Starting phenix.real_space_refine on Tue Feb 20 09:05:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbk_24981/02_2024/7sbk_24981_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbk_24981/02_2024/7sbk_24981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbk_24981/02_2024/7sbk_24981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbk_24981/02_2024/7sbk_24981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbk_24981/02_2024/7sbk_24981_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbk_24981/02_2024/7sbk_24981_neut.pdb" } resolution = 3.1 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= 0.042 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 117 5.16 5 C 17388 2.51 5 N 4416 2.21 5 O 5496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 21": "NH1" <-> "NH2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 646": "NH1" <-> "NH2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B ASP 775": "OD1" <-> "OD2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B ASP 820": "OD1" <-> "OD2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B ARG 1000": "NH1" <-> "NH2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A ASP 796": "OD1" <-> "OD2" Residue "A ASP 820": "OD1" <-> "OD2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C ASP 796": "OD1" <-> "OD2" Residue "C ASP 820": "OD1" <-> "OD2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1127": "OD1" <-> "OD2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1144": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27417 Number of models: 1 Model: "" Number of chains: 39 Chain: "B" Number of atoms: 8624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8624 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 52, 'TRANS': 1048} Chain breaks: 4 Chain: "A" Number of atoms: 8624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8624 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 52, 'TRANS': 1048} Chain breaks: 4 Chain: "C" Number of atoms: 8624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8624 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 52, 'TRANS': 1048} Chain breaks: 4 Chain: "D" 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: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 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: "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: 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 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: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 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: 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: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 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: "V" 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: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 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: 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: 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: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 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: 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: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 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: "g" 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: "h" 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: "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: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.98, per 1000 atoms: 0.55 Number of scatterers: 27417 At special positions: 0 Unit cell: (143.562, 142.737, 193.066, 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 117 16.00 O 5496 8.00 N 4416 7.00 C 17388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.01 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG E 2 " - " MAN E 3 " " NAG F 2 " - " MAN F 3 " " NAG H 2 " - " MAN H 3 " " NAG I 2 " - " MAN I 3 " " NAG K 2 " - " MAN K 3 " " NAG L 2 " - " MAN L 3 " " NAG M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG O 2 " - " MAN O 3 " " NAG P 2 " - " MAN P 3 " " NAG Q 2 " - " MAN Q 3 " " NAG S 2 " - " MAN S 3 " " NAG T 2 " - " MAN T 3 " " NAG V 2 " - " MAN V 3 " " NAG W 2 " - " MAN W 3 " " NAG X 2 " - " MAN X 3 " " NAG Y 2 " - " MAN Y 3 " " NAG Z 2 " - " MAN Z 3 " " NAG a 2 " - " MAN a 3 " " NAG b 2 " - " MAN b 3 " " NAG d 2 " - " MAN d 3 " " NAG e 2 " - " MAN e 3 " " NAG g 2 " - " MAN g 3 " " NAG h 2 " - " MAN h 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 J 1 " - " FUC J 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG U 1 " - " FUC U 3 " " NAG f 1 " - " FUC f 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 149 " " NAG A1403 " - " ASN A 331 " " NAG A1404 " - " ASN A 603 " " NAG A1405 " - " ASN A 657 " " NAG A1406 " - " ASN A 709 " " NAG A1407 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 331 " " NAG B1404 " - " ASN B 603 " " NAG B1405 " - " ASN B 657 " " NAG B1406 " - " ASN B 709 " " NAG B1407 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 603 " " NAG C1405 " - " ASN C 657 " " NAG C1406 " - " ASN C 709 " " NAG C1407 " - " ASN C1158 " " NAG D 1 " - " ASN B 122 " " NAG E 1 " - " ASN B 234 " " NAG F 1 " - " ASN B 282 " " NAG G 1 " - " ASN B 616 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1074 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B 343 " " NAG N 1 " - " ASN B 165 " " NAG O 1 " - " ASN A 122 " " NAG P 1 " - " ASN A 234 " " NAG Q 1 " - " ASN A 282 " " NAG R 1 " - " ASN A 616 " " NAG S 1 " - " ASN A 717 " " NAG T 1 " - " ASN A 801 " " NAG U 1 " - " ASN A1074 " " NAG V 1 " - " ASN A1098 " " NAG W 1 " - " ASN A1134 " " NAG X 1 " - " ASN A 343 " " NAG Y 1 " - " ASN A 165 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C 234 " " NAG b 1 " - " ASN C 282 " " NAG c 1 " - " ASN C 616 " " NAG d 1 " - " ASN C 717 " " NAG e 1 " - " ASN C 801 " " NAG f 1 " - " ASN C1074 " " NAG g 1 " - " ASN C1098 " " NAG h 1 " - " ASN C1134 " " NAG i 1 " - " ASN C 343 " " NAG j 1 " - " ASN C 165 " Time building additional restraints: 12.25 Conformation dependent library (CDL) restraints added in 4.4 seconds 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6186 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 45 sheets defined 27.4% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'B' and resid 154 through 160 removed outlier: 4.425A pdb=" N VAL B 159 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.929A pdb=" N ASN B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 344 removed outlier: 3.633A pdb=" N ALA B 344 " --> pdb=" O GLU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.556A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.166A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.905A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.745A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.042A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) 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: 3.891A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.797A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.607A 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 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: 4.112A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.206A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1160 Processing helix chain 'A' and resid 154 through 160 removed outlier: 4.425A pdb=" N VAL A 159 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.929A pdb=" N ASN A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.633A pdb=" N ALA A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.556A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.165A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.902A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 618 through 624 removed outlier: 4.081A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.042A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) 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: 3.890A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.797A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.607A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.112A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.207A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1160 Processing helix chain 'C' and resid 154 through 160 removed outlier: 4.425A pdb=" N VAL C 159 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.928A pdb=" N ASN C 185 " --> pdb=" O GLY C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.633A pdb=" N ALA C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.557A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.165A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.102A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.614A 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 618 through 624 removed outlier: 4.054A pdb=" N ILE C 624 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.042A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) 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: 3.890A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.797A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.608A 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 Processing helix chain 'C' and resid 919 through 941 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: 4.112A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.208A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1160 Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 31 removed outlier: 8.482A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.540A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.699A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.860A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.138A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.370A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N PHE B 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.088A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.107A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.696A pdb=" N ALA B 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LYS A 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ASN B 703 " --> pdb=" O LYS A 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.977A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.950A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'B' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.438A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.482A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.700A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.859A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.138A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.370A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.088A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.107A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.714A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LYS C 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASN A 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.978A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.950A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.438A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 31 removed outlier: 8.482A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.699A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.860A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.137A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.088A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.107A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.978A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.949A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.438A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1084 hydrogen bonds defined for protein. 2967 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.66 Time building geometry restraints manager: 13.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4401 1.30 - 1.43: 7335 1.43 - 1.57: 16129 1.57 - 1.70: 2 1.70 - 1.83: 147 Bond restraints: 28014 Sorted by residual: bond pdb=" C ARG B1019 " pdb=" O ARG B1019 " ideal model delta sigma weight residual 1.236 1.165 0.071 1.29e-02 6.01e+03 3.02e+01 bond pdb=" CA ARG B1019 " pdb=" C ARG B1019 " ideal model delta sigma weight residual 1.523 1.452 0.071 1.37e-02 5.33e+03 2.71e+01 bond pdb=" N THR C 630 " pdb=" CA THR C 630 " ideal model delta sigma weight residual 1.461 1.505 -0.044 9.20e-03 1.18e+04 2.30e+01 bond pdb=" C4 NAG i 2 " pdb=" O4 NAG i 2 " ideal model delta sigma weight residual 1.409 1.490 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C4 NAG X 2 " pdb=" O4 NAG X 2 " ideal model delta sigma weight residual 1.409 1.490 -0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 28009 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.50: 563 105.50 - 112.93: 13812 112.93 - 120.36: 13429 120.36 - 127.78: 10158 127.78 - 135.21: 141 Bond angle restraints: 38103 Sorted by residual: angle pdb=" N THR C 618 " pdb=" CA THR C 618 " pdb=" C THR C 618 " ideal model delta sigma weight residual 111.69 98.08 13.61 1.23e+00 6.61e-01 1.22e+02 angle pdb=" CA HIS A 625 " pdb=" CB HIS A 625 " pdb=" CG HIS A 625 " ideal model delta sigma weight residual 113.80 121.63 -7.83 1.00e+00 1.00e+00 6.14e+01 angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 112.54 103.06 9.48 1.22e+00 6.72e-01 6.04e+01 angle pdb=" CA HIS B 625 " pdb=" CB HIS B 625 " pdb=" CG HIS B 625 " ideal model delta sigma weight residual 113.80 121.11 -7.31 1.00e+00 1.00e+00 5.35e+01 angle pdb=" OD1 ASN C 149 " pdb=" CG ASN C 149 " pdb=" ND2 ASN C 149 " ideal model delta sigma weight residual 122.60 115.96 6.64 1.00e+00 1.00e+00 4.40e+01 ... (remaining 38098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.12: 17171 25.12 - 50.23: 689 50.23 - 75.35: 206 75.35 - 100.46: 39 100.46 - 125.58: 81 Dihedral angle restraints: 18186 sinusoidal: 8568 harmonic: 9618 Sorted by residual: dihedral pdb=" CA LEU B 517 " pdb=" C LEU B 517 " pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta harmonic sigma weight residual 180.00 150.06 29.94 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 150.07 29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA LEU A 517 " pdb=" C LEU A 517 " pdb=" N LEU A 518 " pdb=" CA LEU A 518 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 ... (remaining 18183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.195: 4405 0.195 - 0.389: 232 0.389 - 0.584: 9 0.584 - 0.778: 1 0.778 - 0.973: 3 Chirality restraints: 4650 Sorted by residual: chirality pdb=" C1 MAN L 3 " pdb=" O4 NAG L 2 " pdb=" C2 MAN L 3 " pdb=" O5 MAN L 3 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-02 2.50e+03 5.39e+01 chirality pdb=" C1 MAN W 3 " pdb=" O4 NAG W 2 " pdb=" C2 MAN W 3 " pdb=" O5 MAN W 3 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-02 2.50e+03 5.33e+01 chirality pdb=" C1 MAN h 3 " pdb=" O4 NAG h 2 " pdb=" C2 MAN h 3 " pdb=" O5 MAN h 3 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-02 2.50e+03 5.29e+01 ... (remaining 4647 not shown) Planarity restraints: 4815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 149 " 0.025 2.00e-02 2.50e+03 1.13e-01 1.60e+02 pdb=" CG ASN B 149 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN B 149 " -0.102 2.00e-02 2.50e+03 pdb=" ND2 ASN B 149 " 0.190 2.00e-02 2.50e+03 pdb=" C1 NAG B1402 " -0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 149 " -0.025 2.00e-02 2.50e+03 1.13e-01 1.59e+02 pdb=" CG ASN C 149 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN C 149 " 0.102 2.00e-02 2.50e+03 pdb=" ND2 ASN C 149 " -0.190 2.00e-02 2.50e+03 pdb=" C1 NAG C1402 " 0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 149 " 0.025 2.00e-02 2.50e+03 1.13e-01 1.59e+02 pdb=" CG ASN A 149 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 149 " -0.102 2.00e-02 2.50e+03 pdb=" ND2 ASN A 149 " 0.190 2.00e-02 2.50e+03 pdb=" C1 NAG A1402 " -0.128 2.00e-02 2.50e+03 ... (remaining 4812 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 1 2.05 - 2.76: 1763 2.76 - 3.48: 38752 3.48 - 4.19: 64316 4.19 - 4.90: 110146 Nonbonded interactions: 214978 Sorted by model distance: nonbonded pdb=" CG PRO C 295 " pdb=" CE1 TYR C 636 " model vdw 1.339 3.740 nonbonded pdb=" CG2 VAL C 608 " pdb=" OH TYR C 636 " model vdw 2.143 3.460 nonbonded pdb=" CG PRO C 295 " pdb=" CZ TYR C 636 " model vdw 2.202 3.660 nonbonded pdb=" OE1 GLU A 298 " pdb=" NE1 TRP A 633 " model vdw 2.209 2.520 nonbonded pdb=" OD2 ASP B 808 " pdb=" NZ LYS B 811 " model vdw 2.220 2.520 ... (remaining 214973 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' and resid 1 through 2) selection = (chain 'E' and resid 1 through 2) selection = (chain 'F' 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) selection = (chain 'K' and resid 1 through 2) selection = (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 'O' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' 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 'Z' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) selection = (chain 'g' 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) } ncs_group { reference = chain 'G' selection = chain 'R' selection = chain 'c' } 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: 0.040 Extract box with map and model: 24.090 Check model and map are aligned: 0.540 Set scattering table: 0.260 Process input model: 74.350 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.081 28014 Z= 0.934 Angle : 1.792 13.612 38103 Z= 1.172 Chirality : 0.108 0.973 4650 Planarity : 0.012 0.088 4761 Dihedral : 17.410 125.578 11874 Min Nonbonded Distance : 1.339 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.29 % Favored : 92.97 % Rotamer: Outliers : 1.49 % Allowed : 4.24 % Favored : 94.27 % Cbeta Deviations : 0.45 % 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: -1.92 (0.13), residues: 3273 helix: -1.42 (0.15), residues: 753 sheet: -0.18 (0.20), residues: 639 loop : -1.63 (0.12), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.138 0.032 TRP B 258 HIS 0.028 0.004 HIS A 625 PHE 0.095 0.015 PHE B 592 TYR 0.112 0.019 TYR C 145 ARG 0.009 0.001 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 748 time to evaluate : 3.343 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: B 140 PHE cc_start: 0.7607 (p90) cc_final: 0.7266 (p90) REVERT: B 205 SER cc_start: 0.8675 (p) cc_final: 0.8364 (t) REVERT: B 208 THR cc_start: 0.8040 (m) cc_final: 0.7670 (p) REVERT: B 224 GLU cc_start: 0.7103 (mp0) cc_final: 0.6744 (mp0) REVERT: B 290 ASP cc_start: 0.7517 (t0) cc_final: 0.7300 (t0) REVERT: B 360 ASN cc_start: 0.8210 (t0) cc_final: 0.7889 (t0) REVERT: B 403 ARG cc_start: 0.7174 (ptm160) cc_final: 0.6964 (ptm160) REVERT: B 455 LEU cc_start: 0.8861 (tp) cc_final: 0.8326 (tp) REVERT: B 580 GLN cc_start: 0.7868 (mt0) cc_final: 0.7652 (mt0) REVERT: B 596 SER cc_start: 0.9062 (m) cc_final: 0.8743 (p) REVERT: B 610 VAL cc_start: 0.9116 (t) cc_final: 0.8805 (m) REVERT: B 642 VAL cc_start: 0.8993 (t) cc_final: 0.8732 (p) REVERT: B 808 ASP cc_start: 0.7054 (t0) cc_final: 0.6717 (t0) REVERT: B 823 PHE cc_start: 0.8348 (m-80) cc_final: 0.8138 (m-80) REVERT: B 850 ILE cc_start: 0.8135 (mp) cc_final: 0.7927 (pt) REVERT: B 902 MET cc_start: 0.8493 (mmm) cc_final: 0.8027 (tpt) REVERT: B 964 LYS cc_start: 0.8613 (mmmm) cc_final: 0.8096 (mtpp) REVERT: B 967 SER cc_start: 0.8630 (m) cc_final: 0.8260 (p) REVERT: B 1050 MET cc_start: 0.8499 (ptp) cc_final: 0.8252 (ptp) REVERT: B 1127 ASP cc_start: 0.7702 (m-30) cc_final: 0.7483 (m-30) REVERT: B 1141 LEU cc_start: 0.8475 (tt) cc_final: 0.8057 (mm) REVERT: A 54 LEU cc_start: 0.8827 (mp) cc_final: 0.8448 (mt) REVERT: A 96 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.4770 (tt0) REVERT: A 129 LYS cc_start: 0.6894 (tttp) cc_final: 0.6659 (ttmm) REVERT: A 195 LYS cc_start: 0.8032 (tttt) cc_final: 0.7635 (tttt) REVERT: A 269 TYR cc_start: 0.6913 (m-80) cc_final: 0.6591 (m-80) REVERT: A 353 TRP cc_start: 0.8526 (p-90) cc_final: 0.8210 (p-90) REVERT: A 360 ASN cc_start: 0.8269 (t0) cc_final: 0.7926 (t0) REVERT: A 396 TYR cc_start: 0.7095 (m-10) cc_final: 0.6647 (m-10) REVERT: A 403 ARG cc_start: 0.7059 (ptm160) cc_final: 0.6254 (ptm160) REVERT: A 453 TYR cc_start: 0.6188 (p90) cc_final: 0.5726 (p90) REVERT: A 455 LEU cc_start: 0.8720 (tp) cc_final: 0.8285 (tp) REVERT: A 596 SER cc_start: 0.9069 (m) cc_final: 0.8816 (p) REVERT: A 642 VAL cc_start: 0.9262 (t) cc_final: 0.8923 (p) REVERT: A 646 ARG cc_start: 0.8062 (tpp80) cc_final: 0.7777 (tpt170) REVERT: A 823 PHE cc_start: 0.8267 (m-80) cc_final: 0.8037 (m-80) REVERT: A 850 ILE cc_start: 0.7995 (mp) cc_final: 0.7794 (pt) REVERT: A 926 GLN cc_start: 0.8718 (mt0) cc_final: 0.8488 (mt0) REVERT: A 986 LYS cc_start: 0.8380 (ttpp) cc_final: 0.7921 (tttm) REVERT: A 990 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7009 (mt-10) REVERT: A 1017 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7457 (tm-30) REVERT: A 1092 GLU cc_start: 0.7211 (pm20) cc_final: 0.6930 (pm20) REVERT: C 54 LEU cc_start: 0.8862 (mp) cc_final: 0.8509 (mp) REVERT: C 96 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.5470 (tt0) REVERT: C 129 LYS cc_start: 0.6911 (tttp) cc_final: 0.6655 (tttt) REVERT: C 276 LEU cc_start: 0.8998 (tp) cc_final: 0.8790 (tp) REVERT: C 360 ASN cc_start: 0.8166 (t0) cc_final: 0.7964 (t0) REVERT: C 383 SER cc_start: 0.8893 (t) cc_final: 0.8679 (p) REVERT: C 402 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7586 (tp) REVERT: C 523 THR cc_start: 0.7906 (OUTLIER) cc_final: 0.7464 (p) REVERT: C 596 SER cc_start: 0.9060 (m) cc_final: 0.8647 (p) REVERT: C 642 VAL cc_start: 0.9130 (t) cc_final: 0.8818 (p) REVERT: C 661 GLU cc_start: 0.7747 (pm20) cc_final: 0.7471 (pm20) REVERT: C 697 MET cc_start: 0.8186 (ptm) cc_final: 0.7904 (ptm) REVERT: C 790 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8448 (mtmm) REVERT: C 902 MET cc_start: 0.8398 (mmm) cc_final: 0.8133 (mmt) REVERT: C 1037 SER cc_start: 0.9021 (t) cc_final: 0.8723 (p) REVERT: C 1041 ASP cc_start: 0.8042 (m-30) cc_final: 0.7796 (m-30) REVERT: C 1045 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8371 (tptp) REVERT: C 1125 ASN cc_start: 0.8360 (p0) cc_final: 0.8067 (p0) REVERT: C 1127 ASP cc_start: 0.7755 (m-30) cc_final: 0.7475 (m-30) outliers start: 43 outliers final: 8 residues processed: 773 average time/residue: 0.4332 time to fit residues: 507.9810 Evaluate side-chains 598 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 586 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 581 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 0.5980 chunk 250 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 168 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 258 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 157 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 chunk 299 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 370 ASN B 751 ASN B 755 GLN B 764 ASN B 777 ASN B 856 ASN B 957 GLN B 969 ASN B1002 GLN A 125 ASN A 317 ASN A 370 ASN A 460 ASN A 777 ASN A 907 ASN A 957 GLN A 969 ASN A1005 GLN A1119 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 460 ASN C 607 GLN C 751 ASN C 777 ASN C 856 ASN C 907 ASN C 969 ASN C1113 GLN C1119 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28014 Z= 0.259 Angle : 0.792 12.786 38103 Z= 0.392 Chirality : 0.051 0.716 4650 Planarity : 0.004 0.039 4761 Dihedral : 14.789 105.231 5955 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.46 % Favored : 95.33 % Rotamer: Outliers : 2.33 % Allowed : 9.06 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3273 helix: 0.95 (0.19), residues: 729 sheet: -0.06 (0.18), residues: 726 loop : -1.32 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 633 HIS 0.009 0.001 HIS B 625 PHE 0.027 0.002 PHE B 347 TYR 0.029 0.002 TYR A 495 ARG 0.006 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 628 time to evaluate : 3.062 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: B 29 THR cc_start: 0.7885 (m) cc_final: 0.7588 (m) REVERT: B 140 PHE cc_start: 0.7593 (p90) cc_final: 0.7295 (p90) REVERT: B 143 VAL cc_start: 0.6990 (OUTLIER) cc_final: 0.6771 (p) REVERT: B 154 GLU cc_start: 0.7514 (mp0) cc_final: 0.7306 (mp0) REVERT: B 177 MET cc_start: 0.5246 (mpp) cc_final: 0.4942 (mmt) REVERT: B 356 LYS cc_start: 0.8941 (tptm) cc_final: 0.8714 (tptp) REVERT: B 360 ASN cc_start: 0.8245 (t0) cc_final: 0.8002 (t0) REVERT: B 406 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7465 (mm-30) REVERT: B 460 ASN cc_start: 0.8250 (m-40) cc_final: 0.7745 (m110) REVERT: B 565 PHE cc_start: 0.6906 (m-10) cc_final: 0.6490 (m-10) REVERT: B 596 SER cc_start: 0.9134 (m) cc_final: 0.8658 (p) REVERT: B 642 VAL cc_start: 0.9024 (t) cc_final: 0.8781 (p) REVERT: B 815 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8793 (ttm110) REVERT: B 990 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7559 (mm-30) REVERT: B 1050 MET cc_start: 0.8311 (ptp) cc_final: 0.8046 (ptm) REVERT: B 1107 ARG cc_start: 0.8173 (mtt90) cc_final: 0.7814 (mtt90) REVERT: A 96 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.5136 (tt0) REVERT: A 99 ASN cc_start: 0.8458 (t0) cc_final: 0.7822 (t0) REVERT: A 129 LYS cc_start: 0.6575 (tttp) cc_final: 0.6313 (ttmm) REVERT: A 206 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8612 (tmtt) REVERT: A 289 VAL cc_start: 0.8882 (t) cc_final: 0.8475 (m) REVERT: A 342 PHE cc_start: 0.8246 (m-80) cc_final: 0.7907 (m-80) REVERT: A 360 ASN cc_start: 0.8397 (t0) cc_final: 0.8032 (t0) REVERT: A 479 PRO cc_start: 0.6190 (Cg_endo) cc_final: 0.5986 (Cg_exo) REVERT: A 492 LEU cc_start: 0.8451 (tp) cc_final: 0.8200 (tp) REVERT: A 565 PHE cc_start: 0.6954 (m-10) cc_final: 0.6545 (m-10) REVERT: A 583 GLU cc_start: 0.7689 (pp20) cc_final: 0.7314 (pp20) REVERT: A 584 ILE cc_start: 0.8920 (mm) cc_final: 0.8616 (mm) REVERT: A 596 SER cc_start: 0.9243 (m) cc_final: 0.8760 (p) REVERT: A 642 VAL cc_start: 0.9174 (t) cc_final: 0.8875 (p) REVERT: A 725 GLU cc_start: 0.7688 (tt0) cc_final: 0.7424 (tt0) REVERT: A 773 GLU cc_start: 0.7769 (tt0) cc_final: 0.7517 (tt0) REVERT: A 904 TYR cc_start: 0.8178 (m-10) cc_final: 0.7722 (m-10) REVERT: A 926 GLN cc_start: 0.8676 (mt0) cc_final: 0.8464 (mt0) REVERT: A 986 LYS cc_start: 0.8211 (ttpp) cc_final: 0.7960 (ttmm) REVERT: A 990 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7138 (mt-10) REVERT: C 99 ASN cc_start: 0.8305 (t0) cc_final: 0.8076 (t0) REVERT: C 129 LYS cc_start: 0.6753 (tttp) cc_final: 0.6370 (tttt) REVERT: C 239 GLN cc_start: 0.7998 (tt0) cc_final: 0.7746 (mt0) REVERT: C 271 GLN cc_start: 0.8472 (mt0) cc_final: 0.8200 (mt0) REVERT: C 275 PHE cc_start: 0.8507 (m-80) cc_final: 0.8298 (m-80) REVERT: C 276 LEU cc_start: 0.8987 (tp) cc_final: 0.8738 (tt) REVERT: C 324 GLU cc_start: 0.7704 (pm20) cc_final: 0.7327 (pm20) REVERT: C 342 PHE cc_start: 0.8072 (m-80) cc_final: 0.7870 (m-80) REVERT: C 383 SER cc_start: 0.8813 (t) cc_final: 0.8426 (p) REVERT: C 434 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8478 (pt) REVERT: C 436 TRP cc_start: 0.6767 (p90) cc_final: 0.6502 (p90) REVERT: C 495 TYR cc_start: 0.5800 (m-80) cc_final: 0.5486 (m-80) REVERT: C 523 THR cc_start: 0.8014 (OUTLIER) cc_final: 0.7559 (p) REVERT: C 562 PHE cc_start: 0.7662 (p90) cc_final: 0.7408 (p90) REVERT: C 565 PHE cc_start: 0.6725 (m-10) cc_final: 0.6516 (m-10) REVERT: C 596 SER cc_start: 0.9153 (m) cc_final: 0.8549 (p) REVERT: C 610 VAL cc_start: 0.8853 (t) cc_final: 0.8631 (m) REVERT: C 820 ASP cc_start: 0.7870 (t0) cc_final: 0.7586 (m-30) REVERT: C 825 LYS cc_start: 0.8783 (tptt) cc_final: 0.8562 (mmtm) REVERT: C 902 MET cc_start: 0.8291 (mmm) cc_final: 0.7915 (mmt) REVERT: C 994 ASP cc_start: 0.7833 (t70) cc_final: 0.7503 (t70) REVERT: C 1037 SER cc_start: 0.9088 (t) cc_final: 0.8820 (p) outliers start: 67 outliers final: 32 residues processed: 664 average time/residue: 0.4183 time to fit residues: 430.1348 Evaluate side-chains 584 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 546 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 821 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 249 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 300 optimal weight: 0.0170 chunk 324 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 297 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN B 751 ASN B 777 ASN B 957 GLN B1002 GLN A 450 ASN A 751 ASN A 907 ASN A1002 GLN C 360 ASN C1005 GLN C1113 GLN C1119 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28014 Z= 0.248 Angle : 0.743 13.371 38103 Z= 0.362 Chirality : 0.050 0.711 4650 Planarity : 0.004 0.034 4761 Dihedral : 13.822 102.716 5953 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.44 % Favored : 94.35 % Rotamer: Outliers : 3.06 % Allowed : 11.15 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3273 helix: 1.25 (0.19), residues: 747 sheet: -0.01 (0.18), residues: 741 loop : -1.38 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 633 HIS 0.005 0.001 HIS C 207 PHE 0.029 0.002 PHE A1148 TYR 0.023 0.002 TYR A 170 ARG 0.013 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 601 time to evaluate : 3.260 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: B 29 THR cc_start: 0.7808 (m) cc_final: 0.7520 (m) REVERT: B 99 ASN cc_start: 0.8102 (t0) cc_final: 0.7866 (t0) REVERT: B 140 PHE cc_start: 0.7576 (p90) cc_final: 0.7249 (p90) REVERT: B 143 VAL cc_start: 0.7028 (OUTLIER) cc_final: 0.6813 (p) REVERT: B 154 GLU cc_start: 0.7519 (mp0) cc_final: 0.7199 (mp0) REVERT: B 168 PHE cc_start: 0.7347 (t80) cc_final: 0.6964 (t80) REVERT: B 360 ASN cc_start: 0.8273 (t0) cc_final: 0.8052 (t0) REVERT: B 452 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7567 (ptm160) REVERT: B 460 ASN cc_start: 0.8074 (m-40) cc_final: 0.7863 (m110) REVERT: B 557 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8275 (ptmt) REVERT: B 565 PHE cc_start: 0.6858 (m-10) cc_final: 0.6422 (m-10) REVERT: B 596 SER cc_start: 0.9117 (m) cc_final: 0.8559 (p) REVERT: B 642 VAL cc_start: 0.9187 (t) cc_final: 0.8892 (p) REVERT: B 646 ARG cc_start: 0.8183 (tpt170) cc_final: 0.7823 (tpt170) REVERT: B 776 LYS cc_start: 0.8492 (tptm) cc_final: 0.8220 (ttpt) REVERT: B 790 LYS cc_start: 0.8464 (mtmm) cc_final: 0.8245 (mtmm) REVERT: B 815 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8779 (tpp80) REVERT: B 825 LYS cc_start: 0.8778 (mmtt) cc_final: 0.8543 (mmtm) REVERT: B 990 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7527 (mm-30) REVERT: B 1050 MET cc_start: 0.8307 (ptp) cc_final: 0.7971 (ptm) REVERT: B 1107 ARG cc_start: 0.8225 (mtt90) cc_final: 0.7914 (mtt90) REVERT: A 96 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.5135 (tt0) REVERT: A 99 ASN cc_start: 0.8457 (t0) cc_final: 0.7774 (t0) REVERT: A 104 TRP cc_start: 0.7610 (m-90) cc_final: 0.7355 (m-90) REVERT: A 121 ASN cc_start: 0.8462 (OUTLIER) cc_final: 0.8244 (m-40) REVERT: A 154 GLU cc_start: 0.7451 (mp0) cc_final: 0.7116 (mp0) REVERT: A 206 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8631 (tmtt) REVERT: A 289 VAL cc_start: 0.8891 (t) cc_final: 0.8516 (m) REVERT: A 342 PHE cc_start: 0.8370 (m-80) cc_final: 0.8009 (m-80) REVERT: A 360 ASN cc_start: 0.8352 (t0) cc_final: 0.7910 (t0) REVERT: A 452 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7917 (ptm-80) REVERT: A 492 LEU cc_start: 0.8509 (tp) cc_final: 0.8255 (tp) REVERT: A 495 TYR cc_start: 0.5375 (m-80) cc_final: 0.5132 (m-80) REVERT: A 523 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7795 (p) REVERT: A 565 PHE cc_start: 0.6957 (m-10) cc_final: 0.6508 (m-10) REVERT: A 583 GLU cc_start: 0.7599 (pp20) cc_final: 0.7338 (pp20) REVERT: A 584 ILE cc_start: 0.8923 (mm) cc_final: 0.8617 (mm) REVERT: A 596 SER cc_start: 0.9236 (m) cc_final: 0.8652 (p) REVERT: A 642 VAL cc_start: 0.9170 (t) cc_final: 0.8881 (p) REVERT: A 725 GLU cc_start: 0.7668 (tt0) cc_final: 0.7411 (tt0) REVERT: A 773 GLU cc_start: 0.7742 (tt0) cc_final: 0.7520 (tt0) REVERT: A 904 TYR cc_start: 0.8207 (m-10) cc_final: 0.7846 (m-10) REVERT: A 964 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8443 (mtmm) REVERT: A 986 LYS cc_start: 0.8190 (ttpp) cc_final: 0.7919 (ttmm) REVERT: A 990 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7123 (mt-10) REVERT: C 96 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.5723 (tt0) REVERT: C 99 ASN cc_start: 0.8238 (t0) cc_final: 0.7843 (t0) REVERT: C 102 ARG cc_start: 0.7353 (mmt90) cc_final: 0.7148 (mmt90) REVERT: C 129 LYS cc_start: 0.6924 (tttp) cc_final: 0.6625 (tptt) REVERT: C 239 GLN cc_start: 0.8027 (tt0) cc_final: 0.7774 (mt0) REVERT: C 275 PHE cc_start: 0.8621 (m-80) cc_final: 0.8323 (m-80) REVERT: C 276 LEU cc_start: 0.8951 (tp) cc_final: 0.8725 (tt) REVERT: C 324 GLU cc_start: 0.7734 (pm20) cc_final: 0.7389 (pm20) REVERT: C 342 PHE cc_start: 0.8114 (m-80) cc_final: 0.7834 (m-80) REVERT: C 383 SER cc_start: 0.8795 (t) cc_final: 0.8413 (p) REVERT: C 406 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7394 (mm-30) REVERT: C 434 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8409 (mm) REVERT: C 436 TRP cc_start: 0.6845 (p90) cc_final: 0.6570 (p90) REVERT: C 452 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7261 (ptm160) REVERT: C 495 TYR cc_start: 0.6101 (m-80) cc_final: 0.5784 (m-80) REVERT: C 565 PHE cc_start: 0.6708 (m-10) cc_final: 0.6313 (m-10) REVERT: C 596 SER cc_start: 0.9137 (m) cc_final: 0.8431 (p) REVERT: C 610 VAL cc_start: 0.8878 (t) cc_final: 0.8554 (m) REVERT: C 820 ASP cc_start: 0.7893 (t0) cc_final: 0.7689 (m-30) REVERT: C 825 LYS cc_start: 0.8860 (tptt) cc_final: 0.8623 (mmtm) REVERT: C 994 ASP cc_start: 0.7784 (t70) cc_final: 0.7498 (t70) REVERT: C 1037 SER cc_start: 0.9111 (t) cc_final: 0.8840 (p) outliers start: 88 outliers final: 49 residues processed: 642 average time/residue: 0.3999 time to fit residues: 401.1768 Evaluate side-chains 609 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 548 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1146 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 143 optimal weight: 0.0040 chunk 201 optimal weight: 1.9990 chunk 301 optimal weight: 0.8980 chunk 318 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 285 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 GLN B 450 ASN B 777 ASN B 957 GLN B1002 GLN B1119 ASN A 751 ASN A 969 ASN A1005 GLN C 360 ASN C1113 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 28014 Z= 0.288 Angle : 0.738 12.872 38103 Z= 0.354 Chirality : 0.048 0.665 4650 Planarity : 0.004 0.055 4761 Dihedral : 13.057 101.381 5953 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.04 % Favored : 94.74 % Rotamer: Outliers : 3.44 % Allowed : 13.02 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3273 helix: 1.59 (0.20), residues: 729 sheet: -0.06 (0.19), residues: 696 loop : -1.26 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 633 HIS 0.006 0.001 HIS A 207 PHE 0.021 0.002 PHE C 140 TYR 0.021 0.002 TYR C1067 ARG 0.029 0.001 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 585 time to evaluate : 2.935 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: B 29 THR cc_start: 0.7841 (m) cc_final: 0.7573 (m) REVERT: B 96 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.4874 (tt0) REVERT: B 99 ASN cc_start: 0.8221 (t0) cc_final: 0.7534 (t0) REVERT: B 104 TRP cc_start: 0.7734 (m-90) cc_final: 0.7474 (m-90) REVERT: B 131 CYS cc_start: 0.4409 (m) cc_final: 0.4153 (m) REVERT: B 140 PHE cc_start: 0.7527 (p90) cc_final: 0.7163 (p90) REVERT: B 143 VAL cc_start: 0.6911 (OUTLIER) cc_final: 0.6693 (p) REVERT: B 153 MET cc_start: 0.6612 (tmm) cc_final: 0.6408 (tpt) REVERT: B 169 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8100 (mm-30) REVERT: B 360 ASN cc_start: 0.8340 (t0) cc_final: 0.8077 (t0) REVERT: B 452 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7533 (ptm160) REVERT: B 460 ASN cc_start: 0.7988 (m-40) cc_final: 0.7500 (m110) REVERT: B 523 THR cc_start: 0.8543 (m) cc_final: 0.8078 (p) REVERT: B 557 LYS cc_start: 0.8749 (mtpt) cc_final: 0.8403 (ptpt) REVERT: B 565 PHE cc_start: 0.6868 (m-10) cc_final: 0.6413 (m-10) REVERT: B 587 ILE cc_start: 0.8873 (mt) cc_final: 0.8594 (tp) REVERT: B 596 SER cc_start: 0.9153 (m) cc_final: 0.8604 (p) REVERT: B 642 VAL cc_start: 0.9280 (t) cc_final: 0.8997 (p) REVERT: B 646 ARG cc_start: 0.8139 (tpt170) cc_final: 0.7729 (tpt170) REVERT: B 825 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8498 (tptt) REVERT: B 912 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8244 (p) REVERT: B 1086 LYS cc_start: 0.8885 (mtmm) cc_final: 0.8675 (mtmm) REVERT: B 1107 ARG cc_start: 0.8277 (mtt90) cc_final: 0.7970 (mtt90) REVERT: A 96 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.5153 (tt0) REVERT: A 99 ASN cc_start: 0.8485 (t0) cc_final: 0.7755 (t0) REVERT: A 153 MET cc_start: 0.6417 (tmm) cc_final: 0.6108 (tpt) REVERT: A 206 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8545 (tmtt) REVERT: A 289 VAL cc_start: 0.8892 (t) cc_final: 0.8514 (m) REVERT: A 342 PHE cc_start: 0.8459 (m-80) cc_final: 0.8193 (m-80) REVERT: A 360 ASN cc_start: 0.8429 (t0) cc_final: 0.7999 (t0) REVERT: A 405 ASP cc_start: 0.7011 (p0) cc_final: 0.5942 (p0) REVERT: A 492 LEU cc_start: 0.8495 (tp) cc_final: 0.8285 (tp) REVERT: A 523 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7842 (p) REVERT: A 557 LYS cc_start: 0.8736 (mtpt) cc_final: 0.8338 (ptpt) REVERT: A 565 PHE cc_start: 0.7019 (m-10) cc_final: 0.6527 (m-10) REVERT: A 583 GLU cc_start: 0.7660 (pp20) cc_final: 0.7438 (pp20) REVERT: A 584 ILE cc_start: 0.8932 (mm) cc_final: 0.8612 (mm) REVERT: A 596 SER cc_start: 0.9229 (m) cc_final: 0.8662 (p) REVERT: A 642 VAL cc_start: 0.9192 (t) cc_final: 0.8841 (p) REVERT: A 725 GLU cc_start: 0.7682 (tt0) cc_final: 0.7419 (tt0) REVERT: A 773 GLU cc_start: 0.7712 (tt0) cc_final: 0.7505 (tt0) REVERT: A 904 TYR cc_start: 0.8191 (m-10) cc_final: 0.7909 (m-10) REVERT: A 985 ASP cc_start: 0.7511 (p0) cc_final: 0.7026 (p0) REVERT: A 986 LYS cc_start: 0.8053 (ttpp) cc_final: 0.7719 (ttmm) REVERT: A 990 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7056 (mt-10) REVERT: C 102 ARG cc_start: 0.7297 (mmt90) cc_final: 0.7061 (mmt90) REVERT: C 129 LYS cc_start: 0.6960 (tttp) cc_final: 0.6636 (tptt) REVERT: C 239 GLN cc_start: 0.8026 (tt0) cc_final: 0.7775 (tp40) REVERT: C 275 PHE cc_start: 0.8628 (m-80) cc_final: 0.8268 (m-80) REVERT: C 276 LEU cc_start: 0.8942 (tp) cc_final: 0.8710 (tp) REVERT: C 277 LEU cc_start: 0.8999 (mt) cc_final: 0.8787 (mp) REVERT: C 289 VAL cc_start: 0.8813 (t) cc_final: 0.8608 (m) REVERT: C 324 GLU cc_start: 0.7791 (pm20) cc_final: 0.7354 (pm20) REVERT: C 342 PHE cc_start: 0.8137 (m-80) cc_final: 0.7818 (m-80) REVERT: C 383 SER cc_start: 0.8867 (t) cc_final: 0.8456 (p) REVERT: C 434 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8376 (mm) REVERT: C 436 TRP cc_start: 0.7008 (p90) cc_final: 0.6712 (p90) REVERT: C 452 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7245 (ptm160) REVERT: C 495 TYR cc_start: 0.6127 (m-80) cc_final: 0.5793 (m-80) REVERT: C 565 PHE cc_start: 0.6574 (m-10) cc_final: 0.6164 (m-10) REVERT: C 596 SER cc_start: 0.9148 (m) cc_final: 0.8494 (p) REVERT: C 820 ASP cc_start: 0.7957 (t0) cc_final: 0.7739 (m-30) REVERT: C 825 LYS cc_start: 0.8893 (tptt) cc_final: 0.8628 (tptt) REVERT: C 850 ILE cc_start: 0.8035 (mp) cc_final: 0.7718 (pt) REVERT: C 994 ASP cc_start: 0.7778 (t70) cc_final: 0.7508 (t70) REVERT: C 1037 SER cc_start: 0.9130 (t) cc_final: 0.8825 (p) outliers start: 99 outliers final: 62 residues processed: 631 average time/residue: 0.4162 time to fit residues: 409.6717 Evaluate side-chains 628 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 556 time to evaluate : 3.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1146 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 237 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 chunk 80 optimal weight: 0.1980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN B 450 ASN B 580 GLN B 777 ASN B 914 ASN B 957 GLN ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1119 ASN A 450 ASN A 751 ASN A 907 ASN A 969 ASN A1010 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C1113 GLN C1142 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 28014 Z= 0.404 Angle : 0.773 12.208 38103 Z= 0.372 Chirality : 0.050 0.710 4650 Planarity : 0.004 0.054 4761 Dihedral : 12.873 103.398 5949 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.45 % Favored : 93.37 % Rotamer: Outliers : 4.27 % Allowed : 14.17 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3273 helix: 1.56 (0.20), residues: 723 sheet: -0.12 (0.19), residues: 672 loop : -1.33 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A 633 HIS 0.006 0.001 HIS A 207 PHE 0.028 0.002 PHE A 347 TYR 0.023 0.002 TYR C1067 ARG 0.014 0.001 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 581 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 THR cc_start: 0.7962 (m) cc_final: 0.7708 (m) REVERT: B 96 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.4771 (tt0) REVERT: B 99 ASN cc_start: 0.8183 (t0) cc_final: 0.7406 (t0) REVERT: B 131 CYS cc_start: 0.4478 (m) cc_final: 0.4256 (m) REVERT: B 140 PHE cc_start: 0.7648 (p90) cc_final: 0.7227 (p90) REVERT: B 143 VAL cc_start: 0.6886 (OUTLIER) cc_final: 0.6636 (p) REVERT: B 168 PHE cc_start: 0.7419 (t80) cc_final: 0.6951 (t80) REVERT: B 169 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.7979 (mm-30) REVERT: B 360 ASN cc_start: 0.8466 (t0) cc_final: 0.8226 (t0) REVERT: B 452 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7391 (ptm160) REVERT: B 460 ASN cc_start: 0.7965 (m-40) cc_final: 0.7660 (m-40) REVERT: B 523 THR cc_start: 0.8664 (m) cc_final: 0.8227 (p) REVERT: B 537 LYS cc_start: 0.8611 (mtpt) cc_final: 0.8162 (ttpt) REVERT: B 557 LYS cc_start: 0.8762 (mtpt) cc_final: 0.8435 (ptpt) REVERT: B 565 PHE cc_start: 0.6998 (m-10) cc_final: 0.6518 (m-10) REVERT: B 587 ILE cc_start: 0.8828 (mt) cc_final: 0.8590 (tp) REVERT: B 596 SER cc_start: 0.9179 (m) cc_final: 0.8649 (p) REVERT: B 642 VAL cc_start: 0.9313 (t) cc_final: 0.9058 (p) REVERT: B 825 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8546 (tptt) REVERT: B 912 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8240 (p) REVERT: B 1107 ARG cc_start: 0.8346 (mtt90) cc_final: 0.7971 (mtt90) REVERT: A 96 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.5655 (tt0) REVERT: A 99 ASN cc_start: 0.8548 (t0) cc_final: 0.7907 (t0) REVERT: A 153 MET cc_start: 0.6293 (tmm) cc_final: 0.6059 (tpt) REVERT: A 169 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7895 (mm-30) REVERT: A 206 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8599 (tmtt) REVERT: A 289 VAL cc_start: 0.8903 (t) cc_final: 0.8514 (m) REVERT: A 360 ASN cc_start: 0.8474 (t0) cc_final: 0.8042 (t0) REVERT: A 405 ASP cc_start: 0.6902 (p0) cc_final: 0.6420 (p0) REVERT: A 523 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8002 (p) REVERT: A 557 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8305 (ptpt) REVERT: A 565 PHE cc_start: 0.7051 (m-10) cc_final: 0.6524 (m-10) REVERT: A 583 GLU cc_start: 0.7674 (pp20) cc_final: 0.7458 (pp20) REVERT: A 584 ILE cc_start: 0.8954 (mm) cc_final: 0.8622 (mm) REVERT: A 596 SER cc_start: 0.9274 (m) cc_final: 0.8656 (p) REVERT: A 633 TRP cc_start: 0.8061 (p-90) cc_final: 0.7727 (p-90) REVERT: A 642 VAL cc_start: 0.9178 (t) cc_final: 0.8858 (p) REVERT: A 725 GLU cc_start: 0.7697 (tt0) cc_final: 0.7405 (tt0) REVERT: A 904 TYR cc_start: 0.8205 (m-10) cc_final: 0.7992 (m-10) REVERT: A 964 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8586 (mtmm) REVERT: A 986 LYS cc_start: 0.8073 (ttpp) cc_final: 0.7716 (ttmm) REVERT: A 990 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7093 (mt-10) REVERT: A 1107 ARG cc_start: 0.8285 (mtt90) cc_final: 0.8051 (mtt90) REVERT: C 96 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.5781 (tt0) REVERT: C 129 LYS cc_start: 0.7085 (tttp) cc_final: 0.6877 (tptt) REVERT: C 271 GLN cc_start: 0.8516 (mt0) cc_final: 0.8304 (mt0) REVERT: C 275 PHE cc_start: 0.8692 (m-80) cc_final: 0.8251 (m-80) REVERT: C 277 LEU cc_start: 0.9006 (mt) cc_final: 0.8793 (mp) REVERT: C 324 GLU cc_start: 0.7875 (pm20) cc_final: 0.7395 (pm20) REVERT: C 349 SER cc_start: 0.7983 (OUTLIER) cc_final: 0.7753 (p) REVERT: C 383 SER cc_start: 0.8912 (t) cc_final: 0.8525 (p) REVERT: C 406 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7696 (mm-30) REVERT: C 436 TRP cc_start: 0.7198 (p90) cc_final: 0.6775 (p90) REVERT: C 452 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7484 (ptm160) REVERT: C 457 ARG cc_start: 0.7227 (tpt-90) cc_final: 0.6942 (ttt90) REVERT: C 523 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8240 (p) REVERT: C 565 PHE cc_start: 0.6679 (m-10) cc_final: 0.6232 (m-10) REVERT: C 596 SER cc_start: 0.9164 (m) cc_final: 0.8552 (p) REVERT: C 776 LYS cc_start: 0.8555 (tptm) cc_final: 0.8338 (ttpt) REVERT: C 820 ASP cc_start: 0.8101 (t0) cc_final: 0.7864 (m-30) REVERT: C 825 LYS cc_start: 0.8892 (tptt) cc_final: 0.8638 (tptt) REVERT: C 994 ASP cc_start: 0.7802 (t70) cc_final: 0.7568 (t70) outliers start: 123 outliers final: 78 residues processed: 638 average time/residue: 0.3898 time to fit residues: 389.2230 Evaluate side-chains 645 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 553 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 1.9990 chunk 287 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 187 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 319 optimal weight: 0.7980 chunk 265 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 580 GLN B 957 GLN B 969 ASN B1119 ASN A 450 ASN A 856 ASN A 907 ASN A 969 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C1113 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28014 Z= 0.244 Angle : 0.728 11.628 38103 Z= 0.346 Chirality : 0.047 0.693 4650 Planarity : 0.004 0.053 4761 Dihedral : 12.051 100.245 5949 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.26 % Favored : 94.56 % Rotamer: Outliers : 3.61 % Allowed : 15.87 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3273 helix: 1.74 (0.20), residues: 723 sheet: 0.01 (0.19), residues: 663 loop : -1.29 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 633 HIS 0.005 0.001 HIS A 207 PHE 0.041 0.002 PHE A 497 TYR 0.019 0.001 TYR C1067 ARG 0.011 0.001 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 585 time to evaluate : 3.124 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: B 29 THR cc_start: 0.7797 (m) cc_final: 0.7548 (m) REVERT: B 96 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.4730 (tt0) REVERT: B 99 ASN cc_start: 0.8167 (t0) cc_final: 0.7407 (t0) REVERT: B 131 CYS cc_start: 0.4477 (m) cc_final: 0.4151 (m) REVERT: B 140 PHE cc_start: 0.7603 (p90) cc_final: 0.7195 (p90) REVERT: B 143 VAL cc_start: 0.6850 (OUTLIER) cc_final: 0.6650 (p) REVERT: B 153 MET cc_start: 0.6424 (tmm) cc_final: 0.6004 (tpt) REVERT: B 169 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8206 (mm-30) REVERT: B 276 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8570 (tt) REVERT: B 289 VAL cc_start: 0.8889 (t) cc_final: 0.8590 (m) REVERT: B 306 PHE cc_start: 0.8798 (m-80) cc_final: 0.8371 (m-80) REVERT: B 360 ASN cc_start: 0.8429 (t0) cc_final: 0.8202 (t0) REVERT: B 452 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7646 (ptm160) REVERT: B 460 ASN cc_start: 0.7899 (m-40) cc_final: 0.7581 (m110) REVERT: B 523 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8214 (p) REVERT: B 537 LYS cc_start: 0.8591 (mtpt) cc_final: 0.8126 (ttpt) REVERT: B 557 LYS cc_start: 0.8764 (mtpt) cc_final: 0.8388 (ptpt) REVERT: B 565 PHE cc_start: 0.6873 (m-10) cc_final: 0.6410 (m-10) REVERT: B 596 SER cc_start: 0.9127 (m) cc_final: 0.8593 (p) REVERT: B 642 VAL cc_start: 0.9316 (t) cc_final: 0.9043 (p) REVERT: B 650 LEU cc_start: 0.8401 (tp) cc_final: 0.8187 (tp) REVERT: B 815 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8091 (mpp80) REVERT: B 825 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8498 (tptt) REVERT: B 912 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8263 (p) REVERT: B 1050 MET cc_start: 0.8272 (ptm) cc_final: 0.8036 (ptm) REVERT: B 1107 ARG cc_start: 0.8307 (mtt90) cc_final: 0.7870 (mtt90) REVERT: A 96 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.5549 (tt0) REVERT: A 99 ASN cc_start: 0.8488 (t0) cc_final: 0.7922 (t0) REVERT: A 169 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8049 (mm-30) REVERT: A 206 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8525 (tmtt) REVERT: A 289 VAL cc_start: 0.8898 (t) cc_final: 0.8529 (m) REVERT: A 360 ASN cc_start: 0.8424 (t0) cc_final: 0.7997 (t0) REVERT: A 452 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7129 (ptm-80) REVERT: A 523 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8041 (p) REVERT: A 557 LYS cc_start: 0.8748 (mtpt) cc_final: 0.8271 (ptpt) REVERT: A 565 PHE cc_start: 0.6994 (m-10) cc_final: 0.6485 (m-10) REVERT: A 583 GLU cc_start: 0.7586 (pp20) cc_final: 0.7207 (pp20) REVERT: A 584 ILE cc_start: 0.8930 (mm) cc_final: 0.8623 (mm) REVERT: A 585 LEU cc_start: 0.8523 (mt) cc_final: 0.8064 (mt) REVERT: A 596 SER cc_start: 0.9241 (m) cc_final: 0.8636 (p) REVERT: A 642 VAL cc_start: 0.9163 (t) cc_final: 0.8816 (p) REVERT: A 675 GLN cc_start: 0.6953 (pp30) cc_final: 0.6563 (tm-30) REVERT: A 725 GLU cc_start: 0.7672 (tt0) cc_final: 0.7367 (tt0) REVERT: A 762 GLN cc_start: 0.8130 (tt0) cc_final: 0.7870 (mt0) REVERT: A 904 TYR cc_start: 0.8205 (m-10) cc_final: 0.7941 (m-10) REVERT: A 964 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8571 (mtmm) REVERT: A 986 LYS cc_start: 0.8002 (ttpp) cc_final: 0.7515 (ttmm) REVERT: A 990 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7072 (mt-10) REVERT: C 271 GLN cc_start: 0.8489 (mt0) cc_final: 0.8247 (mt0) REVERT: C 275 PHE cc_start: 0.8646 (m-80) cc_final: 0.8228 (m-80) REVERT: C 277 LEU cc_start: 0.9007 (mt) cc_final: 0.8793 (mp) REVERT: C 324 GLU cc_start: 0.7926 (pm20) cc_final: 0.7432 (pm20) REVERT: C 383 SER cc_start: 0.8818 (t) cc_final: 0.8433 (p) REVERT: C 406 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7585 (mm-30) REVERT: C 434 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8430 (mm) REVERT: C 436 TRP cc_start: 0.7130 (p90) cc_final: 0.6751 (p90) REVERT: C 452 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7516 (ptm160) REVERT: C 457 ARG cc_start: 0.7198 (tpt-90) cc_final: 0.6908 (ttm-80) REVERT: C 523 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8208 (p) REVERT: C 565 PHE cc_start: 0.6568 (m-10) cc_final: 0.6117 (m-10) REVERT: C 587 ILE cc_start: 0.8779 (mt) cc_final: 0.8523 (tp) REVERT: C 596 SER cc_start: 0.9134 (m) cc_final: 0.8522 (p) REVERT: C 776 LYS cc_start: 0.8534 (tptm) cc_final: 0.8326 (ttpt) REVERT: C 820 ASP cc_start: 0.8003 (t0) cc_final: 0.7781 (m-30) REVERT: C 825 LYS cc_start: 0.8883 (tptt) cc_final: 0.8621 (tptt) REVERT: C 850 ILE cc_start: 0.7991 (mp) cc_final: 0.7694 (pt) REVERT: C 985 ASP cc_start: 0.7686 (p0) cc_final: 0.7351 (p0) REVERT: C 994 ASP cc_start: 0.7737 (t70) cc_final: 0.7492 (t70) REVERT: C 1037 SER cc_start: 0.9143 (t) cc_final: 0.8817 (p) outliers start: 104 outliers final: 64 residues processed: 633 average time/residue: 0.4070 time to fit residues: 404.4742 Evaluate side-chains 642 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 561 time to evaluate : 3.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 233 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 268 optimal weight: 0.2980 chunk 178 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 777 ASN B 957 GLN B1119 ASN A 907 ASN A 969 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C1113 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 28014 Z= 0.280 Angle : 0.737 11.860 38103 Z= 0.349 Chirality : 0.047 0.662 4650 Planarity : 0.004 0.055 4761 Dihedral : 11.253 98.368 5947 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.05 % Favored : 93.77 % Rotamer: Outliers : 3.51 % Allowed : 16.81 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3273 helix: 1.82 (0.20), residues: 720 sheet: -0.16 (0.19), residues: 657 loop : -1.24 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 633 HIS 0.005 0.001 HIS A 207 PHE 0.025 0.002 PHE A 497 TYR 0.020 0.002 TYR C1067 ARG 0.011 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 574 time to evaluate : 3.137 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: B 29 THR cc_start: 0.7862 (m) cc_final: 0.7612 (m) REVERT: B 99 ASN cc_start: 0.8152 (t0) cc_final: 0.7803 (t0) REVERT: B 140 PHE cc_start: 0.7651 (p90) cc_final: 0.7234 (p90) REVERT: B 153 MET cc_start: 0.6464 (tmm) cc_final: 0.6059 (tpt) REVERT: B 169 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8120 (mm-30) REVERT: B 229 LEU cc_start: 0.8188 (pp) cc_final: 0.7899 (pp) REVERT: B 276 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8556 (tt) REVERT: B 289 VAL cc_start: 0.8897 (t) cc_final: 0.8603 (m) REVERT: B 306 PHE cc_start: 0.8821 (m-80) cc_final: 0.8413 (m-80) REVERT: B 360 ASN cc_start: 0.8438 (t0) cc_final: 0.8214 (t0) REVERT: B 452 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7557 (ptm160) REVERT: B 456 PHE cc_start: 0.7578 (m-80) cc_final: 0.7270 (m-80) REVERT: B 460 ASN cc_start: 0.7922 (m-40) cc_final: 0.7612 (m-40) REVERT: B 523 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8290 (p) REVERT: B 537 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8185 (ttpt) REVERT: B 554 GLU cc_start: 0.7353 (mp0) cc_final: 0.7136 (mp0) REVERT: B 557 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8400 (ptpt) REVERT: B 565 PHE cc_start: 0.6913 (m-10) cc_final: 0.6435 (m-10) REVERT: B 596 SER cc_start: 0.9131 (m) cc_final: 0.8601 (p) REVERT: B 642 VAL cc_start: 0.9325 (t) cc_final: 0.9062 (p) REVERT: B 650 LEU cc_start: 0.8388 (tp) cc_final: 0.8178 (tp) REVERT: B 815 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8696 (tpp80) REVERT: B 825 LYS cc_start: 0.8753 (mmtt) cc_final: 0.8475 (tptt) REVERT: B 912 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8263 (p) REVERT: B 1107 ARG cc_start: 0.8313 (mtt90) cc_final: 0.7935 (mtt90) REVERT: A 96 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.5305 (tp30) REVERT: A 99 ASN cc_start: 0.8500 (t0) cc_final: 0.7894 (t0) REVERT: A 169 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8157 (mm-30) REVERT: A 206 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8536 (tmtt) REVERT: A 289 VAL cc_start: 0.8900 (t) cc_final: 0.8529 (m) REVERT: A 342 PHE cc_start: 0.8472 (m-80) cc_final: 0.8242 (m-80) REVERT: A 360 ASN cc_start: 0.8446 (t0) cc_final: 0.8031 (t0) REVERT: A 452 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7201 (ptm-80) REVERT: A 523 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8077 (p) REVERT: A 565 PHE cc_start: 0.7009 (m-10) cc_final: 0.6487 (m-10) REVERT: A 583 GLU cc_start: 0.7640 (pp20) cc_final: 0.7260 (pp20) REVERT: A 584 ILE cc_start: 0.8937 (mm) cc_final: 0.8631 (mm) REVERT: A 585 LEU cc_start: 0.8529 (mt) cc_final: 0.8084 (mt) REVERT: A 596 SER cc_start: 0.9225 (m) cc_final: 0.8655 (p) REVERT: A 642 VAL cc_start: 0.9166 (t) cc_final: 0.8911 (p) REVERT: A 646 ARG cc_start: 0.8086 (tpt170) cc_final: 0.7881 (tpt170) REVERT: A 762 GLN cc_start: 0.8131 (tt0) cc_final: 0.7888 (mt0) REVERT: A 904 TYR cc_start: 0.8205 (m-10) cc_final: 0.7983 (m-10) REVERT: A 964 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8588 (mtmm) REVERT: A 986 LYS cc_start: 0.8041 (ttpp) cc_final: 0.7542 (ttmm) REVERT: A 990 GLU cc_start: 0.7314 (mt-10) cc_final: 0.7090 (mt-10) REVERT: C 96 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.5897 (tt0) REVERT: C 271 GLN cc_start: 0.8478 (mt0) cc_final: 0.8244 (mt0) REVERT: C 275 PHE cc_start: 0.8638 (m-80) cc_final: 0.8170 (m-80) REVERT: C 278 LYS cc_start: 0.8514 (ttmm) cc_final: 0.8281 (ttmt) REVERT: C 324 GLU cc_start: 0.7925 (pm20) cc_final: 0.7565 (pm20) REVERT: C 383 SER cc_start: 0.8808 (t) cc_final: 0.8416 (p) REVERT: C 406 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7596 (mm-30) REVERT: C 436 TRP cc_start: 0.7179 (p90) cc_final: 0.6804 (p90) REVERT: C 452 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7511 (ptm160) REVERT: C 523 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8244 (p) REVERT: C 565 PHE cc_start: 0.6609 (m-10) cc_final: 0.6138 (m-10) REVERT: C 587 ILE cc_start: 0.8783 (mt) cc_final: 0.8553 (tp) REVERT: C 596 SER cc_start: 0.9130 (m) cc_final: 0.8552 (p) REVERT: C 776 LYS cc_start: 0.8527 (tptm) cc_final: 0.8313 (ttpt) REVERT: C 820 ASP cc_start: 0.8037 (t0) cc_final: 0.7816 (m-30) REVERT: C 825 LYS cc_start: 0.8869 (tptt) cc_final: 0.8583 (tptt) REVERT: C 994 ASP cc_start: 0.7745 (t70) cc_final: 0.7507 (t70) REVERT: C 1037 SER cc_start: 0.9148 (t) cc_final: 0.8827 (p) outliers start: 101 outliers final: 67 residues processed: 621 average time/residue: 0.3960 time to fit residues: 387.2487 Evaluate side-chains 643 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 561 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 0.9980 chunk 127 optimal weight: 0.6980 chunk 189 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 202 optimal weight: 0.9980 chunk 216 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 250 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 777 ASN B 957 GLN B1119 ASN A 969 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 914 ASN C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28014 Z= 0.259 Angle : 0.733 10.559 38103 Z= 0.347 Chirality : 0.046 0.671 4650 Planarity : 0.004 0.054 4761 Dihedral : 10.265 95.484 5947 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.32 % Favored : 94.50 % Rotamer: Outliers : 3.26 % Allowed : 17.43 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3273 helix: 1.84 (0.20), residues: 717 sheet: -0.11 (0.19), residues: 657 loop : -1.18 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 633 HIS 0.004 0.001 HIS A 207 PHE 0.032 0.002 PHE A 497 TYR 0.024 0.001 TYR A 495 ARG 0.005 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 581 time to evaluate : 3.112 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: B 29 THR cc_start: 0.7815 (m) cc_final: 0.7566 (m) REVERT: B 52 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8200 (tm-30) REVERT: B 96 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.4885 (tt0) REVERT: B 99 ASN cc_start: 0.8133 (t0) cc_final: 0.7382 (t0) REVERT: B 140 PHE cc_start: 0.7643 (p90) cc_final: 0.7343 (p90) REVERT: B 153 MET cc_start: 0.6416 (tmm) cc_final: 0.6050 (tpt) REVERT: B 169 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: B 276 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8768 (tp) REVERT: B 289 VAL cc_start: 0.8884 (t) cc_final: 0.8646 (m) REVERT: B 360 ASN cc_start: 0.8437 (t0) cc_final: 0.8221 (t0) REVERT: B 452 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7571 (ptm160) REVERT: B 456 PHE cc_start: 0.7658 (m-80) cc_final: 0.7324 (m-80) REVERT: B 460 ASN cc_start: 0.7907 (m-40) cc_final: 0.7586 (m-40) REVERT: B 523 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8247 (p) REVERT: B 537 LYS cc_start: 0.8572 (mtpt) cc_final: 0.8168 (ttpt) REVERT: B 557 LYS cc_start: 0.8750 (mtpt) cc_final: 0.8409 (ptpt) REVERT: B 565 PHE cc_start: 0.6915 (m-10) cc_final: 0.6472 (m-10) REVERT: B 596 SER cc_start: 0.9136 (m) cc_final: 0.8598 (p) REVERT: B 642 VAL cc_start: 0.9333 (t) cc_final: 0.9071 (p) REVERT: B 650 LEU cc_start: 0.8349 (tp) cc_final: 0.8137 (tp) REVERT: B 815 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8707 (tpp80) REVERT: B 825 LYS cc_start: 0.8777 (mmtt) cc_final: 0.8504 (tptt) REVERT: B 912 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8241 (p) REVERT: B 1107 ARG cc_start: 0.8312 (mtt90) cc_final: 0.7934 (mtt90) REVERT: B 1142 GLN cc_start: 0.8477 (tp40) cc_final: 0.8252 (mm-40) REVERT: A 99 ASN cc_start: 0.8472 (t0) cc_final: 0.8252 (t0) REVERT: A 169 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: A 206 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8542 (tmtt) REVERT: A 289 VAL cc_start: 0.8897 (t) cc_final: 0.8530 (m) REVERT: A 360 ASN cc_start: 0.8444 (t0) cc_final: 0.8030 (t0) REVERT: A 452 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7912 (ptm-80) REVERT: A 523 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8095 (p) REVERT: A 565 PHE cc_start: 0.6966 (m-10) cc_final: 0.6447 (m-10) REVERT: A 583 GLU cc_start: 0.7621 (pp20) cc_final: 0.7198 (pp20) REVERT: A 584 ILE cc_start: 0.8930 (mm) cc_final: 0.8624 (mm) REVERT: A 585 LEU cc_start: 0.8532 (mt) cc_final: 0.8058 (mt) REVERT: A 596 SER cc_start: 0.9237 (m) cc_final: 0.8639 (p) REVERT: A 642 VAL cc_start: 0.9205 (t) cc_final: 0.8864 (p) REVERT: A 646 ARG cc_start: 0.8048 (tpt170) cc_final: 0.7817 (tpt170) REVERT: A 725 GLU cc_start: 0.7674 (tt0) cc_final: 0.7377 (tt0) REVERT: A 762 GLN cc_start: 0.8079 (tt0) cc_final: 0.7853 (mt0) REVERT: A 904 TYR cc_start: 0.8216 (m-10) cc_final: 0.7951 (m-10) REVERT: A 964 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8593 (mtmm) REVERT: A 986 LYS cc_start: 0.8021 (ttpp) cc_final: 0.7486 (ttmm) REVERT: A 990 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7046 (mt-10) REVERT: C 275 PHE cc_start: 0.8598 (m-80) cc_final: 0.8177 (m-80) REVERT: C 324 GLU cc_start: 0.7979 (pm20) cc_final: 0.7464 (pm20) REVERT: C 383 SER cc_start: 0.8809 (t) cc_final: 0.8395 (p) REVERT: C 406 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7586 (mm-30) REVERT: C 434 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8586 (mm) REVERT: C 452 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7312 (ptm160) REVERT: C 495 TYR cc_start: 0.6430 (m-80) cc_final: 0.5889 (m-80) REVERT: C 523 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8278 (p) REVERT: C 565 PHE cc_start: 0.6544 (m-10) cc_final: 0.6073 (m-10) REVERT: C 587 ILE cc_start: 0.8811 (mt) cc_final: 0.8599 (tp) REVERT: C 596 SER cc_start: 0.9122 (m) cc_final: 0.8554 (p) REVERT: C 820 ASP cc_start: 0.8029 (t0) cc_final: 0.7816 (m-30) REVERT: C 850 ILE cc_start: 0.8016 (mp) cc_final: 0.7720 (pt) REVERT: C 994 ASP cc_start: 0.7712 (t70) cc_final: 0.7480 (t70) REVERT: C 1037 SER cc_start: 0.9136 (t) cc_final: 0.8834 (p) outliers start: 94 outliers final: 68 residues processed: 622 average time/residue: 0.3913 time to fit residues: 386.1509 Evaluate side-chains 645 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 562 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 0.0770 chunk 304 optimal weight: 0.9980 chunk 278 optimal weight: 0.6980 chunk 296 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 129 optimal weight: 0.3980 chunk 232 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 280 optimal weight: 0.7980 chunk 295 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 777 ASN B1119 ASN A 969 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 28014 Z= 0.225 Angle : 0.727 11.889 38103 Z= 0.343 Chirality : 0.046 0.648 4650 Planarity : 0.004 0.056 4761 Dihedral : 9.334 91.746 5947 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.71 % Favored : 94.10 % Rotamer: Outliers : 3.19 % Allowed : 17.78 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3273 helix: 1.90 (0.20), residues: 717 sheet: -0.05 (0.19), residues: 657 loop : -1.12 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 633 HIS 0.004 0.001 HIS A 207 PHE 0.028 0.001 PHE A 497 TYR 0.018 0.001 TYR C1067 ARG 0.014 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 593 time to evaluate : 3.001 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: B 29 THR cc_start: 0.7746 (m) cc_final: 0.7484 (m) REVERT: B 52 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8178 (tm-30) REVERT: B 96 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.4859 (tt0) REVERT: B 99 ASN cc_start: 0.8116 (t0) cc_final: 0.7376 (t0) REVERT: B 140 PHE cc_start: 0.7612 (p90) cc_final: 0.7304 (p90) REVERT: B 169 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: B 276 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8768 (tp) REVERT: B 289 VAL cc_start: 0.8864 (t) cc_final: 0.8635 (m) REVERT: B 360 ASN cc_start: 0.8372 (t0) cc_final: 0.7945 (t0) REVERT: B 452 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7568 (ptm160) REVERT: B 456 PHE cc_start: 0.7664 (m-80) cc_final: 0.7332 (m-80) REVERT: B 460 ASN cc_start: 0.7882 (m-40) cc_final: 0.7574 (m-40) REVERT: B 523 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8254 (p) REVERT: B 537 LYS cc_start: 0.8577 (mtpt) cc_final: 0.8162 (ttpt) REVERT: B 557 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8300 (ptpt) REVERT: B 565 PHE cc_start: 0.6857 (m-10) cc_final: 0.6393 (m-10) REVERT: B 585 LEU cc_start: 0.8638 (mt) cc_final: 0.8422 (mt) REVERT: B 596 SER cc_start: 0.9127 (m) cc_final: 0.8583 (p) REVERT: B 642 VAL cc_start: 0.9342 (t) cc_final: 0.9004 (p) REVERT: B 650 LEU cc_start: 0.8295 (tp) cc_final: 0.8081 (tp) REVERT: B 825 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8503 (tptt) REVERT: B 912 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8198 (p) REVERT: B 918 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7729 (mt-10) REVERT: B 957 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7885 (tt0) REVERT: B 1107 ARG cc_start: 0.8285 (mtt90) cc_final: 0.7921 (mtt90) REVERT: A 169 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7925 (mp0) REVERT: A 206 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8493 (tmtt) REVERT: A 229 LEU cc_start: 0.8154 (pp) cc_final: 0.7909 (pt) REVERT: A 289 VAL cc_start: 0.8849 (t) cc_final: 0.8489 (m) REVERT: A 360 ASN cc_start: 0.8427 (t0) cc_final: 0.8017 (t0) REVERT: A 452 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7947 (ptm-80) REVERT: A 456 PHE cc_start: 0.7880 (m-80) cc_final: 0.7531 (m-80) REVERT: A 523 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8097 (p) REVERT: A 565 PHE cc_start: 0.6966 (m-10) cc_final: 0.6461 (m-10) REVERT: A 583 GLU cc_start: 0.7603 (pp20) cc_final: 0.7168 (pp20) REVERT: A 584 ILE cc_start: 0.8919 (mm) cc_final: 0.8596 (mm) REVERT: A 585 LEU cc_start: 0.8528 (mt) cc_final: 0.8045 (mt) REVERT: A 596 SER cc_start: 0.9236 (m) cc_final: 0.8639 (p) REVERT: A 642 VAL cc_start: 0.9218 (t) cc_final: 0.8867 (p) REVERT: A 646 ARG cc_start: 0.8013 (tpt170) cc_final: 0.7784 (tpt170) REVERT: A 725 GLU cc_start: 0.7689 (tt0) cc_final: 0.7395 (tt0) REVERT: A 904 TYR cc_start: 0.8221 (m-10) cc_final: 0.7968 (m-10) REVERT: A 964 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8589 (mtmm) REVERT: A 986 LYS cc_start: 0.8000 (ttpp) cc_final: 0.7468 (ttmm) REVERT: A 990 GLU cc_start: 0.7264 (mt-10) cc_final: 0.7030 (mt-10) REVERT: C 96 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6055 (tt0) REVERT: C 169 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7756 (mm-30) REVERT: C 271 GLN cc_start: 0.8421 (mt0) cc_final: 0.8184 (mt0) REVERT: C 275 PHE cc_start: 0.8565 (m-80) cc_final: 0.8213 (m-80) REVERT: C 324 GLU cc_start: 0.7987 (pm20) cc_final: 0.7444 (pm20) REVERT: C 342 PHE cc_start: 0.8313 (m-80) cc_final: 0.7909 (m-80) REVERT: C 383 SER cc_start: 0.8817 (t) cc_final: 0.8372 (p) REVERT: C 406 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7504 (mm-30) REVERT: C 434 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8619 (mm) REVERT: C 452 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7304 (ptm160) REVERT: C 495 TYR cc_start: 0.6395 (m-80) cc_final: 0.5937 (m-80) REVERT: C 523 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8286 (p) REVERT: C 565 PHE cc_start: 0.6486 (m-10) cc_final: 0.6013 (m-10) REVERT: C 596 SER cc_start: 0.9096 (m) cc_final: 0.8556 (p) REVERT: C 633 TRP cc_start: 0.8235 (p-90) cc_final: 0.6960 (p-90) REVERT: C 820 ASP cc_start: 0.7998 (t0) cc_final: 0.7770 (m-30) REVERT: C 825 LYS cc_start: 0.8998 (tppt) cc_final: 0.8620 (tptt) REVERT: C 850 ILE cc_start: 0.8004 (mp) cc_final: 0.7713 (pt) REVERT: C 994 ASP cc_start: 0.7664 (t70) cc_final: 0.7400 (t70) REVERT: C 1037 SER cc_start: 0.9133 (t) cc_final: 0.8880 (p) outliers start: 92 outliers final: 60 residues processed: 637 average time/residue: 0.3886 time to fit residues: 389.6551 Evaluate side-chains 646 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 569 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 821 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 0.0980 chunk 313 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 217 optimal weight: 0.7980 chunk 328 optimal weight: 0.7980 chunk 302 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 644 GLN B 777 ASN B 957 GLN B1005 GLN B1119 ASN A 969 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 777 ASN C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 28014 Z= 0.250 Angle : 0.736 11.074 38103 Z= 0.351 Chirality : 0.046 0.650 4650 Planarity : 0.004 0.057 4761 Dihedral : 8.629 87.362 5947 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.62 % Favored : 94.19 % Rotamer: Outliers : 2.95 % Allowed : 18.40 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3273 helix: 1.83 (0.20), residues: 720 sheet: 0.08 (0.19), residues: 669 loop : -1.16 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 633 HIS 0.004 0.001 HIS A 207 PHE 0.024 0.002 PHE A 497 TYR 0.019 0.001 TYR C1067 ARG 0.007 0.000 ARG B 995 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 578 time to evaluate : 3.066 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: B 29 THR cc_start: 0.7763 (m) cc_final: 0.7503 (m) REVERT: B 52 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8171 (tm-30) REVERT: B 96 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.5032 (tt0) REVERT: B 99 ASN cc_start: 0.8118 (t0) cc_final: 0.7389 (t0) REVERT: B 140 PHE cc_start: 0.7588 (p90) cc_final: 0.7282 (p90) REVERT: B 153 MET cc_start: 0.6052 (tmm) cc_final: 0.5718 (tpt) REVERT: B 169 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: B 276 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8777 (tp) REVERT: B 289 VAL cc_start: 0.8830 (t) cc_final: 0.8587 (m) REVERT: B 324 GLU cc_start: 0.7657 (pt0) cc_final: 0.7405 (pm20) REVERT: B 360 ASN cc_start: 0.8399 (t0) cc_final: 0.7974 (t0) REVERT: B 436 TRP cc_start: 0.6972 (p90) cc_final: 0.6708 (p90) REVERT: B 452 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7570 (ptm160) REVERT: B 456 PHE cc_start: 0.7650 (m-80) cc_final: 0.7326 (m-80) REVERT: B 460 ASN cc_start: 0.7811 (m-40) cc_final: 0.7520 (m-40) REVERT: B 523 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8100 (p) REVERT: B 537 LYS cc_start: 0.8569 (mtpt) cc_final: 0.8060 (ttpt) REVERT: B 565 PHE cc_start: 0.6883 (m-10) cc_final: 0.6435 (m-10) REVERT: B 596 SER cc_start: 0.9129 (m) cc_final: 0.8582 (p) REVERT: B 642 VAL cc_start: 0.9341 (t) cc_final: 0.9075 (p) REVERT: B 650 LEU cc_start: 0.8258 (tp) cc_final: 0.8041 (tp) REVERT: B 825 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8512 (tptt) REVERT: B 912 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8186 (p) REVERT: B 918 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7741 (mt-10) REVERT: B 1107 ARG cc_start: 0.8296 (mtt90) cc_final: 0.8027 (mtt90) REVERT: A 169 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8158 (mm-30) REVERT: A 206 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8510 (tmtt) REVERT: A 229 LEU cc_start: 0.8194 (pp) cc_final: 0.7923 (pt) REVERT: A 289 VAL cc_start: 0.8856 (t) cc_final: 0.8485 (m) REVERT: A 353 TRP cc_start: 0.8668 (p-90) cc_final: 0.8324 (p-90) REVERT: A 360 ASN cc_start: 0.8454 (t0) cc_final: 0.8038 (t0) REVERT: A 452 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7281 (ptm-80) REVERT: A 523 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8146 (p) REVERT: A 565 PHE cc_start: 0.6969 (m-10) cc_final: 0.6479 (m-10) REVERT: A 583 GLU cc_start: 0.7598 (pp20) cc_final: 0.7158 (pp20) REVERT: A 584 ILE cc_start: 0.8925 (mm) cc_final: 0.8597 (mm) REVERT: A 585 LEU cc_start: 0.8531 (mt) cc_final: 0.8047 (mt) REVERT: A 596 SER cc_start: 0.9239 (m) cc_final: 0.8643 (p) REVERT: A 642 VAL cc_start: 0.9215 (t) cc_final: 0.8860 (p) REVERT: A 646 ARG cc_start: 0.8018 (tpt170) cc_final: 0.7784 (tpt170) REVERT: A 725 GLU cc_start: 0.7686 (tt0) cc_final: 0.7422 (tt0) REVERT: A 964 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8599 (mtmm) REVERT: A 986 LYS cc_start: 0.8001 (ttpp) cc_final: 0.7485 (ttmm) REVERT: A 990 GLU cc_start: 0.7262 (mt-10) cc_final: 0.7040 (mt-10) REVERT: C 169 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7794 (mm-30) REVERT: C 188 ASN cc_start: 0.7651 (m-40) cc_final: 0.7106 (t0) REVERT: C 271 GLN cc_start: 0.8441 (mt0) cc_final: 0.8220 (mt0) REVERT: C 275 PHE cc_start: 0.8571 (m-80) cc_final: 0.8251 (m-80) REVERT: C 324 GLU cc_start: 0.8016 (pm20) cc_final: 0.7427 (pm20) REVERT: C 342 PHE cc_start: 0.8358 (m-80) cc_final: 0.7971 (m-80) REVERT: C 383 SER cc_start: 0.8803 (t) cc_final: 0.8348 (p) REVERT: C 406 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7524 (mm-30) REVERT: C 452 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7322 (ptm160) REVERT: C 456 PHE cc_start: 0.7473 (m-80) cc_final: 0.7108 (m-80) REVERT: C 495 TYR cc_start: 0.6385 (m-80) cc_final: 0.5918 (m-80) REVERT: C 523 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8310 (p) REVERT: C 565 PHE cc_start: 0.6505 (m-10) cc_final: 0.6024 (m-10) REVERT: C 596 SER cc_start: 0.9073 (m) cc_final: 0.8549 (p) REVERT: C 633 TRP cc_start: 0.8234 (p-90) cc_final: 0.6941 (p-90) REVERT: C 646 ARG cc_start: 0.8162 (tpt170) cc_final: 0.7781 (mmm160) REVERT: C 850 ILE cc_start: 0.8035 (mp) cc_final: 0.7740 (pt) REVERT: C 994 ASP cc_start: 0.7665 (t70) cc_final: 0.7411 (t70) REVERT: C 1037 SER cc_start: 0.9134 (t) cc_final: 0.8881 (p) outliers start: 85 outliers final: 62 residues processed: 615 average time/residue: 0.3956 time to fit residues: 386.3041 Evaluate side-chains 649 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 573 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 0.8980 chunk 278 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 241 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 262 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 269 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 0.0070 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 762 GLN B 777 ASN B1119 ASN A 125 ASN A 969 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.112625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.090476 restraints weight = 59431.051| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.29 r_work: 0.3259 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28014 Z= 0.256 Angle : 0.736 10.570 38103 Z= 0.351 Chirality : 0.046 0.648 4650 Planarity : 0.004 0.057 4761 Dihedral : 8.209 86.248 5946 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.87 % Favored : 93.95 % Rotamer: Outliers : 2.78 % Allowed : 18.68 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3273 helix: 1.82 (0.20), residues: 720 sheet: 0.06 (0.19), residues: 669 loop : -1.18 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 633 HIS 0.004 0.001 HIS A 207 PHE 0.025 0.002 PHE C 140 TYR 0.023 0.001 TYR C 904 ARG 0.006 0.000 ARG B 995 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8029.16 seconds wall clock time: 146 minutes 9.07 seconds (8769.07 seconds total)