 2.46e-01 7.59e+02 pdb=" C7 NAG C1301 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG C1301 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG C1301 " -0.420 2.00e-02 2.50e+03 pdb=" O7 NAG C1301 " 0.017 2.00e-02 2.50e+03 ... (remaining 7099 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 489 2.62 - 3.19: 35488 3.19 - 3.76: 61350 3.76 - 4.33: 83750 4.33 - 4.90: 134526 Nonbonded interactions: 315603 Sorted by model distance: nonbonded pdb=" OD1 ASN C 540 " pdb=" OG1 THR C 549 " model vdw 2.045 2.440 nonbonded pdb=" OD1 ASN B 540 " pdb=" OG1 THR B 549 " model vdw 2.048 2.440 nonbonded pdb=" O LEU B 966 " pdb=" OG SER B 975 " model vdw 2.059 2.440 nonbonded pdb=" O ALA D 501 " pdb=" OG SER D 507 " model vdw 2.088 2.440 nonbonded pdb=" NH2 ARG D 177 " pdb=" O TYR D 497 " model vdw 2.090 2.520 ... (remaining 315598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 26 through 1149 or resid 1301 through 1313)) selection = (chain 'C' and (resid 26 through 1149 or resid 1301 through 1313)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 14.240 Check model and map are aligned: 0.630 Set scattering table: 0.390 Process input model: 99.670 Find NCS groups from input model: 2.640 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5677 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 : 0.004 0.054 40534 Z= 0.246 Angle : 0.638 11.050 55124 Z= 0.325 Chirality : 0.047 0.421 6286 Planarity : 0.008 0.302 7040 Dihedral : 14.194 89.785 15630 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.07 % Allowed : 0.45 % Favored : 99.48 % 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: -1.75 (0.11), residues: 4824 helix: -1.56 (0.12), residues: 1495 sheet: 0.08 (0.22), residues: 540 loop : -1.15 (0.11), residues: 2789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP D 594 HIS 0.015 0.001 HIS F 540 PHE 0.046 0.001 PHE D 315 TYR 0.017 0.001 TYR F 243 ARG 0.006 0.000 ARG E 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 254 time to evaluate : 4.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 779 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7701 (tm-30) REVERT: B 153 MET cc_start: 0.1872 (pmm) cc_final: 0.1497 (pmm) REVERT: B 915 VAL cc_start: 0.7177 (p) cc_final: 0.6855 (p) REVERT: B 1038 LYS cc_start: 0.5522 (mmtt) cc_final: 0.5219 (mmmt) REVERT: C 42 VAL cc_start: 0.5356 (t) cc_final: 0.4885 (t) REVERT: F 247 LYS cc_start: 0.7651 (mppt) cc_final: 0.7237 (mtmm) REVERT: F 480 MET cc_start: 0.6131 (tmm) cc_final: 0.5915 (tmm) REVERT: F 557 MET cc_start: 0.0501 (ppp) cc_final: 0.0274 (ppp) REVERT: F 579 MET cc_start: 0.2043 (mtt) cc_final: 0.1629 (mtt) REVERT: D 292 ASP cc_start: 0.4617 (m-30) cc_final: 0.4309 (m-30) REVERT: D 376 MET cc_start: -0.0418 (mtt) cc_final: -0.0739 (mtm) REVERT: D 455 MET cc_start: 0.5995 (tmm) cc_final: 0.4903 (ppp) REVERT: D 610 TRP cc_start: 0.7677 (m-90) cc_final: 0.7439 (m-90) REVERT: E 50 TYR cc_start: 0.9496 (t80) cc_final: 0.9240 (t80) REVERT: E 361 CYS cc_start: 0.4262 (m) cc_final: 0.4018 (t) outliers start: 3 outliers final: 2 residues processed: 256 average time/residue: 0.4484 time to fit residues: 200.4912 Evaluate side-chains 196 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 194 time to evaluate : 4.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain D residue 152 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 410 optimal weight: 20.0000 chunk 368 optimal weight: 7.9990 chunk 204 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 196 optimal weight: 6.9990 chunk 380 optimal weight: 30.0000 chunk 147 optimal weight: 8.9990 chunk 231 optimal weight: 0.5980 chunk 283 optimal weight: 10.0000 chunk 441 optimal weight: 20.0000 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN B 450 ASN ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 762 GLN B 777 ASN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 121 ASN C 450 ASN C 751 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 250 ASN F 290 ASN F 330 ASN F 373 HIS F 417 HIS D 330 ASN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS E 330 ASN E 373 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6046 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 40534 Z= 0.322 Angle : 0.693 10.388 55124 Z= 0.359 Chirality : 0.048 0.333 6286 Planarity : 0.005 0.053 7040 Dihedral : 5.976 59.165 6654 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.73 % Allowed : 9.07 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.11), residues: 4824 helix: -0.84 (0.12), residues: 1641 sheet: -0.25 (0.22), residues: 474 loop : -1.35 (0.11), residues: 2709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 163 HIS 0.007 0.002 HIS A1083 PHE 0.028 0.002 PHE B 718 TYR 0.031 0.002 TYR B 917 ARG 0.006 0.001 ARG D 482 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 230 time to evaluate : 4.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1031 GLU cc_start: 0.6276 (mm-30) cc_final: 0.5915 (mm-30) REVERT: B 153 MET cc_start: 0.1138 (pmm) cc_final: 0.0834 (pmm) REVERT: B 710 ASN cc_start: 0.6911 (p0) cc_final: 0.6687 (p0) REVERT: B 902 MET cc_start: 0.7736 (mmp) cc_final: 0.7442 (mmp) REVERT: B 918 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7428 (mt-10) REVERT: C 42 VAL cc_start: 0.6461 (t) cc_final: 0.6108 (t) REVERT: C 1031 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5143 (pp20) REVERT: F 247 LYS cc_start: 0.7880 (mppt) cc_final: 0.7638 (mtmm) REVERT: F 360 MET cc_start: 0.3930 (ppp) cc_final: 0.2795 (ppp) REVERT: F 557 MET cc_start: 0.1038 (ppp) cc_final: 0.0797 (ppp) REVERT: D 455 MET cc_start: 0.6899 (tmm) cc_final: 0.6436 (ppp) REVERT: D 474 MET cc_start: -0.0109 (mmt) cc_final: -0.1227 (mmp) REVERT: E 249 MET cc_start: -0.0832 (OUTLIER) cc_final: -0.3587 (ptt) REVERT: E 332 MET cc_start: -0.0151 (ptt) cc_final: -0.0439 (ptt) REVERT: E 462 MET cc_start: -0.0414 (mmt) cc_final: -0.0661 (mmp) outliers start: 31 outliers final: 16 residues processed: 249 average time/residue: 0.4542 time to fit residues: 198.4968 Evaluate side-chains 207 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 4.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 917 TYR Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1109 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 249 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 245 optimal weight: 50.0000 chunk 136 optimal weight: 9.9990 chunk 367 optimal weight: 40.0000 chunk 300 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 442 optimal weight: 7.9990 chunk 477 optimal weight: 50.0000 chunk 393 optimal weight: 9.9990 chunk 438 optimal weight: 7.9990 chunk 150 optimal weight: 0.8980 chunk 354 optimal weight: 6.9990 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN A 321 GLN A 607 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1002 GLN B1010 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 GLN F 535 HIS D 417 HIS E 175 GLN E 188 ASN E 194 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 40534 Z= 0.469 Angle : 0.837 20.602 55124 Z= 0.439 Chirality : 0.051 0.315 6286 Planarity : 0.006 0.081 7040 Dihedral : 6.466 54.036 6648 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 26.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.70 % Favored : 93.28 % Rotamer: Outliers : 3.13 % Allowed : 13.36 % Favored : 83.51 % 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: -1.83 (0.11), residues: 4824 helix: -0.78 (0.12), residues: 1693 sheet: -1.12 (0.21), residues: 543 loop : -1.51 (0.12), residues: 2588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP E 271 HIS 0.014 0.002 HIS A 655 PHE 0.041 0.003 PHE A1095 TYR 0.062 0.003 TYR A1110 ARG 0.013 0.001 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 181 time to evaluate : 4.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.1318 (pmm) cc_final: 0.0978 (pmm) REVERT: B 196 ASN cc_start: 0.1809 (OUTLIER) cc_final: 0.1482 (t0) REVERT: C 571 ASP cc_start: 0.7447 (t0) cc_final: 0.7212 (t0) REVERT: C 886 TRP cc_start: 0.7737 (OUTLIER) cc_final: 0.7391 (p90) REVERT: C 917 TYR cc_start: 0.5695 (OUTLIER) cc_final: 0.4116 (m-80) REVERT: C 1031 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.5301 (pp20) REVERT: C 1050 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.6205 (pmm) REVERT: F 360 MET cc_start: 0.3801 (ppp) cc_final: 0.2749 (ppp) REVERT: F 455 MET cc_start: -0.0553 (ptt) cc_final: -0.0863 (ptt) REVERT: F 557 MET cc_start: 0.1133 (ppp) cc_final: 0.0902 (ppp) REVERT: D 455 MET cc_start: 0.6364 (tmm) cc_final: 0.6159 (ptt) REVERT: D 474 MET cc_start: 0.0095 (mmt) cc_final: -0.0847 (mmp) REVERT: D 498 CYS cc_start: 0.5375 (t) cc_final: 0.5037 (t) REVERT: E 249 MET cc_start: -0.0848 (OUTLIER) cc_final: -0.3567 (ptt) REVERT: E 332 MET cc_start: -0.0733 (ptt) cc_final: -0.0963 (ptt) REVERT: E 360 MET cc_start: -0.2405 (ptm) cc_final: -0.2664 (ptm) outliers start: 133 outliers final: 68 residues processed: 299 average time/residue: 0.4513 time to fit residues: 235.8692 Evaluate side-chains 229 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 155 time to evaluate : 4.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 802 PHE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 917 TYR Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1109 PHE Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 436 optimal weight: 2.9990 chunk 332 optimal weight: 6.9990 chunk 229 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 443 optimal weight: 8.9990 chunk 469 optimal weight: 30.0000 chunk 231 optimal weight: 1.9990 chunk 420 optimal weight: 40.0000 chunk 126 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN F 265 HIS D 250 ASN E 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40534 Z= 0.219 Angle : 0.578 11.245 55124 Z= 0.297 Chirality : 0.045 0.302 6286 Planarity : 0.004 0.059 7040 Dihedral : 5.685 58.566 6648 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.12 % Allowed : 15.59 % Favored : 82.29 % 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: -1.36 (0.12), residues: 4824 helix: -0.12 (0.13), residues: 1659 sheet: -0.97 (0.21), residues: 539 loop : -1.40 (0.12), residues: 2626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 610 HIS 0.005 0.001 HIS A1048 PHE 0.021 0.001 PHE C1075 TYR 0.019 0.001 TYR B 707 ARG 0.004 0.000 ARG E 460 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 177 time to evaluate : 4.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ILE cc_start: 0.2629 (OUTLIER) cc_final: 0.2101 (tp) REVERT: A 779 GLN cc_start: 0.7987 (tm-30) cc_final: 0.7727 (tm-30) REVERT: A 1050 MET cc_start: 0.7236 (mpp) cc_final: 0.6994 (mpp) REVERT: B 153 MET cc_start: 0.1090 (pmm) cc_final: 0.0764 (pmm) REVERT: B 1038 LYS cc_start: 0.6874 (mmtt) cc_final: 0.6471 (mmtt) REVERT: C 41 LYS cc_start: 0.5917 (OUTLIER) cc_final: 0.5624 (tptp) REVERT: C 201 PHE cc_start: 0.5738 (OUTLIER) cc_final: 0.4882 (t80) REVERT: C 571 ASP cc_start: 0.7140 (t0) cc_final: 0.6901 (t0) REVERT: C 786 LYS cc_start: 0.6765 (pttm) cc_final: 0.6311 (ptpt) REVERT: C 1031 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5167 (pp20) REVERT: C 1050 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6257 (pmm) REVERT: F 360 MET cc_start: 0.3855 (ppp) cc_final: 0.2808 (ppp) REVERT: D 455 MET cc_start: 0.6782 (tmm) cc_final: 0.6513 (ptt) REVERT: D 474 MET cc_start: -0.0357 (mmt) cc_final: -0.1196 (mmp) REVERT: D 498 CYS cc_start: 0.4993 (t) cc_final: 0.4617 (t) REVERT: D 579 MET cc_start: -0.0337 (mmt) cc_final: -0.0903 (mmt) REVERT: E 249 MET cc_start: -0.0740 (OUTLIER) cc_final: -0.3375 (ptt) outliers start: 90 outliers final: 47 residues processed: 250 average time/residue: 0.4353 time to fit residues: 191.3073 Evaluate side-chains 213 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 160 time to evaluate : 4.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1019 ARG Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 917 TYR Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1109 PHE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 573 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 391 optimal weight: 0.4980 chunk 266 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 349 optimal weight: 9.9990 chunk 193 optimal weight: 8.9990 chunk 400 optimal weight: 5.9990 chunk 324 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 239 optimal weight: 2.9990 chunk 421 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40534 Z= 0.202 Angle : 0.548 9.531 55124 Z= 0.281 Chirality : 0.045 0.308 6286 Planarity : 0.004 0.066 7040 Dihedral : 5.292 55.984 6648 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.43 % Allowed : 16.21 % Favored : 81.37 % 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: -1.13 (0.12), residues: 4824 helix: 0.16 (0.13), residues: 1664 sheet: -0.77 (0.22), residues: 489 loop : -1.36 (0.12), residues: 2671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 610 HIS 0.006 0.001 HIS E 505 PHE 0.034 0.001 PHE D 315 TYR 0.018 0.001 TYR B 707 ARG 0.005 0.000 ARG E 460 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 174 time to evaluate : 4.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ILE cc_start: 0.2867 (OUTLIER) cc_final: 0.2255 (tp) REVERT: A 595 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.8164 (p) REVERT: A 779 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7695 (tm-30) REVERT: A 1050 MET cc_start: 0.7330 (mpp) cc_final: 0.7028 (mpp) REVERT: B 56 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8198 (tp) REVERT: B 153 MET cc_start: 0.1199 (pmm) cc_final: 0.0879 (pmm) REVERT: B 177 MET cc_start: 0.1789 (mmt) cc_final: 0.1289 (mmt) REVERT: B 196 ASN cc_start: 0.2258 (OUTLIER) cc_final: 0.1534 (t0) REVERT: B 1031 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6206 (pp20) REVERT: B 1038 LYS cc_start: 0.6819 (mmtt) cc_final: 0.6577 (mmtt) REVERT: B 1106 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7847 (tm-30) REVERT: C 201 PHE cc_start: 0.5811 (OUTLIER) cc_final: 0.5053 (t80) REVERT: C 544 ASN cc_start: 0.6071 (OUTLIER) cc_final: 0.5847 (p0) REVERT: C 571 ASP cc_start: 0.7106 (t0) cc_final: 0.6837 (t0) REVERT: C 1031 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5193 (pp20) REVERT: C 1050 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6316 (pmm) REVERT: F 360 MET cc_start: 0.3896 (ppp) cc_final: 0.2832 (ppp) REVERT: F 601 ASN cc_start: -0.2628 (OUTLIER) cc_final: -0.2928 (m-40) REVERT: D 408 MET cc_start: -0.1915 (ttt) cc_final: -0.2184 (ttp) REVERT: D 474 MET cc_start: -0.0581 (mmp) cc_final: -0.1387 (mmp) REVERT: D 498 CYS cc_start: 0.5005 (t) cc_final: 0.4624 (t) REVERT: D 579 MET cc_start: -0.0075 (mmt) cc_final: -0.0648 (mmt) REVERT: E 249 MET cc_start: -0.1030 (OUTLIER) cc_final: -0.3667 (ptt) REVERT: E 360 MET cc_start: -0.2443 (ptm) cc_final: -0.2748 (ptm) outliers start: 103 outliers final: 60 residues processed: 261 average time/residue: 0.4302 time to fit residues: 199.1777 Evaluate side-chains 238 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 166 time to evaluate : 4.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1019 ARG Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 917 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1109 PHE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 601 ASN Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 366 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 158 optimal weight: 0.9990 chunk 423 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 275 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 470 optimal weight: 0.8980 chunk 390 optimal weight: 50.0000 chunk 217 optimal weight: 9.9990 chunk 39 optimal weight: 0.0570 chunk 155 optimal weight: 6.9990 chunk 246 optimal weight: 0.0870 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 644 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN D 340 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 40534 Z= 0.146 Angle : 0.525 9.472 55124 Z= 0.264 Chirality : 0.045 0.317 6286 Planarity : 0.004 0.068 7040 Dihedral : 4.911 56.639 6648 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.96 % Allowed : 17.15 % Favored : 80.90 % 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: -0.95 (0.12), residues: 4824 helix: 0.34 (0.13), residues: 1669 sheet: -0.63 (0.22), residues: 517 loop : -1.29 (0.12), residues: 2638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 610 HIS 0.005 0.001 HIS B1048 PHE 0.024 0.001 PHE D 315 TYR 0.015 0.001 TYR B1067 ARG 0.004 0.000 ARG E 460 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 191 time to evaluate : 4.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ILE cc_start: 0.2812 (OUTLIER) cc_final: 0.2131 (tp) REVERT: A 595 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8231 (p) REVERT: A 779 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7660 (tm-30) REVERT: A 802 PHE cc_start: 0.7112 (m-80) cc_final: 0.6872 (m-80) REVERT: A 1050 MET cc_start: 0.7396 (mpp) cc_final: 0.7194 (mpp) REVERT: B 153 MET cc_start: 0.1063 (pmm) cc_final: 0.0782 (pmm) REVERT: B 177 MET cc_start: 0.1771 (mmt) cc_final: 0.1373 (mmt) REVERT: B 1031 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6202 (pp20) REVERT: C 544 ASN cc_start: 0.5925 (OUTLIER) cc_final: 0.5693 (p0) REVERT: C 571 ASP cc_start: 0.7127 (t0) cc_final: 0.6885 (t0) REVERT: C 595 VAL cc_start: 0.7975 (OUTLIER) cc_final: 0.7686 (p) REVERT: C 1050 MET cc_start: 0.6707 (OUTLIER) cc_final: 0.6032 (pmm) REVERT: F 249 MET cc_start: 0.4691 (ppp) cc_final: 0.4360 (ppp) REVERT: F 360 MET cc_start: 0.3985 (ppp) cc_final: 0.2905 (ppp) REVERT: F 579 MET cc_start: 0.2704 (mtt) cc_final: 0.2332 (mpp) REVERT: D 182 GLU cc_start: 0.8539 (tm-30) cc_final: 0.7710 (mp0) REVERT: D 474 MET cc_start: -0.0502 (mmp) cc_final: -0.1497 (mmp) REVERT: D 579 MET cc_start: -0.0238 (mmt) cc_final: -0.0802 (mmt) REVERT: E 249 MET cc_start: -0.0932 (OUTLIER) cc_final: -0.3565 (ptt) REVERT: E 579 MET cc_start: -0.2698 (tmm) cc_final: -0.3242 (tpt) outliers start: 83 outliers final: 44 residues processed: 256 average time/residue: 0.4552 time to fit residues: 204.9270 Evaluate side-chains 222 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 171 time to evaluate : 4.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 917 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1109 PHE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 573 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 453 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 267 optimal weight: 6.9990 chunk 343 optimal weight: 50.0000 chunk 266 optimal weight: 5.9990 chunk 395 optimal weight: 0.2980 chunk 262 optimal weight: 2.9990 chunk 468 optimal weight: 9.9990 chunk 293 optimal weight: 0.7980 chunk 285 optimal weight: 8.9990 chunk 216 optimal weight: 20.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.5872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 40534 Z= 0.267 Angle : 0.611 16.378 55124 Z= 0.310 Chirality : 0.045 0.320 6286 Planarity : 0.004 0.066 7040 Dihedral : 5.094 54.856 6648 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.26 % Allowed : 17.55 % Favored : 80.19 % 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: -1.00 (0.12), residues: 4824 helix: 0.32 (0.13), residues: 1674 sheet: -0.77 (0.22), residues: 516 loop : -1.30 (0.12), residues: 2634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 610 HIS 0.008 0.001 HIS A 655 PHE 0.035 0.002 PHE C 888 TYR 0.022 0.001 TYR B 707 ARG 0.011 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 181 time to evaluate : 4.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ILE cc_start: 0.3271 (OUTLIER) cc_final: 0.2651 (tp) REVERT: A 753 LEU cc_start: 0.8636 (pp) cc_final: 0.8411 (pp) REVERT: A 779 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7801 (tm-30) REVERT: A 898 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7603 (t80) REVERT: A 1050 MET cc_start: 0.7255 (mpp) cc_final: 0.6995 (mpp) REVERT: B 153 MET cc_start: 0.1719 (pmm) cc_final: 0.1442 (pmm) REVERT: B 177 MET cc_start: 0.2226 (mmt) cc_final: 0.1934 (mmt) REVERT: B 196 ASN cc_start: 0.2343 (OUTLIER) cc_final: 0.2088 (p0) REVERT: B 544 ASN cc_start: 0.7005 (OUTLIER) cc_final: 0.6799 (p0) REVERT: C 201 PHE cc_start: 0.5843 (OUTLIER) cc_final: 0.5251 (t80) REVERT: C 544 ASN cc_start: 0.5499 (OUTLIER) cc_final: 0.5217 (p0) REVERT: C 571 ASP cc_start: 0.7218 (t0) cc_final: 0.6910 (t0) REVERT: C 786 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6463 (pttm) REVERT: C 1050 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6274 (pmm) REVERT: F 249 MET cc_start: 0.4762 (ppp) cc_final: 0.4490 (ppp) REVERT: F 360 MET cc_start: 0.3679 (ppp) cc_final: 0.2539 (ppp) REVERT: F 601 ASN cc_start: -0.2536 (OUTLIER) cc_final: -0.2818 (m-40) REVERT: D 474 MET cc_start: -0.0319 (mmp) cc_final: -0.1276 (mmp) REVERT: D 579 MET cc_start: 0.0101 (mmt) cc_final: -0.0515 (mmt) REVERT: E 249 MET cc_start: -0.0863 (OUTLIER) cc_final: -0.3549 (ptt) REVERT: E 579 MET cc_start: -0.2768 (tmm) cc_final: -0.3057 (tpt) outliers start: 96 outliers final: 67 residues processed: 261 average time/residue: 0.4420 time to fit residues: 203.4457 Evaluate side-chains 243 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 166 time to evaluate : 4.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 1019 ARG Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 802 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 917 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1109 PHE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 601 ASN Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 573 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 289 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 92 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 297 optimal weight: 3.9990 chunk 319 optimal weight: 30.0000 chunk 231 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 368 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6358 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40534 Z= 0.166 Angle : 0.551 12.715 55124 Z= 0.276 Chirality : 0.044 0.317 6286 Planarity : 0.004 0.067 7040 Dihedral : 4.916 56.672 6648 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.93 % Allowed : 18.30 % Favored : 79.76 % 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: -0.90 (0.12), residues: 4824 helix: 0.43 (0.13), residues: 1679 sheet: -0.72 (0.22), residues: 535 loop : -1.26 (0.12), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1102 HIS 0.006 0.001 HIS B1048 PHE 0.034 0.001 PHE C 888 TYR 0.015 0.001 TYR B 707 ARG 0.007 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 177 time to evaluate : 4.271 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: A 231 ILE cc_start: 0.3340 (OUTLIER) cc_final: 0.2703 (tp) REVERT: A 595 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8139 (p) REVERT: A 779 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7742 (tm-30) REVERT: A 1050 MET cc_start: 0.7490 (mpp) cc_final: 0.7202 (mpp) REVERT: B 153 MET cc_start: 0.1804 (pmm) cc_final: 0.1548 (pmm) REVERT: B 177 MET cc_start: 0.2013 (mmt) cc_final: 0.1784 (mmt) REVERT: C 201 PHE cc_start: 0.5945 (OUTLIER) cc_final: 0.5251 (t80) REVERT: C 544 ASN cc_start: 0.5567 (OUTLIER) cc_final: 0.5304 (p0) REVERT: C 571 ASP cc_start: 0.7344 (t0) cc_final: 0.7048 (t0) REVERT: C 786 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6456 (pttm) REVERT: F 249 MET cc_start: 0.4774 (ppp) cc_final: 0.4528 (ppp) REVERT: F 360 MET cc_start: 0.4103 (ppp) cc_final: 0.2992 (ppp) REVERT: F 579 MET cc_start: 0.2534 (mtt) cc_final: 0.2236 (mpp) REVERT: F 601 ASN cc_start: -0.2432 (OUTLIER) cc_final: -0.2730 (m-40) REVERT: D 383 MET cc_start: -0.1049 (mtt) cc_final: -0.2486 (tmm) REVERT: D 474 MET cc_start: -0.0549 (mmp) cc_final: -0.1569 (mmp) REVERT: D 480 MET cc_start: -0.0006 (ppp) cc_final: -0.0392 (ppp) REVERT: D 579 MET cc_start: -0.0072 (mmt) cc_final: -0.0710 (mmt) REVERT: E 123 MET cc_start: -0.4990 (ptt) cc_final: -0.5211 (ppp) REVERT: E 249 MET cc_start: -0.0932 (OUTLIER) cc_final: -0.3599 (ptt) REVERT: E 270 MET cc_start: 0.5455 (ppp) cc_final: 0.5108 (mmp) REVERT: E 579 MET cc_start: -0.2953 (tmm) cc_final: -0.3171 (tpt) outliers start: 82 outliers final: 58 residues processed: 242 average time/residue: 0.4452 time to fit residues: 189.6082 Evaluate side-chains 236 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 171 time to evaluate : 4.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1019 ARG Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 917 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1109 PHE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 601 ASN Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 573 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 426 optimal weight: 0.6980 chunk 448 optimal weight: 0.7980 chunk 409 optimal weight: 6.9990 chunk 436 optimal weight: 0.9980 chunk 262 optimal weight: 0.1980 chunk 190 optimal weight: 0.9980 chunk 342 optimal weight: 30.0000 chunk 133 optimal weight: 30.0000 chunk 394 optimal weight: 8.9990 chunk 412 optimal weight: 4.9990 chunk 434 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 544 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN F 60 GLN F 64 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 40534 Z= 0.150 Angle : 0.545 13.130 55124 Z= 0.271 Chirality : 0.044 0.320 6286 Planarity : 0.004 0.068 7040 Dihedral : 4.752 55.754 6648 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.79 % Allowed : 18.52 % Favored : 79.69 % 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: -0.83 (0.12), residues: 4824 helix: 0.49 (0.13), residues: 1673 sheet: -0.72 (0.22), residues: 528 loop : -1.20 (0.12), residues: 2623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 271 HIS 0.007 0.001 HIS B1048 PHE 0.030 0.001 PHE C 888 TYR 0.014 0.001 TYR B1067 ARG 0.006 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 183 time to evaluate : 4.476 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: A 231 ILE cc_start: 0.3453 (OUTLIER) cc_final: 0.2811 (tp) REVERT: A 595 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8154 (p) REVERT: A 753 LEU cc_start: 0.8458 (pp) cc_final: 0.7871 (tt) REVERT: A 779 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7708 (tm-30) REVERT: A 1050 MET cc_start: 0.7481 (mpp) cc_final: 0.7150 (mpp) REVERT: B 153 MET cc_start: 0.1781 (pmm) cc_final: 0.1555 (pmm) REVERT: B 177 MET cc_start: 0.1945 (mmt) cc_final: 0.1693 (mmt) REVERT: B 196 ASN cc_start: 0.1989 (OUTLIER) cc_final: 0.1695 (t0) REVERT: C 201 PHE cc_start: 0.5817 (OUTLIER) cc_final: 0.5223 (t80) REVERT: C 544 ASN cc_start: 0.5956 (OUTLIER) cc_final: 0.5711 (p0) REVERT: C 571 ASP cc_start: 0.7292 (t0) cc_final: 0.7033 (t0) REVERT: C 595 VAL cc_start: 0.7918 (OUTLIER) cc_final: 0.7608 (p) REVERT: C 786 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6442 (pttm) REVERT: F 190 MET cc_start: 0.2544 (mpp) cc_final: 0.2315 (mpp) REVERT: F 249 MET cc_start: 0.4669 (ppp) cc_final: 0.4419 (ppp) REVERT: F 360 MET cc_start: 0.4118 (ppp) cc_final: 0.2991 (ppp) REVERT: F 579 MET cc_start: 0.2637 (mtt) cc_final: 0.2320 (mpp) REVERT: D 323 MET cc_start: -0.2564 (tpt) cc_final: -0.3031 (tpt) REVERT: D 383 MET cc_start: -0.1052 (mtt) cc_final: -0.2589 (tmm) REVERT: D 474 MET cc_start: -0.0638 (mmp) cc_final: -0.1615 (mmp) REVERT: D 480 MET cc_start: -0.0043 (ppp) cc_final: -0.0375 (ppp) REVERT: D 579 MET cc_start: -0.0262 (mmt) cc_final: -0.0765 (mmt) REVERT: E 123 MET cc_start: -0.5005 (ptt) cc_final: -0.5235 (ppp) REVERT: E 249 MET cc_start: -0.0877 (OUTLIER) cc_final: -0.3479 (ptt) REVERT: E 270 MET cc_start: 0.5611 (ppp) cc_final: 0.5140 (mmp) REVERT: E 376 MET cc_start: -0.5368 (ttp) cc_final: -0.5822 (ttp) outliers start: 76 outliers final: 57 residues processed: 245 average time/residue: 0.4495 time to fit residues: 195.6392 Evaluate side-chains 237 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 172 time to evaluate : 4.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 917 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 573 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 286 optimal weight: 0.7980 chunk 461 optimal weight: 1.9990 chunk 281 optimal weight: 0.9980 chunk 218 optimal weight: 0.9990 chunk 320 optimal weight: 9.9990 chunk 484 optimal weight: 30.0000 chunk 445 optimal weight: 50.0000 chunk 385 optimal weight: 20.0000 chunk 40 optimal weight: 40.0000 chunk 297 optimal weight: 0.7980 chunk 236 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN F 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.6005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.165 40534 Z= 0.196 Angle : 0.699 59.200 55124 Z= 0.384 Chirality : 0.045 0.510 6286 Planarity : 0.004 0.069 7040 Dihedral : 4.751 55.747 6648 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.98 % Favored : 95.00 % Rotamer: Outliers : 1.67 % Allowed : 18.68 % Favored : 79.65 % Cbeta Deviations : 0.02 % 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: -0.82 (0.12), residues: 4824 helix: 0.49 (0.13), residues: 1673 sheet: -0.71 (0.22), residues: 528 loop : -1.20 (0.12), residues: 2623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 271 HIS 0.006 0.001 HIS B1048 PHE 0.028 0.001 PHE C 888 TYR 0.015 0.001 TYR B1067 ARG 0.006 0.000 ARG A1039 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 171 time to evaluate : 4.968 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: A 231 ILE cc_start: 0.3447 (OUTLIER) cc_final: 0.2811 (tp) REVERT: A 595 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8154 (p) REVERT: A 753 LEU cc_start: 0.8493 (pp) cc_final: 0.7916 (tt) REVERT: A 779 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7728 (tm-30) REVERT: A 1050 MET cc_start: 0.7450 (mpp) cc_final: 0.7143 (mpp) REVERT: B 153 MET cc_start: 0.1780 (pmm) cc_final: 0.1556 (pmm) REVERT: B 177 MET cc_start: 0.1944 (mmt) cc_final: 0.1691 (mmt) REVERT: B 196 ASN cc_start: 0.1991 (OUTLIER) cc_final: 0.1696 (t0) REVERT: C 201 PHE cc_start: 0.5816 (OUTLIER) cc_final: 0.5219 (t80) REVERT: C 544 ASN cc_start: 0.5960 (OUTLIER) cc_final: 0.5714 (p0) REVERT: C 571 ASP cc_start: 0.7295 (t0) cc_final: 0.7036 (t0) REVERT: C 595 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7609 (p) REVERT: F 190 MET cc_start: 0.2545 (mpp) cc_final: 0.2314 (mpp) REVERT: F 249 MET cc_start: 0.4671 (ppp) cc_final: 0.4417 (ppp) REVERT: F 360 MET cc_start: 0.4113 (ppp) cc_final: 0.2991 (ppp) REVERT: F 579 MET cc_start: 0.2686 (mtt) cc_final: 0.2357 (mpp) REVERT: D 323 MET cc_start: -0.2560 (tpt) cc_final: -0.3035 (tpt) REVERT: D 383 MET cc_start: -0.1054 (mtt) cc_final: -0.2603 (tmm) REVERT: D 474 MET cc_start: -0.0636 (mmp) cc_final: -0.1602 (mmp) REVERT: D 579 MET cc_start: -0.0131 (mmt) cc_final: -0.0797 (mmt) REVERT: E 123 MET cc_start: -0.5006 (ptt) cc_final: -0.5334 (ppp) REVERT: E 249 MET cc_start: -0.0879 (OUTLIER) cc_final: -0.3483 (ptt) REVERT: E 270 MET cc_start: 0.5690 (ppp) cc_final: 0.5132 (mmp) REVERT: E 376 MET cc_start: -0.5378 (ttp) cc_final: -0.5861 (ttp) outliers start: 71 outliers final: 59 residues processed: 229 average time/residue: 0.4415 time to fit residues: 182.0835 Evaluate side-chains 237 residues out of total 4278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 171 time to evaluate : 4.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 917 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 573 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 306 optimal weight: 4.9990 chunk 410 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 355 optimal weight: 30.0000 chunk 56 optimal weight: 0.1980 chunk 107 optimal weight: 0.5980 chunk 386 optimal weight: 50.0000 chunk 161 optimal weight: 8.9990 chunk 396 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN F 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.116857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.079210 restraints weight = 297181.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.077672 restraints weight = 194181.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.077232 restraints weight = 126483.342| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.165 40534 Z= 0.196 Angle : 0.696 55.079 55124 Z= 0.384 Chirality : 0.045 0.527 6286 Planarity : 0.004 0.069 7040 Dihedral : 4.751 55.747 6648 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.98 % Favored : 95.00 % Rotamer: Outliers : 1.55 % Allowed : 18.82 % Favored : 79.62 % Cbeta Deviations : 0.02 % 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: -0.82 (0.12), residues: 4824 helix: 0.49 (0.13), residues: 1673 sheet: -0.71 (0.22), residues: 528 loop : -1.20 (0.12), residues: 2623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 271 HIS 0.006 0.001 HIS B1048 PHE 0.028 0.001 PHE C 888 TYR 0.015 0.001 TYR B1067 ARG 0.006 0.000 ARG A1039 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7360.36 seconds wall clock time: 135 minutes 30.19 seconds (8130.19 seconds total)