Starting phenix.real_space_refine on Tue Feb 20 11:22:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to4_26029/02_2024/7to4_26029.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to4_26029/02_2024/7to4_26029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to4_26029/02_2024/7to4_26029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to4_26029/02_2024/7to4_26029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to4_26029/02_2024/7to4_26029.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to4_26029/02_2024/7to4_26029.pdb" } resolution = 3.4 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= 0.003 sd= 0.040 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 120 5.16 5 C 17613 2.51 5 N 4473 2.21 5 O 5466 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 PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 843": "OD1" <-> "OD2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 936": "OD1" <-> "OD2" Residue "A PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A ASP 994": "OD1" <-> "OD2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "A ASP 1139": "OD1" <-> "OD2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A ASP 1146": "OD1" <-> "OD2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C ARG 634": "NH1" <-> "NH2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C ASP 820": "OD1" <-> "OD2" Residue "C PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 839": "OD1" <-> "OD2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1146": "OD1" <-> "OD2" Residue "C ASP 1153": "OD1" <-> "OD2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27672 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8737 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 54, 'TRANS': 1057} Chain breaks: 4 Chain: "B" Number of atoms: 8789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8789 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 3 Chain: "C" Number of atoms: 8789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8789 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 3 Chain: "D" 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: "E" 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: "F" 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" 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: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" 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: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" 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: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" 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: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" 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: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 15.21, per 1000 atoms: 0.55 Number of scatterers: 27672 At special positions: 0 Unit cell: (148.57, 138.61, 220.78, 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 120 16.00 O 5466 8.00 N 4473 7.00 C 17613 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.06 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.06 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=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 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=2.01 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=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.01 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.02 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=2.06 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.01 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 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 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 ALPHA1-4 " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG M 2 " - " MAN M 3 " " NAG O 2 " - " MAN O 3 " " NAG Q 2 " - " MAN Q 3 " " NAG R 2 " - " MAN R 3 " " NAG T 2 " - " MAN T 3 " " NAG U 2 " - " MAN U 3 " " NAG W 2 " - " MAN W 3 " " NAG Y 2 " - " MAN Y 3 " " NAG Z 2 " - " MAN Z 3 " " NAG b 2 " - " MAN b 3 " " NAG c 2 " - " MAN c 3 " " NAG e 2 " - " MAN e 3 " " NAG f 2 " - " MAN f 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1158 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1158 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 616 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 17 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN B 165 " " NAG O 1 " - " ASN B 282 " " NAG P 1 " - " ASN B 616 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 17 " " NAG W 1 " - " ASN C 122 " " NAG X 1 " - " ASN C 165 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 282 " " NAG a 1 " - " ASN C 616 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Time building additional restraints: 12.94 Conformation dependent library (CDL) restraints added in 5.0 seconds 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6298 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 51 sheets defined 27.7% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.557A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.597A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.133A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 634 through 638 removed outlier: 3.557A pdb=" N SER A 637 " --> pdb=" O ARG A 634 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 634 through 638' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.483A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.213A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 842 through 847 removed outlier: 3.697A pdb=" N ALA A 845 " --> pdb=" O GLY A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.751A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.519A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.604A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.104A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.678A pdb=" N GLU A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1161 Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.652A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 372 removed outlier: 3.805A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.071A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.161A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.600A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.049A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.105A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 826 removed outlier: 4.207A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.704A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.708A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.554A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.521A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.178A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.867A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1141 through 1161 removed outlier: 3.923A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 150 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.865A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.754A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 removed outlier: 4.090A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.393A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 635 through 639 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.955A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 756 Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.102A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.266A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 842 through 847 removed outlier: 3.601A pdb=" N ALA C 846 " --> pdb=" O ASP C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.584A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.566A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.772A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 4.039A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.539A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.116A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 982 removed outlier: 3.599A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1033 removed outlier: 4.509A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1160 removed outlier: 4.139A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.981A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.735A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.571A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.735A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.685A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.663A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.090A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 144 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.992A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.047A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.606A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.606A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.289A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.148A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.696A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.887A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.596A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.572A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.669A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.961A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 158 through 160 removed outlier: 8.048A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 12.662A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.840A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 11.687A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 11.603A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE B 144 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC8, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.405A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.108A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.934A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLU B 516 " --> pdb=" O THR B 393 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.086A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.415A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.934A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.890A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.418A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.752A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.809A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.199A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.812A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.853A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.703A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE C 144 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.891A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.197A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.974A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.974A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.603A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.330A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.330A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.204A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.787A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1109 hydrogen bonds defined for protein. 2982 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: 14.35 Time building geometry restraints manager: 13.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4409 1.29 - 1.43: 7540 1.43 - 1.56: 16190 1.56 - 1.70: 2 1.70 - 1.83: 150 Bond restraints: 28291 Sorted by residual: bond pdb=" CA LEU C 118 " pdb=" C LEU C 118 " ideal model delta sigma weight residual 1.522 1.620 -0.097 1.18e-02 7.18e+03 6.81e+01 bond pdb=" C ARG A 983 " pdb=" O ARG A 983 " ideal model delta sigma weight residual 1.236 1.157 0.079 1.11e-02 8.12e+03 5.10e+01 bond pdb=" C ARG B1014 " pdb=" O ARG B1014 " ideal model delta sigma weight residual 1.236 1.174 0.062 1.22e-02 6.72e+03 2.57e+01 bond pdb=" C ARG A1019 " pdb=" O ARG A1019 " ideal model delta sigma weight residual 1.237 1.178 0.059 1.16e-02 7.43e+03 2.57e+01 bond pdb=" C ARG C1019 " pdb=" O ARG C1019 " ideal model delta sigma weight residual 1.236 1.176 0.060 1.22e-02 6.72e+03 2.42e+01 ... (remaining 28286 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.68: 671 105.68 - 113.23: 14062 113.23 - 120.79: 14566 120.79 - 128.35: 9060 128.35 - 135.91: 107 Bond angle restraints: 38466 Sorted by residual: angle pdb=" N ASN C 164 " pdb=" CA ASN C 164 " pdb=" C ASN C 164 " ideal model delta sigma weight residual 110.97 123.12 -12.15 1.09e+00 8.42e-01 1.24e+02 angle pdb=" N ARG A1091 " pdb=" CA ARG A1091 " pdb=" C ARG A1091 " ideal model delta sigma weight residual 111.03 102.31 8.72 1.11e+00 8.12e-01 6.18e+01 angle pdb=" N TYR A 421 " pdb=" CA TYR A 421 " pdb=" C TYR A 421 " ideal model delta sigma weight residual 113.50 122.46 -8.96 1.23e+00 6.61e-01 5.31e+01 angle pdb=" CA ASP B 389 " pdb=" CB ASP B 389 " pdb=" CG ASP B 389 " ideal model delta sigma weight residual 112.60 119.79 -7.19 1.00e+00 1.00e+00 5.16e+01 angle pdb=" N ILE C 834 " pdb=" CA ILE C 834 " pdb=" C ILE C 834 " ideal model delta sigma weight residual 109.30 118.64 -9.34 1.31e+00 5.83e-01 5.08e+01 ... (remaining 38461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.33: 17256 25.33 - 50.65: 709 50.65 - 75.98: 145 75.98 - 101.31: 43 101.31 - 126.64: 43 Dihedral angle restraints: 18196 sinusoidal: 8414 harmonic: 9782 Sorted by residual: dihedral pdb=" C ASN C 122 " pdb=" N ASN C 122 " pdb=" CA ASN C 122 " pdb=" CB ASN C 122 " ideal model delta harmonic sigma weight residual -122.60 -138.91 16.31 0 2.50e+00 1.60e-01 4.26e+01 dihedral pdb=" C CYS C1126 " pdb=" N CYS C1126 " pdb=" CA CYS C1126 " pdb=" CB CYS C1126 " ideal model delta harmonic sigma weight residual -122.60 -137.29 14.69 0 2.50e+00 1.60e-01 3.45e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual -86.00 -36.03 -49.97 1 1.00e+01 1.00e-02 3.42e+01 ... (remaining 18193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.320: 4583 0.320 - 0.639: 37 0.639 - 0.959: 7 0.959 - 1.279: 3 1.279 - 1.598: 5 Chirality restraints: 4635 Sorted by residual: chirality pdb=" C1 MAN Z 3 " pdb=" O4 NAG Z 2 " pdb=" C2 MAN Z 3 " pdb=" O5 MAN Z 3 " both_signs ideal model delta sigma weight residual False 2.40 2.61 -0.21 2.00e-02 2.50e+03 1.10e+02 chirality pdb=" C1 MAN f 3 " pdb=" O4 NAG f 2 " pdb=" C2 MAN f 3 " pdb=" O5 MAN f 3 " both_signs ideal model delta sigma weight residual False 2.40 2.59 -0.19 2.00e-02 2.50e+03 9.34e+01 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.39e+01 ... (remaining 4632 not shown) Planarity restraints: 4881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.103 2.00e-02 2.50e+03 1.47e-01 2.69e+02 pdb=" CG ASN C 234 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.032 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " 0.256 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " -0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 104 " -0.144 2.00e-02 2.50e+03 7.54e-02 1.42e+02 pdb=" CG TRP A 104 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP A 104 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 104 " 0.070 2.00e-02 2.50e+03 pdb=" NE1 TRP A 104 " 0.053 2.00e-02 2.50e+03 pdb=" CE2 TRP A 104 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 104 " 0.106 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 104 " -0.091 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 104 " 0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP A 104 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " 0.100 2.00e-02 2.50e+03 1.05e-01 1.37e+02 pdb=" CG ASN A1074 " -0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " -0.160 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.125 2.00e-02 2.50e+03 ... (remaining 4878 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 81 2.59 - 3.17: 22407 3.17 - 3.74: 41775 3.74 - 4.32: 58970 4.32 - 4.90: 94396 Nonbonded interactions: 217629 Sorted by model distance: nonbonded pdb=" O ASN B 17 " pdb=" OD1 ASN B 17 " model vdw 2.009 3.040 nonbonded pdb=" O ASN C 17 " pdb=" OD1 ASN C 17 " model vdw 2.138 3.040 nonbonded pdb=" O4 NAG S 1 " pdb=" O7 NAG S 2 " model vdw 2.210 2.440 nonbonded pdb=" N GLN C 836 " pdb=" OE1 GLN C 836 " model vdw 2.211 2.520 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.251 2.520 ... (remaining 217624 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' and (resid 14 through 1162 or resid 1301 through 1307)) selection = (chain 'B' and (resid 14 through 626 or resid 633 through 679 or resid 687 throu \ gh 1162 or resid 1301 through 1307)) selection = (chain 'C' and (resid 14 through 626 or resid 633 through 679 or resid 687 throu \ gh 1162 or resid 1301 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'V' selection = chain 'X' selection = chain 'a' } ncs_group { reference = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 22.820 Check model and map are aligned: 0.420 Set scattering table: 0.270 Process input model: 79.390 Find NCS groups from input model: 2.860 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.015 0.097 28291 Z= 0.960 Angle : 1.899 12.147 38466 Z= 1.241 Chirality : 0.129 1.598 4635 Planarity : 0.013 0.093 4827 Dihedral : 16.215 126.636 11763 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.78 % Allowed : 7.19 % Favored : 92.03 % Rotamer: Outliers : 2.60 % Allowed : 5.77 % Favored : 91.63 % Cbeta Deviations : 0.64 % 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: -2.22 (0.13), residues: 3324 helix: -1.76 (0.15), residues: 775 sheet: 0.03 (0.21), residues: 533 loop : -1.85 (0.12), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.144 0.026 TRP A 104 HIS 0.022 0.007 HIS A1159 PHE 0.097 0.016 PHE B 898 TYR 0.120 0.021 TYR B 660 ARG 0.019 0.001 ARG C 493 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 747 time to evaluate : 3.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PRO cc_start: 0.7665 (Cg_endo) cc_final: 0.7387 (Cg_exo) REVERT: A 52 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8067 (tm-30) REVERT: A 62 VAL cc_start: 0.8763 (m) cc_final: 0.8539 (p) REVERT: A 116 SER cc_start: 0.8853 (m) cc_final: 0.8576 (m) REVERT: A 120 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8733 (m) REVERT: A 190 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7728 (mmm-85) REVERT: A 197 ILE cc_start: 0.8709 (mm) cc_final: 0.8507 (mm) REVERT: A 224 GLU cc_start: 0.8442 (mp0) cc_final: 0.8187 (mp0) REVERT: A 228 ASP cc_start: 0.7630 (p0) cc_final: 0.7415 (p0) REVERT: A 309 GLU cc_start: 0.8510 (mp0) cc_final: 0.8237 (mp0) REVERT: A 319 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7552 (tpt170) REVERT: A 338 PHE cc_start: 0.7831 (m-80) cc_final: 0.7601 (p90) REVERT: A 380 TYR cc_start: 0.6165 (t80) cc_final: 0.5772 (t80) REVERT: A 424 LYS cc_start: 0.5081 (tptt) cc_final: 0.4573 (tttm) REVERT: A 541 PHE cc_start: 0.6328 (p90) cc_final: 0.5760 (p90) REVERT: A 565 PHE cc_start: 0.7774 (p90) cc_final: 0.7545 (p90) REVERT: A 588 THR cc_start: 0.9018 (m) cc_final: 0.8792 (t) REVERT: A 740 MET cc_start: 0.9044 (tpt) cc_final: 0.8737 (tpp) REVERT: A 773 GLU cc_start: 0.8340 (tt0) cc_final: 0.8023 (tt0) REVERT: A 780 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8133 (mm-30) REVERT: A 811 LYS cc_start: 0.7983 (mmtt) cc_final: 0.7237 (tmtt) REVERT: A 814 LYS cc_start: 0.8181 (mmtm) cc_final: 0.7699 (mmmt) REVERT: A 819 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8373 (mt-10) REVERT: A 820 ASP cc_start: 0.8739 (t70) cc_final: 0.8478 (m-30) REVERT: A 848 ASP cc_start: 0.8429 (t0) cc_final: 0.7573 (p0) REVERT: A 849 LEU cc_start: 0.8750 (mt) cc_final: 0.8329 (mm) REVERT: A 854 LYS cc_start: 0.9288 (tttt) cc_final: 0.9034 (tttt) REVERT: A 856 LYS cc_start: 0.9159 (mptt) cc_final: 0.8887 (mptt) REVERT: A 921 LYS cc_start: 0.8811 (mtpp) cc_final: 0.8484 (mtpp) REVERT: A 925 ASN cc_start: 0.8795 (m110) cc_final: 0.8579 (m-40) REVERT: A 935 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8601 (tm-30) REVERT: A 936 ASP cc_start: 0.8845 (m-30) cc_final: 0.8512 (m-30) REVERT: A 950 ASP cc_start: 0.8464 (p0) cc_final: 0.8111 (p0) REVERT: A 964 LYS cc_start: 0.8784 (mtpp) cc_final: 0.8582 (mtpp) REVERT: A 975 SER cc_start: 0.8758 (p) cc_final: 0.8506 (p) REVERT: A 1005 GLN cc_start: 0.8438 (mm-40) cc_final: 0.7964 (mm-40) REVERT: A 1019 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8064 (ttp-110) REVERT: A 1072 GLU cc_start: 0.8837 (pm20) cc_final: 0.8355 (pm20) REVERT: A 1073 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8461 (mtpp) REVERT: A 1107 ARG cc_start: 0.7859 (mtt180) cc_final: 0.7340 (mtt-85) REVERT: B 41 LYS cc_start: 0.8618 (mmmm) cc_final: 0.8410 (mmmm) REVERT: B 92 PHE cc_start: 0.8691 (t80) cc_final: 0.8305 (t80) REVERT: B 133 PHE cc_start: 0.7069 (m-80) cc_final: 0.6564 (m-10) REVERT: B 196 ASN cc_start: 0.7978 (t0) cc_final: 0.7685 (t0) REVERT: B 197 ILE cc_start: 0.9020 (tp) cc_final: 0.8708 (pt) REVERT: B 200 TYR cc_start: 0.7650 (m-80) cc_final: 0.7008 (m-80) REVERT: B 202 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8289 (mmmt) REVERT: B 203 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8588 (tt) REVERT: B 204 TYR cc_start: 0.8984 (m-80) cc_final: 0.8604 (m-80) REVERT: B 275 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8518 (t80) REVERT: B 323 THR cc_start: 0.8705 (t) cc_final: 0.8251 (p) REVERT: B 388 ASN cc_start: 0.8346 (t0) cc_final: 0.8135 (t0) REVERT: B 422 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.6997 (p0) REVERT: B 607 GLN cc_start: 0.8696 (tt0) cc_final: 0.8489 (tp40) REVERT: B 643 PHE cc_start: 0.8555 (t80) cc_final: 0.8262 (t80) REVERT: B 646 ARG cc_start: 0.7892 (ttt90) cc_final: 0.7597 (ttt90) REVERT: B 654 GLU cc_start: 0.8529 (tp30) cc_final: 0.8325 (tp30) REVERT: B 675 GLN cc_start: 0.7695 (pp30) cc_final: 0.7429 (pp30) REVERT: B 751 ASN cc_start: 0.8769 (m110) cc_final: 0.8482 (m110) REVERT: B 755 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8058 (mp10) REVERT: B 765 ARG cc_start: 0.8389 (ttm-80) cc_final: 0.8014 (ttm-80) REVERT: B 780 GLU cc_start: 0.8653 (tp30) cc_final: 0.8252 (tp30) REVERT: B 814 LYS cc_start: 0.8550 (mptt) cc_final: 0.8201 (mmmt) REVERT: B 900 MET cc_start: 0.8739 (tpp) cc_final: 0.8381 (mtp) REVERT: B 964 LYS cc_start: 0.9297 (tppt) cc_final: 0.9016 (mmmm) REVERT: B 994 ASP cc_start: 0.8474 (t0) cc_final: 0.8195 (t0) REVERT: B 1005 GLN cc_start: 0.8876 (tp-100) cc_final: 0.8516 (tp40) REVERT: B 1041 ASP cc_start: 0.8538 (t0) cc_final: 0.8074 (t0) REVERT: C 34 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8505 (mtp85) REVERT: C 79 PHE cc_start: 0.6099 (OUTLIER) cc_final: 0.5891 (m-80) REVERT: C 102 ARG cc_start: 0.7164 (mtp180) cc_final: 0.6547 (mtp180) REVERT: C 154 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6924 (tm-30) REVERT: C 175 PHE cc_start: 0.6191 (t80) cc_final: 0.5544 (m-80) REVERT: C 207 HIS cc_start: 0.7974 (t-90) cc_final: 0.7683 (t70) REVERT: C 218 GLN cc_start: 0.8246 (tt0) cc_final: 0.7989 (tt0) REVERT: C 224 GLU cc_start: 0.8478 (mp0) cc_final: 0.8122 (mp0) REVERT: C 320 VAL cc_start: 0.8948 (t) cc_final: 0.8451 (m) REVERT: C 360 ASN cc_start: 0.8931 (t0) cc_final: 0.8662 (t0) REVERT: C 365 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7780 (t80) REVERT: C 377 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.7061 (t80) REVERT: C 456 PHE cc_start: 0.7416 (m-80) cc_final: 0.7192 (m-10) REVERT: C 547 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8594 (mmmm) REVERT: C 559 PHE cc_start: 0.8330 (m-10) cc_final: 0.7983 (m-10) REVERT: C 564 GLN cc_start: 0.8685 (tp-100) cc_final: 0.8336 (tp40) REVERT: C 565 PHE cc_start: 0.8909 (m-80) cc_final: 0.8682 (m-10) REVERT: C 568 ASP cc_start: 0.7860 (t0) cc_final: 0.7525 (t0) REVERT: C 571 ASP cc_start: 0.7858 (t0) cc_final: 0.7431 (t0) REVERT: C 577 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8579 (ttm170) REVERT: C 584 ILE cc_start: 0.8900 (mm) cc_final: 0.8411 (mm) REVERT: C 610 VAL cc_start: 0.9252 (t) cc_final: 0.8937 (m) REVERT: C 613 GLN cc_start: 0.7975 (mt0) cc_final: 0.7616 (mt0) REVERT: C 661 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7700 (tm-30) REVERT: C 765 ARG cc_start: 0.8454 (ptp-110) cc_final: 0.8207 (mtm110) REVERT: C 780 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8183 (mm-30) REVERT: C 849 LEU cc_start: 0.8779 (mt) cc_final: 0.8552 (tp) REVERT: C 854 LYS cc_start: 0.9183 (tptp) cc_final: 0.8969 (tptp) REVERT: C 855 PHE cc_start: 0.8500 (m-10) cc_final: 0.8056 (m-80) REVERT: C 935 GLN cc_start: 0.8996 (tt0) cc_final: 0.8636 (tt0) REVERT: C 950 ASP cc_start: 0.8373 (p0) cc_final: 0.7826 (p0) REVERT: C 954 HIS cc_start: 0.8222 (m-70) cc_final: 0.8001 (m170) REVERT: C 957 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7963 (tm-30) REVERT: C 991 VAL cc_start: 0.9436 (t) cc_final: 0.9208 (t) REVERT: C 1019 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8422 (ttt-90) outliers start: 76 outliers final: 13 residues processed: 793 average time/residue: 0.4421 time to fit residues: 526.1595 Evaluate side-chains 627 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 599 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1019 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 281 optimal weight: 0.0570 chunk 252 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 261 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 158 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 302 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 314 GLN A 417 ASN A 481 ASN A 536 ASN A 658 ASN A 901 GLN A 925 ASN B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1023 ASN B1119 ASN C 146 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 564 GLN C 675 GLN C 907 ASN C 913 GLN ** C 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28291 Z= 0.232 Angle : 0.807 10.817 38466 Z= 0.402 Chirality : 0.052 0.626 4635 Planarity : 0.005 0.058 4827 Dihedral : 12.708 110.282 5747 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 2.87 % Allowed : 11.31 % Favored : 85.82 % 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: -0.98 (0.14), residues: 3324 helix: 0.57 (0.18), residues: 782 sheet: -0.05 (0.19), residues: 638 loop : -1.43 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 353 HIS 0.011 0.001 HIS B 207 PHE 0.045 0.002 PHE A 133 TYR 0.036 0.002 TYR C 636 ARG 0.012 0.001 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 616 time to evaluate : 3.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PRO cc_start: 0.7477 (Cg_endo) cc_final: 0.7117 (Cg_exo) REVERT: A 41 LYS cc_start: 0.8999 (mmmm) cc_final: 0.8433 (mmmm) REVERT: A 52 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8079 (tm-30) REVERT: A 62 VAL cc_start: 0.8758 (m) cc_final: 0.8513 (p) REVERT: A 111 ASP cc_start: 0.8324 (p0) cc_final: 0.7447 (t70) REVERT: A 129 LYS cc_start: 0.8592 (tttt) cc_final: 0.8219 (ttmm) REVERT: A 135 PHE cc_start: 0.7375 (m-80) cc_final: 0.7174 (m-80) REVERT: A 190 ARG cc_start: 0.8266 (mmm160) cc_final: 0.7701 (mmm-85) REVERT: A 195 LYS cc_start: 0.8506 (ttpp) cc_final: 0.8142 (ttpt) REVERT: A 224 GLU cc_start: 0.8397 (mp0) cc_final: 0.8153 (mp0) REVERT: A 228 ASP cc_start: 0.7628 (p0) cc_final: 0.7318 (p0) REVERT: A 287 ASP cc_start: 0.8558 (t0) cc_final: 0.8321 (t0) REVERT: A 306 PHE cc_start: 0.8316 (m-10) cc_final: 0.7890 (m-10) REVERT: A 456 PHE cc_start: 0.8092 (m-10) cc_final: 0.7879 (m-10) REVERT: A 565 PHE cc_start: 0.7662 (p90) cc_final: 0.7401 (p90) REVERT: A 588 THR cc_start: 0.9048 (m) cc_final: 0.8787 (t) REVERT: A 740 MET cc_start: 0.9026 (tpt) cc_final: 0.8717 (tpp) REVERT: A 752 LEU cc_start: 0.9417 (mm) cc_final: 0.9186 (mp) REVERT: A 773 GLU cc_start: 0.8508 (tt0) cc_final: 0.8074 (tt0) REVERT: A 780 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8131 (mm-30) REVERT: A 819 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8069 (mt-10) REVERT: A 820 ASP cc_start: 0.8538 (t70) cc_final: 0.8323 (m-30) REVERT: A 823 PHE cc_start: 0.7975 (m-80) cc_final: 0.7431 (t80) REVERT: A 848 ASP cc_start: 0.8576 (t0) cc_final: 0.7651 (p0) REVERT: A 849 LEU cc_start: 0.8623 (mt) cc_final: 0.8267 (mm) REVERT: A 851 CYS cc_start: 0.7694 (t) cc_final: 0.7258 (t) REVERT: A 854 LYS cc_start: 0.9274 (tttt) cc_final: 0.9002 (tttt) REVERT: A 856 LYS cc_start: 0.9202 (mptt) cc_final: 0.8856 (mptt) REVERT: A 867 ASP cc_start: 0.8333 (m-30) cc_final: 0.8124 (m-30) REVERT: A 921 LYS cc_start: 0.8747 (mtpp) cc_final: 0.8521 (mtmm) REVERT: A 935 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8536 (tm-30) REVERT: A 936 ASP cc_start: 0.8786 (m-30) cc_final: 0.8576 (m-30) REVERT: A 986 LYS cc_start: 0.8961 (mmtm) cc_final: 0.8752 (mmtm) REVERT: A 1019 ARG cc_start: 0.8502 (ttp-110) cc_final: 0.8086 (ttp-110) REVERT: A 1072 GLU cc_start: 0.8649 (pm20) cc_final: 0.8261 (pm20) REVERT: A 1148 PHE cc_start: 0.6418 (OUTLIER) cc_final: 0.5857 (t80) REVERT: B 41 LYS cc_start: 0.8722 (mmmm) cc_final: 0.8493 (mmmm) REVERT: B 52 GLN cc_start: 0.8535 (tp40) cc_final: 0.8042 (tp40) REVERT: B 65 PHE cc_start: 0.8540 (m-10) cc_final: 0.8257 (m-10) REVERT: B 191 GLU cc_start: 0.7629 (mp0) cc_final: 0.7294 (pm20) REVERT: B 200 TYR cc_start: 0.7711 (m-80) cc_final: 0.7509 (m-80) REVERT: B 202 LYS cc_start: 0.8766 (mmmt) cc_final: 0.8411 (mmtm) REVERT: B 204 TYR cc_start: 0.8950 (m-80) cc_final: 0.8728 (m-80) REVERT: B 237 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7721 (ptt90) REVERT: B 305 SER cc_start: 0.9088 (t) cc_final: 0.8861 (t) REVERT: B 388 ASN cc_start: 0.8396 (t0) cc_final: 0.8065 (t0) REVERT: B 518 LEU cc_start: 0.9250 (mm) cc_final: 0.8966 (tp) REVERT: B 571 ASP cc_start: 0.8765 (t0) cc_final: 0.8110 (t0) REVERT: B 646 ARG cc_start: 0.8036 (ttt90) cc_final: 0.7823 (ttt90) REVERT: B 654 GLU cc_start: 0.8529 (tp30) cc_final: 0.8255 (tp30) REVERT: B 690 GLN cc_start: 0.7877 (mm110) cc_final: 0.7654 (mm110) REVERT: B 751 ASN cc_start: 0.8875 (m-40) cc_final: 0.8543 (m-40) REVERT: B 755 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8095 (mp10) REVERT: B 780 GLU cc_start: 0.8657 (tp30) cc_final: 0.8443 (tp30) REVERT: B 868 GLU cc_start: 0.8427 (mp0) cc_final: 0.8144 (mp0) REVERT: B 936 ASP cc_start: 0.8383 (m-30) cc_final: 0.8170 (m-30) REVERT: B 983 ARG cc_start: 0.8564 (mpp80) cc_final: 0.8291 (ptp90) REVERT: B 1005 GLN cc_start: 0.9009 (tp-100) cc_final: 0.8583 (tp40) REVERT: B 1010 GLN cc_start: 0.8762 (mt0) cc_final: 0.8499 (mm-40) REVERT: B 1072 GLU cc_start: 0.8548 (pm20) cc_final: 0.8142 (pm20) REVERT: C 81 ASN cc_start: 0.8629 (m-40) cc_final: 0.8233 (m-40) REVERT: C 133 PHE cc_start: 0.7645 (m-80) cc_final: 0.7430 (m-80) REVERT: C 154 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6938 (tm-30) REVERT: C 175 PHE cc_start: 0.6004 (t80) cc_final: 0.5526 (m-80) REVERT: C 224 GLU cc_start: 0.8471 (mp0) cc_final: 0.7913 (mp0) REVERT: C 242 LEU cc_start: 0.8569 (mm) cc_final: 0.8065 (mm) REVERT: C 360 ASN cc_start: 0.8968 (t0) cc_final: 0.8459 (t0) REVERT: C 377 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.7053 (t80) REVERT: C 547 LYS cc_start: 0.8931 (mtpp) cc_final: 0.8563 (mtpp) REVERT: C 564 GLN cc_start: 0.8900 (tp40) cc_final: 0.8589 (tp40) REVERT: C 568 ASP cc_start: 0.7811 (t0) cc_final: 0.7290 (t0) REVERT: C 574 ASP cc_start: 0.7974 (p0) cc_final: 0.7608 (p0) REVERT: C 610 VAL cc_start: 0.9272 (t) cc_final: 0.8979 (m) REVERT: C 613 GLN cc_start: 0.7885 (mt0) cc_final: 0.7664 (mt0) REVERT: C 646 ARG cc_start: 0.8921 (tpp80) cc_final: 0.8668 (tpp80) REVERT: C 661 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7429 (tm-30) REVERT: C 675 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7501 (pp30) REVERT: C 759 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7496 (t80) REVERT: C 773 GLU cc_start: 0.8675 (tt0) cc_final: 0.7918 (tm-30) REVERT: C 777 ASN cc_start: 0.8534 (m-40) cc_final: 0.7545 (m110) REVERT: C 819 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8045 (mt-10) REVERT: C 855 PHE cc_start: 0.8514 (m-10) cc_final: 0.8234 (m-80) REVERT: C 950 ASP cc_start: 0.8184 (p0) cc_final: 0.7906 (p0) REVERT: C 957 GLN cc_start: 0.8242 (tm-30) cc_final: 0.8016 (tm-30) REVERT: C 988 GLU cc_start: 0.7899 (tp30) cc_final: 0.7493 (tp30) REVERT: C 1144 GLU cc_start: 0.8515 (mp0) cc_final: 0.8284 (mp0) outliers start: 84 outliers final: 47 residues processed: 654 average time/residue: 0.4140 time to fit residues: 419.0673 Evaluate side-chains 599 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 545 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 251 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 chunk 327 optimal weight: 0.9980 chunk 269 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 755 GLN A 901 GLN A 907 ASN A 957 GLN A1002 GLN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 125 ASN B 207 HIS B 784 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN C 957 GLN C1002 GLN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 28291 Z= 0.330 Angle : 0.776 9.962 38466 Z= 0.382 Chirality : 0.050 0.552 4635 Planarity : 0.005 0.066 4827 Dihedral : 11.592 111.202 5707 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.05 % Favored : 93.92 % Rotamer: Outliers : 4.00 % Allowed : 12.85 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.81 (0.14), residues: 3324 helix: 1.02 (0.19), residues: 773 sheet: -0.19 (0.18), residues: 675 loop : -1.38 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 436 HIS 0.008 0.001 HIS C 66 PHE 0.027 0.002 PHE A 133 TYR 0.035 0.002 TYR C 636 ARG 0.008 0.001 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 579 time to evaluate : 3.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9078 (mmmm) cc_final: 0.8499 (mmmm) REVERT: A 52 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8211 (tm-30) REVERT: A 129 LYS cc_start: 0.8829 (tttt) cc_final: 0.8336 (ttmm) REVERT: A 190 ARG cc_start: 0.8313 (mmm160) cc_final: 0.7661 (mmm-85) REVERT: A 224 GLU cc_start: 0.8364 (mp0) cc_final: 0.8085 (mp0) REVERT: A 228 ASP cc_start: 0.7735 (p0) cc_final: 0.7400 (p0) REVERT: A 266 TYR cc_start: 0.7886 (m-80) cc_final: 0.7589 (m-80) REVERT: A 287 ASP cc_start: 0.8619 (t0) cc_final: 0.8337 (t0) REVERT: A 306 PHE cc_start: 0.8365 (m-10) cc_final: 0.7855 (m-10) REVERT: A 309 GLU cc_start: 0.8443 (mp0) cc_final: 0.8202 (mp0) REVERT: A 456 PHE cc_start: 0.8222 (m-10) cc_final: 0.7989 (m-10) REVERT: A 532 ASN cc_start: 0.7370 (OUTLIER) cc_final: 0.6500 (p0) REVERT: A 588 THR cc_start: 0.9050 (m) cc_final: 0.8784 (t) REVERT: A 607 GLN cc_start: 0.8156 (mp10) cc_final: 0.7543 (mp10) REVERT: A 658 ASN cc_start: 0.8221 (t0) cc_final: 0.8017 (t0) REVERT: A 663 ASP cc_start: 0.8322 (t0) cc_final: 0.7944 (t0) REVERT: A 740 MET cc_start: 0.9072 (tpt) cc_final: 0.8850 (tpp) REVERT: A 752 LEU cc_start: 0.9441 (mm) cc_final: 0.9208 (mp) REVERT: A 780 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8097 (mm-30) REVERT: A 819 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8159 (mt-10) REVERT: A 820 ASP cc_start: 0.8518 (t70) cc_final: 0.8268 (m-30) REVERT: A 823 PHE cc_start: 0.7999 (m-80) cc_final: 0.7333 (t80) REVERT: A 848 ASP cc_start: 0.8542 (t0) cc_final: 0.8111 (t0) REVERT: A 854 LYS cc_start: 0.9245 (tttt) cc_final: 0.9004 (tttt) REVERT: A 856 LYS cc_start: 0.9215 (mptt) cc_final: 0.8939 (mptt) REVERT: A 935 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8667 (tm-30) REVERT: A 936 ASP cc_start: 0.8844 (m-30) cc_final: 0.8527 (m-30) REVERT: A 1045 LYS cc_start: 0.8730 (mmmm) cc_final: 0.8355 (mmtm) REVERT: A 1072 GLU cc_start: 0.8729 (pm20) cc_final: 0.8388 (pm20) REVERT: B 41 LYS cc_start: 0.8757 (mmmm) cc_final: 0.8446 (mmmm) REVERT: B 52 GLN cc_start: 0.8346 (tp40) cc_final: 0.7812 (tp40) REVERT: B 65 PHE cc_start: 0.8584 (m-10) cc_final: 0.8358 (m-10) REVERT: B 92 PHE cc_start: 0.8398 (t80) cc_final: 0.8163 (t80) REVERT: B 190 ARG cc_start: 0.7973 (mmt-90) cc_final: 0.7510 (mmt-90) REVERT: B 200 TYR cc_start: 0.7662 (m-80) cc_final: 0.7382 (m-80) REVERT: B 202 LYS cc_start: 0.8788 (mmmt) cc_final: 0.8462 (mmtm) REVERT: B 204 TYR cc_start: 0.8914 (m-80) cc_final: 0.8692 (m-80) REVERT: B 218 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8317 (tm-30) REVERT: B 237 ARG cc_start: 0.8088 (mtm-85) cc_final: 0.7716 (ptt90) REVERT: B 304 LYS cc_start: 0.9011 (mmmm) cc_final: 0.8746 (mmmm) REVERT: B 354 ASN cc_start: 0.8125 (t0) cc_final: 0.7698 (p0) REVERT: B 365 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.6958 (p90) REVERT: B 388 ASN cc_start: 0.8370 (t0) cc_final: 0.8034 (t0) REVERT: B 452 LEU cc_start: 0.8794 (mp) cc_final: 0.8452 (mp) REVERT: B 518 LEU cc_start: 0.9291 (mm) cc_final: 0.8971 (tp) REVERT: B 571 ASP cc_start: 0.8789 (t0) cc_final: 0.8196 (t0) REVERT: B 654 GLU cc_start: 0.8570 (tp30) cc_final: 0.8301 (tp30) REVERT: B 661 GLU cc_start: 0.8254 (pm20) cc_final: 0.7936 (pm20) REVERT: B 755 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8118 (mp10) REVERT: B 868 GLU cc_start: 0.8484 (mp0) cc_final: 0.8273 (mp0) REVERT: B 1005 GLN cc_start: 0.9006 (tp-100) cc_final: 0.8613 (tp40) REVERT: B 1010 GLN cc_start: 0.8786 (mt0) cc_final: 0.8537 (mm-40) REVERT: B 1091 ARG cc_start: 0.8202 (ttm170) cc_final: 0.7769 (ttm110) REVERT: B 1118 ASP cc_start: 0.8143 (t0) cc_final: 0.7886 (t0) REVERT: C 63 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8529 (p) REVERT: C 129 LYS cc_start: 0.8162 (tttt) cc_final: 0.7950 (ttmt) REVERT: C 154 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7132 (tm-30) REVERT: C 191 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7684 (mt-10) REVERT: C 224 GLU cc_start: 0.8492 (mp0) cc_final: 0.8044 (mp0) REVERT: C 242 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8347 (mm) REVERT: C 360 ASN cc_start: 0.8958 (t0) cc_final: 0.8521 (t0) REVERT: C 365 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7374 (t80) REVERT: C 377 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.7092 (t80) REVERT: C 516 GLU cc_start: 0.7898 (tp30) cc_final: 0.7541 (tp30) REVERT: C 547 LYS cc_start: 0.8927 (mtpp) cc_final: 0.8558 (mtpp) REVERT: C 564 GLN cc_start: 0.8891 (tp40) cc_final: 0.8424 (tp40) REVERT: C 568 ASP cc_start: 0.7963 (t0) cc_final: 0.7546 (t0) REVERT: C 574 ASP cc_start: 0.8086 (p0) cc_final: 0.7740 (p0) REVERT: C 610 VAL cc_start: 0.9239 (t) cc_final: 0.8929 (m) REVERT: C 613 GLN cc_start: 0.7835 (mt0) cc_final: 0.7567 (mt0) REVERT: C 646 ARG cc_start: 0.8946 (tpp80) cc_final: 0.8241 (ttp80) REVERT: C 661 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7398 (tm-30) REVERT: C 819 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8188 (mt-10) REVERT: C 855 PHE cc_start: 0.8603 (m-10) cc_final: 0.8278 (m-10) REVERT: C 950 ASP cc_start: 0.8229 (p0) cc_final: 0.7880 (p0) REVERT: C 988 GLU cc_start: 0.8008 (tp30) cc_final: 0.7789 (tp30) outliers start: 117 outliers final: 76 residues processed: 648 average time/residue: 0.4108 time to fit residues: 415.0890 Evaluate side-chains 621 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 536 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 299 optimal weight: 2.9990 chunk 227 optimal weight: 0.3980 chunk 157 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 203 optimal weight: 0.8980 chunk 304 optimal weight: 0.8980 chunk 321 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 907 ASN B 125 ASN B 207 HIS B 955 ASN B1005 GLN C 188 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28291 Z= 0.226 Angle : 0.721 10.797 38466 Z= 0.351 Chirality : 0.048 0.574 4635 Planarity : 0.004 0.068 4827 Dihedral : 10.775 108.762 5707 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.23 % Favored : 94.74 % Rotamer: Outliers : 3.79 % Allowed : 15.41 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.65 (0.14), residues: 3324 helix: 1.23 (0.19), residues: 775 sheet: -0.04 (0.18), residues: 692 loop : -1.36 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 436 HIS 0.008 0.001 HIS A1083 PHE 0.041 0.002 PHE A 823 TYR 0.021 0.001 TYR C 636 ARG 0.006 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 547 time to evaluate : 3.919 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 41 LYS cc_start: 0.9093 (mmmm) cc_final: 0.8565 (mmmm) REVERT: A 129 LYS cc_start: 0.8940 (tttt) cc_final: 0.8216 (ttmm) REVERT: A 190 ARG cc_start: 0.8320 (mmm160) cc_final: 0.7725 (mmm-85) REVERT: A 224 GLU cc_start: 0.8363 (mp0) cc_final: 0.8077 (mp0) REVERT: A 228 ASP cc_start: 0.7703 (p0) cc_final: 0.7371 (p0) REVERT: A 266 TYR cc_start: 0.7890 (m-80) cc_final: 0.7483 (m-80) REVERT: A 287 ASP cc_start: 0.8624 (t0) cc_final: 0.8367 (t0) REVERT: A 306 PHE cc_start: 0.8344 (m-10) cc_final: 0.7948 (m-10) REVERT: A 309 GLU cc_start: 0.8412 (mp0) cc_final: 0.8163 (mp0) REVERT: A 319 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7565 (tpt170) REVERT: A 392 PHE cc_start: 0.7268 (m-10) cc_final: 0.6640 (m-80) REVERT: A 532 ASN cc_start: 0.7284 (OUTLIER) cc_final: 0.6400 (p0) REVERT: A 588 THR cc_start: 0.9060 (m) cc_final: 0.8802 (t) REVERT: A 740 MET cc_start: 0.9045 (tpt) cc_final: 0.8841 (tpp) REVERT: A 773 GLU cc_start: 0.8360 (tt0) cc_final: 0.8136 (tp30) REVERT: A 780 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8074 (mm-30) REVERT: A 819 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8057 (mt-10) REVERT: A 820 ASP cc_start: 0.8491 (t70) cc_final: 0.8190 (t0) REVERT: A 823 PHE cc_start: 0.7845 (m-80) cc_final: 0.7487 (m-10) REVERT: A 848 ASP cc_start: 0.8561 (t0) cc_final: 0.7715 (p0) REVERT: A 854 LYS cc_start: 0.9239 (tttt) cc_final: 0.9025 (tptm) REVERT: A 867 ASP cc_start: 0.8504 (m-30) cc_final: 0.8116 (t0) REVERT: A 935 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8520 (tm-30) REVERT: A 1045 LYS cc_start: 0.8748 (mmmm) cc_final: 0.8397 (mmtm) REVERT: A 1072 GLU cc_start: 0.8703 (pm20) cc_final: 0.8353 (pm20) REVERT: B 41 LYS cc_start: 0.8730 (mmmm) cc_final: 0.8483 (mmmm) REVERT: B 52 GLN cc_start: 0.8383 (tp40) cc_final: 0.7807 (tp40) REVERT: B 65 PHE cc_start: 0.8570 (m-10) cc_final: 0.8351 (m-10) REVERT: B 176 LEU cc_start: 0.6364 (OUTLIER) cc_final: 0.5943 (mt) REVERT: B 190 ARG cc_start: 0.7679 (mmt-90) cc_final: 0.7434 (mmt-90) REVERT: B 200 TYR cc_start: 0.7592 (m-80) cc_final: 0.7366 (m-80) REVERT: B 202 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8516 (mmtm) REVERT: B 237 ARG cc_start: 0.8051 (mtm-85) cc_final: 0.7711 (ptt90) REVERT: B 304 LYS cc_start: 0.8992 (mmmm) cc_final: 0.8733 (mmmm) REVERT: B 354 ASN cc_start: 0.8109 (t0) cc_final: 0.7696 (p0) REVERT: B 365 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6945 (p90) REVERT: B 474 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7652 (pt0) REVERT: B 518 LEU cc_start: 0.9262 (mm) cc_final: 0.8913 (tp) REVERT: B 571 ASP cc_start: 0.8788 (t0) cc_final: 0.8197 (t0) REVERT: B 646 ARG cc_start: 0.8058 (ttt90) cc_final: 0.7779 (ttt90) REVERT: B 654 GLU cc_start: 0.8529 (tp30) cc_final: 0.8255 (tp30) REVERT: B 661 GLU cc_start: 0.8227 (pm20) cc_final: 0.7907 (pm20) REVERT: B 780 GLU cc_start: 0.8666 (tp30) cc_final: 0.8342 (tp30) REVERT: B 1005 GLN cc_start: 0.8928 (tp40) cc_final: 0.8561 (tp40) REVERT: B 1010 GLN cc_start: 0.8767 (mt0) cc_final: 0.8539 (mm-40) REVERT: B 1091 ARG cc_start: 0.8149 (ttm170) cc_final: 0.7901 (ttm170) REVERT: C 63 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8508 (p) REVERT: C 129 LYS cc_start: 0.8289 (tttt) cc_final: 0.8028 (ttmt) REVERT: C 191 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7670 (mt-10) REVERT: C 207 HIS cc_start: 0.8360 (t70) cc_final: 0.8152 (t70) REVERT: C 218 GLN cc_start: 0.8197 (tt0) cc_final: 0.7981 (mt0) REVERT: C 224 GLU cc_start: 0.8501 (mp0) cc_final: 0.8065 (mp0) REVERT: C 306 PHE cc_start: 0.8592 (m-80) cc_final: 0.8382 (m-80) REVERT: C 360 ASN cc_start: 0.8932 (t0) cc_final: 0.8489 (t0) REVERT: C 365 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7334 (t80) REVERT: C 377 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.7174 (t80) REVERT: C 386 LYS cc_start: 0.8804 (mttp) cc_final: 0.8448 (mttm) REVERT: C 516 GLU cc_start: 0.7782 (tp30) cc_final: 0.7404 (tp30) REVERT: C 547 LYS cc_start: 0.8933 (mtpp) cc_final: 0.8559 (mtpp) REVERT: C 564 GLN cc_start: 0.8865 (tp40) cc_final: 0.8538 (tp40) REVERT: C 571 ASP cc_start: 0.7927 (t0) cc_final: 0.7696 (t0) REVERT: C 610 VAL cc_start: 0.9226 (t) cc_final: 0.8918 (m) REVERT: C 613 GLN cc_start: 0.7882 (mt0) cc_final: 0.7667 (mt0) REVERT: C 646 ARG cc_start: 0.8969 (tpp80) cc_final: 0.8242 (ttp80) REVERT: C 661 GLU cc_start: 0.7571 (tm-30) cc_final: 0.6998 (tm-30) REVERT: C 819 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8179 (mt-10) REVERT: C 855 PHE cc_start: 0.8569 (m-10) cc_final: 0.8239 (m-10) REVERT: C 918 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8275 (mt-10) REVERT: C 950 ASP cc_start: 0.8204 (p0) cc_final: 0.7855 (p0) REVERT: C 988 GLU cc_start: 0.7964 (tp30) cc_final: 0.7716 (tp30) outliers start: 111 outliers final: 75 residues processed: 609 average time/residue: 0.3982 time to fit residues: 381.2941 Evaluate side-chains 601 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 517 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 268 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 239 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 274 optimal weight: 0.2980 chunk 222 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 chunk 288 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28291 Z= 0.256 Angle : 0.711 10.597 38466 Z= 0.345 Chirality : 0.048 0.558 4635 Planarity : 0.004 0.091 4827 Dihedral : 10.261 107.926 5701 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.08 % Favored : 93.89 % Rotamer: Outliers : 4.34 % Allowed : 15.75 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.61 (0.14), residues: 3324 helix: 1.32 (0.19), residues: 774 sheet: -0.06 (0.18), residues: 697 loop : -1.34 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 436 HIS 0.010 0.001 HIS B 207 PHE 0.029 0.002 PHE A 823 TYR 0.029 0.001 TYR C 636 ARG 0.007 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 541 time to evaluate : 3.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9097 (mmmm) cc_final: 0.8544 (mmmm) REVERT: A 129 LYS cc_start: 0.8888 (tttt) cc_final: 0.8343 (ttmm) REVERT: A 190 ARG cc_start: 0.8326 (mmm160) cc_final: 0.7755 (mmm-85) REVERT: A 214 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6990 (ttp80) REVERT: A 224 GLU cc_start: 0.8330 (mp0) cc_final: 0.8051 (mp0) REVERT: A 228 ASP cc_start: 0.7800 (p0) cc_final: 0.7440 (p0) REVERT: A 266 TYR cc_start: 0.7920 (m-80) cc_final: 0.7445 (m-80) REVERT: A 287 ASP cc_start: 0.8670 (t0) cc_final: 0.8415 (t0) REVERT: A 306 PHE cc_start: 0.8386 (m-10) cc_final: 0.8012 (m-10) REVERT: A 309 GLU cc_start: 0.8401 (mp0) cc_final: 0.8148 (mp0) REVERT: A 319 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7611 (tpt170) REVERT: A 532 ASN cc_start: 0.7329 (OUTLIER) cc_final: 0.6468 (p0) REVERT: A 588 THR cc_start: 0.9078 (m) cc_final: 0.8825 (t) REVERT: A 780 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8054 (mm-30) REVERT: A 819 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8090 (mt-10) REVERT: A 823 PHE cc_start: 0.7772 (m-80) cc_final: 0.7461 (m-10) REVERT: A 848 ASP cc_start: 0.8579 (t0) cc_final: 0.7764 (p0) REVERT: A 854 LYS cc_start: 0.9227 (tttt) cc_final: 0.8948 (tptp) REVERT: A 867 ASP cc_start: 0.8470 (m-30) cc_final: 0.8228 (m-30) REVERT: A 935 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8536 (tm-30) REVERT: A 1072 GLU cc_start: 0.8720 (pm20) cc_final: 0.8381 (pm20) REVERT: B 41 LYS cc_start: 0.8736 (mmmm) cc_final: 0.8505 (mtpp) REVERT: B 52 GLN cc_start: 0.8369 (tp40) cc_final: 0.7813 (tp-100) REVERT: B 202 LYS cc_start: 0.8823 (mmmt) cc_final: 0.8497 (mmtm) REVERT: B 237 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7729 (ptt90) REVERT: B 304 LYS cc_start: 0.8992 (mmmm) cc_final: 0.8732 (mmmm) REVERT: B 354 ASN cc_start: 0.8113 (t0) cc_final: 0.7706 (p0) REVERT: B 365 TYR cc_start: 0.7326 (OUTLIER) cc_final: 0.6860 (p90) REVERT: B 452 LEU cc_start: 0.8897 (mp) cc_final: 0.8491 (mt) REVERT: B 474 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7522 (pt0) REVERT: B 518 LEU cc_start: 0.9258 (mm) cc_final: 0.9040 (tp) REVERT: B 537 LYS cc_start: 0.9036 (mttt) cc_final: 0.8789 (mttp) REVERT: B 571 ASP cc_start: 0.8817 (t0) cc_final: 0.8235 (t0) REVERT: B 646 ARG cc_start: 0.8104 (ttt90) cc_final: 0.7653 (mtp180) REVERT: B 654 GLU cc_start: 0.8542 (tp30) cc_final: 0.8310 (tp30) REVERT: B 661 GLU cc_start: 0.8246 (pm20) cc_final: 0.7888 (pm20) REVERT: B 755 GLN cc_start: 0.8621 (pt0) cc_final: 0.8263 (mp10) REVERT: B 765 ARG cc_start: 0.8539 (ttm110) cc_final: 0.7859 (ttm110) REVERT: B 780 GLU cc_start: 0.8667 (tp30) cc_final: 0.8342 (tp30) REVERT: B 848 ASP cc_start: 0.7576 (t0) cc_final: 0.7181 (p0) REVERT: B 1005 GLN cc_start: 0.8905 (tp40) cc_final: 0.8572 (tp40) REVERT: B 1010 GLN cc_start: 0.8771 (mt0) cc_final: 0.8554 (mm-40) REVERT: B 1091 ARG cc_start: 0.8188 (ttm170) cc_final: 0.7980 (ttm170) REVERT: C 63 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8533 (p) REVERT: C 129 LYS cc_start: 0.8415 (tttt) cc_final: 0.8119 (ttmt) REVERT: C 191 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7638 (mt-10) REVERT: C 218 GLN cc_start: 0.8181 (tt0) cc_final: 0.7939 (tt0) REVERT: C 224 GLU cc_start: 0.8503 (mp0) cc_final: 0.8077 (mp0) REVERT: C 306 PHE cc_start: 0.8625 (m-80) cc_final: 0.8353 (m-80) REVERT: C 360 ASN cc_start: 0.8925 (t0) cc_final: 0.8460 (t0) REVERT: C 365 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.7343 (t80) REVERT: C 377 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.7074 (t80) REVERT: C 386 LYS cc_start: 0.8772 (mttp) cc_final: 0.8434 (mttm) REVERT: C 516 GLU cc_start: 0.7792 (tp30) cc_final: 0.7382 (tp30) REVERT: C 547 LYS cc_start: 0.8931 (mtpp) cc_final: 0.8559 (mtpp) REVERT: C 564 GLN cc_start: 0.8840 (tp40) cc_final: 0.8514 (tp40) REVERT: C 571 ASP cc_start: 0.7961 (t0) cc_final: 0.7674 (t0) REVERT: C 610 VAL cc_start: 0.9225 (t) cc_final: 0.8932 (m) REVERT: C 613 GLN cc_start: 0.7874 (mt0) cc_final: 0.7669 (mt0) REVERT: C 646 ARG cc_start: 0.8977 (tpp80) cc_final: 0.8253 (tpp80) REVERT: C 661 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7187 (tm-30) REVERT: C 773 GLU cc_start: 0.8513 (tt0) cc_final: 0.7643 (tm-30) REVERT: C 819 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8209 (mt-10) REVERT: C 855 PHE cc_start: 0.8592 (m-10) cc_final: 0.8273 (m-10) REVERT: C 918 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8275 (mt-10) REVERT: C 950 ASP cc_start: 0.8218 (p0) cc_final: 0.7835 (p0) REVERT: C 988 GLU cc_start: 0.7991 (tp30) cc_final: 0.7744 (tp30) outliers start: 127 outliers final: 92 residues processed: 615 average time/residue: 0.4126 time to fit residues: 396.4857 Evaluate side-chains 627 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 526 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 108 optimal weight: 0.9980 chunk 289 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 322 optimal weight: 2.9990 chunk 267 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 169 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 207 HIS B 955 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 954 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28291 Z= 0.228 Angle : 0.702 10.718 38466 Z= 0.340 Chirality : 0.047 0.559 4635 Planarity : 0.004 0.078 4827 Dihedral : 9.787 105.942 5700 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.78 % Favored : 94.16 % Rotamer: Outliers : 4.48 % Allowed : 16.36 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.51 (0.14), residues: 3324 helix: 1.43 (0.19), residues: 781 sheet: -0.06 (0.18), residues: 709 loop : -1.28 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 436 HIS 0.009 0.001 HIS C 954 PHE 0.034 0.002 PHE A 456 TYR 0.024 0.001 TYR C 636 ARG 0.022 0.001 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 550 time to evaluate : 3.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9106 (mmmm) cc_final: 0.8560 (mmmm) REVERT: A 129 LYS cc_start: 0.8878 (tttt) cc_final: 0.8131 (tttt) REVERT: A 190 ARG cc_start: 0.8351 (mmm160) cc_final: 0.7786 (mmm-85) REVERT: A 195 LYS cc_start: 0.8088 (mttt) cc_final: 0.7848 (mttt) REVERT: A 214 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6969 (ttp80) REVERT: A 228 ASP cc_start: 0.7729 (p0) cc_final: 0.7346 (p0) REVERT: A 287 ASP cc_start: 0.8697 (t0) cc_final: 0.8391 (t0) REVERT: A 319 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7561 (tpt170) REVERT: A 588 THR cc_start: 0.9052 (m) cc_final: 0.8804 (t) REVERT: A 646 ARG cc_start: 0.8401 (mtp180) cc_final: 0.7876 (mmm-85) REVERT: A 780 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8119 (mm-30) REVERT: A 819 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8053 (mt-10) REVERT: A 823 PHE cc_start: 0.7729 (m-80) cc_final: 0.7388 (m-10) REVERT: A 848 ASP cc_start: 0.8542 (t0) cc_final: 0.7667 (p0) REVERT: A 854 LYS cc_start: 0.9272 (tttt) cc_final: 0.8923 (tptp) REVERT: A 867 ASP cc_start: 0.8455 (m-30) cc_final: 0.8172 (m-30) REVERT: A 935 GLN cc_start: 0.8998 (tm130) cc_final: 0.8573 (tm-30) REVERT: A 1005 GLN cc_start: 0.8814 (tp40) cc_final: 0.8298 (tp40) REVERT: A 1045 LYS cc_start: 0.8660 (mmmm) cc_final: 0.8260 (tptt) REVERT: A 1072 GLU cc_start: 0.8695 (pm20) cc_final: 0.8356 (pm20) REVERT: B 52 GLN cc_start: 0.8345 (tp40) cc_final: 0.7784 (tp-100) REVERT: B 119 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8885 (tp) REVERT: B 156 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5609 (mm-30) REVERT: B 176 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6012 (mt) REVERT: B 202 LYS cc_start: 0.8828 (mmmt) cc_final: 0.8519 (mmtm) REVERT: B 237 ARG cc_start: 0.8068 (mtm-85) cc_final: 0.7725 (ptt90) REVERT: B 354 ASN cc_start: 0.8110 (t0) cc_final: 0.7696 (p0) REVERT: B 365 TYR cc_start: 0.7309 (OUTLIER) cc_final: 0.6895 (p90) REVERT: B 451 TYR cc_start: 0.6545 (m-10) cc_final: 0.6328 (m-10) REVERT: B 452 LEU cc_start: 0.8908 (mp) cc_final: 0.8529 (mt) REVERT: B 474 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7590 (pt0) REVERT: B 571 ASP cc_start: 0.8827 (t0) cc_final: 0.8238 (t0) REVERT: B 646 ARG cc_start: 0.8093 (ttt90) cc_final: 0.7681 (mtp180) REVERT: B 654 GLU cc_start: 0.8514 (tp30) cc_final: 0.8280 (tp30) REVERT: B 661 GLU cc_start: 0.8236 (pm20) cc_final: 0.7877 (pm20) REVERT: B 675 GLN cc_start: 0.7807 (mt0) cc_final: 0.7491 (pp30) REVERT: B 755 GLN cc_start: 0.8603 (pt0) cc_final: 0.8281 (mp10) REVERT: B 765 ARG cc_start: 0.8528 (ttm110) cc_final: 0.8083 (mtm-85) REVERT: B 780 GLU cc_start: 0.8658 (tp30) cc_final: 0.8326 (tp30) REVERT: B 848 ASP cc_start: 0.7569 (t0) cc_final: 0.7193 (p0) REVERT: B 1005 GLN cc_start: 0.8881 (tp40) cc_final: 0.8571 (tp40) REVERT: B 1010 GLN cc_start: 0.8757 (mt0) cc_final: 0.8459 (mm-40) REVERT: B 1091 ARG cc_start: 0.8177 (ttm170) cc_final: 0.7948 (ttm170) REVERT: C 63 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8533 (p) REVERT: C 129 LYS cc_start: 0.8435 (tttt) cc_final: 0.7864 (tptp) REVERT: C 168 PHE cc_start: 0.8538 (t80) cc_final: 0.7990 (t80) REVERT: C 191 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7667 (mt-10) REVERT: C 224 GLU cc_start: 0.8498 (mp0) cc_final: 0.8076 (mp0) REVERT: C 236 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8613 (p) REVERT: C 306 PHE cc_start: 0.8659 (m-80) cc_final: 0.8421 (m-80) REVERT: C 316 SER cc_start: 0.8852 (m) cc_final: 0.8548 (p) REVERT: C 360 ASN cc_start: 0.8896 (t0) cc_final: 0.8429 (t0) REVERT: C 365 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.7241 (t80) REVERT: C 377 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.7151 (t80) REVERT: C 386 LYS cc_start: 0.8749 (mttp) cc_final: 0.8246 (mmmm) REVERT: C 516 GLU cc_start: 0.7749 (tp30) cc_final: 0.7348 (tp30) REVERT: C 547 LYS cc_start: 0.8931 (mtpp) cc_final: 0.8557 (mtpp) REVERT: C 564 GLN cc_start: 0.8811 (tp40) cc_final: 0.8486 (tp40) REVERT: C 571 ASP cc_start: 0.8008 (t0) cc_final: 0.7723 (t0) REVERT: C 610 VAL cc_start: 0.9221 (t) cc_final: 0.8924 (m) REVERT: C 613 GLN cc_start: 0.7837 (mt0) cc_final: 0.7625 (mt0) REVERT: C 646 ARG cc_start: 0.8969 (tpp80) cc_final: 0.8249 (tpp80) REVERT: C 661 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7115 (tm-30) REVERT: C 773 GLU cc_start: 0.8483 (tt0) cc_final: 0.7483 (tm-30) REVERT: C 777 ASN cc_start: 0.8514 (m-40) cc_final: 0.7121 (m110) REVERT: C 819 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8219 (mt-10) REVERT: C 855 PHE cc_start: 0.8617 (m-10) cc_final: 0.8243 (m-10) REVERT: C 918 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8268 (mt-10) REVERT: C 950 ASP cc_start: 0.8159 (p0) cc_final: 0.7785 (p0) REVERT: C 988 GLU cc_start: 0.7965 (tp30) cc_final: 0.7700 (tp30) REVERT: C 1019 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8073 (ttm-80) REVERT: C 1072 GLU cc_start: 0.8389 (pp20) cc_final: 0.8008 (pp20) outliers start: 131 outliers final: 95 residues processed: 628 average time/residue: 0.4044 time to fit residues: 396.3077 Evaluate side-chains 633 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 526 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 310 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 271 optimal weight: 0.9990 chunk 179 optimal weight: 0.8980 chunk 320 optimal weight: 0.9980 chunk 200 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 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 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 207 HIS B 675 GLN B 953 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 28291 Z= 0.267 Angle : 0.719 12.148 38466 Z= 0.348 Chirality : 0.048 0.547 4635 Planarity : 0.004 0.079 4827 Dihedral : 9.480 105.759 5695 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.54 % Allowed : 16.91 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.51 (0.14), residues: 3324 helix: 1.42 (0.19), residues: 779 sheet: -0.08 (0.18), residues: 714 loop : -1.26 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 436 HIS 0.009 0.001 HIS B 207 PHE 0.052 0.002 PHE A 456 TYR 0.025 0.001 TYR C 636 ARG 0.009 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 537 time to evaluate : 3.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9093 (mmmm) cc_final: 0.8864 (mmmm) REVERT: A 115 GLN cc_start: 0.8857 (tp40) cc_final: 0.8401 (tp-100) REVERT: A 129 LYS cc_start: 0.8867 (tttt) cc_final: 0.8378 (tttt) REVERT: A 177 MET cc_start: 0.6511 (ppp) cc_final: 0.6192 (tmm) REVERT: A 190 ARG cc_start: 0.8353 (mmm160) cc_final: 0.7844 (mmm-85) REVERT: A 204 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: A 214 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.7008 (ttp80) REVERT: A 224 GLU cc_start: 0.8251 (mp0) cc_final: 0.7819 (mp0) REVERT: A 228 ASP cc_start: 0.7710 (p0) cc_final: 0.7320 (p0) REVERT: A 287 ASP cc_start: 0.8709 (t0) cc_final: 0.8401 (t0) REVERT: A 319 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7614 (tpt170) REVERT: A 392 PHE cc_start: 0.7309 (m-10) cc_final: 0.6618 (m-80) REVERT: A 588 THR cc_start: 0.9044 (m) cc_final: 0.8808 (t) REVERT: A 646 ARG cc_start: 0.8478 (mtp180) cc_final: 0.8029 (mmm-85) REVERT: A 780 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8106 (mm-30) REVERT: A 819 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8097 (mt-10) REVERT: A 823 PHE cc_start: 0.7765 (m-80) cc_final: 0.7404 (m-10) REVERT: A 848 ASP cc_start: 0.8490 (t0) cc_final: 0.7952 (m-30) REVERT: A 854 LYS cc_start: 0.9279 (tttt) cc_final: 0.8931 (tptp) REVERT: A 867 ASP cc_start: 0.8461 (m-30) cc_final: 0.8122 (m-30) REVERT: A 935 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8579 (tm-30) REVERT: A 1045 LYS cc_start: 0.8652 (mmmm) cc_final: 0.8291 (mmtm) REVERT: A 1072 GLU cc_start: 0.8728 (pm20) cc_final: 0.8393 (pm20) REVERT: B 52 GLN cc_start: 0.8342 (tp40) cc_final: 0.7774 (tp-100) REVERT: B 156 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.5005 (mp0) REVERT: B 176 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6050 (mt) REVERT: B 202 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8518 (mmtm) REVERT: B 224 GLU cc_start: 0.8177 (mp0) cc_final: 0.7946 (mp0) REVERT: B 354 ASN cc_start: 0.8151 (t0) cc_final: 0.7737 (p0) REVERT: B 365 TYR cc_start: 0.7300 (OUTLIER) cc_final: 0.6834 (p90) REVERT: B 452 LEU cc_start: 0.8907 (mp) cc_final: 0.8542 (mt) REVERT: B 474 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7491 (pt0) REVERT: B 537 LYS cc_start: 0.9059 (mttt) cc_final: 0.8809 (mttp) REVERT: B 571 ASP cc_start: 0.8847 (t0) cc_final: 0.8271 (t0) REVERT: B 646 ARG cc_start: 0.8077 (ttt90) cc_final: 0.7624 (mtp180) REVERT: B 654 GLU cc_start: 0.8529 (tp30) cc_final: 0.8298 (tp30) REVERT: B 661 GLU cc_start: 0.8247 (pm20) cc_final: 0.7883 (pm20) REVERT: B 755 GLN cc_start: 0.8623 (pt0) cc_final: 0.8341 (mp10) REVERT: B 765 ARG cc_start: 0.8543 (ttm110) cc_final: 0.8116 (mtm-85) REVERT: B 773 GLU cc_start: 0.8638 (tp30) cc_final: 0.8071 (tp30) REVERT: B 780 GLU cc_start: 0.8658 (tp30) cc_final: 0.8337 (tp30) REVERT: B 820 ASP cc_start: 0.8921 (t0) cc_final: 0.8625 (m-30) REVERT: B 848 ASP cc_start: 0.7680 (t0) cc_final: 0.7258 (p0) REVERT: B 1005 GLN cc_start: 0.8889 (tp40) cc_final: 0.8580 (tp40) REVERT: B 1010 GLN cc_start: 0.8760 (mt0) cc_final: 0.8470 (mm-40) REVERT: B 1019 ARG cc_start: 0.7897 (ttt90) cc_final: 0.7488 (ttt90) REVERT: B 1091 ARG cc_start: 0.8181 (ttm170) cc_final: 0.7914 (ttm170) REVERT: C 63 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8547 (p) REVERT: C 129 LYS cc_start: 0.8456 (tttt) cc_final: 0.7994 (ttmm) REVERT: C 190 ARG cc_start: 0.8385 (tpt170) cc_final: 0.7998 (mmm160) REVERT: C 191 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7635 (mt-10) REVERT: C 218 GLN cc_start: 0.8135 (tt0) cc_final: 0.7908 (mt0) REVERT: C 224 GLU cc_start: 0.8453 (mp0) cc_final: 0.8029 (mp0) REVERT: C 236 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8621 (p) REVERT: C 306 PHE cc_start: 0.8689 (m-80) cc_final: 0.8487 (m-80) REVERT: C 316 SER cc_start: 0.8870 (m) cc_final: 0.8576 (p) REVERT: C 360 ASN cc_start: 0.8910 (t0) cc_final: 0.8440 (t0) REVERT: C 365 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7247 (t80) REVERT: C 377 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.6842 (t80) REVERT: C 386 LYS cc_start: 0.8768 (mttp) cc_final: 0.8471 (mmtm) REVERT: C 403 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6320 (mmm-85) REVERT: C 516 GLU cc_start: 0.7790 (tp30) cc_final: 0.7373 (tp30) REVERT: C 547 LYS cc_start: 0.8937 (mtpp) cc_final: 0.8571 (mtpp) REVERT: C 564 GLN cc_start: 0.8812 (tp40) cc_final: 0.8491 (tp40) REVERT: C 571 ASP cc_start: 0.8046 (t0) cc_final: 0.7761 (t0) REVERT: C 610 VAL cc_start: 0.9223 (t) cc_final: 0.8931 (m) REVERT: C 613 GLN cc_start: 0.7844 (mt0) cc_final: 0.7634 (mt0) REVERT: C 646 ARG cc_start: 0.8966 (tpp80) cc_final: 0.8236 (tpp80) REVERT: C 661 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7082 (tm-30) REVERT: C 773 GLU cc_start: 0.8487 (tt0) cc_final: 0.7589 (tm-30) REVERT: C 777 ASN cc_start: 0.8502 (m-40) cc_final: 0.7265 (m110) REVERT: C 819 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8235 (mt-10) REVERT: C 855 PHE cc_start: 0.8588 (m-10) cc_final: 0.8220 (m-10) REVERT: C 918 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8282 (mt-10) REVERT: C 950 ASP cc_start: 0.8137 (p0) cc_final: 0.7816 (p0) REVERT: C 988 GLU cc_start: 0.7999 (tp30) cc_final: 0.7734 (tp30) REVERT: C 1002 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8174 (mp10) REVERT: C 1072 GLU cc_start: 0.8412 (pp20) cc_final: 0.8008 (pp20) outliers start: 133 outliers final: 97 residues processed: 620 average time/residue: 0.4129 time to fit residues: 403.1252 Evaluate side-chains 634 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 523 time to evaluate : 3.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 198 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 218 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 252 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1002 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 394 ASN B 439 ASN B 675 GLN B 949 GLN B 953 ASN B 955 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 28291 Z= 0.324 Angle : 0.753 11.219 38466 Z= 0.367 Chirality : 0.048 0.531 4635 Planarity : 0.005 0.079 4827 Dihedral : 9.295 106.850 5692 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.44 % Allowed : 17.59 % Favored : 77.96 % 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: -0.59 (0.14), residues: 3324 helix: 1.38 (0.19), residues: 772 sheet: -0.10 (0.18), residues: 709 loop : -1.33 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 436 HIS 0.012 0.001 HIS B 207 PHE 0.048 0.002 PHE A 456 TYR 0.025 0.002 TYR A 351 ARG 0.019 0.001 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 533 time to evaluate : 3.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9098 (mmmm) cc_final: 0.8866 (mmmm) REVERT: A 129 LYS cc_start: 0.8867 (tttt) cc_final: 0.8361 (tttt) REVERT: A 177 MET cc_start: 0.6559 (ppp) cc_final: 0.6312 (tmm) REVERT: A 190 ARG cc_start: 0.8364 (mmm160) cc_final: 0.7822 (mmm-85) REVERT: A 204 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.8352 (m-80) REVERT: A 214 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6841 (ttp80) REVERT: A 215 ASP cc_start: 0.7307 (p0) cc_final: 0.6854 (p0) REVERT: A 228 ASP cc_start: 0.7765 (p0) cc_final: 0.7341 (p0) REVERT: A 266 TYR cc_start: 0.7945 (m-80) cc_final: 0.7264 (m-80) REVERT: A 287 ASP cc_start: 0.8750 (t0) cc_final: 0.8453 (t0) REVERT: A 306 PHE cc_start: 0.8503 (m-80) cc_final: 0.8123 (m-10) REVERT: A 588 THR cc_start: 0.9016 (m) cc_final: 0.8769 (t) REVERT: A 780 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8111 (mm-30) REVERT: A 819 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8138 (mt-10) REVERT: A 823 PHE cc_start: 0.7770 (m-80) cc_final: 0.7381 (m-10) REVERT: A 848 ASP cc_start: 0.8440 (t0) cc_final: 0.7981 (m-30) REVERT: A 854 LYS cc_start: 0.9281 (tttt) cc_final: 0.8935 (tptp) REVERT: A 867 ASP cc_start: 0.8470 (m-30) cc_final: 0.8082 (m-30) REVERT: A 935 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8616 (tm-30) REVERT: A 1045 LYS cc_start: 0.8683 (mmmm) cc_final: 0.8327 (mmtm) REVERT: A 1072 GLU cc_start: 0.8755 (pm20) cc_final: 0.8421 (pm20) REVERT: B 52 GLN cc_start: 0.8370 (tp40) cc_final: 0.7758 (tp-100) REVERT: B 125 ASN cc_start: 0.7688 (OUTLIER) cc_final: 0.7404 (p0) REVERT: B 156 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.5756 (mm-30) REVERT: B 202 LYS cc_start: 0.8849 (mmmt) cc_final: 0.8540 (mmtm) REVERT: B 224 GLU cc_start: 0.8167 (mp0) cc_final: 0.7939 (mp0) REVERT: B 354 ASN cc_start: 0.8118 (t0) cc_final: 0.7698 (p0) REVERT: B 365 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.6703 (p90) REVERT: B 452 LEU cc_start: 0.8919 (mp) cc_final: 0.8542 (mt) REVERT: B 474 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7516 (pt0) REVERT: B 537 LYS cc_start: 0.9111 (mttt) cc_final: 0.8854 (mttp) REVERT: B 571 ASP cc_start: 0.8882 (t0) cc_final: 0.8324 (t0) REVERT: B 646 ARG cc_start: 0.8055 (ttt90) cc_final: 0.7565 (mtp180) REVERT: B 654 GLU cc_start: 0.8537 (tp30) cc_final: 0.8302 (tp30) REVERT: B 661 GLU cc_start: 0.8276 (pm20) cc_final: 0.7923 (pm20) REVERT: B 765 ARG cc_start: 0.8571 (ttm110) cc_final: 0.8154 (mtm-85) REVERT: B 780 GLU cc_start: 0.8659 (tp30) cc_final: 0.8319 (tp30) REVERT: B 786 LYS cc_start: 0.8564 (mttt) cc_final: 0.8324 (mmmt) REVERT: B 820 ASP cc_start: 0.8947 (t0) cc_final: 0.8653 (m-30) REVERT: B 848 ASP cc_start: 0.7622 (t0) cc_final: 0.7269 (p0) REVERT: B 868 GLU cc_start: 0.8562 (mp0) cc_final: 0.8306 (mp0) REVERT: B 1005 GLN cc_start: 0.8916 (tp40) cc_final: 0.8598 (tp40) REVERT: B 1010 GLN cc_start: 0.8766 (mt0) cc_final: 0.8484 (mm-40) REVERT: B 1072 GLU cc_start: 0.8699 (pm20) cc_final: 0.8095 (pm20) REVERT: B 1091 ARG cc_start: 0.8161 (ttm170) cc_final: 0.7882 (ttm170) REVERT: C 63 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8538 (p) REVERT: C 129 LYS cc_start: 0.8523 (tttt) cc_final: 0.8003 (ttmt) REVERT: C 190 ARG cc_start: 0.8394 (tpt170) cc_final: 0.7995 (mmm160) REVERT: C 224 GLU cc_start: 0.8459 (mp0) cc_final: 0.8022 (mp0) REVERT: C 236 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8668 (p) REVERT: C 306 PHE cc_start: 0.8757 (m-80) cc_final: 0.8476 (m-80) REVERT: C 316 SER cc_start: 0.8909 (m) cc_final: 0.8591 (p) REVERT: C 360 ASN cc_start: 0.8945 (t0) cc_final: 0.8482 (t0) REVERT: C 365 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.7187 (t80) REVERT: C 377 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.7062 (t80) REVERT: C 403 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6466 (mmm-85) REVERT: C 516 GLU cc_start: 0.7855 (tp30) cc_final: 0.7364 (tp30) REVERT: C 547 LYS cc_start: 0.8945 (mtpp) cc_final: 0.8589 (mtpp) REVERT: C 564 GLN cc_start: 0.8809 (tp40) cc_final: 0.8480 (tp40) REVERT: C 571 ASP cc_start: 0.8076 (t0) cc_final: 0.7847 (t0) REVERT: C 610 VAL cc_start: 0.9237 (t) cc_final: 0.8941 (m) REVERT: C 613 GLN cc_start: 0.7840 (mt0) cc_final: 0.7601 (mt0) REVERT: C 646 ARG cc_start: 0.8962 (tpp80) cc_final: 0.8228 (tpp80) REVERT: C 661 GLU cc_start: 0.7578 (tm-30) cc_final: 0.6963 (tm-30) REVERT: C 773 GLU cc_start: 0.8474 (tt0) cc_final: 0.7623 (tm-30) REVERT: C 811 LYS cc_start: 0.8727 (tppt) cc_final: 0.8238 (ttmm) REVERT: C 819 GLU cc_start: 0.8594 (mt-10) cc_final: 0.7791 (mm-30) REVERT: C 855 PHE cc_start: 0.8664 (m-10) cc_final: 0.8316 (m-10) REVERT: C 918 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8299 (mt-10) REVERT: C 950 ASP cc_start: 0.8180 (p0) cc_final: 0.7849 (p0) REVERT: C 988 GLU cc_start: 0.8087 (tp30) cc_final: 0.7828 (tp30) REVERT: C 1002 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8268 (mp10) outliers start: 130 outliers final: 102 residues processed: 612 average time/residue: 0.4254 time to fit residues: 408.1083 Evaluate side-chains 638 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 523 time to evaluate : 7.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 291 optimal weight: 0.8980 chunk 307 optimal weight: 0.6980 chunk 280 optimal weight: 0.0370 chunk 299 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 234 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 270 optimal weight: 4.9990 chunk 282 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1088 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 675 GLN B 953 ASN B 955 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 965 GLN C1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28291 Z= 0.217 Angle : 0.721 12.182 38466 Z= 0.349 Chirality : 0.047 0.571 4635 Planarity : 0.004 0.067 4827 Dihedral : 8.751 106.981 5688 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.96 % Allowed : 18.45 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3324 helix: 1.41 (0.19), residues: 778 sheet: -0.07 (0.18), residues: 702 loop : -1.21 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 436 HIS 0.011 0.001 HIS B 954 PHE 0.043 0.002 PHE A 456 TYR 0.020 0.001 TYR C 636 ARG 0.009 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 542 time to evaluate : 3.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9094 (mmmm) cc_final: 0.8863 (mmmm) REVERT: A 102 ARG cc_start: 0.7011 (mmm-85) cc_final: 0.6801 (mmm-85) REVERT: A 115 GLN cc_start: 0.8805 (tp40) cc_final: 0.8297 (tp-100) REVERT: A 129 LYS cc_start: 0.8825 (tttt) cc_final: 0.8328 (tttt) REVERT: A 190 ARG cc_start: 0.8370 (mmm160) cc_final: 0.7864 (mmm-85) REVERT: A 204 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.8314 (m-80) REVERT: A 224 GLU cc_start: 0.8229 (mp0) cc_final: 0.7908 (mp0) REVERT: A 228 ASP cc_start: 0.7721 (p0) cc_final: 0.7288 (p0) REVERT: A 287 ASP cc_start: 0.8696 (t0) cc_final: 0.8378 (t0) REVERT: A 306 PHE cc_start: 0.8477 (m-80) cc_final: 0.8085 (m-10) REVERT: A 392 PHE cc_start: 0.7308 (m-10) cc_final: 0.6630 (m-80) REVERT: A 588 THR cc_start: 0.9012 (m) cc_final: 0.8769 (t) REVERT: A 780 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8133 (mm-30) REVERT: A 819 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8070 (mt-10) REVERT: A 823 PHE cc_start: 0.7743 (m-80) cc_final: 0.7316 (m-10) REVERT: A 848 ASP cc_start: 0.8399 (t0) cc_final: 0.7952 (m-30) REVERT: A 854 LYS cc_start: 0.9271 (tttt) cc_final: 0.8942 (tptp) REVERT: A 867 ASP cc_start: 0.8452 (m-30) cc_final: 0.8038 (m-30) REVERT: A 935 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8601 (tm-30) REVERT: A 1045 LYS cc_start: 0.8691 (mmmm) cc_final: 0.8308 (mmtm) REVERT: A 1072 GLU cc_start: 0.8677 (pm20) cc_final: 0.8347 (pm20) REVERT: B 52 GLN cc_start: 0.8335 (tp40) cc_final: 0.7738 (tp-100) REVERT: B 156 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.5821 (mm-30) REVERT: B 202 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8577 (mmtm) REVERT: B 220 PHE cc_start: 0.8405 (t80) cc_final: 0.8025 (t80) REVERT: B 224 GLU cc_start: 0.8131 (mp0) cc_final: 0.7912 (mp0) REVERT: B 237 ARG cc_start: 0.8149 (mtm-85) cc_final: 0.7804 (ptt-90) REVERT: B 354 ASN cc_start: 0.8118 (t0) cc_final: 0.7393 (p0) REVERT: B 365 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.6851 (p90) REVERT: B 452 LEU cc_start: 0.8922 (mp) cc_final: 0.8578 (mt) REVERT: B 474 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7484 (pt0) REVERT: B 537 LYS cc_start: 0.9062 (mttt) cc_final: 0.8806 (mttp) REVERT: B 571 ASP cc_start: 0.8867 (t0) cc_final: 0.8283 (t0) REVERT: B 646 ARG cc_start: 0.8063 (ttt90) cc_final: 0.7771 (mtp180) REVERT: B 654 GLU cc_start: 0.8531 (tp30) cc_final: 0.8291 (tp30) REVERT: B 661 GLU cc_start: 0.8213 (pm20) cc_final: 0.7836 (pm20) REVERT: B 765 ARG cc_start: 0.8560 (ttm110) cc_final: 0.8146 (mtm-85) REVERT: B 780 GLU cc_start: 0.8650 (tp30) cc_final: 0.8337 (tp30) REVERT: B 786 LYS cc_start: 0.8553 (mttt) cc_final: 0.8308 (mmmt) REVERT: B 820 ASP cc_start: 0.8885 (t0) cc_final: 0.8518 (m-30) REVERT: B 848 ASP cc_start: 0.7608 (t0) cc_final: 0.7259 (p0) REVERT: B 1005 GLN cc_start: 0.8892 (tp40) cc_final: 0.8582 (tp40) REVERT: B 1072 GLU cc_start: 0.8647 (pm20) cc_final: 0.8059 (pm20) REVERT: B 1091 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7854 (ttm170) REVERT: C 63 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8535 (p) REVERT: C 129 LYS cc_start: 0.8422 (tttt) cc_final: 0.7982 (ttmm) REVERT: C 190 ARG cc_start: 0.8384 (tpt170) cc_final: 0.8017 (mmm160) REVERT: C 191 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7639 (mt-10) REVERT: C 214 GLU cc_start: 0.7790 (pm20) cc_final: 0.7393 (pm20) REVERT: C 218 GLN cc_start: 0.8178 (mt0) cc_final: 0.7929 (mt0) REVERT: C 224 GLU cc_start: 0.8451 (mp0) cc_final: 0.8038 (mp0) REVERT: C 236 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8584 (p) REVERT: C 306 PHE cc_start: 0.8730 (m-80) cc_final: 0.8463 (m-80) REVERT: C 316 SER cc_start: 0.8875 (m) cc_final: 0.8518 (p) REVERT: C 360 ASN cc_start: 0.8884 (t0) cc_final: 0.8428 (t0) REVERT: C 365 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.7113 (t80) REVERT: C 377 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.6904 (t80) REVERT: C 386 LYS cc_start: 0.8792 (mttp) cc_final: 0.8495 (mttm) REVERT: C 516 GLU cc_start: 0.7750 (tp30) cc_final: 0.7280 (tp30) REVERT: C 547 LYS cc_start: 0.8942 (mtpp) cc_final: 0.8566 (mtpp) REVERT: C 564 GLN cc_start: 0.8800 (tp40) cc_final: 0.8338 (tp40) REVERT: C 571 ASP cc_start: 0.8064 (t0) cc_final: 0.7831 (t0) REVERT: C 610 VAL cc_start: 0.9221 (t) cc_final: 0.8927 (m) REVERT: C 613 GLN cc_start: 0.7854 (mt0) cc_final: 0.7642 (mt0) REVERT: C 646 ARG cc_start: 0.8971 (tpp80) cc_final: 0.8215 (tpp80) REVERT: C 661 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7093 (tm-30) REVERT: C 773 GLU cc_start: 0.8457 (tt0) cc_final: 0.7583 (tm-30) REVERT: C 777 ASN cc_start: 0.8422 (m-40) cc_final: 0.7069 (m110) REVERT: C 811 LYS cc_start: 0.8727 (tppt) cc_final: 0.8263 (ttmm) REVERT: C 819 GLU cc_start: 0.8532 (mt-10) cc_final: 0.7754 (mm-30) REVERT: C 918 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8266 (mt-10) REVERT: C 935 GLN cc_start: 0.8870 (tt0) cc_final: 0.8313 (tm-30) REVERT: C 950 ASP cc_start: 0.8164 (p0) cc_final: 0.7856 (p0) REVERT: C 953 ASN cc_start: 0.8737 (m-40) cc_final: 0.8480 (m-40) REVERT: C 988 GLU cc_start: 0.7982 (tp30) cc_final: 0.7711 (tp30) REVERT: C 1002 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8220 (mp10) outliers start: 116 outliers final: 93 residues processed: 612 average time/residue: 0.4253 time to fit residues: 407.2903 Evaluate side-chains 625 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 522 time to evaluate : 3.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 196 optimal weight: 0.5980 chunk 316 optimal weight: 0.6980 chunk 193 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 331 optimal weight: 0.8980 chunk 305 optimal weight: 0.5980 chunk 264 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1002 GLN B 675 GLN B1002 GLN C 239 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C 935 GLN C1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28291 Z= 0.226 Angle : 0.729 12.085 38466 Z= 0.353 Chirality : 0.047 0.565 4635 Planarity : 0.005 0.079 4827 Dihedral : 8.514 106.715 5688 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.72 % Favored : 94.25 % Rotamer: Outliers : 3.83 % Allowed : 18.65 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3324 helix: 1.46 (0.19), residues: 770 sheet: -0.01 (0.18), residues: 702 loop : -1.22 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP C 436 HIS 0.005 0.001 HIS B1083 PHE 0.041 0.002 PHE A 456 TYR 0.018 0.001 TYR C 636 ARG 0.010 0.000 ARG B1019 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 533 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9088 (mmmm) cc_final: 0.8861 (mmmm) REVERT: A 115 GLN cc_start: 0.8802 (tp40) cc_final: 0.8298 (tp-100) REVERT: A 129 LYS cc_start: 0.8821 (tttt) cc_final: 0.8265 (tttp) REVERT: A 135 PHE cc_start: 0.7411 (m-80) cc_final: 0.7184 (m-80) REVERT: A 190 ARG cc_start: 0.8381 (mmm160) cc_final: 0.7874 (mmm-85) REVERT: A 204 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.8310 (m-80) REVERT: A 224 GLU cc_start: 0.8207 (mp0) cc_final: 0.7857 (mp0) REVERT: A 228 ASP cc_start: 0.7689 (p0) cc_final: 0.7284 (p0) REVERT: A 287 ASP cc_start: 0.8699 (t0) cc_final: 0.8387 (t0) REVERT: A 306 PHE cc_start: 0.8489 (m-80) cc_final: 0.7970 (m-10) REVERT: A 392 PHE cc_start: 0.7340 (m-10) cc_final: 0.6649 (m-80) REVERT: A 588 THR cc_start: 0.8990 (m) cc_final: 0.8737 (t) REVERT: A 780 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8131 (mm-30) REVERT: A 819 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8056 (mt-10) REVERT: A 823 PHE cc_start: 0.7721 (m-80) cc_final: 0.7344 (m-80) REVERT: A 848 ASP cc_start: 0.8369 (t0) cc_final: 0.7960 (m-30) REVERT: A 854 LYS cc_start: 0.9266 (tttt) cc_final: 0.8919 (tptp) REVERT: A 867 ASP cc_start: 0.8422 (m-30) cc_final: 0.8030 (m-30) REVERT: A 935 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8595 (tm-30) REVERT: A 990 GLU cc_start: 0.7732 (pm20) cc_final: 0.7531 (pm20) REVERT: A 1045 LYS cc_start: 0.8676 (mmmm) cc_final: 0.8328 (tptt) REVERT: A 1072 GLU cc_start: 0.8683 (pm20) cc_final: 0.8360 (pm20) REVERT: B 52 GLN cc_start: 0.8331 (tp40) cc_final: 0.7749 (tp-100) REVERT: B 156 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.5568 (mm-30) REVERT: B 202 LYS cc_start: 0.8849 (mmmt) cc_final: 0.8579 (mmtm) REVERT: B 220 PHE cc_start: 0.8405 (t80) cc_final: 0.8062 (t80) REVERT: B 224 GLU cc_start: 0.8144 (mp0) cc_final: 0.7931 (mp0) REVERT: B 365 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.6835 (p90) REVERT: B 452 LEU cc_start: 0.8932 (mp) cc_final: 0.8585 (mt) REVERT: B 474 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7507 (pt0) REVERT: B 537 LYS cc_start: 0.9051 (mttt) cc_final: 0.8795 (mttp) REVERT: B 571 ASP cc_start: 0.8869 (t0) cc_final: 0.8296 (t0) REVERT: B 646 ARG cc_start: 0.8071 (ttt90) cc_final: 0.7773 (mtp180) REVERT: B 654 GLU cc_start: 0.8535 (tp30) cc_final: 0.8301 (tp30) REVERT: B 661 GLU cc_start: 0.8202 (pm20) cc_final: 0.7826 (pm20) REVERT: B 765 ARG cc_start: 0.8549 (ttm110) cc_final: 0.8140 (mtm-85) REVERT: B 780 GLU cc_start: 0.8673 (tp30) cc_final: 0.8370 (tp30) REVERT: B 786 LYS cc_start: 0.8547 (mttt) cc_final: 0.8307 (mmmt) REVERT: B 820 ASP cc_start: 0.8866 (t0) cc_final: 0.8493 (m-30) REVERT: B 848 ASP cc_start: 0.7600 (t0) cc_final: 0.7256 (p0) REVERT: B 1005 GLN cc_start: 0.8891 (tp40) cc_final: 0.8559 (tp40) REVERT: B 1072 GLU cc_start: 0.8642 (pm20) cc_final: 0.8048 (pm20) REVERT: B 1091 ARG cc_start: 0.8153 (ttm170) cc_final: 0.7850 (ttm170) REVERT: C 41 LYS cc_start: 0.8978 (mmmm) cc_final: 0.8724 (mmmm) REVERT: C 63 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8514 (p) REVERT: C 129 LYS cc_start: 0.8428 (tttt) cc_final: 0.7987 (ttmm) REVERT: C 190 ARG cc_start: 0.8376 (tpt170) cc_final: 0.8006 (mmm160) REVERT: C 218 GLN cc_start: 0.8163 (mt0) cc_final: 0.7908 (mt0) REVERT: C 224 GLU cc_start: 0.8432 (mp0) cc_final: 0.8007 (mp0) REVERT: C 236 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8585 (p) REVERT: C 306 PHE cc_start: 0.8752 (m-80) cc_final: 0.8491 (m-80) REVERT: C 316 SER cc_start: 0.8836 (m) cc_final: 0.8564 (p) REVERT: C 360 ASN cc_start: 0.8863 (t0) cc_final: 0.8416 (t0) REVERT: C 377 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6852 (t80) REVERT: C 516 GLU cc_start: 0.7686 (tp30) cc_final: 0.7227 (tp30) REVERT: C 547 LYS cc_start: 0.8941 (mtpp) cc_final: 0.8557 (mtpp) REVERT: C 564 GLN cc_start: 0.8791 (tp40) cc_final: 0.8330 (tp40) REVERT: C 571 ASP cc_start: 0.8068 (t0) cc_final: 0.7827 (t0) REVERT: C 610 VAL cc_start: 0.9218 (t) cc_final: 0.8923 (m) REVERT: C 613 GLN cc_start: 0.7857 (mt0) cc_final: 0.7649 (mt0) REVERT: C 646 ARG cc_start: 0.8975 (tpp80) cc_final: 0.8211 (tpp80) REVERT: C 661 GLU cc_start: 0.7494 (tm-30) cc_final: 0.7103 (tm-30) REVERT: C 773 GLU cc_start: 0.8471 (tt0) cc_final: 0.7595 (tm-30) REVERT: C 777 ASN cc_start: 0.8378 (m-40) cc_final: 0.7028 (m110) REVERT: C 811 LYS cc_start: 0.8727 (tppt) cc_final: 0.8275 (ttmm) REVERT: C 819 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7815 (mm-30) REVERT: C 918 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8274 (mt-10) REVERT: C 950 ASP cc_start: 0.8177 (p0) cc_final: 0.7863 (p0) REVERT: C 953 ASN cc_start: 0.8760 (m-40) cc_final: 0.8525 (m-40) REVERT: C 988 GLU cc_start: 0.7966 (tp30) cc_final: 0.7693 (tp30) outliers start: 112 outliers final: 96 residues processed: 601 average time/residue: 0.4147 time to fit residues: 391.5940 Evaluate side-chains 623 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 519 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 209 optimal weight: 2.9990 chunk 281 optimal weight: 5.9990 chunk 80 optimal weight: 0.0670 chunk 243 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 264 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 271 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 0.0050 overall best weight: 0.9734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.097864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.076477 restraints weight = 76197.434| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 4.00 r_work: 0.3069 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.280 28291 Z= 0.368 Angle : 0.909 59.200 38466 Z= 0.501 Chirality : 0.049 0.775 4635 Planarity : 0.005 0.148 4827 Dihedral : 8.508 106.703 5687 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.72 % Favored : 94.25 % Rotamer: Outliers : 3.79 % Allowed : 18.86 % Favored : 77.35 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3324 helix: 1.42 (0.19), residues: 770 sheet: -0.00 (0.18), residues: 702 loop : -1.22 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.004 TRP C 436 HIS 0.005 0.001 HIS B1083 PHE 0.054 0.002 PHE C 374 TYR 0.039 0.001 TYR C 495 ARG 0.011 0.000 ARG B1019 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8306.79 seconds wall clock time: 150 minutes 52.05 seconds (9052.05 seconds total)