Starting phenix.real_space_refine on Wed Mar 20 06:44:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1u_24123/03_2024/7n1u_24123_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1u_24123/03_2024/7n1u_24123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1u_24123/03_2024/7n1u_24123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1u_24123/03_2024/7n1u_24123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1u_24123/03_2024/7n1u_24123_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1u_24123/03_2024/7n1u_24123_neut.pdb" } resolution = 3.14 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= 0.043 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 16908 2.51 5 N 4299 2.21 5 O 5298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 737": "OD1" <-> "OD2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "B PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 737": "OD1" <-> "OD2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "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: 26619 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8421 Classifications: {'peptide': 1075} Link IDs: {'PTRANS': 52, 'TRANS': 1022} Chain breaks: 5 Chain: "B" Number of atoms: 8421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8421 Classifications: {'peptide': 1075} Link IDs: {'PTRANS': 52, 'TRANS': 1022} Chain breaks: 5 Chain: "C" Number of atoms: 8421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8421 Classifications: {'peptide': 1075} Link IDs: {'PTRANS': 52, 'TRANS': 1022} Chain breaks: 5 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 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: "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: 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: "T" 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: "U" 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: "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: 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: "X" 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: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 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: 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: 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: "i" 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: "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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 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: 13.54, per 1000 atoms: 0.51 Number of scatterers: 26619 At special positions: 0 Unit cell: (155.113, 155.938, 196.366, 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 5298 8.00 N 4299 7.00 C 16908 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=2.78 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.81 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.01 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.90 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 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=2.78 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.89 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=1.99 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.57 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.58 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.65 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.75 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.01 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.94 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.97 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.99 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.85 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.60 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.06 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.70 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.64 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.54 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.42 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.66 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.98 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.74 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.34 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=2.10 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.68 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 M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG X 2 " - " MAN X 3 " " NAG Y 2 " - " MAN Y 3 " " NAG i 2 " - " MAN i 3 " " NAG j 2 " - " MAN j 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 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " BETA1-6 " NAG L 1 " - " FUC L 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG W 1 " - " FUC W 3 " " NAG h 1 " - " FUC h 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1403 " - " ASN A 331 " " NAG A1405 " - " ASN A 603 " " NAG A1406 " - " ASN A 657 " " NAG A1407 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 331 " " NAG B1404 " - " ASN B 343 " " NAG B1405 " - " ASN B 603 " " NAG B1406 " - " ASN B 657 " " NAG B1407 " - " ASN B 709 " " NAG C1401 " - " ASN C 61 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 343 " " NAG C1405 " - " ASN C 603 " " 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 122 " " NAG F 1 " - " ASN A 165 " " NAG H 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 616 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 17 " " NAG Q 1 " - " ASN B 165 " " NAG S 1 " - " ASN B 282 " " NAG T 1 " - " ASN B 616 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 801 " " NAG W 1 " - " ASN B1074 " " NAG X 1 " - " ASN B1098 " " NAG Y 1 " - " ASN B1134 " " NAG Z 1 " - " ASN C 17 " " NAG a 1 " - " ASN C 122 " " NAG c 1 " - " ASN C 234 " " NAG d 1 " - " ASN C 282 " " NAG e 1 " - " ASN C 616 " " NAG f 1 " - " ASN C 717 " " NAG g 1 " - " ASN C 801 " " NAG h 1 " - " ASN C1074 " " NAG i 1 " - " ASN C1098 " " NAG j 1 " - " ASN C1134 " Time building additional restraints: 11.90 Conformation dependent library (CDL) restraints added in 5.0 seconds 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6042 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 48 sheets defined 27.3% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.711A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 4.061A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.725A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.453A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.691A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.567A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.717A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 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: 3.948A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.433A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1159 removed outlier: 3.756A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.267A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.538A 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: 4.962A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.342A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.632A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.728A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.529A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (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 758 through 783 removed outlier: 3.603A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.646A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.518A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.549A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.570A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.795A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.530A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1160 removed outlier: 3.538A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.004A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.726A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.116A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.111A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.446A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.515A 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: 3.668A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.542A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.530A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) 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: 3.825A 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 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.763A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1159 removed outlier: 4.718A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU C1151 " --> pdb=" O SER C1147 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.845A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.231A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.235A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.855A 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: 7.165A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.791A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.653A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.100A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.259A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.898A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.435A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.968A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.437A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LYS C 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ASN A 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.737A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.891A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.804A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.712A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.293A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.747A 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: 7.732A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.973A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.654A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.927A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.504A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.162A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 448 through 454 removed outlier: 6.106A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) 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: 5.997A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.606A pdb=" N GLN B1071 " --> pdb=" O ILE B 716 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.606A pdb=" N GLN B1071 " --> pdb=" O ILE B 716 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (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 787 through 788 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.416A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.781A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.669A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.792A 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: 6.040A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 142 through 143 removed outlier: 6.573A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.966A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 6.828A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.300A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.976A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.650A 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 715 removed outlier: 3.716A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.936A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.331A 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: 4.480A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1113 hydrogen bonds defined for protein. 3054 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.46 Time building geometry restraints manager: 12.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5292 1.33 - 1.45: 6726 1.45 - 1.58: 15042 1.58 - 1.70: 0 1.70 - 1.83: 144 Bond restraints: 27204 Sorted by residual: bond pdb=" CA PRO C 792 " pdb=" C PRO C 792 " ideal model delta sigma weight residual 1.514 1.543 -0.028 5.50e-03 3.31e+04 2.66e+01 bond pdb=" N CYS C 15 " pdb=" CA CYS C 15 " ideal model delta sigma weight residual 1.457 1.514 -0.057 1.23e-02 6.61e+03 2.12e+01 bond pdb=" C5 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.413 1.498 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C5 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.413 1.496 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C5 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.413 1.492 -0.079 2.00e-02 2.50e+03 1.57e+01 ... (remaining 27199 not shown) Histogram of bond angle deviations from ideal: 96.95 - 104.67: 406 104.67 - 112.39: 12369 112.39 - 120.11: 12965 120.11 - 127.83: 11139 127.83 - 135.56: 117 Bond angle restraints: 36996 Sorted by residual: angle pdb=" N ARG A1107 " pdb=" CA ARG A1107 " pdb=" C ARG A1107 " ideal model delta sigma weight residual 112.34 123.59 -11.25 1.30e+00 5.92e-01 7.49e+01 angle pdb=" OD1 ASN C1074 " pdb=" CG ASN C1074 " pdb=" ND2 ASN C1074 " ideal model delta sigma weight residual 122.60 114.21 8.39 1.00e+00 1.00e+00 7.04e+01 angle pdb=" OD1 ASN B1074 " pdb=" CG ASN B1074 " pdb=" ND2 ASN B1074 " ideal model delta sigma weight residual 122.60 114.23 8.37 1.00e+00 1.00e+00 7.01e+01 angle pdb=" N ARG C1107 " pdb=" CA ARG C1107 " pdb=" C ARG C1107 " ideal model delta sigma weight residual 112.34 123.12 -10.78 1.30e+00 5.92e-01 6.88e+01 angle pdb=" N ARG B 214 " pdb=" CA ARG B 214 " pdb=" C ARG B 214 " ideal model delta sigma weight residual 112.03 122.64 -10.61 1.31e+00 5.83e-01 6.56e+01 ... (remaining 36991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.39: 16574 24.39 - 48.79: 692 48.79 - 73.18: 151 73.18 - 97.58: 43 97.58 - 121.97: 21 Dihedral angle restraints: 17481 sinusoidal: 8091 harmonic: 9390 Sorted by residual: dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -171.06 85.06 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -165.40 79.40 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -12.57 -73.43 1 1.00e+01 1.00e-02 6.86e+01 ... (remaining 17478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.616: 4444 0.616 - 1.232: 9 1.232 - 1.848: 3 1.848 - 2.464: 1 2.464 - 3.080: 1 Chirality restraints: 4458 Sorted by residual: chirality pdb=" C1 NAG B1403 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1403 " pdb=" O5 NAG B1403 " both_signs ideal model delta sigma weight residual False -2.40 0.68 -3.08 2.00e-01 2.50e+01 2.37e+02 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.49 -1.91 2.00e-01 2.50e+01 9.09e+01 chirality pdb=" C1 FUC W 3 " pdb=" O6 NAG W 1 " pdb=" C2 FUC W 3 " pdb=" O5 FUC W 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.84e+01 ... (remaining 4455 not shown) Planarity restraints: 4698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " -0.319 2.00e-02 2.50e+03 3.28e-01 1.35e+03 pdb=" CG ASN B 343 " 0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " 0.553 2.00e-02 2.50e+03 pdb=" C1 NAG B1404 " -0.348 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " -0.311 2.00e-02 2.50e+03 3.13e-01 1.23e+03 pdb=" CG ASN C 343 " 0.097 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " 0.522 2.00e-02 2.50e+03 pdb=" C1 NAG C1404 " -0.334 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 61 " -0.069 2.00e-02 2.50e+03 2.28e-01 6.49e+02 pdb=" CG ASN C 61 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN C 61 " -0.141 2.00e-02 2.50e+03 pdb=" ND2 ASN C 61 " 0.405 2.00e-02 2.50e+03 pdb=" C1 NAG C1401 " -0.258 2.00e-02 2.50e+03 ... (remaining 4695 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 83 2.58 - 3.16: 21422 3.16 - 3.74: 40140 3.74 - 4.32: 57496 4.32 - 4.90: 92987 Nonbonded interactions: 212128 Sorted by model distance: nonbonded pdb=" ND2 ASN B 234 " pdb=" C1 NAG R 1 " model vdw 2.003 3.550 nonbonded pdb=" ND2 ASN C 149 " pdb=" C1 NAG C1402 " model vdw 2.023 3.550 nonbonded pdb=" ND2 ASN C 149 " pdb=" O5 NAG C1402 " model vdw 2.030 2.520 nonbonded pdb=" CD ARG B 454 " pdb=" CD1 LEU B 492 " model vdw 2.037 3.860 nonbonded pdb=" ND2 ASN A 149 " pdb=" C1 NAG A1402 " model vdw 2.045 3.550 ... (remaining 212123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.100 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: 23.280 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 75.790 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.390 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: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 : 0.013 0.085 27204 Z= 0.872 Angle : 1.765 11.560 36996 Z= 1.165 Chirality : 0.129 3.080 4458 Planarity : 0.012 0.122 4650 Dihedral : 14.945 121.970 11313 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.05 % Favored : 93.70 % Rotamer: Outliers : 1.56 % Allowed : 5.17 % Favored : 93.27 % Cbeta Deviations : 0.23 % 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: -1.65 (0.13), residues: 3189 helix: -1.36 (0.16), residues: 714 sheet: 0.24 (0.21), residues: 549 loop : -1.43 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.182 0.024 TRP A 258 HIS 0.017 0.004 HIS B1048 PHE 0.101 0.013 PHE A 718 TYR 0.112 0.018 TYR A 495 ARG 0.011 0.001 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 757 time to evaluate : 3.093 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 54 LEU cc_start: 0.8501 (mt) cc_final: 0.8202 (mt) REVERT: A 125 ASN cc_start: 0.7291 (OUTLIER) cc_final: 0.7062 (p0) REVERT: A 133 PHE cc_start: 0.7142 (m-80) cc_final: 0.6873 (m-80) REVERT: A 140 PHE cc_start: 0.7790 (p90) cc_final: 0.7136 (p90) REVERT: A 188 ASN cc_start: 0.7844 (t0) cc_final: 0.7091 (t0) REVERT: A 205 SER cc_start: 0.8932 (p) cc_final: 0.8588 (t) REVERT: A 207 HIS cc_start: 0.7172 (t-170) cc_final: 0.6673 (t-90) REVERT: A 224 GLU cc_start: 0.7458 (mp0) cc_final: 0.7184 (mp0) REVERT: A 244 LEU cc_start: 0.5148 (mt) cc_final: 0.4649 (mt) REVERT: A 278 LYS cc_start: 0.8411 (ttmm) cc_final: 0.8009 (ttmt) REVERT: A 286 THR cc_start: 0.8800 (m) cc_final: 0.8547 (p) REVERT: A 306 PHE cc_start: 0.8536 (m-80) cc_final: 0.8252 (m-80) REVERT: A 323 THR cc_start: 0.8759 (p) cc_final: 0.8453 (p) REVERT: A 324 GLU cc_start: 0.7492 (pm20) cc_final: 0.7039 (pm20) REVERT: A 391 CYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6094 (m) REVERT: A 392 PHE cc_start: 0.8375 (m-80) cc_final: 0.7954 (m-80) REVERT: A 425 LEU cc_start: 0.7735 (mt) cc_final: 0.7056 (mt) REVERT: A 555 SER cc_start: 0.7938 (t) cc_final: 0.7497 (t) REVERT: A 563 GLN cc_start: 0.7550 (mt0) cc_final: 0.7291 (mt0) REVERT: A 586 ASP cc_start: 0.7946 (m-30) cc_final: 0.7441 (m-30) REVERT: A 588 THR cc_start: 0.8762 (m) cc_final: 0.8469 (t) REVERT: A 664 ILE cc_start: 0.9118 (mt) cc_final: 0.8862 (mm) REVERT: A 776 LYS cc_start: 0.7976 (tmmt) cc_final: 0.7688 (ttpt) REVERT: A 780 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7259 (mm-30) REVERT: A 816 SER cc_start: 0.8803 (p) cc_final: 0.8530 (p) REVERT: A 904 TYR cc_start: 0.7836 (m-10) cc_final: 0.7505 (m-80) REVERT: A 907 ASN cc_start: 0.8931 (t0) cc_final: 0.8679 (t0) REVERT: A 933 LYS cc_start: 0.8353 (mtpp) cc_final: 0.8110 (mtpp) REVERT: A 945 LEU cc_start: 0.8738 (mm) cc_final: 0.8501 (mm) REVERT: A 957 GLN cc_start: 0.7659 (tt0) cc_final: 0.7450 (tt0) REVERT: A 986 LYS cc_start: 0.8595 (ttmm) cc_final: 0.8187 (ttmm) REVERT: A 990 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7861 (mm-30) REVERT: A 994 ASP cc_start: 0.7504 (t0) cc_final: 0.7150 (t0) REVERT: A 1102 TRP cc_start: 0.8842 (m100) cc_final: 0.8585 (m100) REVERT: B 99 ASN cc_start: 0.8308 (m-40) cc_final: 0.7951 (m-40) REVERT: B 137 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7506 (t0) REVERT: B 157 PHE cc_start: 0.7077 (p90) cc_final: 0.6691 (p90) REVERT: B 237 ARG cc_start: 0.7395 (ptt-90) cc_final: 0.7090 (ptt-90) REVERT: B 278 LYS cc_start: 0.8376 (ttmm) cc_final: 0.8059 (ttmm) REVERT: B 306 PHE cc_start: 0.8740 (m-80) cc_final: 0.8457 (m-80) REVERT: B 309 GLU cc_start: 0.8035 (mp0) cc_final: 0.7569 (mp0) REVERT: B 360 ASN cc_start: 0.8084 (t0) cc_final: 0.7839 (t0) REVERT: B 428 ASP cc_start: 0.8179 (p0) cc_final: 0.7888 (p0) REVERT: B 541 PHE cc_start: 0.8723 (p90) cc_final: 0.8496 (p90) REVERT: B 560 LEU cc_start: 0.8446 (mp) cc_final: 0.8033 (mp) REVERT: B 563 GLN cc_start: 0.7470 (mt0) cc_final: 0.7262 (mt0) REVERT: B 565 PHE cc_start: 0.7626 (m-80) cc_final: 0.7338 (m-80) REVERT: B 586 ASP cc_start: 0.7835 (m-30) cc_final: 0.7396 (m-30) REVERT: B 619 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7641 (mm-30) REVERT: B 646 ARG cc_start: 0.7720 (mmt180) cc_final: 0.7496 (mmm160) REVERT: B 776 LYS cc_start: 0.8534 (tppt) cc_final: 0.8300 (tppt) REVERT: B 816 SER cc_start: 0.8479 (p) cc_final: 0.8250 (p) REVERT: B 907 ASN cc_start: 0.8916 (t0) cc_final: 0.8672 (t0) REVERT: B 918 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7428 (mt-10) REVERT: B 957 GLN cc_start: 0.7652 (tm-30) cc_final: 0.7285 (tm-30) REVERT: B 960 ASN cc_start: 0.8401 (t0) cc_final: 0.8101 (t0) REVERT: B 979 ASP cc_start: 0.7837 (t0) cc_final: 0.7527 (t0) REVERT: B 985 ASP cc_start: 0.7227 (p0) cc_final: 0.6766 (p0) REVERT: B 986 LYS cc_start: 0.8537 (tmmt) cc_final: 0.8315 (tmtt) REVERT: B 990 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7716 (mm-30) REVERT: B 994 ASP cc_start: 0.7534 (t0) cc_final: 0.7215 (t0) REVERT: C 39 PRO cc_start: 0.8865 (Cg_endo) cc_final: 0.8643 (Cg_exo) REVERT: C 40 ASP cc_start: 0.7998 (m-30) cc_final: 0.7781 (m-30) REVERT: C 54 LEU cc_start: 0.8485 (mt) cc_final: 0.8125 (mt) REVERT: C 133 PHE cc_start: 0.7241 (m-80) cc_final: 0.6715 (m-80) REVERT: C 179 LEU cc_start: 0.8324 (tp) cc_final: 0.8115 (tp) REVERT: C 190 ARG cc_start: 0.7243 (mmm-85) cc_final: 0.6967 (mmm-85) REVERT: C 195 LYS cc_start: 0.8440 (mtmt) cc_final: 0.8227 (mtpt) REVERT: C 203 ILE cc_start: 0.8770 (mt) cc_final: 0.8278 (pt) REVERT: C 207 HIS cc_start: 0.7147 (t-90) cc_final: 0.6396 (t-90) REVERT: C 224 GLU cc_start: 0.7438 (mp0) cc_final: 0.7094 (mp0) REVERT: C 280 ASN cc_start: 0.8468 (p0) cc_final: 0.8027 (p0) REVERT: C 457 ARG cc_start: 0.6727 (tpm170) cc_final: 0.6318 (tpt90) REVERT: C 523 THR cc_start: 0.8244 (p) cc_final: 0.8041 (t) REVERT: C 563 GLN cc_start: 0.7721 (mt0) cc_final: 0.7415 (mt0) REVERT: C 584 ILE cc_start: 0.8282 (mm) cc_final: 0.7736 (mm) REVERT: C 588 THR cc_start: 0.8690 (m) cc_final: 0.8472 (t) REVERT: C 596 SER cc_start: 0.8919 (t) cc_final: 0.8654 (m) REVERT: C 619 GLU cc_start: 0.8161 (mp0) cc_final: 0.7710 (mp0) REVERT: C 654 GLU cc_start: 0.7522 (pt0) cc_final: 0.7245 (pt0) REVERT: C 664 ILE cc_start: 0.8878 (mp) cc_final: 0.8638 (mm) REVERT: C 936 ASP cc_start: 0.7903 (m-30) cc_final: 0.7685 (m-30) REVERT: C 985 ASP cc_start: 0.7255 (p0) cc_final: 0.6911 (p0) REVERT: C 990 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7866 (mm-30) REVERT: C 1102 TRP cc_start: 0.8917 (m100) cc_final: 0.8654 (m100) REVERT: C 1127 ASP cc_start: 0.7619 (t70) cc_final: 0.7394 (t0) REVERT: C 1142 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7166 (tm-30) outliers start: 44 outliers final: 3 residues processed: 782 average time/residue: 0.3997 time to fit residues: 476.8722 Evaluate side-chains 623 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 617 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 318 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 291 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 234 ASN A 493 GLN A 804 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 14 GLN B 30 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 207 HIS B 394 ASN B 564 GLN B 613 GLN B 751 ASN B 872 GLN B 926 GLN B 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1119 ASN B1158 ASN C 137 ASN C 149 ASN C 196 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1119 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27204 Z= 0.254 Angle : 0.770 10.129 36996 Z= 0.386 Chirality : 0.051 0.822 4458 Planarity : 0.004 0.052 4650 Dihedral : 10.870 110.960 5519 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.95 % Allowed : 10.13 % Favored : 87.92 % 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: -0.57 (0.14), residues: 3189 helix: 0.89 (0.19), residues: 711 sheet: -0.15 (0.18), residues: 657 loop : -0.98 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 64 HIS 0.006 0.001 HIS A 66 PHE 0.030 0.002 PHE C 565 TYR 0.028 0.002 TYR B 453 ARG 0.005 0.001 ARG C1091 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 625 time to evaluate : 2.942 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: A 140 PHE cc_start: 0.8158 (p90) cc_final: 0.7767 (p90) REVERT: A 202 LYS cc_start: 0.8800 (mptt) cc_final: 0.8592 (mptt) REVERT: A 224 GLU cc_start: 0.7577 (mp0) cc_final: 0.7295 (mp0) REVERT: A 228 ASP cc_start: 0.7216 (m-30) cc_final: 0.6991 (m-30) REVERT: A 278 LYS cc_start: 0.8512 (ttmm) cc_final: 0.7961 (ttmt) REVERT: A 286 THR cc_start: 0.8997 (m) cc_final: 0.8652 (p) REVERT: A 306 PHE cc_start: 0.8497 (m-80) cc_final: 0.8261 (m-80) REVERT: A 323 THR cc_start: 0.8697 (p) cc_final: 0.8396 (p) REVERT: A 324 GLU cc_start: 0.7492 (pm20) cc_final: 0.7064 (pm20) REVERT: A 414 GLN cc_start: 0.5848 (mm-40) cc_final: 0.5644 (tp-100) REVERT: A 463 PRO cc_start: 0.8176 (Cg_exo) cc_final: 0.7939 (Cg_endo) REVERT: A 560 LEU cc_start: 0.8585 (mm) cc_final: 0.8121 (mm) REVERT: A 563 GLN cc_start: 0.7571 (mt0) cc_final: 0.7353 (mt0) REVERT: A 586 ASP cc_start: 0.7709 (m-30) cc_final: 0.7426 (m-30) REVERT: A 664 ILE cc_start: 0.9050 (mt) cc_final: 0.8738 (mp) REVERT: A 816 SER cc_start: 0.8470 (p) cc_final: 0.8143 (p) REVERT: A 907 ASN cc_start: 0.8878 (t0) cc_final: 0.8643 (t0) REVERT: A 945 LEU cc_start: 0.8721 (mm) cc_final: 0.8424 (mm) REVERT: A 990 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7804 (mm-30) REVERT: A 994 ASP cc_start: 0.7656 (t0) cc_final: 0.7341 (t0) REVERT: B 18 LEU cc_start: 0.7051 (mm) cc_final: 0.6447 (tp) REVERT: B 80 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.5932 (p0) REVERT: B 99 ASN cc_start: 0.8493 (m-40) cc_final: 0.8292 (m-40) REVERT: B 137 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7710 (t0) REVERT: B 224 GLU cc_start: 0.7584 (mp0) cc_final: 0.7204 (pm20) REVERT: B 278 LYS cc_start: 0.8492 (ttmm) cc_final: 0.8186 (ttpt) REVERT: B 302 THR cc_start: 0.9191 (m) cc_final: 0.8727 (p) REVERT: B 428 ASP cc_start: 0.8094 (p0) cc_final: 0.7696 (p0) REVERT: B 559 PHE cc_start: 0.8012 (m-80) cc_final: 0.7783 (m-80) REVERT: B 586 ASP cc_start: 0.7570 (m-30) cc_final: 0.7262 (m-30) REVERT: B 619 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7557 (mp0) REVERT: B 646 ARG cc_start: 0.7764 (mmt180) cc_final: 0.7429 (mmm160) REVERT: B 776 LYS cc_start: 0.8544 (tppt) cc_final: 0.8324 (tppt) REVERT: B 816 SER cc_start: 0.8462 (p) cc_final: 0.8243 (p) REVERT: B 907 ASN cc_start: 0.8891 (t0) cc_final: 0.8640 (t0) REVERT: B 957 GLN cc_start: 0.7661 (tm-30) cc_final: 0.7315 (tm-30) REVERT: B 979 ASP cc_start: 0.7883 (t0) cc_final: 0.7597 (t0) REVERT: B 994 ASP cc_start: 0.7524 (t0) cc_final: 0.7173 (t0) REVERT: C 40 ASP cc_start: 0.8059 (m-30) cc_final: 0.7804 (m-30) REVERT: C 86 PHE cc_start: 0.8624 (t80) cc_final: 0.8379 (t80) REVERT: C 133 PHE cc_start: 0.7257 (m-80) cc_final: 0.6670 (m-80) REVERT: C 203 ILE cc_start: 0.8857 (mt) cc_final: 0.8371 (pt) REVERT: C 224 GLU cc_start: 0.7436 (mp0) cc_final: 0.7107 (mp0) REVERT: C 278 LYS cc_start: 0.8301 (tttm) cc_final: 0.8020 (ttpt) REVERT: C 280 ASN cc_start: 0.8491 (p0) cc_final: 0.8172 (p0) REVERT: C 281 GLU cc_start: 0.7808 (pm20) cc_final: 0.7487 (pm20) REVERT: C 564 GLN cc_start: 0.6573 (tm-30) cc_final: 0.6357 (tm-30) REVERT: C 619 GLU cc_start: 0.8108 (mp0) cc_final: 0.7601 (mp0) REVERT: C 773 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7237 (tt0) REVERT: C 823 PHE cc_start: 0.7942 (t80) cc_final: 0.7712 (t80) REVERT: C 918 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7785 (mt-10) REVERT: C 936 ASP cc_start: 0.7924 (m-30) cc_final: 0.7645 (m-30) REVERT: C 990 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7758 (mm-30) outliers start: 55 outliers final: 31 residues processed: 646 average time/residue: 0.3848 time to fit residues: 388.4065 Evaluate side-chains 591 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 557 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 773 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 chunk 315 optimal weight: 2.9990 chunk 260 optimal weight: 0.8980 chunk 289 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 935 GLN B 14 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 207 HIS ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 762 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS B1119 ASN B1135 ASN C 388 ASN C 762 GLN C 804 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.154 27204 Z= 0.380 Angle : 0.769 12.365 36996 Z= 0.380 Chirality : 0.050 0.699 4458 Planarity : 0.004 0.078 4650 Dihedral : 10.443 109.280 5512 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.26 % Allowed : 12.82 % Favored : 83.92 % 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: -0.45 (0.14), residues: 3189 helix: 1.45 (0.20), residues: 684 sheet: -0.37 (0.18), residues: 660 loop : -0.96 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 353 HIS 0.008 0.001 HIS A 66 PHE 0.022 0.002 PHE B 306 TYR 0.027 0.002 TYR A 904 ARG 0.008 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 596 time to evaluate : 3.135 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 140 PHE cc_start: 0.8331 (p90) cc_final: 0.8024 (p90) REVERT: A 190 ARG cc_start: 0.7691 (mpt-90) cc_final: 0.7319 (mpt-90) REVERT: A 202 LYS cc_start: 0.8783 (mptt) cc_final: 0.8516 (mptt) REVERT: A 224 GLU cc_start: 0.7723 (mp0) cc_final: 0.7407 (mp0) REVERT: A 278 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8311 (ttmt) REVERT: A 287 ASP cc_start: 0.8050 (m-30) cc_final: 0.7698 (m-30) REVERT: A 291 CYS cc_start: 0.5940 (t) cc_final: 0.5663 (t) REVERT: A 323 THR cc_start: 0.8623 (p) cc_final: 0.8389 (p) REVERT: A 324 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7085 (pm20) REVERT: A 429 PHE cc_start: 0.8352 (t80) cc_final: 0.8149 (t80) REVERT: A 586 ASP cc_start: 0.7589 (m-30) cc_final: 0.7291 (m-30) REVERT: A 599 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8496 (p) REVERT: A 675 GLN cc_start: 0.7286 (mm-40) cc_final: 0.7044 (mt0) REVERT: A 773 GLU cc_start: 0.7744 (tp30) cc_final: 0.7523 (tp30) REVERT: A 816 SER cc_start: 0.8685 (p) cc_final: 0.8411 (p) REVERT: A 819 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7613 (mt-10) REVERT: A 904 TYR cc_start: 0.7764 (m-80) cc_final: 0.7497 (m-80) REVERT: A 907 ASN cc_start: 0.8937 (t0) cc_final: 0.8611 (t0) REVERT: A 990 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7781 (mm-30) REVERT: A 994 ASP cc_start: 0.7845 (t0) cc_final: 0.7285 (t0) REVERT: B 18 LEU cc_start: 0.7118 (mm) cc_final: 0.6534 (tp) REVERT: B 80 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.5712 (p0) REVERT: B 223 LEU cc_start: 0.8667 (mt) cc_final: 0.8376 (mt) REVERT: B 278 LYS cc_start: 0.8523 (ttmm) cc_final: 0.8151 (ttmm) REVERT: B 302 THR cc_start: 0.9179 (m) cc_final: 0.8716 (p) REVERT: B 310 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8779 (tttp) REVERT: B 414 GLN cc_start: 0.6458 (tp-100) cc_final: 0.6039 (tp40) REVERT: B 428 ASP cc_start: 0.8070 (p0) cc_final: 0.7722 (p0) REVERT: B 559 PHE cc_start: 0.8008 (m-80) cc_final: 0.7774 (m-80) REVERT: B 560 LEU cc_start: 0.8292 (mp) cc_final: 0.7687 (mp) REVERT: B 563 GLN cc_start: 0.7584 (mt0) cc_final: 0.7111 (mt0) REVERT: B 586 ASP cc_start: 0.7482 (m-30) cc_final: 0.7015 (m-30) REVERT: B 816 SER cc_start: 0.8598 (p) cc_final: 0.8378 (p) REVERT: B 907 ASN cc_start: 0.8928 (t0) cc_final: 0.8678 (t0) REVERT: B 957 GLN cc_start: 0.7586 (tm-30) cc_final: 0.7137 (tm-30) REVERT: B 979 ASP cc_start: 0.7898 (t0) cc_final: 0.7596 (t0) REVERT: B 994 ASP cc_start: 0.7630 (t0) cc_final: 0.7322 (t0) REVERT: C 40 ASP cc_start: 0.8053 (m-30) cc_final: 0.7839 (m-30) REVERT: C 133 PHE cc_start: 0.7358 (m-80) cc_final: 0.6613 (m-80) REVERT: C 540 ASN cc_start: 0.8688 (m110) cc_final: 0.8415 (m-40) REVERT: C 564 GLN cc_start: 0.6788 (tm-30) cc_final: 0.6422 (tm-30) REVERT: C 619 GLU cc_start: 0.7949 (mp0) cc_final: 0.7473 (mp0) REVERT: C 773 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7233 (tt0) REVERT: C 808 ASP cc_start: 0.7470 (t0) cc_final: 0.7041 (t0) REVERT: C 936 ASP cc_start: 0.7943 (m-30) cc_final: 0.7656 (m-30) REVERT: C 990 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7709 (mm-30) REVERT: C 1142 GLN cc_start: 0.8148 (tm-30) cc_final: 0.7869 (tm-30) outliers start: 92 outliers final: 57 residues processed: 644 average time/residue: 0.3828 time to fit residues: 383.3439 Evaluate side-chains 617 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 555 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 0.9980 chunk 219 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 196 optimal weight: 0.9980 chunk 293 optimal weight: 0.9990 chunk 310 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 277 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A1119 ASN B 14 GLN B 207 HIS B 580 GLN B 658 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1119 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27204 Z= 0.255 Angle : 0.707 12.342 36996 Z= 0.345 Chirality : 0.048 0.637 4458 Planarity : 0.004 0.046 4650 Dihedral : 9.810 107.215 5512 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.40 % Allowed : 14.77 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3189 helix: 1.76 (0.20), residues: 687 sheet: -0.06 (0.18), residues: 642 loop : -0.98 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 104 HIS 0.007 0.001 HIS A 66 PHE 0.033 0.002 PHE B 157 TYR 0.023 0.002 TYR B 453 ARG 0.006 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 589 time to evaluate : 3.254 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 140 PHE cc_start: 0.8295 (p90) cc_final: 0.8023 (p90) REVERT: A 202 LYS cc_start: 0.8750 (mptt) cc_final: 0.8468 (mptt) REVERT: A 224 GLU cc_start: 0.7709 (mp0) cc_final: 0.7463 (mp0) REVERT: A 237 ARG cc_start: 0.8240 (ttp-170) cc_final: 0.7823 (ttt-90) REVERT: A 278 LYS cc_start: 0.8593 (ttmm) cc_final: 0.8317 (ttmt) REVERT: A 291 CYS cc_start: 0.5967 (t) cc_final: 0.5637 (t) REVERT: A 323 THR cc_start: 0.8589 (p) cc_final: 0.8385 (p) REVERT: A 324 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7007 (pm20) REVERT: A 414 GLN cc_start: 0.5820 (mm-40) cc_final: 0.5543 (tp-100) REVERT: A 429 PHE cc_start: 0.8383 (t80) cc_final: 0.8146 (t80) REVERT: A 586 ASP cc_start: 0.7605 (m-30) cc_final: 0.7324 (m-30) REVERT: A 599 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8521 (p) REVERT: A 675 GLN cc_start: 0.7266 (mm-40) cc_final: 0.7032 (mt0) REVERT: A 773 GLU cc_start: 0.7749 (tp30) cc_final: 0.7508 (tp30) REVERT: A 816 SER cc_start: 0.8656 (p) cc_final: 0.8435 (p) REVERT: A 819 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7584 (mt-10) REVERT: A 904 TYR cc_start: 0.7759 (m-80) cc_final: 0.7433 (m-80) REVERT: A 907 ASN cc_start: 0.8868 (t0) cc_final: 0.8538 (t0) REVERT: A 1102 TRP cc_start: 0.8836 (m100) cc_final: 0.8382 (m100) REVERT: B 18 LEU cc_start: 0.7120 (mm) cc_final: 0.6606 (tp) REVERT: B 80 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6585 (p0) REVERT: B 207 HIS cc_start: 0.7000 (t70) cc_final: 0.6751 (t-90) REVERT: B 237 ARG cc_start: 0.7730 (ptt-90) cc_final: 0.7480 (tmm-80) REVERT: B 278 LYS cc_start: 0.8510 (ttmm) cc_final: 0.8129 (ttmm) REVERT: B 309 GLU cc_start: 0.8031 (mp0) cc_final: 0.7605 (mp0) REVERT: B 428 ASP cc_start: 0.8028 (p0) cc_final: 0.7699 (p0) REVERT: B 586 ASP cc_start: 0.7464 (m-30) cc_final: 0.6965 (m-30) REVERT: B 644 GLN cc_start: 0.8382 (tp40) cc_final: 0.8128 (tp40) REVERT: B 773 GLU cc_start: 0.7674 (tp30) cc_final: 0.7411 (tp30) REVERT: B 816 SER cc_start: 0.8606 (p) cc_final: 0.8329 (p) REVERT: B 907 ASN cc_start: 0.8883 (t0) cc_final: 0.8635 (t0) REVERT: B 957 GLN cc_start: 0.7403 (tm130) cc_final: 0.7137 (tm-30) REVERT: B 979 ASP cc_start: 0.7816 (t0) cc_final: 0.7535 (t0) REVERT: C 14 GLN cc_start: 0.6910 (OUTLIER) cc_final: 0.6647 (pp30) REVERT: C 40 ASP cc_start: 0.8010 (m-30) cc_final: 0.7793 (m-30) REVERT: C 102 ARG cc_start: 0.7991 (mmp-170) cc_final: 0.7769 (mmp-170) REVERT: C 129 LYS cc_start: 0.8060 (mttt) cc_final: 0.7838 (mttt) REVERT: C 224 GLU cc_start: 0.7414 (mp0) cc_final: 0.7056 (mp0) REVERT: C 280 ASN cc_start: 0.8595 (p0) cc_final: 0.8264 (p0) REVERT: C 540 ASN cc_start: 0.8647 (m110) cc_final: 0.8402 (m-40) REVERT: C 563 GLN cc_start: 0.7691 (mt0) cc_final: 0.7340 (mt0) REVERT: C 564 GLN cc_start: 0.6952 (tm-30) cc_final: 0.6535 (tm-30) REVERT: C 808 ASP cc_start: 0.7482 (t0) cc_final: 0.7019 (t0) REVERT: C 936 ASP cc_start: 0.7932 (m-30) cc_final: 0.7652 (m-30) REVERT: C 990 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7623 (mm-30) REVERT: C 1142 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7532 (tm-30) outliers start: 96 outliers final: 55 residues processed: 640 average time/residue: 0.3877 time to fit residues: 387.5515 Evaluate side-chains 624 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 565 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 0.9990 chunk 176 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 264 optimal weight: 4.9990 chunk 214 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 278 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN B 14 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 481 ASN C 914 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 27204 Z= 0.352 Angle : 0.738 13.379 36996 Z= 0.360 Chirality : 0.048 0.599 4458 Planarity : 0.004 0.048 4650 Dihedral : 9.544 107.370 5510 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.58 % Rotamer: Outliers : 4.18 % Allowed : 15.44 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3189 helix: 1.69 (0.20), residues: 687 sheet: -0.15 (0.18), residues: 654 loop : -1.00 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 152 HIS 0.008 0.001 HIS A 66 PHE 0.022 0.002 PHE B 759 TYR 0.025 0.002 TYR C1067 ARG 0.007 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 588 time to evaluate : 2.958 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 140 PHE cc_start: 0.8353 (p90) cc_final: 0.8096 (p90) REVERT: A 202 LYS cc_start: 0.8753 (mptt) cc_final: 0.8496 (mmmt) REVERT: A 224 GLU cc_start: 0.7718 (mp0) cc_final: 0.7474 (mp0) REVERT: A 278 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8312 (ttmt) REVERT: A 279 TYR cc_start: 0.8472 (m-80) cc_final: 0.8049 (m-80) REVERT: A 414 GLN cc_start: 0.5870 (mm-40) cc_final: 0.5643 (tp-100) REVERT: A 429 PHE cc_start: 0.8400 (t80) cc_final: 0.8115 (t80) REVERT: A 563 GLN cc_start: 0.7666 (mt0) cc_final: 0.7251 (mt0) REVERT: A 586 ASP cc_start: 0.7575 (m-30) cc_final: 0.7288 (m-30) REVERT: A 599 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8521 (p) REVERT: A 675 GLN cc_start: 0.7253 (mm-40) cc_final: 0.7007 (mt0) REVERT: A 773 GLU cc_start: 0.7733 (tp30) cc_final: 0.7433 (tp30) REVERT: A 819 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7636 (mt-10) REVERT: A 904 TYR cc_start: 0.7791 (m-80) cc_final: 0.7439 (m-80) REVERT: A 907 ASN cc_start: 0.8905 (t0) cc_final: 0.8583 (t0) REVERT: A 912 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8335 (p) REVERT: A 994 ASP cc_start: 0.7932 (t0) cc_final: 0.7336 (t0) REVERT: A 1102 TRP cc_start: 0.8848 (m100) cc_final: 0.8430 (m100) REVERT: B 18 LEU cc_start: 0.7074 (mm) cc_final: 0.6544 (tp) REVERT: B 278 LYS cc_start: 0.8541 (ttmm) cc_final: 0.8132 (ttmm) REVERT: B 408 ARG cc_start: 0.7953 (ppt170) cc_final: 0.7383 (ppt170) REVERT: B 414 GLN cc_start: 0.6277 (tp40) cc_final: 0.5519 (tp40) REVERT: B 428 ASP cc_start: 0.8041 (p0) cc_final: 0.7749 (p0) REVERT: B 586 ASP cc_start: 0.7455 (m-30) cc_final: 0.6928 (m-30) REVERT: B 644 GLN cc_start: 0.8374 (tp40) cc_final: 0.8134 (tp40) REVERT: B 773 GLU cc_start: 0.7706 (tp30) cc_final: 0.7424 (tp30) REVERT: B 816 SER cc_start: 0.8659 (p) cc_final: 0.8372 (p) REVERT: B 825 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8130 (ttmm) REVERT: B 907 ASN cc_start: 0.8915 (t0) cc_final: 0.8670 (t0) REVERT: B 957 GLN cc_start: 0.7444 (tm130) cc_final: 0.7168 (tm-30) REVERT: B 979 ASP cc_start: 0.7816 (t0) cc_final: 0.7533 (t0) REVERT: B 994 ASP cc_start: 0.7682 (t0) cc_final: 0.7364 (t0) REVERT: C 14 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6785 (pp30) REVERT: C 129 LYS cc_start: 0.8133 (mttt) cc_final: 0.7859 (mttt) REVERT: C 224 GLU cc_start: 0.7462 (mp0) cc_final: 0.7090 (mp0) REVERT: C 326 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8557 (pt) REVERT: C 563 GLN cc_start: 0.7739 (mt0) cc_final: 0.7402 (mt0) REVERT: C 564 GLN cc_start: 0.7079 (tm-30) cc_final: 0.6563 (tm-30) REVERT: C 808 ASP cc_start: 0.7459 (t0) cc_final: 0.6991 (t0) REVERT: C 936 ASP cc_start: 0.7914 (m-30) cc_final: 0.7615 (m-30) REVERT: C 990 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7616 (mm-30) outliers start: 118 outliers final: 81 residues processed: 649 average time/residue: 0.3904 time to fit residues: 396.1160 Evaluate side-chains 639 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 553 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1159 HIS Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 104 optimal weight: 0.8980 chunk 279 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 310 optimal weight: 0.9990 chunk 257 optimal weight: 4.9990 chunk 143 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 163 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN A 955 ASN B 137 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 27204 Z= 0.228 Angle : 0.686 13.354 36996 Z= 0.334 Chirality : 0.046 0.558 4458 Planarity : 0.004 0.045 4650 Dihedral : 8.853 105.958 5510 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.54 % Allowed : 16.68 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.14), residues: 3189 helix: 1.90 (0.20), residues: 687 sheet: -0.01 (0.18), residues: 672 loop : -0.97 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 104 HIS 0.007 0.001 HIS A 66 PHE 0.028 0.001 PHE C 133 TYR 0.023 0.001 TYR B 453 ARG 0.007 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 588 time to evaluate : 2.446 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 140 PHE cc_start: 0.8300 (p90) cc_final: 0.8077 (p90) REVERT: A 202 LYS cc_start: 0.8778 (mptt) cc_final: 0.8537 (mmmt) REVERT: A 224 GLU cc_start: 0.7691 (mp0) cc_final: 0.7486 (mp0) REVERT: A 237 ARG cc_start: 0.8111 (ttp-170) cc_final: 0.7593 (ttp80) REVERT: A 278 LYS cc_start: 0.8613 (ttmm) cc_final: 0.8333 (ttmt) REVERT: A 279 TYR cc_start: 0.8430 (m-80) cc_final: 0.8035 (m-80) REVERT: A 392 PHE cc_start: 0.8245 (m-80) cc_final: 0.7903 (m-80) REVERT: A 414 GLN cc_start: 0.5838 (mm-40) cc_final: 0.5379 (tp-100) REVERT: A 429 PHE cc_start: 0.8398 (t80) cc_final: 0.8146 (t80) REVERT: A 563 GLN cc_start: 0.7693 (mt0) cc_final: 0.7303 (mt0) REVERT: A 584 ILE cc_start: 0.8590 (mm) cc_final: 0.8359 (mm) REVERT: A 586 ASP cc_start: 0.7569 (m-30) cc_final: 0.7255 (m-30) REVERT: A 599 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8541 (p) REVERT: A 619 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7102 (mm-30) REVERT: A 675 GLN cc_start: 0.7199 (mm-40) cc_final: 0.6982 (mt0) REVERT: A 773 GLU cc_start: 0.7712 (tp30) cc_final: 0.7492 (tp30) REVERT: A 904 TYR cc_start: 0.7772 (m-80) cc_final: 0.7450 (m-80) REVERT: A 907 ASN cc_start: 0.8849 (t0) cc_final: 0.8530 (t0) REVERT: A 912 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8482 (p) REVERT: A 994 ASP cc_start: 0.7893 (t0) cc_final: 0.7348 (t0) REVERT: A 1102 TRP cc_start: 0.8800 (m100) cc_final: 0.8374 (m100) REVERT: B 18 LEU cc_start: 0.7076 (mm) cc_final: 0.6596 (tp) REVERT: B 80 ASP cc_start: 0.7156 (OUTLIER) cc_final: 0.5736 (p0) REVERT: B 278 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8112 (ttmm) REVERT: B 309 GLU cc_start: 0.7981 (mp0) cc_final: 0.7547 (mp0) REVERT: B 310 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8764 (ptmt) REVERT: B 408 ARG cc_start: 0.7951 (ppt170) cc_final: 0.7280 (ppt170) REVERT: B 414 GLN cc_start: 0.6205 (tp40) cc_final: 0.5417 (tp40) REVERT: B 428 ASP cc_start: 0.8025 (p0) cc_final: 0.7738 (p0) REVERT: B 453 TYR cc_start: 0.7435 (p90) cc_final: 0.7206 (p90) REVERT: B 586 ASP cc_start: 0.7456 (m-30) cc_final: 0.6940 (m-30) REVERT: B 644 GLN cc_start: 0.8419 (tp40) cc_final: 0.8194 (tp40) REVERT: B 773 GLU cc_start: 0.7682 (tp30) cc_final: 0.7424 (tp30) REVERT: B 816 SER cc_start: 0.8668 (p) cc_final: 0.8393 (p) REVERT: B 825 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8095 (ttmm) REVERT: B 904 TYR cc_start: 0.7678 (m-10) cc_final: 0.7472 (m-80) REVERT: B 907 ASN cc_start: 0.8870 (t0) cc_final: 0.8617 (t0) REVERT: B 957 GLN cc_start: 0.7391 (tm130) cc_final: 0.7076 (tm-30) REVERT: B 979 ASP cc_start: 0.7767 (t0) cc_final: 0.7499 (t0) REVERT: C 14 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6757 (pp30) REVERT: C 153 MET cc_start: 0.7878 (pmm) cc_final: 0.7642 (pmm) REVERT: C 224 GLU cc_start: 0.7476 (mp0) cc_final: 0.7106 (mp0) REVERT: C 280 ASN cc_start: 0.8660 (p0) cc_final: 0.8375 (p0) REVERT: C 281 GLU cc_start: 0.8160 (pm20) cc_final: 0.7914 (pm20) REVERT: C 326 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8543 (pt) REVERT: C 409 GLN cc_start: 0.7905 (mt0) cc_final: 0.7335 (mp10) REVERT: C 494 SER cc_start: 0.7682 (OUTLIER) cc_final: 0.7443 (t) REVERT: C 563 GLN cc_start: 0.7737 (mt0) cc_final: 0.7415 (mt0) REVERT: C 564 GLN cc_start: 0.7138 (tm-30) cc_final: 0.6611 (tm-30) REVERT: C 808 ASP cc_start: 0.7487 (t0) cc_final: 0.7028 (t0) REVERT: C 936 ASP cc_start: 0.7892 (m-30) cc_final: 0.7595 (m-30) REVERT: C 983 ARG cc_start: 0.8040 (mtp180) cc_final: 0.7800 (mtp180) REVERT: C 990 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7562 (mm-30) REVERT: C 1102 TRP cc_start: 0.8939 (m100) cc_final: 0.8515 (m100) outliers start: 100 outliers final: 64 residues processed: 639 average time/residue: 0.3995 time to fit residues: 393.9067 Evaluate side-chains 640 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 568 time to evaluate : 3.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 299 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 226 optimal weight: 0.0270 chunk 175 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 309 optimal weight: 0.0970 chunk 193 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 142 optimal weight: 0.3980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 115 GLN C 271 GLN C 388 ASN C 784 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27204 Z= 0.194 Angle : 0.666 14.355 36996 Z= 0.324 Chirality : 0.046 0.521 4458 Planarity : 0.004 0.042 4650 Dihedral : 8.193 103.322 5510 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.75 % Allowed : 17.32 % Favored : 78.92 % 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: -0.07 (0.14), residues: 3189 helix: 2.06 (0.20), residues: 690 sheet: 0.03 (0.18), residues: 702 loop : -0.94 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 152 HIS 0.006 0.001 HIS A 66 PHE 0.028 0.001 PHE C 133 TYR 0.022 0.001 TYR B 453 ARG 0.010 0.001 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 583 time to evaluate : 2.917 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 202 LYS cc_start: 0.8783 (mptt) cc_final: 0.8545 (mmmt) REVERT: A 237 ARG cc_start: 0.8016 (ttp-170) cc_final: 0.7662 (ttp80) REVERT: A 278 LYS cc_start: 0.8630 (ttmm) cc_final: 0.8347 (ttmt) REVERT: A 279 TYR cc_start: 0.8419 (m-80) cc_final: 0.8037 (m-80) REVERT: A 304 LYS cc_start: 0.8906 (mtpt) cc_final: 0.8573 (mmtm) REVERT: A 374 PHE cc_start: 0.7614 (m-80) cc_final: 0.7399 (m-80) REVERT: A 392 PHE cc_start: 0.8090 (m-80) cc_final: 0.7556 (m-80) REVERT: A 414 GLN cc_start: 0.5726 (mm-40) cc_final: 0.5309 (tp-100) REVERT: A 422 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7092 (p0) REVERT: A 429 PHE cc_start: 0.8392 (t80) cc_final: 0.8140 (t80) REVERT: A 563 GLN cc_start: 0.7675 (mt0) cc_final: 0.7242 (mt0) REVERT: A 586 ASP cc_start: 0.7611 (m-30) cc_final: 0.7277 (m-30) REVERT: A 591 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8113 (t) REVERT: A 599 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8551 (p) REVERT: A 675 GLN cc_start: 0.7206 (mm-40) cc_final: 0.6990 (mt0) REVERT: A 773 GLU cc_start: 0.7664 (tp30) cc_final: 0.7459 (tp30) REVERT: A 904 TYR cc_start: 0.7770 (m-80) cc_final: 0.7416 (m-80) REVERT: A 907 ASN cc_start: 0.8810 (t0) cc_final: 0.8504 (t0) REVERT: A 912 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8475 (p) REVERT: A 994 ASP cc_start: 0.7866 (t0) cc_final: 0.7310 (t0) REVERT: A 1102 TRP cc_start: 0.8770 (m100) cc_final: 0.8394 (m100) REVERT: B 18 LEU cc_start: 0.6993 (mm) cc_final: 0.6542 (tp) REVERT: B 177 MET cc_start: 0.3223 (pmm) cc_final: 0.2795 (pmm) REVERT: B 278 LYS cc_start: 0.8490 (ttmm) cc_final: 0.8068 (ttmm) REVERT: B 309 GLU cc_start: 0.8007 (mp0) cc_final: 0.7499 (mp0) REVERT: B 310 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8767 (ptmt) REVERT: B 386 LYS cc_start: 0.9011 (mmmt) cc_final: 0.8702 (mmmm) REVERT: B 408 ARG cc_start: 0.7955 (ppt170) cc_final: 0.7239 (ppt170) REVERT: B 414 GLN cc_start: 0.6217 (tp40) cc_final: 0.5407 (tp40) REVERT: B 428 ASP cc_start: 0.8019 (p0) cc_final: 0.7734 (p0) REVERT: B 442 ASP cc_start: 0.6840 (p0) cc_final: 0.6398 (p0) REVERT: B 563 GLN cc_start: 0.7655 (mt0) cc_final: 0.7451 (mp10) REVERT: B 586 ASP cc_start: 0.7461 (m-30) cc_final: 0.6951 (m-30) REVERT: B 619 GLU cc_start: 0.7496 (mp0) cc_final: 0.7296 (mp0) REVERT: B 773 GLU cc_start: 0.7690 (tp30) cc_final: 0.7424 (tp30) REVERT: B 776 LYS cc_start: 0.8556 (tppp) cc_final: 0.8321 (tppt) REVERT: B 816 SER cc_start: 0.8684 (p) cc_final: 0.8405 (p) REVERT: B 825 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8133 (ttmm) REVERT: B 907 ASN cc_start: 0.8857 (t0) cc_final: 0.8600 (t0) REVERT: B 912 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8532 (p) REVERT: B 957 GLN cc_start: 0.7354 (tm130) cc_final: 0.7053 (tm-30) REVERT: B 979 ASP cc_start: 0.7785 (t0) cc_final: 0.7505 (t0) REVERT: C 153 MET cc_start: 0.7794 (pmm) cc_final: 0.7514 (pmm) REVERT: C 224 GLU cc_start: 0.7451 (mp0) cc_final: 0.7074 (mp0) REVERT: C 269 TYR cc_start: 0.7669 (m-10) cc_final: 0.7410 (m-80) REVERT: C 278 LYS cc_start: 0.8320 (tttm) cc_final: 0.8045 (ttpt) REVERT: C 280 ASN cc_start: 0.8639 (p0) cc_final: 0.8359 (p0) REVERT: C 281 GLU cc_start: 0.8215 (pm20) cc_final: 0.7997 (pm20) REVERT: C 319 ARG cc_start: 0.7957 (mtp-110) cc_final: 0.7687 (mtp-110) REVERT: C 326 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8479 (pt) REVERT: C 409 GLN cc_start: 0.7890 (mt0) cc_final: 0.7055 (mt0) REVERT: C 457 ARG cc_start: 0.6747 (OUTLIER) cc_final: 0.6383 (tpt90) REVERT: C 494 SER cc_start: 0.7599 (OUTLIER) cc_final: 0.7388 (t) REVERT: C 563 GLN cc_start: 0.7731 (mt0) cc_final: 0.7430 (mt0) REVERT: C 564 GLN cc_start: 0.7163 (tm-30) cc_final: 0.6635 (tm-30) REVERT: C 776 LYS cc_start: 0.8648 (tppp) cc_final: 0.8402 (tptp) REVERT: C 808 ASP cc_start: 0.7467 (t0) cc_final: 0.7020 (t0) REVERT: C 936 ASP cc_start: 0.7885 (m-30) cc_final: 0.7590 (m-30) REVERT: C 983 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7762 (mtp180) REVERT: C 990 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7585 (mm-30) REVERT: C 1102 TRP cc_start: 0.8911 (m100) cc_final: 0.8486 (m100) outliers start: 106 outliers final: 65 residues processed: 637 average time/residue: 0.3863 time to fit residues: 380.5503 Evaluate side-chains 634 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 559 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 191 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.0670 chunk 196 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 152 optimal weight: 0.4980 chunk 28 optimal weight: 0.1980 chunk 243 optimal weight: 0.2980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 580 GLN C 784 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27204 Z= 0.182 Angle : 0.661 15.125 36996 Z= 0.320 Chirality : 0.045 0.496 4458 Planarity : 0.004 0.073 4650 Dihedral : 7.721 101.722 5510 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.98 % Allowed : 18.31 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3189 helix: 2.16 (0.20), residues: 690 sheet: 0.10 (0.18), residues: 702 loop : -0.89 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 152 HIS 0.007 0.001 HIS A 66 PHE 0.028 0.001 PHE C 133 TYR 0.027 0.001 TYR C1138 ARG 0.011 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 582 time to evaluate : 2.788 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: A 191 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6853 (mm-30) REVERT: A 202 LYS cc_start: 0.8783 (mptt) cc_final: 0.8540 (mmmt) REVERT: A 237 ARG cc_start: 0.7991 (ttp-170) cc_final: 0.7656 (ttp80) REVERT: A 278 LYS cc_start: 0.8615 (ttmm) cc_final: 0.8336 (ttmt) REVERT: A 279 TYR cc_start: 0.8359 (m-80) cc_final: 0.8001 (m-80) REVERT: A 304 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8572 (mmtm) REVERT: A 346 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7365 (ttp-110) REVERT: A 347 PHE cc_start: 0.7484 (m-10) cc_final: 0.7142 (m-10) REVERT: A 374 PHE cc_start: 0.7614 (m-80) cc_final: 0.7383 (m-80) REVERT: A 392 PHE cc_start: 0.8112 (m-80) cc_final: 0.7677 (m-80) REVERT: A 414 GLN cc_start: 0.5728 (mm-40) cc_final: 0.5278 (tp-100) REVERT: A 422 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.7021 (p0) REVERT: A 429 PHE cc_start: 0.8401 (t80) cc_final: 0.8166 (t80) REVERT: A 563 GLN cc_start: 0.7642 (mt0) cc_final: 0.7223 (mt0) REVERT: A 586 ASP cc_start: 0.7611 (m-30) cc_final: 0.7278 (m-30) REVERT: A 599 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8565 (p) REVERT: A 646 ARG cc_start: 0.7967 (mmt180) cc_final: 0.7756 (mmt180) REVERT: A 675 GLN cc_start: 0.7211 (mm-40) cc_final: 0.6991 (mt0) REVERT: A 773 GLU cc_start: 0.7651 (tp30) cc_final: 0.7231 (tp30) REVERT: A 904 TYR cc_start: 0.7756 (m-80) cc_final: 0.7410 (m-80) REVERT: A 907 ASN cc_start: 0.8798 (t0) cc_final: 0.8491 (t0) REVERT: A 912 THR cc_start: 0.8806 (OUTLIER) cc_final: 0.8486 (p) REVERT: A 1102 TRP cc_start: 0.8746 (m100) cc_final: 0.8368 (m100) REVERT: B 18 LEU cc_start: 0.6972 (mm) cc_final: 0.6518 (tp) REVERT: B 129 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7927 (mmtt) REVERT: B 177 MET cc_start: 0.3259 (pmm) cc_final: 0.2849 (pmm) REVERT: B 277 LEU cc_start: 0.8712 (mp) cc_final: 0.8466 (mp) REVERT: B 278 LYS cc_start: 0.8400 (ttmm) cc_final: 0.8088 (ttpt) REVERT: B 360 ASN cc_start: 0.8141 (t0) cc_final: 0.7806 (t0) REVERT: B 386 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8596 (mmmm) REVERT: B 408 ARG cc_start: 0.7989 (ppt170) cc_final: 0.7272 (ppt170) REVERT: B 414 GLN cc_start: 0.6279 (tp40) cc_final: 0.5521 (tp40) REVERT: B 428 ASP cc_start: 0.8023 (p0) cc_final: 0.7741 (p0) REVERT: B 442 ASP cc_start: 0.6859 (p0) cc_final: 0.6473 (p0) REVERT: B 563 GLN cc_start: 0.7653 (mt0) cc_final: 0.7427 (mp10) REVERT: B 586 ASP cc_start: 0.7490 (m-30) cc_final: 0.7006 (m-30) REVERT: B 773 GLU cc_start: 0.7695 (tp30) cc_final: 0.7433 (tp30) REVERT: B 776 LYS cc_start: 0.8595 (tppp) cc_final: 0.8342 (tppt) REVERT: B 816 SER cc_start: 0.8704 (p) cc_final: 0.8414 (p) REVERT: B 825 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8137 (ttmm) REVERT: B 907 ASN cc_start: 0.8859 (t0) cc_final: 0.8593 (t0) REVERT: B 912 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8535 (p) REVERT: B 957 GLN cc_start: 0.7333 (tm130) cc_final: 0.7032 (tm-30) REVERT: B 979 ASP cc_start: 0.7768 (t0) cc_final: 0.7499 (t0) REVERT: C 224 GLU cc_start: 0.7435 (mp0) cc_final: 0.7048 (mp0) REVERT: C 278 LYS cc_start: 0.8315 (tttm) cc_final: 0.7947 (ttmm) REVERT: C 280 ASN cc_start: 0.8597 (p0) cc_final: 0.8311 (p0) REVERT: C 319 ARG cc_start: 0.7953 (mtp-110) cc_final: 0.7674 (mtp-110) REVERT: C 409 GLN cc_start: 0.7976 (mt0) cc_final: 0.7594 (mt0) REVERT: C 457 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.6364 (tpt90) REVERT: C 494 SER cc_start: 0.7605 (OUTLIER) cc_final: 0.7235 (t) REVERT: C 563 GLN cc_start: 0.7720 (mt0) cc_final: 0.7317 (mt0) REVERT: C 564 GLN cc_start: 0.7171 (tm-30) cc_final: 0.6667 (tm-30) REVERT: C 776 LYS cc_start: 0.8654 (tppp) cc_final: 0.8416 (tptp) REVERT: C 808 ASP cc_start: 0.7469 (t0) cc_final: 0.7030 (t0) REVERT: C 936 ASP cc_start: 0.7849 (m-30) cc_final: 0.7543 (m-30) REVERT: C 990 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7591 (mm-30) REVERT: C 1004 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8398 (tt) REVERT: C 1102 TRP cc_start: 0.8904 (m100) cc_final: 0.8496 (m100) outliers start: 84 outliers final: 59 residues processed: 626 average time/residue: 0.4185 time to fit residues: 409.9584 Evaluate side-chains 632 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 563 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 281 optimal weight: 0.8980 chunk 296 optimal weight: 0.0370 chunk 270 optimal weight: 3.9990 chunk 288 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 chunk 287 optimal weight: 0.8980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN C 388 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS C1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27204 Z= 0.232 Angle : 0.679 15.336 36996 Z= 0.331 Chirality : 0.046 0.490 4458 Planarity : 0.004 0.068 4650 Dihedral : 7.504 101.860 5510 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.29 % Allowed : 18.10 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.14), residues: 3189 helix: 2.08 (0.20), residues: 687 sheet: 0.03 (0.18), residues: 699 loop : -0.85 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 258 HIS 0.007 0.001 HIS A 66 PHE 0.026 0.001 PHE A 92 TYR 0.025 0.001 TYR C1138 ARG 0.010 0.001 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 581 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6878 (mm-30) REVERT: A 202 LYS cc_start: 0.8784 (mptt) cc_final: 0.8539 (mmmt) REVERT: A 237 ARG cc_start: 0.8031 (ttp-170) cc_final: 0.7613 (ttp80) REVERT: A 278 LYS cc_start: 0.8636 (ttmm) cc_final: 0.8301 (ttmt) REVERT: A 279 TYR cc_start: 0.8390 (m-80) cc_final: 0.8031 (m-80) REVERT: A 346 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7362 (ttp-110) REVERT: A 374 PHE cc_start: 0.7700 (m-80) cc_final: 0.7441 (m-80) REVERT: A 392 PHE cc_start: 0.8294 (m-80) cc_final: 0.7845 (m-80) REVERT: A 422 ASN cc_start: 0.7720 (OUTLIER) cc_final: 0.7073 (p0) REVERT: A 429 PHE cc_start: 0.8418 (t80) cc_final: 0.8157 (t80) REVERT: A 563 GLN cc_start: 0.7687 (mt0) cc_final: 0.7250 (mt0) REVERT: A 586 ASP cc_start: 0.7621 (m-30) cc_final: 0.7298 (m-30) REVERT: A 599 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8577 (p) REVERT: A 646 ARG cc_start: 0.7985 (mmt180) cc_final: 0.7784 (mmt180) REVERT: A 675 GLN cc_start: 0.7228 (mm-40) cc_final: 0.7010 (mt0) REVERT: A 904 TYR cc_start: 0.7786 (m-80) cc_final: 0.7427 (m-80) REVERT: A 907 ASN cc_start: 0.8820 (t0) cc_final: 0.8517 (t0) REVERT: A 912 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8460 (p) REVERT: A 994 ASP cc_start: 0.7892 (t70) cc_final: 0.7338 (t0) REVERT: A 1102 TRP cc_start: 0.8766 (m100) cc_final: 0.8372 (m100) REVERT: B 18 LEU cc_start: 0.6911 (mm) cc_final: 0.6467 (tp) REVERT: B 129 LYS cc_start: 0.8240 (mmtt) cc_final: 0.8020 (mmtt) REVERT: B 177 MET cc_start: 0.3151 (pmm) cc_final: 0.2712 (pmm) REVERT: B 277 LEU cc_start: 0.8728 (mp) cc_final: 0.8514 (mp) REVERT: B 278 LYS cc_start: 0.8379 (ttmm) cc_final: 0.7971 (ttmm) REVERT: B 386 LYS cc_start: 0.9022 (mmmt) cc_final: 0.8596 (mmmm) REVERT: B 408 ARG cc_start: 0.7923 (ppt170) cc_final: 0.7232 (ppt170) REVERT: B 414 GLN cc_start: 0.6276 (tp40) cc_final: 0.5632 (tp40) REVERT: B 428 ASP cc_start: 0.8022 (p0) cc_final: 0.7749 (p0) REVERT: B 437 ASN cc_start: 0.6902 (m-40) cc_final: 0.6437 (m110) REVERT: B 586 ASP cc_start: 0.7501 (m-30) cc_final: 0.7011 (m-30) REVERT: B 773 GLU cc_start: 0.7708 (tp30) cc_final: 0.7431 (tp30) REVERT: B 816 SER cc_start: 0.8729 (p) cc_final: 0.8429 (p) REVERT: B 825 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8145 (ttmm) REVERT: B 907 ASN cc_start: 0.8869 (t0) cc_final: 0.8605 (t0) REVERT: B 912 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8535 (p) REVERT: B 957 GLN cc_start: 0.7343 (tm130) cc_final: 0.7037 (tm-30) REVERT: B 979 ASP cc_start: 0.7779 (t0) cc_final: 0.7497 (t0) REVERT: C 224 GLU cc_start: 0.7459 (mp0) cc_final: 0.7072 (mp0) REVERT: C 278 LYS cc_start: 0.8346 (tttm) cc_final: 0.8136 (ttpt) REVERT: C 280 ASN cc_start: 0.8631 (p0) cc_final: 0.8343 (p0) REVERT: C 319 ARG cc_start: 0.7947 (mtp-110) cc_final: 0.7685 (mtp-110) REVERT: C 424 LYS cc_start: 0.6822 (tptt) cc_final: 0.6611 (mmtm) REVERT: C 442 ASP cc_start: 0.7348 (p0) cc_final: 0.7129 (p0) REVERT: C 457 ARG cc_start: 0.6727 (OUTLIER) cc_final: 0.6374 (tpt90) REVERT: C 494 SER cc_start: 0.7621 (OUTLIER) cc_final: 0.7388 (t) REVERT: C 563 GLN cc_start: 0.7711 (mt0) cc_final: 0.7383 (mt0) REVERT: C 564 GLN cc_start: 0.7235 (tm-30) cc_final: 0.6678 (tm-30) REVERT: C 776 LYS cc_start: 0.8638 (tppp) cc_final: 0.8409 (tptp) REVERT: C 808 ASP cc_start: 0.7546 (t0) cc_final: 0.7102 (t0) REVERT: C 904 TYR cc_start: 0.7569 (m-80) cc_final: 0.7313 (m-10) REVERT: C 912 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8498 (p) REVERT: C 936 ASP cc_start: 0.7835 (m-30) cc_final: 0.7543 (m-30) REVERT: C 990 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7594 (mm-30) REVERT: C 1102 TRP cc_start: 0.8916 (m100) cc_final: 0.8494 (m100) outliers start: 93 outliers final: 74 residues processed: 636 average time/residue: 0.3875 time to fit residues: 381.4415 Evaluate side-chains 655 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 571 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 189 optimal weight: 1.9990 chunk 304 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 chunk 319 optimal weight: 0.0050 chunk 294 optimal weight: 1.9990 chunk 254 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 196 optimal weight: 0.7980 chunk 156 optimal weight: 0.4980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A1002 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27204 Z= 0.193 Angle : 0.672 15.671 36996 Z= 0.327 Chirality : 0.046 0.475 4458 Planarity : 0.004 0.055 4650 Dihedral : 7.219 100.591 5510 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.94 % Allowed : 18.88 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3189 helix: 1.99 (0.20), residues: 705 sheet: 0.01 (0.18), residues: 705 loop : -0.79 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 104 HIS 0.006 0.001 HIS A 66 PHE 0.025 0.001 PHE A 92 TYR 0.024 0.001 TYR C1138 ARG 0.010 0.001 ARG B 765 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 595 time to evaluate : 2.728 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 191 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6817 (mm-30) REVERT: A 202 LYS cc_start: 0.8786 (mptt) cc_final: 0.8537 (mmmt) REVERT: A 237 ARG cc_start: 0.8027 (ttp-170) cc_final: 0.7782 (ttp80) REVERT: A 278 LYS cc_start: 0.8640 (ttmm) cc_final: 0.8296 (ttmt) REVERT: A 279 TYR cc_start: 0.8362 (m-80) cc_final: 0.8013 (m-80) REVERT: A 309 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7943 (mm-30) REVERT: A 346 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7320 (ttp-110) REVERT: A 347 PHE cc_start: 0.7431 (m-10) cc_final: 0.6933 (m-80) REVERT: A 374 PHE cc_start: 0.7696 (m-80) cc_final: 0.7432 (m-80) REVERT: A 378 LYS cc_start: 0.7864 (tmtt) cc_final: 0.7601 (tptt) REVERT: A 422 ASN cc_start: 0.7690 (OUTLIER) cc_final: 0.7068 (p0) REVERT: A 429 PHE cc_start: 0.8415 (t80) cc_final: 0.8168 (t80) REVERT: A 534 VAL cc_start: 0.9258 (OUTLIER) cc_final: 0.8988 (m) REVERT: A 563 GLN cc_start: 0.7668 (mt0) cc_final: 0.7239 (mt0) REVERT: A 586 ASP cc_start: 0.7611 (m-30) cc_final: 0.7268 (m-30) REVERT: A 599 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8588 (p) REVERT: A 675 GLN cc_start: 0.7218 (mm-40) cc_final: 0.7005 (mt0) REVERT: A 904 TYR cc_start: 0.7773 (m-80) cc_final: 0.7460 (m-80) REVERT: A 907 ASN cc_start: 0.8793 (t0) cc_final: 0.8498 (t0) REVERT: A 912 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8481 (p) REVERT: A 994 ASP cc_start: 0.7883 (t70) cc_final: 0.7306 (t0) REVERT: A 1102 TRP cc_start: 0.8745 (m100) cc_final: 0.8356 (m100) REVERT: B 18 LEU cc_start: 0.6800 (mm) cc_final: 0.6430 (tp) REVERT: B 129 LYS cc_start: 0.8249 (mmtt) cc_final: 0.7967 (mmtt) REVERT: B 177 MET cc_start: 0.3222 (pmm) cc_final: 0.2807 (pmm) REVERT: B 188 ASN cc_start: 0.6742 (t0) cc_final: 0.5941 (t0) REVERT: B 277 LEU cc_start: 0.8741 (mp) cc_final: 0.8531 (mp) REVERT: B 278 LYS cc_start: 0.8373 (ttmm) cc_final: 0.7961 (ttmm) REVERT: B 360 ASN cc_start: 0.8134 (t0) cc_final: 0.7806 (t0) REVERT: B 386 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8586 (mmmm) REVERT: B 408 ARG cc_start: 0.7949 (ppt170) cc_final: 0.7315 (ppt170) REVERT: B 414 GLN cc_start: 0.6328 (tp40) cc_final: 0.5759 (tp40) REVERT: B 428 ASP cc_start: 0.8015 (p0) cc_final: 0.7745 (p0) REVERT: B 437 ASN cc_start: 0.6857 (m-40) cc_final: 0.6330 (m110) REVERT: B 442 ASP cc_start: 0.6889 (p0) cc_final: 0.6580 (p0) REVERT: B 586 ASP cc_start: 0.7503 (m-30) cc_final: 0.7011 (m-30) REVERT: B 773 GLU cc_start: 0.7700 (tp30) cc_final: 0.7436 (tp30) REVERT: B 816 SER cc_start: 0.8732 (p) cc_final: 0.8432 (p) REVERT: B 825 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8137 (ttmm) REVERT: B 907 ASN cc_start: 0.8866 (t0) cc_final: 0.8604 (t0) REVERT: B 912 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8538 (p) REVERT: B 957 GLN cc_start: 0.7318 (tm130) cc_final: 0.7017 (tm-30) REVERT: B 979 ASP cc_start: 0.7761 (t0) cc_final: 0.7490 (t0) REVERT: C 190 ARG cc_start: 0.7374 (mmm-85) cc_final: 0.5450 (mmt90) REVERT: C 224 GLU cc_start: 0.7472 (mp0) cc_final: 0.7055 (mp0) REVERT: C 319 ARG cc_start: 0.7946 (mtp-110) cc_final: 0.7672 (mtp-110) REVERT: C 442 ASP cc_start: 0.7298 (p0) cc_final: 0.7078 (p0) REVERT: C 457 ARG cc_start: 0.6704 (OUTLIER) cc_final: 0.6336 (tpt90) REVERT: C 494 SER cc_start: 0.7625 (OUTLIER) cc_final: 0.7406 (t) REVERT: C 563 GLN cc_start: 0.7725 (mt0) cc_final: 0.7402 (mt0) REVERT: C 564 GLN cc_start: 0.7258 (tm-30) cc_final: 0.6693 (tm-30) REVERT: C 776 LYS cc_start: 0.8632 (tppp) cc_final: 0.8391 (tptp) REVERT: C 808 ASP cc_start: 0.7538 (t0) cc_final: 0.7081 (t0) REVERT: C 904 TYR cc_start: 0.7481 (m-80) cc_final: 0.7266 (m-10) REVERT: C 912 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8510 (p) REVERT: C 936 ASP cc_start: 0.7824 (m-30) cc_final: 0.7502 (m-30) REVERT: C 990 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7588 (mm-30) REVERT: C 1041 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7947 (t0) REVERT: C 1102 TRP cc_start: 0.8899 (m100) cc_final: 0.8490 (m100) outliers start: 83 outliers final: 64 residues processed: 640 average time/residue: 0.3821 time to fit residues: 377.5965 Evaluate side-chains 648 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 572 time to evaluate : 2.876 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 202 optimal weight: 0.9990 chunk 271 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 234 optimal weight: 0.4980 chunk 37 optimal weight: 0.2980 chunk 70 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 261 optimal weight: 0.0770 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 777 ASN A 804 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.102091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.084045 restraints weight = 64627.779| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.15 r_work: 0.3199 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 27204 Z= 0.199 Angle : 0.676 15.548 36996 Z= 0.329 Chirality : 0.045 0.461 4458 Planarity : 0.004 0.113 4650 Dihedral : 7.074 99.528 5510 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.08 % Allowed : 18.92 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3189 helix: 2.00 (0.20), residues: 705 sheet: 0.05 (0.18), residues: 699 loop : -0.80 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.017 0.001 HIS C 207 PHE 0.025 0.001 PHE A 92 TYR 0.024 0.001 TYR C1138 ARG 0.017 0.001 ARG C 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7488.09 seconds wall clock time: 135 minutes 18.42 seconds (8118.42 seconds total)