Starting phenix.real_space_refine on Wed Mar 20 08:02:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1x_24126/03_2024/7n1x_24126.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1x_24126/03_2024/7n1x_24126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1x_24126/03_2024/7n1x_24126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1x_24126/03_2024/7n1x_24126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1x_24126/03_2024/7n1x_24126.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1x_24126/03_2024/7n1x_24126.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.044 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 114 5.16 5 C 17037 2.51 5 N 4338 2.21 5 O 5321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" 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 TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1150": "OE1" <-> "OE2" Residue "A ASP 1153": "OD1" <-> "OD2" Residue "A TYR 1155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1107": "NH1" <-> "NH2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 936": "OD1" <-> "OD2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1084": "OD1" <-> "OD2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26810 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8434 Classifications: {'peptide': 1077} Link IDs: {'PTRANS': 52, 'TRANS': 1024} Chain breaks: 5 Chain: "B" Number of atoms: 8522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8522 Classifications: {'peptide': 1088} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1035} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8554 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 53, 'TRANS': 1038} Chain breaks: 4 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: 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: "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: 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: "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: 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: "R" 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: "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: 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: "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: 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: 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: "c" 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: "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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" 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 Time building chain proxies: 14.50, per 1000 atoms: 0.54 Number of scatterers: 26810 At special positions: 0 Unit cell: (155.938, 154.288, 216.168, 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 114 16.00 O 5321 8.00 N 4338 7.00 C 17037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.02 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=2.06 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=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " 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=2.05 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=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.06 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=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.00 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.05 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.06 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.01 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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 T 2 " - " MAN T 3 " " NAG U 2 " - " MAN U 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 A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 149 " " NAG A1404 " - " ASN A 165 " " NAG A1405 " - " ASN A 234 " " NAG A1406 " - " ASN A 282 " " NAG A1407 " - " ASN A 343 " " NAG A1408 " - " ASN A 603 " " NAG A1409 " - " ASN A 657 " " NAG A1410 " - " ASN A 709 " " NAG A1411 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 234 " " NAG B1404 " - " ASN B 331 " " NAG B1405 " - " ASN B 343 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B 709 " " NAG B1409 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 343 " " NAG C1406 " - " ASN C 657 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 331 " " 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: 12.29 Conformation dependent library (CDL) restraints added in 5.1 seconds 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6102 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 48 sheets defined 26.3% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 368 removed outlier: 4.646A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.516A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.638A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.931A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.119A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.614A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 856 No H-bonds generated for 'chain 'A' and resid 854 through 856' Processing helix chain 'A' and resid 866 through 882 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.775A 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 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.570A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (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: 3.794A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 954 " --> pdb=" O ASP A 950 " (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 989 through 1033 removed outlier: 3.999A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1161 removed outlier: 3.853A pdb=" N LYS A1149 " --> pdb=" O LEU A1145 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU A1152 " --> pdb=" O PHE A1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.092A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.878A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 5.447A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 618 through 623 removed outlier: 4.013A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.672A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.808A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 3.570A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 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: 3.633A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.568A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.258A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 978 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.003A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 3.510A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B1151 " --> pdb=" O SER B1147 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.675A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.046A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.531A pdb=" N ILE C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 406 through 411' Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.665A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 639 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.614A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.620A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.516A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.585A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.731A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.582A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.758A 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: 3.555A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.167A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1159 removed outlier: 4.134A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.789A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 11.218A pdb=" N SER A 221 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ARG A 34 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LEU A 223 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.148A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.562A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.618A 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: 13.353A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 13.045A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.614A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.276A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.109A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.813A 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 319 removed outlier: 4.780A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.525A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.769A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.769A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.451A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.424A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.256A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.256A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.503A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 removed outlier: 9.249A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.244A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.077A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.212A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.953A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.811A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.220A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.334A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.551A pdb=" N GLN B1071 " --> pdb=" O ILE B 716 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.243A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.765A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.621A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.352A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.627A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 142 through 144 removed outlier: 6.300A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.090A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.308A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.181A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.371A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.514A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.514A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.447A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.416A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1063 hydrogen bonds defined for protein. 2898 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: 11.79 Time building geometry restraints manager: 13.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4356 1.30 - 1.43: 7337 1.43 - 1.56: 15563 1.56 - 1.70: 4 1.70 - 1.83: 144 Bond restraints: 27404 Sorted by residual: bond pdb=" C ARG B1014 " pdb=" O ARG B1014 " ideal model delta sigma weight residual 1.237 1.172 0.064 1.19e-02 7.06e+03 2.91e+01 bond pdb=" N ARG C1000 " pdb=" CA ARG C1000 " ideal model delta sigma weight residual 1.459 1.401 0.059 1.20e-02 6.94e+03 2.39e+01 bond pdb=" CA ARG A1014 " pdb=" CB ARG A1014 " ideal model delta sigma weight residual 1.529 1.451 0.077 1.62e-02 3.81e+03 2.28e+01 bond pdb=" N ARG A 509 " pdb=" CA ARG A 509 " ideal model delta sigma weight residual 1.457 1.515 -0.058 1.23e-02 6.61e+03 2.20e+01 bond pdb=" CA ARG C 466 " pdb=" C ARG C 466 " ideal model delta sigma weight residual 1.520 1.575 -0.055 1.20e-02 6.94e+03 2.09e+01 ... (remaining 27399 not shown) Histogram of bond angle deviations from ideal: 96.49 - 104.42: 363 104.42 - 112.34: 11948 112.34 - 120.27: 14252 120.27 - 128.19: 10611 128.19 - 136.11: 104 Bond angle restraints: 37278 Sorted by residual: angle pdb=" OD1 ASN C 61 " pdb=" CG ASN C 61 " pdb=" ND2 ASN C 61 " ideal model delta sigma weight residual 122.60 114.14 8.46 1.00e+00 1.00e+00 7.15e+01 angle pdb=" OD1 ASN B 331 " pdb=" CG ASN B 331 " pdb=" ND2 ASN B 331 " ideal model delta sigma weight residual 122.60 114.92 7.68 1.00e+00 1.00e+00 5.90e+01 angle pdb=" CB ASN C 61 " pdb=" CG ASN C 61 " pdb=" ND2 ASN C 61 " ideal model delta sigma weight residual 116.40 127.55 -11.15 1.50e+00 4.44e-01 5.53e+01 angle pdb=" CB ASN B 331 " pdb=" CG ASN B 331 " pdb=" ND2 ASN B 331 " ideal model delta sigma weight residual 116.40 127.25 -10.85 1.50e+00 4.44e-01 5.24e+01 angle pdb=" CA ASP A 570 " pdb=" CB ASP A 570 " pdb=" CG ASP A 570 " ideal model delta sigma weight residual 112.60 119.67 -7.07 1.00e+00 1.00e+00 5.00e+01 ... (remaining 37273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.75: 16685 25.75 - 51.50: 662 51.50 - 77.25: 131 77.25 - 103.00: 43 103.00 - 128.75: 16 Dihedral angle restraints: 17537 sinusoidal: 8052 harmonic: 9485 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -155.73 69.73 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 156.66 -63.66 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CA GLY B 526 " pdb=" C GLY B 526 " pdb=" N PRO B 527 " pdb=" CA PRO B 527 " ideal model delta harmonic sigma weight residual -180.00 -150.25 -29.75 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 17534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.684: 4477 0.684 - 1.369: 6 1.369 - 2.053: 1 2.053 - 2.738: 3 2.738 - 3.422: 1 Chirality restraints: 4488 Sorted by residual: chirality pdb=" C1 NAG A1402 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A1402 " pdb=" O5 NAG A1402 " both_signs ideal model delta sigma weight residual False -2.40 1.02 -3.42 2.00e-01 2.50e+01 2.93e+02 chirality pdb=" C1 NAG B1405 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1405 " pdb=" O5 NAG B1405 " both_signs ideal model delta sigma weight residual False -2.40 0.32 -2.72 2.00e-01 2.50e+01 1.85e+02 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 0.20 -2.60 2.00e-01 2.50e+01 1.69e+02 ... (remaining 4485 not shown) Planarity restraints: 4745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.343 2.00e-02 2.50e+03 3.70e-01 1.71e+03 pdb=" CG ASN A 343 " 0.119 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.614 2.00e-02 2.50e+03 pdb=" C1 NAG A1407 " -0.420 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " -0.279 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" CG ASN B 343 " 0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " 0.052 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " 0.479 2.00e-02 2.50e+03 pdb=" C1 NAG B1405 " -0.354 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 17 " -0.243 2.00e-02 2.50e+03 2.41e-01 7.29e+02 pdb=" CG ASN B 17 " 0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN B 17 " 0.062 2.00e-02 2.50e+03 pdb=" ND2 ASN B 17 " 0.381 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " -0.277 2.00e-02 2.50e+03 ... (remaining 4742 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.17: 18 2.17 - 2.85: 7546 2.85 - 3.53: 37581 3.53 - 4.22: 63806 4.22 - 4.90: 105353 Nonbonded interactions: 214304 Sorted by model distance: nonbonded pdb=" NH2 ARG B 905 " pdb=" O LEU B1049 " model vdw 1.484 2.520 nonbonded pdb=" O MET B 900 " pdb=" CD2 TYR B 904 " model vdw 1.609 3.340 nonbonded pdb=" O HIS C 66 " pdb=" NH1 ARG C 78 " model vdw 1.711 2.520 nonbonded pdb=" OE1 GLU B 132 " pdb=" ND2 ASN B 165 " model vdw 1.725 2.520 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 1.823 2.520 ... (remaining 214299 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 826 or resid 855 through 1162 or resid 1401 thr \ ough 1408)) selection = (chain 'B' and (resid 14 through 623 or resid 641 through 826 or resid 855 throu \ gh 1162 or resid 1401 through 1408)) selection = (chain 'C' and (resid 14 through 623 or resid 641 through 826 or resid 855 throu \ gh 1162 or resid 1401 through 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } 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 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.570 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: 23.020 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 75.030 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.370 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 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 : 0.014 0.089 27404 Z= 0.916 Angle : 1.895 13.022 37278 Z= 1.244 Chirality : 0.142 3.422 4488 Planarity : 0.014 0.120 4690 Dihedral : 15.454 128.749 11309 Min Nonbonded Distance : 1.484 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.13 % Favored : 91.25 % Rotamer: Outliers : 1.97 % Allowed : 6.22 % Favored : 91.82 % Cbeta Deviations : 0.43 % 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: -2.39 (0.13), residues: 3223 helix: -2.19 (0.16), residues: 704 sheet: -0.17 (0.21), residues: 546 loop : -1.83 (0.13), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.197 0.039 TRP C 258 HIS 0.016 0.004 HIS B1083 PHE 0.117 0.016 PHE A1121 TYR 0.107 0.020 TYR A 674 ARG 0.022 0.001 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 797 time to evaluate : 2.964 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: A 40 ASP cc_start: 0.6386 (p0) cc_final: 0.6138 (p0) REVERT: A 64 TRP cc_start: 0.6383 (t60) cc_final: 0.5990 (t60) REVERT: A 81 ASN cc_start: 0.7920 (p0) cc_final: 0.7694 (p0) REVERT: A 144 TYR cc_start: 0.7887 (m-80) cc_final: 0.7568 (m-80) REVERT: A 304 LYS cc_start: 0.7982 (tptt) cc_final: 0.7718 (tptt) REVERT: A 364 ASP cc_start: 0.6241 (t0) cc_final: 0.6000 (t70) REVERT: A 551 VAL cc_start: 0.7927 (t) cc_final: 0.7691 (p) REVERT: A 571 ASP cc_start: 0.7124 (m-30) cc_final: 0.6550 (m-30) REVERT: A 740 MET cc_start: 0.7666 (mtm) cc_final: 0.7332 (mtm) REVERT: A 755 GLN cc_start: 0.7277 (tp-100) cc_final: 0.7039 (tp-100) REVERT: A 777 ASN cc_start: 0.7834 (m-40) cc_final: 0.7578 (m-40) REVERT: A 779 GLN cc_start: 0.7765 (tt0) cc_final: 0.7516 (tt0) REVERT: A 788 ILE cc_start: 0.7874 (mm) cc_final: 0.7664 (mp) REVERT: A 806 LEU cc_start: 0.8648 (mm) cc_final: 0.8374 (mm) REVERT: A 825 LYS cc_start: 0.7469 (mttm) cc_final: 0.7048 (tttp) REVERT: A 870 ILE cc_start: 0.8341 (mt) cc_final: 0.7992 (mp) REVERT: A 935 GLN cc_start: 0.7054 (mt0) cc_final: 0.6780 (mt0) REVERT: A 936 ASP cc_start: 0.7865 (t0) cc_final: 0.7625 (t70) REVERT: A 957 GLN cc_start: 0.7073 (tp40) cc_final: 0.6798 (tp40) REVERT: A 1005 GLN cc_start: 0.7542 (mm-40) cc_final: 0.7247 (mm-40) REVERT: A 1148 PHE cc_start: 0.6268 (m-80) cc_final: 0.5954 (m-10) REVERT: B 48 LEU cc_start: 0.8138 (mp) cc_final: 0.7758 (mt) REVERT: B 53 ASP cc_start: 0.7327 (m-30) cc_final: 0.6826 (m-30) REVERT: B 129 LYS cc_start: 0.7795 (mmtm) cc_final: 0.7546 (mmtt) REVERT: B 141 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6252 (tp) REVERT: B 152 TRP cc_start: 0.3053 (m100) cc_final: 0.1912 (m100) REVERT: B 157 PHE cc_start: 0.5838 (t80) cc_final: 0.5065 (t80) REVERT: B 226 LEU cc_start: 0.7633 (mp) cc_final: 0.7368 (mp) REVERT: B 227 VAL cc_start: 0.7851 (p) cc_final: 0.7536 (t) REVERT: B 238 PHE cc_start: 0.6764 (p90) cc_final: 0.5699 (p90) REVERT: B 286 THR cc_start: 0.7599 (m) cc_final: 0.7364 (p) REVERT: B 293 LEU cc_start: 0.7897 (tt) cc_final: 0.7681 (tt) REVERT: B 304 LYS cc_start: 0.7727 (mtmm) cc_final: 0.7294 (tmmt) REVERT: B 310 LYS cc_start: 0.8791 (tttt) cc_final: 0.8403 (tmtt) REVERT: B 313 TYR cc_start: 0.7822 (m-80) cc_final: 0.7604 (m-80) REVERT: B 402 ILE cc_start: 0.7584 (tp) cc_final: 0.7333 (mm) REVERT: B 421 TYR cc_start: 0.3912 (p90) cc_final: 0.3387 (p90) REVERT: B 468 ILE cc_start: 0.7122 (pt) cc_final: 0.6894 (tp) REVERT: B 540 ASN cc_start: 0.7504 (t0) cc_final: 0.7302 (t0) REVERT: B 581 THR cc_start: 0.7079 (p) cc_final: 0.6738 (p) REVERT: B 611 LEU cc_start: 0.8620 (tp) cc_final: 0.8319 (tp) REVERT: B 613 GLN cc_start: 0.7547 (mt0) cc_final: 0.7157 (mt0) REVERT: B 644 GLN cc_start: 0.6620 (tp40) cc_final: 0.6413 (tp40) REVERT: B 659 SER cc_start: 0.7594 (m) cc_final: 0.7392 (t) REVERT: B 664 ILE cc_start: 0.8135 (mm) cc_final: 0.7587 (mm) REVERT: B 693 ILE cc_start: 0.8213 (pt) cc_final: 0.8004 (pt) REVERT: B 720 ILE cc_start: 0.8560 (mm) cc_final: 0.8139 (mm) REVERT: B 776 LYS cc_start: 0.8406 (tmtt) cc_final: 0.8129 (tttt) REVERT: B 806 LEU cc_start: 0.8811 (mt) cc_final: 0.8443 (mt) REVERT: B 877 LEU cc_start: 0.8438 (mt) cc_final: 0.8197 (mt) REVERT: B 895 GLN cc_start: 0.7615 (pm20) cc_final: 0.7224 (pm20) REVERT: B 907 ASN cc_start: 0.8152 (m-40) cc_final: 0.7338 (m110) REVERT: B 918 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7474 (tp30) REVERT: B 950 ASP cc_start: 0.7425 (m-30) cc_final: 0.7154 (m-30) REVERT: B 953 ASN cc_start: 0.7760 (m-40) cc_final: 0.7547 (m-40) REVERT: B 957 GLN cc_start: 0.7967 (tt0) cc_final: 0.7752 (tt0) REVERT: B 1037 SER cc_start: 0.8400 (t) cc_final: 0.8061 (p) REVERT: B 1096 VAL cc_start: 0.8336 (m) cc_final: 0.7914 (p) REVERT: B 1135 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.7825 (m-40) REVERT: C 36 VAL cc_start: 0.7942 (t) cc_final: 0.7717 (m) REVERT: C 170 TYR cc_start: 0.6534 (m-80) cc_final: 0.6256 (m-80) REVERT: C 190 ARG cc_start: 0.7020 (mmt180) cc_final: 0.6682 (mmm-85) REVERT: C 271 GLN cc_start: 0.7954 (mp10) cc_final: 0.7644 (mp10) REVERT: C 278 LYS cc_start: 0.7963 (ttpt) cc_final: 0.7736 (ttpt) REVERT: C 290 ASP cc_start: 0.6874 (t0) cc_final: 0.6596 (t0) REVERT: C 298 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8044 (mm-30) REVERT: C 313 TYR cc_start: 0.7445 (m-80) cc_final: 0.7231 (m-10) REVERT: C 353 TRP cc_start: 0.3185 (p-90) cc_final: 0.2686 (p-90) REVERT: C 355 ARG cc_start: 0.6715 (mtp85) cc_final: 0.6263 (mtp85) REVERT: C 388 ASN cc_start: 0.7289 (p0) cc_final: 0.6921 (p0) REVERT: C 392 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6986 (m-80) REVERT: C 402 ILE cc_start: 0.7444 (pt) cc_final: 0.7206 (pt) REVERT: C 403 ARG cc_start: 0.5330 (OUTLIER) cc_final: 0.4506 (ttp-170) REVERT: C 429 PHE cc_start: 0.7476 (t80) cc_final: 0.7146 (t80) REVERT: C 466 ARG cc_start: 0.4125 (OUTLIER) cc_final: 0.3275 (ttp80) REVERT: C 568 ASP cc_start: 0.6036 (t0) cc_final: 0.5230 (t0) REVERT: C 585 LEU cc_start: 0.7172 (mm) cc_final: 0.6923 (mp) REVERT: C 673 SER cc_start: 0.7018 (t) cc_final: 0.6159 (m) REVERT: C 699 LEU cc_start: 0.7517 (mp) cc_final: 0.7302 (mp) REVERT: C 779 GLN cc_start: 0.8041 (pp30) cc_final: 0.7470 (pp30) REVERT: C 864 LEU cc_start: 0.8005 (tp) cc_final: 0.7773 (tt) REVERT: C 873 TYR cc_start: 0.7850 (m-80) cc_final: 0.7293 (m-80) REVERT: C 877 LEU cc_start: 0.8521 (mt) cc_final: 0.8243 (mt) REVERT: C 915 VAL cc_start: 0.8348 (t) cc_final: 0.8100 (t) REVERT: C 919 ASN cc_start: 0.8100 (m-40) cc_final: 0.7701 (m110) REVERT: C 1008 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.8055 (p) REVERT: C 1067 TYR cc_start: 0.8063 (t80) cc_final: 0.7547 (t80) REVERT: C 1145 LEU cc_start: 0.7857 (tp) cc_final: 0.7482 (tp) outliers start: 56 outliers final: 19 residues processed: 834 average time/residue: 0.4011 time to fit residues: 512.6014 Evaluate side-chains 659 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 634 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 1008 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 0.9990 chunk 245 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 253 optimal weight: 0.2980 chunk 98 optimal weight: 0.5980 chunk 154 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 294 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 99 ASN A 580 GLN A 655 HIS A 751 ASN A 901 GLN A 926 GLN A 954 GLN A 965 GLN B 317 ASN B 409 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 762 GLN B 907 ASN B 925 ASN B 954 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN C 52 GLN C 360 ASN C 487 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 954 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27404 Z= 0.235 Angle : 0.816 13.184 37278 Z= 0.415 Chirality : 0.052 0.665 4488 Planarity : 0.005 0.064 4690 Dihedral : 11.697 109.552 5509 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 3.58 % Allowed : 11.38 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3223 helix: -0.32 (0.19), residues: 721 sheet: -0.19 (0.20), residues: 617 loop : -1.36 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 64 HIS 0.012 0.002 HIS A 146 PHE 0.034 0.002 PHE C 157 TYR 0.027 0.002 TYR B 451 ARG 0.005 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 640 time to evaluate : 3.038 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: A 64 TRP cc_start: 0.6658 (t60) cc_final: 0.6349 (t60) REVERT: A 121 ASN cc_start: 0.5816 (t0) cc_final: 0.5458 (t0) REVERT: A 146 HIS cc_start: 0.5000 (p-80) cc_final: 0.3735 (m-70) REVERT: A 388 ASN cc_start: 0.4998 (m-40) cc_final: 0.4294 (t0) REVERT: A 396 TYR cc_start: 0.5741 (m-80) cc_final: 0.4781 (m-80) REVERT: A 551 VAL cc_start: 0.8108 (t) cc_final: 0.7792 (p) REVERT: A 565 PHE cc_start: 0.6880 (m-80) cc_final: 0.6642 (m-10) REVERT: A 660 TYR cc_start: 0.7667 (m-80) cc_final: 0.7305 (m-80) REVERT: A 779 GLN cc_start: 0.7777 (tt0) cc_final: 0.7509 (tt0) REVERT: A 806 LEU cc_start: 0.8628 (mm) cc_final: 0.8367 (mm) REVERT: A 1146 ASP cc_start: 0.8094 (m-30) cc_final: 0.7170 (m-30) REVERT: B 43 PHE cc_start: 0.7440 (t80) cc_final: 0.7099 (t80) REVERT: B 66 HIS cc_start: 0.5770 (m90) cc_final: 0.5531 (m90) REVERT: B 152 TRP cc_start: 0.2636 (m100) cc_final: 0.2121 (m100) REVERT: B 157 PHE cc_start: 0.5693 (t80) cc_final: 0.5288 (t80) REVERT: B 227 VAL cc_start: 0.7749 (p) cc_final: 0.7275 (t) REVERT: B 238 PHE cc_start: 0.6957 (p90) cc_final: 0.5937 (p90) REVERT: B 271 GLN cc_start: 0.7856 (mt0) cc_final: 0.7079 (mm110) REVERT: B 286 THR cc_start: 0.7799 (m) cc_final: 0.7471 (p) REVERT: B 293 LEU cc_start: 0.7534 (tt) cc_final: 0.7238 (tt) REVERT: B 409 GLN cc_start: 0.6119 (OUTLIER) cc_final: 0.5873 (tt0) REVERT: B 439 ASN cc_start: 0.6898 (t0) cc_final: 0.6318 (p0) REVERT: B 462 LYS cc_start: 0.6957 (tptt) cc_final: 0.6529 (tttp) REVERT: B 468 ILE cc_start: 0.7140 (pt) cc_final: 0.6898 (tp) REVERT: B 480 CYS cc_start: 0.4560 (OUTLIER) cc_final: 0.3546 (t) REVERT: B 495 TYR cc_start: 0.6225 (m-80) cc_final: 0.6019 (m-10) REVERT: B 540 ASN cc_start: 0.7413 (t0) cc_final: 0.7139 (t0) REVERT: B 565 PHE cc_start: 0.6634 (m-80) cc_final: 0.6181 (m-80) REVERT: B 567 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.5458 (mmm160) REVERT: B 611 LEU cc_start: 0.8679 (tp) cc_final: 0.8438 (tp) REVERT: B 693 ILE cc_start: 0.8135 (pt) cc_final: 0.7927 (pt) REVERT: B 748 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7363 (pm20) REVERT: B 773 GLU cc_start: 0.7459 (tp30) cc_final: 0.7220 (tp30) REVERT: B 788 ILE cc_start: 0.7682 (mm) cc_final: 0.7464 (mm) REVERT: B 806 LEU cc_start: 0.8747 (mt) cc_final: 0.8543 (mt) REVERT: B 918 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7437 (tp30) REVERT: B 950 ASP cc_start: 0.7447 (m-30) cc_final: 0.7127 (m-30) REVERT: B 957 GLN cc_start: 0.8051 (tt0) cc_final: 0.7841 (tt0) REVERT: B 1037 SER cc_start: 0.8399 (t) cc_final: 0.8089 (p) REVERT: B 1041 ASP cc_start: 0.7481 (t0) cc_final: 0.7268 (t0) REVERT: C 63 THR cc_start: 0.7383 (p) cc_final: 0.7057 (p) REVERT: C 170 TYR cc_start: 0.6468 (m-80) cc_final: 0.6251 (m-80) REVERT: C 190 ARG cc_start: 0.7113 (mmt180) cc_final: 0.6696 (mmm-85) REVERT: C 204 TYR cc_start: 0.7004 (m-80) cc_final: 0.6580 (m-80) REVERT: C 237 ARG cc_start: 0.6500 (ptt180) cc_final: 0.6142 (ptt-90) REVERT: C 274 THR cc_start: 0.7645 (m) cc_final: 0.7248 (t) REVERT: C 278 LYS cc_start: 0.7954 (ttpt) cc_final: 0.7721 (ttpt) REVERT: C 290 ASP cc_start: 0.6677 (t0) cc_final: 0.6360 (t0) REVERT: C 298 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7937 (mm-30) REVERT: C 324 GLU cc_start: 0.6259 (pm20) cc_final: 0.5953 (pm20) REVERT: C 355 ARG cc_start: 0.7049 (mtp85) cc_final: 0.6731 (mtp85) REVERT: C 466 ARG cc_start: 0.4067 (OUTLIER) cc_final: 0.3656 (ttp80) REVERT: C 489 TYR cc_start: 0.7072 (m-80) cc_final: 0.6868 (m-80) REVERT: C 510 VAL cc_start: 0.7349 (t) cc_final: 0.7086 (t) REVERT: C 541 PHE cc_start: 0.7835 (p90) cc_final: 0.7576 (p90) REVERT: C 570 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.7031 (m-30) REVERT: C 576 VAL cc_start: 0.8088 (p) cc_final: 0.7874 (t) REVERT: C 588 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7938 (p) REVERT: C 673 SER cc_start: 0.7031 (t) cc_final: 0.6307 (m) REVERT: C 697 MET cc_start: 0.6370 (OUTLIER) cc_final: 0.6032 (ptm) REVERT: C 825 LYS cc_start: 0.7299 (tppt) cc_final: 0.6853 (tppt) REVERT: C 902 MET cc_start: 0.8382 (mmm) cc_final: 0.8064 (mmm) REVERT: C 919 ASN cc_start: 0.7976 (m-40) cc_final: 0.7442 (m110) REVERT: C 991 VAL cc_start: 0.8459 (t) cc_final: 0.7849 (t) REVERT: C 1058 HIS cc_start: 0.7603 (m-70) cc_final: 0.7379 (m170) outliers start: 102 outliers final: 49 residues processed: 700 average time/residue: 0.4060 time to fit residues: 445.3656 Evaluate side-chains 625 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 568 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 200 optimal weight: 0.2980 chunk 81 optimal weight: 0.7980 chunk 294 optimal weight: 0.8980 chunk 318 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 292 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 236 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 173 GLN A 493 GLN A 580 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 115 GLN B 394 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 644 GLN B 703 ASN B 762 GLN B 856 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN C 52 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 388 ASN C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C1054 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27404 Z= 0.243 Angle : 0.752 10.294 37278 Z= 0.378 Chirality : 0.049 0.580 4488 Planarity : 0.005 0.075 4690 Dihedral : 10.984 110.564 5485 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.97 % Allowed : 14.40 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.14), residues: 3223 helix: 0.10 (0.19), residues: 724 sheet: -0.38 (0.20), residues: 622 loop : -1.34 (0.13), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 436 HIS 0.010 0.002 HIS A 146 PHE 0.029 0.002 PHE C 377 TYR 0.026 0.002 TYR A 365 ARG 0.012 0.001 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 616 time to evaluate : 2.759 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 64 TRP cc_start: 0.6670 (t60) cc_final: 0.6442 (t60) REVERT: A 146 HIS cc_start: 0.4852 (p-80) cc_final: 0.3470 (m-70) REVERT: A 154 GLU cc_start: 0.5571 (pp20) cc_final: 0.4639 (mt-10) REVERT: A 304 LYS cc_start: 0.8023 (tptt) cc_final: 0.7689 (tptt) REVERT: A 388 ASN cc_start: 0.5024 (m-40) cc_final: 0.4232 (t0) REVERT: A 396 TYR cc_start: 0.5863 (m-80) cc_final: 0.4737 (m-80) REVERT: A 565 PHE cc_start: 0.6856 (m-80) cc_final: 0.6631 (m-80) REVERT: A 773 GLU cc_start: 0.7211 (tt0) cc_final: 0.6882 (tt0) REVERT: A 779 GLN cc_start: 0.7880 (tt0) cc_final: 0.7535 (tt0) REVERT: A 780 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7379 (tt0) REVERT: A 950 ASP cc_start: 0.7414 (m-30) cc_final: 0.7195 (m-30) REVERT: A 1031 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6619 (mp0) REVERT: A 1034 LEU cc_start: 0.8393 (mp) cc_final: 0.8165 (mt) REVERT: A 1145 LEU cc_start: 0.6948 (pp) cc_final: 0.6729 (mp) REVERT: B 41 LYS cc_start: 0.8325 (pttt) cc_final: 0.8096 (mttp) REVERT: B 43 PHE cc_start: 0.7287 (t80) cc_final: 0.6975 (t80) REVERT: B 94 SER cc_start: 0.6423 (p) cc_final: 0.6168 (m) REVERT: B 152 TRP cc_start: 0.2818 (m100) cc_final: 0.2180 (m100) REVERT: B 157 PHE cc_start: 0.5756 (t80) cc_final: 0.5313 (t80) REVERT: B 286 THR cc_start: 0.7777 (m) cc_final: 0.7487 (p) REVERT: B 354 ASN cc_start: 0.7491 (OUTLIER) cc_final: 0.7110 (m-40) REVERT: B 387 LEU cc_start: 0.8145 (mt) cc_final: 0.7720 (tp) REVERT: B 439 ASN cc_start: 0.6770 (t0) cc_final: 0.6414 (p0) REVERT: B 453 TYR cc_start: 0.5588 (p90) cc_final: 0.5379 (p90) REVERT: B 457 ARG cc_start: 0.4883 (tpt90) cc_final: 0.4303 (ttp80) REVERT: B 468 ILE cc_start: 0.7104 (pt) cc_final: 0.6870 (tp) REVERT: B 480 CYS cc_start: 0.4561 (OUTLIER) cc_final: 0.3558 (t) REVERT: B 540 ASN cc_start: 0.7411 (t0) cc_final: 0.7130 (t0) REVERT: B 565 PHE cc_start: 0.6519 (m-80) cc_final: 0.6089 (m-80) REVERT: B 567 ARG cc_start: 0.6570 (OUTLIER) cc_final: 0.5450 (mmm160) REVERT: B 664 ILE cc_start: 0.8098 (mm) cc_final: 0.7761 (mm) REVERT: B 693 ILE cc_start: 0.8137 (pt) cc_final: 0.7935 (pt) REVERT: B 704 SER cc_start: 0.7299 (t) cc_final: 0.7013 (m) REVERT: B 806 LEU cc_start: 0.8684 (mt) cc_final: 0.8479 (mt) REVERT: B 873 TYR cc_start: 0.7962 (m-10) cc_final: 0.7675 (m-10) REVERT: B 895 GLN cc_start: 0.7586 (pm20) cc_final: 0.7335 (pm20) REVERT: B 900 MET cc_start: 0.8207 (mmp) cc_final: 0.7942 (mmt) REVERT: B 918 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7518 (tp30) REVERT: B 950 ASP cc_start: 0.7394 (m-30) cc_final: 0.7119 (m-30) REVERT: B 969 ASN cc_start: 0.6643 (t0) cc_final: 0.6272 (t0) REVERT: B 1037 SER cc_start: 0.8407 (t) cc_final: 0.8108 (p) REVERT: B 1041 ASP cc_start: 0.7604 (t0) cc_final: 0.7382 (t0) REVERT: C 41 LYS cc_start: 0.7778 (mttp) cc_final: 0.7407 (mtmm) REVERT: C 44 ARG cc_start: 0.6095 (mtt180) cc_final: 0.5892 (mtm180) REVERT: C 170 TYR cc_start: 0.6650 (m-80) cc_final: 0.6350 (m-80) REVERT: C 204 TYR cc_start: 0.6852 (m-80) cc_final: 0.6500 (m-80) REVERT: C 237 ARG cc_start: 0.6432 (ptt180) cc_final: 0.6062 (ptt-90) REVERT: C 271 GLN cc_start: 0.7975 (mp10) cc_final: 0.7711 (mp10) REVERT: C 274 THR cc_start: 0.7711 (m) cc_final: 0.7335 (t) REVERT: C 298 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8096 (mm-30) REVERT: C 319 ARG cc_start: 0.7457 (mpt-90) cc_final: 0.7050 (mmt90) REVERT: C 324 GLU cc_start: 0.6281 (pm20) cc_final: 0.6006 (pm20) REVERT: C 355 ARG cc_start: 0.7092 (mtp85) cc_final: 0.6793 (mtp85) REVERT: C 570 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.7102 (m-30) REVERT: C 588 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.7914 (p) REVERT: C 673 SER cc_start: 0.7014 (t) cc_final: 0.6312 (m) REVERT: C 825 LYS cc_start: 0.7307 (tppt) cc_final: 0.6853 (tppt) REVERT: C 919 ASN cc_start: 0.8028 (m-40) cc_final: 0.7485 (m110) REVERT: C 1058 HIS cc_start: 0.7651 (m-70) cc_final: 0.7422 (m170) outliers start: 113 outliers final: 65 residues processed: 676 average time/residue: 0.3835 time to fit residues: 408.0983 Evaluate side-chains 635 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 563 time to evaluate : 3.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 295 optimal weight: 0.7980 chunk 313 optimal weight: 0.6980 chunk 154 optimal weight: 0.9980 chunk 280 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 613 GLN A 955 ASN A 969 ASN A1011 GLN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 755 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 388 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 27404 Z= 0.350 Angle : 0.829 11.907 37278 Z= 0.417 Chirality : 0.051 0.546 4488 Planarity : 0.006 0.129 4690 Dihedral : 11.122 113.290 5477 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.85 % Allowed : 16.86 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.14), residues: 3223 helix: -0.12 (0.19), residues: 715 sheet: -0.59 (0.19), residues: 649 loop : -1.65 (0.13), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 436 HIS 0.010 0.002 HIS A1064 PHE 0.026 0.003 PHE B 306 TYR 0.029 0.003 TYR A 365 ARG 0.015 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 596 time to evaluate : 2.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7363 (p0) cc_final: 0.6969 (p0) REVERT: A 146 HIS cc_start: 0.4801 (p-80) cc_final: 0.3571 (m-70) REVERT: A 269 TYR cc_start: 0.6757 (m-80) cc_final: 0.6355 (m-80) REVERT: A 388 ASN cc_start: 0.5131 (m-40) cc_final: 0.4292 (t0) REVERT: A 424 LYS cc_start: 0.5293 (tppt) cc_final: 0.4893 (tppt) REVERT: A 460 ASN cc_start: 0.3274 (OUTLIER) cc_final: 0.2973 (m-40) REVERT: A 565 PHE cc_start: 0.6975 (m-80) cc_final: 0.6694 (m-80) REVERT: A 773 GLU cc_start: 0.7312 (tt0) cc_final: 0.7112 (tt0) REVERT: A 779 GLN cc_start: 0.7860 (tt0) cc_final: 0.7565 (tt0) REVERT: A 780 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: A 788 ILE cc_start: 0.7746 (mm) cc_final: 0.7541 (mp) REVERT: A 904 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.5357 (m-10) REVERT: A 950 ASP cc_start: 0.7613 (m-30) cc_final: 0.7268 (m-30) REVERT: A 1031 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: A 1034 LEU cc_start: 0.8487 (mp) cc_final: 0.8274 (mt) REVERT: B 43 PHE cc_start: 0.7162 (t80) cc_final: 0.6951 (t80) REVERT: B 49 HIS cc_start: 0.7669 (OUTLIER) cc_final: 0.7052 (t-170) REVERT: B 152 TRP cc_start: 0.3176 (m100) cc_final: 0.2436 (m100) REVERT: B 157 PHE cc_start: 0.5809 (t80) cc_final: 0.5444 (t80) REVERT: B 286 THR cc_start: 0.7790 (m) cc_final: 0.7490 (p) REVERT: B 293 LEU cc_start: 0.7908 (tt) cc_final: 0.7615 (tt) REVERT: B 354 ASN cc_start: 0.7411 (OUTLIER) cc_final: 0.7064 (m-40) REVERT: B 387 LEU cc_start: 0.8133 (mt) cc_final: 0.7762 (tp) REVERT: B 439 ASN cc_start: 0.6788 (t0) cc_final: 0.6322 (p0) REVERT: B 457 ARG cc_start: 0.4973 (tpt90) cc_final: 0.4468 (ttp80) REVERT: B 480 CYS cc_start: 0.4686 (OUTLIER) cc_final: 0.3876 (t) REVERT: B 540 ASN cc_start: 0.7431 (t0) cc_final: 0.7195 (t0) REVERT: B 567 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.5459 (mmm160) REVERT: B 748 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7374 (pm20) REVERT: B 788 ILE cc_start: 0.7305 (mm) cc_final: 0.7086 (mm) REVERT: B 873 TYR cc_start: 0.8047 (m-10) cc_final: 0.7791 (m-10) REVERT: B 900 MET cc_start: 0.8150 (mmp) cc_final: 0.7888 (mmt) REVERT: B 918 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7538 (tp30) REVERT: B 950 ASP cc_start: 0.7323 (m-30) cc_final: 0.7101 (m-30) REVERT: B 969 ASN cc_start: 0.6706 (t0) cc_final: 0.6341 (t0) REVERT: B 1028 LYS cc_start: 0.7632 (mtpp) cc_final: 0.7238 (mttp) REVERT: B 1037 SER cc_start: 0.8441 (t) cc_final: 0.8192 (p) REVERT: B 1041 ASP cc_start: 0.7707 (t0) cc_final: 0.7396 (t0) REVERT: C 106 PHE cc_start: 0.6597 (m-10) cc_final: 0.6383 (m-10) REVERT: C 200 TYR cc_start: 0.6011 (m-80) cc_final: 0.5729 (m-80) REVERT: C 204 TYR cc_start: 0.6837 (m-80) cc_final: 0.6456 (m-80) REVERT: C 271 GLN cc_start: 0.7950 (mp10) cc_final: 0.7708 (mp10) REVERT: C 274 THR cc_start: 0.7658 (m) cc_final: 0.7271 (t) REVERT: C 298 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8098 (mm-30) REVERT: C 319 ARG cc_start: 0.7539 (mpt-90) cc_final: 0.7131 (mmt90) REVERT: C 324 GLU cc_start: 0.6331 (pm20) cc_final: 0.6056 (pm20) REVERT: C 392 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.6770 (m-80) REVERT: C 570 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.6892 (p0) REVERT: C 588 THR cc_start: 0.8222 (OUTLIER) cc_final: 0.7886 (p) REVERT: C 825 LYS cc_start: 0.7370 (tppt) cc_final: 0.6920 (tppt) REVERT: C 919 ASN cc_start: 0.8002 (m-40) cc_final: 0.7506 (m110) REVERT: C 1017 GLU cc_start: 0.6565 (mt-10) cc_final: 0.6321 (mt-10) REVERT: C 1058 HIS cc_start: 0.7648 (m-70) cc_final: 0.7444 (m170) outliers start: 138 outliers final: 92 residues processed: 679 average time/residue: 0.3997 time to fit residues: 427.4945 Evaluate side-chains 653 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 549 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 0.6980 chunk 177 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 233 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 267 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 281 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 580 GLN A 613 GLN B 354 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 755 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 474 GLN C 487 ASN C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27404 Z= 0.261 Angle : 0.753 11.200 37278 Z= 0.377 Chirality : 0.049 0.508 4488 Planarity : 0.005 0.068 4690 Dihedral : 10.600 110.144 5477 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.36 % Allowed : 18.86 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.14), residues: 3223 helix: 0.16 (0.19), residues: 717 sheet: -0.71 (0.19), residues: 633 loop : -1.64 (0.13), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 886 HIS 0.007 0.001 HIS A 146 PHE 0.033 0.002 PHE B 306 TYR 0.026 0.002 TYR A 365 ARG 0.005 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 596 time to evaluate : 2.894 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: A 146 HIS cc_start: 0.4493 (p-80) cc_final: 0.3305 (m-70) REVERT: A 304 LYS cc_start: 0.7996 (tptt) cc_final: 0.7703 (tptt) REVERT: A 565 PHE cc_start: 0.6938 (m-80) cc_final: 0.6699 (m-10) REVERT: A 586 ASP cc_start: 0.7854 (m-30) cc_final: 0.7288 (m-30) REVERT: A 697 MET cc_start: 0.6738 (tpt) cc_final: 0.6491 (tpp) REVERT: A 773 GLU cc_start: 0.7319 (tt0) cc_final: 0.7074 (tt0) REVERT: A 779 GLN cc_start: 0.7899 (tt0) cc_final: 0.7593 (tt0) REVERT: A 780 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7374 (tt0) REVERT: A 945 LEU cc_start: 0.7913 (mm) cc_final: 0.7709 (mm) REVERT: A 950 ASP cc_start: 0.7626 (m-30) cc_final: 0.7297 (m-30) REVERT: A 1031 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6617 (mp0) REVERT: A 1034 LEU cc_start: 0.8464 (mp) cc_final: 0.8229 (mt) REVERT: A 1115 ILE cc_start: 0.8652 (mp) cc_final: 0.8172 (tp) REVERT: B 119 ILE cc_start: 0.6744 (mp) cc_final: 0.6093 (tt) REVERT: B 152 TRP cc_start: 0.3246 (m100) cc_final: 0.2492 (m100) REVERT: B 157 PHE cc_start: 0.5780 (t80) cc_final: 0.5443 (t80) REVERT: B 293 LEU cc_start: 0.7993 (tt) cc_final: 0.7677 (tt) REVERT: B 309 GLU cc_start: 0.8060 (tp30) cc_final: 0.7800 (tp30) REVERT: B 387 LEU cc_start: 0.8129 (mt) cc_final: 0.7761 (tp) REVERT: B 439 ASN cc_start: 0.6838 (t0) cc_final: 0.6300 (p0) REVERT: B 457 ARG cc_start: 0.4916 (tpt90) cc_final: 0.4469 (ttp80) REVERT: B 462 LYS cc_start: 0.7382 (tppt) cc_final: 0.7038 (tptt) REVERT: B 540 ASN cc_start: 0.7456 (t0) cc_final: 0.7214 (t0) REVERT: B 699 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7673 (mp) REVERT: B 748 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7317 (pm20) REVERT: B 789 TYR cc_start: 0.7183 (m-80) cc_final: 0.6506 (m-80) REVERT: B 873 TYR cc_start: 0.8044 (m-10) cc_final: 0.7809 (m-10) REVERT: B 895 GLN cc_start: 0.7613 (pm20) cc_final: 0.7361 (pm20) REVERT: B 900 MET cc_start: 0.8084 (mmp) cc_final: 0.7878 (mmt) REVERT: B 901 GLN cc_start: 0.8053 (tt0) cc_final: 0.7811 (tt0) REVERT: B 918 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7550 (tp30) REVERT: B 950 ASP cc_start: 0.7268 (m-30) cc_final: 0.7017 (m-30) REVERT: B 969 ASN cc_start: 0.6781 (t0) cc_final: 0.6403 (t0) REVERT: B 1028 LYS cc_start: 0.7597 (mtpp) cc_final: 0.7245 (mttp) REVERT: B 1037 SER cc_start: 0.8415 (t) cc_final: 0.8174 (p) REVERT: B 1041 ASP cc_start: 0.7676 (t0) cc_final: 0.7458 (t0) REVERT: C 21 ARG cc_start: 0.5139 (ttt-90) cc_final: 0.4692 (mtt-85) REVERT: C 204 TYR cc_start: 0.6687 (m-80) cc_final: 0.6251 (m-80) REVERT: C 271 GLN cc_start: 0.7932 (mp10) cc_final: 0.7588 (mp10) REVERT: C 274 THR cc_start: 0.7670 (m) cc_final: 0.7281 (t) REVERT: C 290 ASP cc_start: 0.6764 (t0) cc_final: 0.6541 (t0) REVERT: C 298 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8013 (mm-30) REVERT: C 319 ARG cc_start: 0.7520 (mpt-90) cc_final: 0.7094 (mmt90) REVERT: C 324 GLU cc_start: 0.6347 (pm20) cc_final: 0.6103 (pm20) REVERT: C 331 ASN cc_start: 0.1427 (OUTLIER) cc_final: 0.0696 (p0) REVERT: C 392 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.6856 (m-80) REVERT: C 429 PHE cc_start: 0.7259 (t80) cc_final: 0.6917 (t80) REVERT: C 576 VAL cc_start: 0.8175 (OUTLIER) cc_final: 0.7968 (t) REVERT: C 588 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7875 (p) REVERT: C 825 LYS cc_start: 0.7330 (tppt) cc_final: 0.6913 (tppt) REVERT: C 919 ASN cc_start: 0.8014 (m-40) cc_final: 0.7522 (m110) REVERT: C 1058 HIS cc_start: 0.7645 (m-70) cc_final: 0.7431 (m170) outliers start: 124 outliers final: 86 residues processed: 666 average time/residue: 0.3763 time to fit residues: 396.7381 Evaluate side-chains 658 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 564 time to evaluate : 3.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 3.9990 chunk 282 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 183 optimal weight: 0.0980 chunk 77 optimal weight: 4.9990 chunk 313 optimal weight: 0.9990 chunk 260 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 164 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 394 ASN B 422 ASN B 703 ASN B 755 GLN B 787 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C1054 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27404 Z= 0.192 Angle : 0.697 11.794 37278 Z= 0.345 Chirality : 0.047 0.461 4488 Planarity : 0.004 0.060 4690 Dihedral : 9.759 107.448 5477 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.14 % Allowed : 19.85 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.14), residues: 3223 helix: 0.62 (0.20), residues: 708 sheet: -0.72 (0.19), residues: 630 loop : -1.48 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 353 HIS 0.005 0.001 HIS B 66 PHE 0.030 0.002 PHE B 306 TYR 0.022 0.002 TYR A 365 ARG 0.007 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 604 time to evaluate : 2.800 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 121 ASN cc_start: 0.7138 (p0) cc_final: 0.6534 (t0) REVERT: A 146 HIS cc_start: 0.4506 (p-80) cc_final: 0.3327 (m-70) REVERT: A 270 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6914 (tp) REVERT: A 304 LYS cc_start: 0.7995 (tptt) cc_final: 0.7641 (tptt) REVERT: A 388 ASN cc_start: 0.5028 (m-40) cc_final: 0.3926 (t0) REVERT: A 586 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7319 (m-30) REVERT: A 697 MET cc_start: 0.6651 (tpt) cc_final: 0.6402 (tpp) REVERT: A 779 GLN cc_start: 0.7882 (tt0) cc_final: 0.7598 (tt0) REVERT: A 780 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: A 950 ASP cc_start: 0.7545 (m-30) cc_final: 0.7212 (m-30) REVERT: A 1034 LEU cc_start: 0.8456 (mp) cc_final: 0.8232 (mt) REVERT: A 1115 ILE cc_start: 0.8654 (mp) cc_final: 0.8209 (tp) REVERT: B 119 ILE cc_start: 0.6819 (mp) cc_final: 0.6201 (tt) REVERT: B 152 TRP cc_start: 0.2977 (m100) cc_final: 0.2355 (m100) REVERT: B 157 PHE cc_start: 0.5804 (t80) cc_final: 0.5476 (t80) REVERT: B 206 LYS cc_start: 0.7600 (tptt) cc_final: 0.7340 (tppt) REVERT: B 266 TYR cc_start: 0.7014 (m-80) cc_final: 0.6740 (m-80) REVERT: B 293 LEU cc_start: 0.7985 (tt) cc_final: 0.7621 (tt) REVERT: B 309 GLU cc_start: 0.7998 (tp30) cc_final: 0.7772 (tp30) REVERT: B 314 GLN cc_start: 0.8112 (tp40) cc_final: 0.7733 (tp40) REVERT: B 387 LEU cc_start: 0.8132 (mt) cc_final: 0.7766 (tp) REVERT: B 396 TYR cc_start: 0.5084 (m-10) cc_final: 0.4679 (m-10) REVERT: B 409 GLN cc_start: 0.6488 (mt0) cc_final: 0.6213 (tt0) REVERT: B 422 ASN cc_start: 0.4988 (m-40) cc_final: 0.4776 (m110) REVERT: B 439 ASN cc_start: 0.6843 (t0) cc_final: 0.6363 (p0) REVERT: B 457 ARG cc_start: 0.4873 (tpt90) cc_final: 0.4391 (ttp80) REVERT: B 540 ASN cc_start: 0.7474 (t0) cc_final: 0.7198 (t0) REVERT: B 704 SER cc_start: 0.7300 (t) cc_final: 0.6980 (m) REVERT: B 748 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7345 (pm20) REVERT: B 753 LEU cc_start: 0.8057 (tp) cc_final: 0.7844 (tp) REVERT: B 900 MET cc_start: 0.8000 (mmp) cc_final: 0.7734 (mmt) REVERT: B 918 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7508 (tp30) REVERT: B 950 ASP cc_start: 0.7311 (m-30) cc_final: 0.7039 (m-30) REVERT: B 969 ASN cc_start: 0.6822 (t0) cc_final: 0.6409 (t0) REVERT: B 990 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7216 (pt0) REVERT: B 1037 SER cc_start: 0.8415 (t) cc_final: 0.8192 (p) REVERT: C 21 ARG cc_start: 0.5225 (ttt-90) cc_final: 0.4735 (mtt-85) REVERT: C 38 TYR cc_start: 0.7787 (m-80) cc_final: 0.7295 (m-10) REVERT: C 41 LYS cc_start: 0.7642 (mttp) cc_final: 0.7337 (mtmm) REVERT: C 204 TYR cc_start: 0.6726 (m-80) cc_final: 0.6228 (m-80) REVERT: C 271 GLN cc_start: 0.7970 (mp10) cc_final: 0.7720 (mp10) REVERT: C 274 THR cc_start: 0.7798 (m) cc_final: 0.7161 (t) REVERT: C 319 ARG cc_start: 0.7552 (mpt-90) cc_final: 0.7175 (mmt90) REVERT: C 324 GLU cc_start: 0.6320 (pm20) cc_final: 0.6063 (pm20) REVERT: C 331 ASN cc_start: 0.1714 (OUTLIER) cc_final: 0.1027 (p0) REVERT: C 429 PHE cc_start: 0.7139 (t80) cc_final: 0.6891 (t80) REVERT: C 542 ASN cc_start: 0.7460 (t0) cc_final: 0.6388 (m110) REVERT: C 576 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7954 (t) REVERT: C 654 GLU cc_start: 0.7050 (mp0) cc_final: 0.6835 (mm-30) REVERT: C 825 LYS cc_start: 0.7315 (tppt) cc_final: 0.6897 (tppt) REVERT: C 919 ASN cc_start: 0.8022 (m-40) cc_final: 0.7569 (m110) REVERT: C 954 GLN cc_start: 0.7283 (mt0) cc_final: 0.6925 (mt0) REVERT: C 970 PHE cc_start: 0.7610 (m-80) cc_final: 0.7042 (m-80) outliers start: 118 outliers final: 88 residues processed: 672 average time/residue: 0.3797 time to fit residues: 404.7377 Evaluate side-chains 659 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 565 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 3.9990 chunk 35 optimal weight: 0.0060 chunk 178 optimal weight: 0.6980 chunk 228 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 263 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 chunk 312 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 190 optimal weight: 0.4980 chunk 144 optimal weight: 2.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 755 GLN B 787 GLN B 954 GLN B 955 ASN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C1058 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27404 Z= 0.203 Angle : 0.701 11.509 37278 Z= 0.347 Chirality : 0.047 0.444 4488 Planarity : 0.004 0.062 4690 Dihedral : 9.270 107.251 5473 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.81 % Allowed : 19.56 % Favored : 75.62 % 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: -1.12 (0.14), residues: 3223 helix: 0.80 (0.20), residues: 705 sheet: -0.68 (0.20), residues: 616 loop : -1.40 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 353 HIS 0.006 0.001 HIS B1088 PHE 0.035 0.002 PHE C 157 TYR 0.022 0.002 TYR A 365 ARG 0.009 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 580 time to evaluate : 3.231 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 121 ASN cc_start: 0.7193 (p0) cc_final: 0.6463 (t0) REVERT: A 146 HIS cc_start: 0.4244 (p-80) cc_final: 0.3098 (m-70) REVERT: A 187 LYS cc_start: 0.6534 (OUTLIER) cc_final: 0.6321 (tppt) REVERT: A 269 TYR cc_start: 0.6827 (m-80) cc_final: 0.6326 (m-80) REVERT: A 270 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6911 (tp) REVERT: A 304 LYS cc_start: 0.8008 (tptt) cc_final: 0.7636 (tptt) REVERT: A 388 ASN cc_start: 0.5034 (m-40) cc_final: 0.4121 (t0) REVERT: A 560 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7573 (mp) REVERT: A 586 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7321 (m-30) REVERT: A 697 MET cc_start: 0.6640 (tpt) cc_final: 0.6367 (tpp) REVERT: A 779 GLN cc_start: 0.7896 (tt0) cc_final: 0.7628 (tt0) REVERT: A 780 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: A 950 ASP cc_start: 0.7529 (m-30) cc_final: 0.7180 (m-30) REVERT: A 1115 ILE cc_start: 0.8662 (mp) cc_final: 0.8246 (tp) REVERT: B 104 TRP cc_start: 0.6821 (m-90) cc_final: 0.6567 (m-90) REVERT: B 119 ILE cc_start: 0.6736 (mp) cc_final: 0.6080 (tt) REVERT: B 152 TRP cc_start: 0.2895 (m100) cc_final: 0.2289 (m100) REVERT: B 293 LEU cc_start: 0.8064 (tt) cc_final: 0.7759 (tt) REVERT: B 309 GLU cc_start: 0.8014 (tp30) cc_final: 0.7714 (tp30) REVERT: B 314 GLN cc_start: 0.8114 (tp40) cc_final: 0.7680 (tp40) REVERT: B 387 LEU cc_start: 0.8128 (mt) cc_final: 0.7757 (tp) REVERT: B 396 TYR cc_start: 0.5119 (m-10) cc_final: 0.4732 (m-10) REVERT: B 409 GLN cc_start: 0.6511 (mt0) cc_final: 0.6261 (tt0) REVERT: B 439 ASN cc_start: 0.6835 (t0) cc_final: 0.6299 (p0) REVERT: B 457 ARG cc_start: 0.4934 (tpt90) cc_final: 0.4433 (ttp80) REVERT: B 462 LYS cc_start: 0.7436 (tppt) cc_final: 0.6696 (tttp) REVERT: B 480 CYS cc_start: 0.4746 (OUTLIER) cc_final: 0.3856 (t) REVERT: B 540 ASN cc_start: 0.7470 (t0) cc_final: 0.7172 (t0) REVERT: B 704 SER cc_start: 0.7282 (t) cc_final: 0.6969 (m) REVERT: B 748 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7341 (pm20) REVERT: B 753 LEU cc_start: 0.8074 (tp) cc_final: 0.7827 (tp) REVERT: B 900 MET cc_start: 0.7993 (mmp) cc_final: 0.7783 (mmt) REVERT: B 918 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7438 (tp30) REVERT: B 936 ASP cc_start: 0.8047 (m-30) cc_final: 0.7657 (m-30) REVERT: B 950 ASP cc_start: 0.7251 (m-30) cc_final: 0.7004 (m-30) REVERT: B 957 GLN cc_start: 0.8019 (tt0) cc_final: 0.7781 (tt0) REVERT: B 969 ASN cc_start: 0.6820 (t0) cc_final: 0.6404 (t0) REVERT: B 990 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7268 (mm-30) REVERT: C 18 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.5491 (mt) REVERT: C 21 ARG cc_start: 0.5154 (ttt-90) cc_final: 0.4748 (mtt-85) REVERT: C 38 TYR cc_start: 0.7776 (m-80) cc_final: 0.7346 (m-10) REVERT: C 41 LYS cc_start: 0.7626 (mttp) cc_final: 0.7291 (mtmm) REVERT: C 204 TYR cc_start: 0.6699 (m-80) cc_final: 0.6198 (m-80) REVERT: C 271 GLN cc_start: 0.7949 (mp10) cc_final: 0.7576 (mp10) REVERT: C 319 ARG cc_start: 0.7534 (mpt-90) cc_final: 0.7144 (mmt90) REVERT: C 324 GLU cc_start: 0.6337 (pm20) cc_final: 0.6070 (pm20) REVERT: C 392 PHE cc_start: 0.7290 (OUTLIER) cc_final: 0.6885 (m-80) REVERT: C 429 PHE cc_start: 0.7201 (t80) cc_final: 0.6895 (t80) REVERT: C 542 ASN cc_start: 0.7579 (t0) cc_final: 0.6481 (m110) REVERT: C 576 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7943 (t) REVERT: C 617 CYS cc_start: 0.6091 (OUTLIER) cc_final: 0.5782 (m) REVERT: C 654 GLU cc_start: 0.7081 (mp0) cc_final: 0.6837 (mm-30) REVERT: C 825 LYS cc_start: 0.7295 (tppt) cc_final: 0.6895 (tppt) REVERT: C 919 ASN cc_start: 0.8045 (m-40) cc_final: 0.7561 (m110) REVERT: C 954 GLN cc_start: 0.7297 (mt0) cc_final: 0.6966 (mt0) REVERT: C 970 PHE cc_start: 0.7590 (m-80) cc_final: 0.7058 (m-80) outliers start: 137 outliers final: 99 residues processed: 664 average time/residue: 0.3770 time to fit residues: 397.1325 Evaluate side-chains 665 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 555 time to evaluate : 3.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 186 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 chunk 212 optimal weight: 0.0050 chunk 154 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 245 optimal weight: 0.6980 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN B 703 ASN B 755 GLN B 954 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27404 Z= 0.208 Angle : 0.706 11.642 37278 Z= 0.348 Chirality : 0.047 0.435 4488 Planarity : 0.005 0.100 4690 Dihedral : 8.970 106.927 5471 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.60 % Allowed : 19.99 % Favored : 75.41 % 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: -1.09 (0.14), residues: 3223 helix: 0.82 (0.20), residues: 705 sheet: -0.74 (0.20), residues: 631 loop : -1.35 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 353 HIS 0.026 0.002 HIS C1058 PHE 0.044 0.002 PHE B 92 TYR 0.021 0.002 TYR A 365 ARG 0.019 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 572 time to evaluate : 3.018 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 121 ASN cc_start: 0.7175 (p0) cc_final: 0.6421 (t0) REVERT: A 133 PHE cc_start: 0.6205 (m-80) cc_final: 0.5967 (m-80) REVERT: A 146 HIS cc_start: 0.4126 (p-80) cc_final: 0.2942 (m-70) REVERT: A 270 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6914 (tp) REVERT: A 304 LYS cc_start: 0.8018 (tptt) cc_final: 0.7639 (tptt) REVERT: A 314 GLN cc_start: 0.6533 (OUTLIER) cc_final: 0.6298 (tp40) REVERT: A 388 ASN cc_start: 0.5025 (m-40) cc_final: 0.4103 (t0) REVERT: A 559 PHE cc_start: 0.7279 (m-10) cc_final: 0.7076 (m-10) REVERT: A 560 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7609 (mp) REVERT: A 567 ARG cc_start: 0.7391 (mtm-85) cc_final: 0.6926 (mtt90) REVERT: A 586 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7308 (m-30) REVERT: A 613 GLN cc_start: 0.7627 (mt0) cc_final: 0.7086 (mt0) REVERT: A 697 MET cc_start: 0.6638 (tpt) cc_final: 0.6374 (tpp) REVERT: A 780 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: A 950 ASP cc_start: 0.7525 (m-30) cc_final: 0.7163 (m-30) REVERT: A 1002 GLN cc_start: 0.7432 (mt0) cc_final: 0.7175 (mt0) REVERT: A 1050 MET cc_start: 0.6634 (OUTLIER) cc_final: 0.6381 (pmm) REVERT: A 1071 GLN cc_start: 0.7411 (mp10) cc_final: 0.7192 (mp10) REVERT: A 1115 ILE cc_start: 0.8673 (mp) cc_final: 0.8275 (tp) REVERT: B 66 HIS cc_start: 0.5959 (OUTLIER) cc_final: 0.5122 (m90) REVERT: B 104 TRP cc_start: 0.6900 (m-90) cc_final: 0.6624 (m-90) REVERT: B 119 ILE cc_start: 0.6723 (mp) cc_final: 0.6077 (tt) REVERT: B 152 TRP cc_start: 0.2896 (m100) cc_final: 0.2285 (m100) REVERT: B 293 LEU cc_start: 0.8108 (tt) cc_final: 0.7820 (tt) REVERT: B 309 GLU cc_start: 0.7996 (tp30) cc_final: 0.7714 (tp30) REVERT: B 314 GLN cc_start: 0.8125 (tp40) cc_final: 0.7739 (tp40) REVERT: B 387 LEU cc_start: 0.8144 (mt) cc_final: 0.7758 (tp) REVERT: B 396 TYR cc_start: 0.5131 (m-10) cc_final: 0.4737 (m-10) REVERT: B 409 GLN cc_start: 0.6496 (mt0) cc_final: 0.6250 (tt0) REVERT: B 439 ASN cc_start: 0.6835 (t0) cc_final: 0.6294 (p0) REVERT: B 457 ARG cc_start: 0.4935 (tpt90) cc_final: 0.4430 (ttp80) REVERT: B 480 CYS cc_start: 0.4779 (OUTLIER) cc_final: 0.3907 (t) REVERT: B 540 ASN cc_start: 0.7456 (t0) cc_final: 0.7161 (t0) REVERT: B 704 SER cc_start: 0.7286 (t) cc_final: 0.6981 (m) REVERT: B 748 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7357 (pm20) REVERT: B 753 LEU cc_start: 0.8101 (tp) cc_final: 0.7863 (tp) REVERT: B 900 MET cc_start: 0.7993 (mmp) cc_final: 0.7745 (mmt) REVERT: B 916 LEU cc_start: 0.8470 (tt) cc_final: 0.8230 (tp) REVERT: B 918 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7452 (tp30) REVERT: B 957 GLN cc_start: 0.8026 (tt0) cc_final: 0.7764 (tt0) REVERT: B 969 ASN cc_start: 0.6802 (t0) cc_final: 0.6407 (t0) REVERT: B 990 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7060 (mt-10) REVERT: B 1041 ASP cc_start: 0.7712 (t0) cc_final: 0.7495 (t0) REVERT: C 18 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.5355 (mt) REVERT: C 21 ARG cc_start: 0.5238 (ttt-90) cc_final: 0.4748 (mtt-85) REVERT: C 38 TYR cc_start: 0.7786 (m-80) cc_final: 0.7365 (m-10) REVERT: C 41 LYS cc_start: 0.7620 (mttp) cc_final: 0.7300 (mtmm) REVERT: C 83 VAL cc_start: 0.7853 (OUTLIER) cc_final: 0.7541 (p) REVERT: C 134 GLN cc_start: 0.6515 (mm110) cc_final: 0.6303 (mm110) REVERT: C 204 TYR cc_start: 0.6648 (m-80) cc_final: 0.6171 (m-80) REVERT: C 271 GLN cc_start: 0.7951 (mp10) cc_final: 0.7582 (mp10) REVERT: C 274 THR cc_start: 0.7456 (m) cc_final: 0.7204 (t) REVERT: C 319 ARG cc_start: 0.7554 (mpt-90) cc_final: 0.7219 (mmt90) REVERT: C 324 GLU cc_start: 0.6290 (pm20) cc_final: 0.6036 (pm20) REVERT: C 331 ASN cc_start: 0.1571 (OUTLIER) cc_final: 0.0910 (p0) REVERT: C 351 TYR cc_start: 0.4917 (p90) cc_final: 0.4614 (p90) REVERT: C 392 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6874 (m-80) REVERT: C 429 PHE cc_start: 0.7291 (t80) cc_final: 0.7062 (t80) REVERT: C 542 ASN cc_start: 0.7577 (t0) cc_final: 0.6556 (m110) REVERT: C 576 VAL cc_start: 0.8243 (OUTLIER) cc_final: 0.7998 (t) REVERT: C 617 CYS cc_start: 0.6090 (OUTLIER) cc_final: 0.5790 (m) REVERT: C 654 GLU cc_start: 0.7102 (mp0) cc_final: 0.6860 (mm-30) REVERT: C 673 SER cc_start: 0.7055 (t) cc_final: 0.6319 (m) REVERT: C 825 LYS cc_start: 0.7236 (tppt) cc_final: 0.6868 (tppt) REVERT: C 919 ASN cc_start: 0.8031 (m-40) cc_final: 0.7595 (m110) REVERT: C 954 GLN cc_start: 0.7286 (mt0) cc_final: 0.6983 (mt0) outliers start: 131 outliers final: 101 residues processed: 644 average time/residue: 0.3756 time to fit residues: 384.8159 Evaluate side-chains 671 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 555 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 0.0970 chunk 299 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 291 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 228 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 262 optimal weight: 0.8980 chunk 275 optimal weight: 3.9990 chunk 289 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 755 GLN B 954 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 487 ASN C 603 ASN C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27404 Z= 0.223 Angle : 0.712 11.252 37278 Z= 0.353 Chirality : 0.047 0.428 4488 Planarity : 0.005 0.097 4690 Dihedral : 8.779 106.636 5471 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.53 % Allowed : 20.55 % Favored : 74.92 % 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: -1.11 (0.14), residues: 3223 helix: 0.75 (0.20), residues: 712 sheet: -0.75 (0.20), residues: 637 loop : -1.35 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 353 HIS 0.005 0.001 HIS B1088 PHE 0.054 0.002 PHE B 92 TYR 0.021 0.002 TYR A 365 ARG 0.010 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 567 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7162 (p0) cc_final: 0.6395 (t0) REVERT: A 133 PHE cc_start: 0.6200 (m-80) cc_final: 0.5982 (m-80) REVERT: A 146 HIS cc_start: 0.4160 (p-80) cc_final: 0.2893 (m90) REVERT: A 270 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6919 (tp) REVERT: A 304 LYS cc_start: 0.8024 (tptt) cc_final: 0.7630 (tptt) REVERT: A 314 GLN cc_start: 0.6586 (OUTLIER) cc_final: 0.6328 (tp40) REVERT: A 560 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7680 (mp) REVERT: A 586 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7329 (m-30) REVERT: A 697 MET cc_start: 0.6664 (tpt) cc_final: 0.6397 (tpp) REVERT: A 780 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: A 824 ASN cc_start: 0.6759 (m-40) cc_final: 0.6251 (m110) REVERT: A 950 ASP cc_start: 0.7540 (m-30) cc_final: 0.7131 (m-30) REVERT: A 1002 GLN cc_start: 0.7408 (mt0) cc_final: 0.7162 (mt0) REVERT: A 1031 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6600 (mp0) REVERT: A 1115 ILE cc_start: 0.8679 (mp) cc_final: 0.8282 (tp) REVERT: B 66 HIS cc_start: 0.5890 (OUTLIER) cc_final: 0.5047 (m90) REVERT: B 119 ILE cc_start: 0.6754 (mp) cc_final: 0.6089 (tt) REVERT: B 152 TRP cc_start: 0.2945 (m100) cc_final: 0.2393 (m100) REVERT: B 293 LEU cc_start: 0.8124 (tt) cc_final: 0.7815 (tt) REVERT: B 314 GLN cc_start: 0.8144 (tp40) cc_final: 0.7763 (tp40) REVERT: B 387 LEU cc_start: 0.8106 (mt) cc_final: 0.7727 (tp) REVERT: B 396 TYR cc_start: 0.5193 (m-10) cc_final: 0.4829 (m-10) REVERT: B 409 GLN cc_start: 0.6512 (mt0) cc_final: 0.6268 (tt0) REVERT: B 439 ASN cc_start: 0.6858 (t0) cc_final: 0.6303 (p0) REVERT: B 457 ARG cc_start: 0.4965 (tpt90) cc_final: 0.4456 (ttp80) REVERT: B 480 CYS cc_start: 0.4787 (OUTLIER) cc_final: 0.3946 (t) REVERT: B 540 ASN cc_start: 0.7439 (t0) cc_final: 0.7130 (t0) REVERT: B 704 SER cc_start: 0.7301 (t) cc_final: 0.6995 (m) REVERT: B 748 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7345 (pm20) REVERT: B 753 LEU cc_start: 0.8111 (tp) cc_final: 0.7883 (tp) REVERT: B 900 MET cc_start: 0.7996 (mmp) cc_final: 0.7753 (mmt) REVERT: B 916 LEU cc_start: 0.8500 (tt) cc_final: 0.8235 (tp) REVERT: B 918 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7417 (tp30) REVERT: B 936 ASP cc_start: 0.7890 (m-30) cc_final: 0.7503 (m-30) REVERT: B 957 GLN cc_start: 0.8019 (tt0) cc_final: 0.7750 (tt0) REVERT: B 969 ASN cc_start: 0.6777 (t0) cc_final: 0.6382 (t0) REVERT: B 990 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7258 (mm-30) REVERT: B 1041 ASP cc_start: 0.7739 (t0) cc_final: 0.7519 (t0) REVERT: C 18 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.5418 (mt) REVERT: C 21 ARG cc_start: 0.5322 (ttt-90) cc_final: 0.4812 (mtt-85) REVERT: C 38 TYR cc_start: 0.7754 (m-80) cc_final: 0.7359 (m-10) REVERT: C 41 LYS cc_start: 0.7620 (mttp) cc_final: 0.7284 (mtmm) REVERT: C 83 VAL cc_start: 0.7853 (OUTLIER) cc_final: 0.7554 (p) REVERT: C 134 GLN cc_start: 0.6530 (mm110) cc_final: 0.6291 (mm110) REVERT: C 204 TYR cc_start: 0.6601 (m-80) cc_final: 0.6146 (m-80) REVERT: C 271 GLN cc_start: 0.7939 (mp10) cc_final: 0.7594 (mp10) REVERT: C 274 THR cc_start: 0.7472 (m) cc_final: 0.7268 (t) REVERT: C 290 ASP cc_start: 0.6751 (t0) cc_final: 0.6485 (t0) REVERT: C 319 ARG cc_start: 0.7581 (mpt-90) cc_final: 0.7269 (mmt90) REVERT: C 324 GLU cc_start: 0.6296 (pm20) cc_final: 0.6045 (pm20) REVERT: C 331 ASN cc_start: 0.1632 (OUTLIER) cc_final: 0.1064 (p0) REVERT: C 351 TYR cc_start: 0.4963 (p90) cc_final: 0.4599 (p90) REVERT: C 392 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.6922 (m-80) REVERT: C 542 ASN cc_start: 0.7583 (t0) cc_final: 0.6604 (m110) REVERT: C 576 VAL cc_start: 0.8249 (OUTLIER) cc_final: 0.7969 (t) REVERT: C 588 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.7819 (p) REVERT: C 617 CYS cc_start: 0.6112 (OUTLIER) cc_final: 0.5809 (m) REVERT: C 654 GLU cc_start: 0.7122 (mp0) cc_final: 0.6861 (mm-30) REVERT: C 673 SER cc_start: 0.7046 (t) cc_final: 0.6298 (m) REVERT: C 825 LYS cc_start: 0.7248 (tppt) cc_final: 0.6948 (tppt) REVERT: C 919 ASN cc_start: 0.8010 (m-40) cc_final: 0.7560 (m110) REVERT: C 954 GLN cc_start: 0.7344 (mt0) cc_final: 0.7047 (mt0) REVERT: C 970 PHE cc_start: 0.7310 (m-80) cc_final: 0.7045 (m-80) outliers start: 129 outliers final: 100 residues processed: 636 average time/residue: 0.3768 time to fit residues: 381.7144 Evaluate side-chains 673 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 557 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 0.9990 chunk 307 optimal weight: 0.6980 chunk 187 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 213 optimal weight: 0.6980 chunk 322 optimal weight: 0.8980 chunk 297 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 198 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 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 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 755 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.172 27404 Z= 0.268 Angle : 0.815 59.139 37278 Z= 0.430 Chirality : 0.048 0.530 4488 Planarity : 0.005 0.097 4690 Dihedral : 8.771 106.477 5471 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.04 % Allowed : 21.29 % Favored : 74.68 % Cbeta Deviations : 0.03 % 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: -1.12 (0.14), residues: 3223 helix: 0.75 (0.20), residues: 712 sheet: -0.77 (0.20), residues: 637 loop : -1.36 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 353 HIS 0.005 0.001 HIS A 49 PHE 0.062 0.003 PHE B 92 TYR 0.023 0.002 TYR A 365 ARG 0.012 0.001 ARG A 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 558 time to evaluate : 3.008 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: A 121 ASN cc_start: 0.7165 (p0) cc_final: 0.6393 (t0) REVERT: A 133 PHE cc_start: 0.6206 (m-80) cc_final: 0.5990 (m-80) REVERT: A 146 HIS cc_start: 0.4152 (p-80) cc_final: 0.2892 (m90) REVERT: A 270 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6920 (tp) REVERT: A 304 LYS cc_start: 0.8011 (tptt) cc_final: 0.7627 (tptt) REVERT: A 314 GLN cc_start: 0.6546 (OUTLIER) cc_final: 0.6331 (tp40) REVERT: A 560 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7692 (mp) REVERT: A 586 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7301 (m-30) REVERT: A 697 MET cc_start: 0.6661 (tpt) cc_final: 0.6397 (tpp) REVERT: A 780 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: A 824 ASN cc_start: 0.6756 (m-40) cc_final: 0.6249 (m110) REVERT: A 950 ASP cc_start: 0.7532 (m-30) cc_final: 0.7131 (m-30) REVERT: A 1002 GLN cc_start: 0.7407 (mt0) cc_final: 0.7161 (mt0) REVERT: A 1031 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6596 (mp0) REVERT: A 1115 ILE cc_start: 0.8678 (mp) cc_final: 0.8281 (tp) REVERT: B 66 HIS cc_start: 0.5894 (OUTLIER) cc_final: 0.5357 (m90) REVERT: B 119 ILE cc_start: 0.6743 (mp) cc_final: 0.6090 (tt) REVERT: B 152 TRP cc_start: 0.2943 (m100) cc_final: 0.2392 (m100) REVERT: B 266 TYR cc_start: 0.7426 (m-80) cc_final: 0.7184 (m-80) REVERT: B 293 LEU cc_start: 0.8124 (tt) cc_final: 0.7811 (tt) REVERT: B 314 GLN cc_start: 0.8147 (tp40) cc_final: 0.7764 (tp40) REVERT: B 387 LEU cc_start: 0.8097 (mt) cc_final: 0.7727 (tp) REVERT: B 396 TYR cc_start: 0.5193 (m-10) cc_final: 0.4827 (m-10) REVERT: B 409 GLN cc_start: 0.6515 (mt0) cc_final: 0.6267 (tt0) REVERT: B 439 ASN cc_start: 0.6861 (t0) cc_final: 0.6305 (p0) REVERT: B 457 ARG cc_start: 0.4964 (tpt90) cc_final: 0.4455 (ttp80) REVERT: B 480 CYS cc_start: 0.4787 (OUTLIER) cc_final: 0.3946 (t) REVERT: B 540 ASN cc_start: 0.7435 (t0) cc_final: 0.7128 (t0) REVERT: B 704 SER cc_start: 0.7311 (t) cc_final: 0.7007 (m) REVERT: B 748 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7344 (pm20) REVERT: B 753 LEU cc_start: 0.8110 (tp) cc_final: 0.7867 (tp) REVERT: B 773 GLU cc_start: 0.7450 (tp30) cc_final: 0.7223 (tp30) REVERT: B 900 MET cc_start: 0.8002 (mmp) cc_final: 0.7752 (mmt) REVERT: B 916 LEU cc_start: 0.8507 (tt) cc_final: 0.8237 (tp) REVERT: B 918 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7419 (tp30) REVERT: B 936 ASP cc_start: 0.7879 (m-30) cc_final: 0.7502 (m-30) REVERT: B 957 GLN cc_start: 0.8022 (tt0) cc_final: 0.7749 (tt0) REVERT: B 969 ASN cc_start: 0.6771 (t0) cc_final: 0.6384 (t0) REVERT: B 990 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7256 (mm-30) REVERT: B 1041 ASP cc_start: 0.7740 (t0) cc_final: 0.7517 (t0) REVERT: C 18 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.5416 (mt) REVERT: C 21 ARG cc_start: 0.5324 (ttt-90) cc_final: 0.4809 (mtt-85) REVERT: C 38 TYR cc_start: 0.7753 (m-80) cc_final: 0.7381 (m-10) REVERT: C 41 LYS cc_start: 0.7624 (mttp) cc_final: 0.7281 (mtmm) REVERT: C 83 VAL cc_start: 0.7852 (OUTLIER) cc_final: 0.7554 (p) REVERT: C 134 GLN cc_start: 0.6534 (mm110) cc_final: 0.6286 (mm110) REVERT: C 204 TYR cc_start: 0.6602 (m-80) cc_final: 0.6150 (m-80) REVERT: C 271 GLN cc_start: 0.7941 (mp10) cc_final: 0.7583 (mp10) REVERT: C 274 THR cc_start: 0.7473 (m) cc_final: 0.7255 (t) REVERT: C 319 ARG cc_start: 0.7576 (mpt-90) cc_final: 0.7262 (mmt90) REVERT: C 324 GLU cc_start: 0.6298 (pm20) cc_final: 0.6053 (pm20) REVERT: C 331 ASN cc_start: 0.1637 (OUTLIER) cc_final: 0.1071 (p0) REVERT: C 351 TYR cc_start: 0.4945 (p90) cc_final: 0.4601 (p90) REVERT: C 392 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.6942 (m-80) REVERT: C 542 ASN cc_start: 0.7606 (t0) cc_final: 0.6612 (m110) REVERT: C 576 VAL cc_start: 0.8232 (OUTLIER) cc_final: 0.7972 (t) REVERT: C 617 CYS cc_start: 0.6116 (OUTLIER) cc_final: 0.5800 (m) REVERT: C 661 GLU cc_start: 0.7156 (tp30) cc_final: 0.6766 (tm-30) REVERT: C 673 SER cc_start: 0.7037 (t) cc_final: 0.6300 (m) REVERT: C 825 LYS cc_start: 0.7286 (tppt) cc_final: 0.6951 (tppt) REVERT: C 919 ASN cc_start: 0.8002 (m-40) cc_final: 0.7556 (m110) REVERT: C 954 GLN cc_start: 0.7347 (mt0) cc_final: 0.7045 (mt0) REVERT: C 970 PHE cc_start: 0.7307 (m-80) cc_final: 0.7048 (m-80) outliers start: 115 outliers final: 99 residues processed: 621 average time/residue: 0.3838 time to fit residues: 381.4457 Evaluate side-chains 669 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 555 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 0.8980 chunk 273 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 257 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 264 optimal weight: 0.0050 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.085010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.069670 restraints weight = 107628.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.071759 restraints weight = 60275.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.073131 restraints weight = 39571.049| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.172 27404 Z= 0.268 Angle : 0.815 59.138 37278 Z= 0.430 Chirality : 0.049 0.530 4488 Planarity : 0.005 0.097 4690 Dihedral : 8.771 106.477 5471 Min Nonbonded Distance : 1.529 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.00 % Allowed : 21.32 % Favored : 74.68 % Cbeta Deviations : 0.03 % 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: -1.12 (0.14), residues: 3223 helix: 0.75 (0.20), residues: 712 sheet: -0.77 (0.20), residues: 637 loop : -1.36 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 353 HIS 0.005 0.001 HIS A 49 PHE 0.062 0.003 PHE B 92 TYR 0.023 0.002 TYR A 365 ARG 0.012 0.001 ARG A 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7514.93 seconds wall clock time: 136 minutes 0.69 seconds (8160.69 seconds total)