Starting phenix.real_space_refine on Thu Dec 14 03:04:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zge_11203/12_2023/6zge_11203.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zge_11203/12_2023/6zge_11203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zge_11203/12_2023/6zge_11203.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zge_11203/12_2023/6zge_11203.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zge_11203/12_2023/6zge_11203.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zge_11203/12_2023/6zge_11203.pdb" } resolution = 2.6 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= 0.005 sd= 0.208 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17121 2.51 5 N 4395 2.21 5 O 5355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 936": "OD1" <-> "OD2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 442": "OD1" <-> "OD2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 775": "OD1" <-> "OD2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 936": "OD1" <-> "OD2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 936": "OD1" <-> "OD2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 26991 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8603 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 bond proxies already assigned to first conformer: 8768 Chain: "B" Number of atoms: 8603 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 bond proxies already assigned to first conformer: 8768 Chain: "C" Number of atoms: 8603 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 bond proxies already assigned to first conformer: 8768 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "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 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Time building chain proxies: 25.90, per 1000 atoms: 0.96 Number of scatterers: 26991 At special positions: 0 Unit cell: (151.093, 150.006, 179.355, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5355 8.00 N 4395 7.00 C 17121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.05 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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-ASN " NAG A1307 " - " ASN A 149 " " NAG A1312 " - " ASN A 282 " " NAG A1313 " - " ASN A 331 " " NAG A1314 " - " ASN A 343 " " NAG A1317 " - " ASN A 657 " " NAG A1318 " - " ASN A 709 " " NAG A1323 " - " ASN A1074 " " NAG B1307 " - " ASN B 149 " " NAG B1312 " - " ASN B 282 " " NAG B1313 " - " ASN B 331 " " NAG B1314 " - " ASN B 343 " " NAG B1317 " - " ASN B 657 " " NAG B1318 " - " ASN B 709 " " NAG B1323 " - " ASN B1074 " " NAG C1307 " - " ASN C 149 " " NAG C1312 " - " ASN C 282 " " NAG C1313 " - " ASN C 331 " " NAG C1314 " - " ASN C 343 " " NAG C1317 " - " ASN C 657 " " NAG C1318 " - " ASN C 709 " " NAG C1323 " - " ASN C1074 " " NAG D 1 " - " ASN A 61 " " NAG E 1 " - " ASN A 17 " " NAG F 1 " - " ASN A 122 " " NAG G 1 " - " ASN A 165 " " NAG H 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 616 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 61 " " NAG O 1 " - " ASN B 17 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 165 " " NAG R 1 " - " ASN B 234 " " NAG S 1 " - " ASN B 616 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 61 " " NAG Y 1 " - " ASN C 17 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C 165 " " NAG b 1 " - " ASN C 234 " " NAG c 1 " - " ASN C 616 " " NAG d 1 " - " ASN C 717 " " NAG e 1 " - " ASN C 801 " " NAG f 1 " - " ASN C1098 " " NAG g 1 " - " ASN C1134 " Time building additional restraints: 11.64 Conformation dependent library (CDL) restraints added in 9.6 seconds 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6168 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 42 sheets defined 24.2% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.653A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.191A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 756 through 783 removed outlier: 3.751A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 836 through 840 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.137A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.209A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.438A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.653A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.191A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.751A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 836 through 840 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.137A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.209A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.438A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.653A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.191A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.751A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 836 through 840 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.138A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.210A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.438A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.205A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.030A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.877A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 163 removed outlier: 6.624A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.290A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.417A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.334A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.322A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.629A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.070A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.406A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.205A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.030A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.876A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 151 through 163 removed outlier: 6.624A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.417A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.335A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.321A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.629A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.070A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.406A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.204A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.029A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.877A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 151 through 163 removed outlier: 6.624A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.290A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AD7, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.417A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.334A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.321A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.629A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.071A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.406A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 1056 hydrogen bonds defined for protein. 2856 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: 11.72 Time building geometry restraints manager: 11.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8310 1.34 - 1.47: 7203 1.47 - 1.59: 11889 1.59 - 1.72: 0 1.72 - 1.85: 150 Bond restraints: 27552 Sorted by residual: bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.85e+00 bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" CB ASP B 228 " pdb=" CG ASP B 228 " ideal model delta sigma weight residual 1.516 1.467 0.049 2.50e-02 1.60e+03 3.81e+00 bond pdb=" CB ASP A 228 " pdb=" CG ASP A 228 " ideal model delta sigma weight residual 1.516 1.467 0.049 2.50e-02 1.60e+03 3.80e+00 bond pdb=" C1 NAG f 2 " pdb=" O5 NAG f 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.80e+00 ... (remaining 27547 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.36: 655 106.36 - 113.33: 15112 113.33 - 120.29: 9932 120.29 - 127.25: 11549 127.25 - 134.21: 246 Bond angle restraints: 37494 Sorted by residual: angle pdb=" N CYS C 525 " pdb=" CA CYS C 525 " pdb=" C CYS C 525 " ideal model delta sigma weight residual 110.80 119.21 -8.41 2.13e+00 2.20e-01 1.56e+01 angle pdb=" N CYS A 525 " pdb=" CA CYS A 525 " pdb=" C CYS A 525 " ideal model delta sigma weight residual 110.80 119.21 -8.41 2.13e+00 2.20e-01 1.56e+01 angle pdb=" N CYS B 525 " pdb=" CA CYS B 525 " pdb=" C CYS B 525 " ideal model delta sigma weight residual 110.80 119.19 -8.39 2.13e+00 2.20e-01 1.55e+01 angle pdb=" CA LEU B 241 " pdb=" CB LEU B 241 " pdb=" CG LEU B 241 " ideal model delta sigma weight residual 116.30 128.02 -11.72 3.50e+00 8.16e-02 1.12e+01 angle pdb=" CA LEU A 241 " pdb=" CB LEU A 241 " pdb=" CG LEU A 241 " ideal model delta sigma weight residual 116.30 128.02 -11.72 3.50e+00 8.16e-02 1.12e+01 ... (remaining 37489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 16240 17.58 - 35.16: 908 35.16 - 52.74: 189 52.74 - 70.32: 98 70.32 - 87.90: 28 Dihedral angle restraints: 17463 sinusoidal: 7857 harmonic: 9606 Sorted by residual: dihedral pdb=" CA HIS C 66 " pdb=" C HIS C 66 " pdb=" N ALA C 67 " pdb=" CA ALA C 67 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA HIS A 66 " pdb=" C HIS A 66 " pdb=" N ALA A 67 " pdb=" CA ALA A 67 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA HIS B 66 " pdb=" C HIS B 66 " pdb=" N ALA B 67 " pdb=" CA ALA B 67 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 17460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2960 0.062 - 0.124: 1323 0.124 - 0.186: 158 0.186 - 0.248: 14 0.248 - 0.310: 3 Chirality restraints: 4458 Sorted by residual: chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A 149 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 149 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 149 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 4455 not shown) Planarity restraints: 4806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 539 " 0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C VAL B 539 " -0.068 2.00e-02 2.50e+03 pdb=" O VAL B 539 " 0.025 2.00e-02 2.50e+03 pdb=" N ASN B 540 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 539 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C VAL C 539 " 0.067 2.00e-02 2.50e+03 pdb=" O VAL C 539 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN C 540 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 539 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C VAL A 539 " 0.067 2.00e-02 2.50e+03 pdb=" O VAL A 539 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN A 540 " -0.023 2.00e-02 2.50e+03 ... (remaining 4803 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 9045 2.86 - 3.37: 21969 3.37 - 3.88: 43388 3.88 - 4.39: 50567 4.39 - 4.90: 87089 Nonbonded interactions: 212058 Sorted by model distance: nonbonded pdb=" OD1 ASN A 777 " pdb=" NH1BARG A1019 " model vdw 2.344 2.520 nonbonded pdb=" OD1 ASN B 777 " pdb=" NH1BARG B1019 " model vdw 2.345 2.520 nonbonded pdb=" OD1 ASN C 777 " pdb=" NH1BARG C1019 " model vdw 2.345 2.520 nonbonded pdb=" O SER B 477 " pdb=" OG1 THR B 478 " model vdw 2.347 2.440 nonbonded pdb=" O SER A 477 " pdb=" OG1 THR A 478 " model vdw 2.347 2.440 ... (remaining 212053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1146 or resid 1307 through 1323)) selection = (chain 'B' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1146 or resid 1307 through 1323)) selection = (chain 'C' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1146 or resid 1307 through 1323)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.960 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: 0.030 Extract box with map and model: 14.290 Check model and map are aligned: 0.390 Set scattering table: 0.210 Process input model: 88.680 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.540 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:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 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 : 0.010 0.080 27552 Z= 0.645 Angle : 0.941 11.722 37494 Z= 0.509 Chirality : 0.063 0.310 4458 Planarity : 0.005 0.039 4755 Dihedral : 12.776 87.897 11160 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.22 % Rotamer: Outliers : 0.73 % Allowed : 3.24 % Favored : 96.03 % 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: -0.97 (0.14), residues: 3270 helix: 0.91 (0.19), residues: 711 sheet: 0.39 (0.18), residues: 777 loop : -1.87 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 886 HIS 0.008 0.002 HIS B 49 PHE 0.022 0.004 PHE A 592 TYR 0.024 0.003 TYR C 265 ARG 0.008 0.001 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 408 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 3 residues processed: 426 average time/residue: 1.4267 time to fit residues: 703.6362 Evaluate side-chains 256 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 253 time to evaluate : 3.247 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 4.2847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 0.5980 chunk 247 optimal weight: 0.8980 chunk 137 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 132 optimal weight: 0.1980 chunk 256 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 155 optimal weight: 7.9990 chunk 190 optimal weight: 0.9980 chunk 296 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 146 HIS A 218 GLN A 239 GLN A 245 HIS A 394 ASN A 440 ASN A 474 GLN A 493 GLN A 501 ASN A 540 ASN A 563 GLN A 580 GLN A 641 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 925 ASN A 954 GLN A 969 ASN A1023 ASN A1036 GLN A1064 HIS B 99 ASN B 146 HIS B 239 GLN B 245 HIS B 394 ASN B 474 GLN B 501 ASN B 540 ASN B 580 GLN B 641 ASN B 658 ASN B 675 GLN B 690 GLN B 751 ASN B 925 ASN B 955 ASN B1023 ASN B1036 GLN B1064 HIS C 99 ASN C 146 HIS C 188 ASN C 207 HIS C 218 GLN C 239 GLN C 245 HIS C 394 ASN C 474 GLN C 501 ASN C 540 ASN C 580 GLN C 641 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 925 ASN C1023 ASN C1036 GLN C1064 HIS Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 27552 Z= 0.192 Angle : 0.639 16.202 37494 Z= 0.333 Chirality : 0.049 0.436 4458 Planarity : 0.004 0.045 4755 Dihedral : 7.739 59.242 5256 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.62 % Favored : 96.14 % Rotamer: Outliers : 1.46 % Allowed : 8.52 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: -0.72 (0.14), residues: 3270 helix: 1.30 (0.20), residues: 711 sheet: 0.44 (0.19), residues: 759 loop : -1.72 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS C1064 PHE 0.014 0.001 PHE B 643 TYR 0.017 0.001 TYR A 904 ARG 0.004 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 327 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 16 residues processed: 348 average time/residue: 1.3812 time to fit residues: 562.0981 Evaluate side-chains 284 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 268 time to evaluate : 3.045 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 9 residues processed: 7 average time/residue: 0.8665 time to fit residues: 11.7946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 165 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 297 optimal weight: 4.9990 chunk 321 optimal weight: 3.9990 chunk 264 optimal weight: 0.0070 chunk 295 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 238 optimal weight: 0.0970 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN B 66 HIS B 99 ASN B 658 ASN B 690 GLN B 779 GLN B 969 ASN C 99 ASN C 207 HIS C 211 ASN C 394 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 787 GLN C1005 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 27552 Z= 0.196 Angle : 0.606 12.824 37494 Z= 0.317 Chirality : 0.048 0.440 4458 Planarity : 0.004 0.048 4755 Dihedral : 7.088 58.254 5256 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.11 % Favored : 95.80 % Rotamer: Outliers : 1.67 % Allowed : 9.99 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -0.57 (0.14), residues: 3270 helix: 1.46 (0.20), residues: 711 sheet: 0.65 (0.19), residues: 750 loop : -1.69 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 152 HIS 0.004 0.001 HIS B 146 PHE 0.012 0.001 PHE A 643 TYR 0.029 0.001 TYR A 904 ARG 0.003 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 282 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 22 residues processed: 308 average time/residue: 1.3303 time to fit residues: 484.9484 Evaluate side-chains 277 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 255 time to evaluate : 2.784 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 13 residues processed: 9 average time/residue: 0.8163 time to fit residues: 13.1725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 293 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 chunk 298 optimal weight: 0.1980 chunk 316 optimal weight: 0.0050 chunk 155 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 563 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A1005 GLN B 99 ASN B 164 ASN B 690 GLN C 99 ASN C 164 ASN C 207 HIS ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 27552 Z= 0.181 Angle : 0.587 9.528 37494 Z= 0.306 Chirality : 0.047 0.385 4458 Planarity : 0.004 0.049 4755 Dihedral : 6.745 59.997 5256 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 2.05 % Allowed : 10.40 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.14), residues: 3270 helix: 1.57 (0.20), residues: 708 sheet: 0.80 (0.18), residues: 780 loop : -1.68 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 152 HIS 0.002 0.001 HIS A 146 PHE 0.026 0.001 PHE A 133 TYR 0.018 0.001 TYR B 265 ARG 0.003 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 271 time to evaluate : 2.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 27 residues processed: 310 average time/residue: 1.2792 time to fit residues: 470.9534 Evaluate side-chains 285 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 258 time to evaluate : 3.182 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 18 residues processed: 9 average time/residue: 1.0077 time to fit residues: 15.0109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 263 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 235 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 269 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 394 ASN A 563 GLN A 613 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A1054 GLN B 99 ASN B 690 GLN B1054 GLN C 99 ASN C 207 HIS C 493 GLN C 762 GLN C 787 GLN C 901 GLN C1054 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 27552 Z= 0.412 Angle : 0.761 18.703 37494 Z= 0.400 Chirality : 0.054 0.506 4458 Planarity : 0.005 0.050 4755 Dihedral : 6.992 59.885 5256 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.22 % Rotamer: Outliers : 2.23 % Allowed : 10.89 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.14), residues: 3270 helix: 0.97 (0.19), residues: 714 sheet: 0.61 (0.18), residues: 759 loop : -1.84 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 152 HIS 0.006 0.001 HIS C1064 PHE 0.022 0.003 PHE A 802 TYR 0.028 0.003 TYR B 265 ARG 0.008 0.001 ARG B1000 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 279 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 42 residues processed: 321 average time/residue: 1.2603 time to fit residues: 479.6017 Evaluate side-chains 303 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 261 time to evaluate : 3.086 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 27 residues processed: 15 average time/residue: 0.7288 time to fit residues: 18.4949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 106 optimal weight: 0.0270 chunk 284 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 185 optimal weight: 0.9980 chunk 78 optimal weight: 0.4980 chunk 316 optimal weight: 1.9990 chunk 262 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 66 HIS A 314 GLN A 563 GLN A 613 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN B 99 ASN C 99 ASN C 207 HIS C 901 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 27552 Z= 0.206 Angle : 0.649 20.217 37494 Z= 0.336 Chirality : 0.048 0.410 4458 Planarity : 0.004 0.049 4755 Dihedral : 6.638 59.756 5256 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.26 % Rotamer: Outliers : 1.70 % Allowed : 11.86 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: -0.58 (0.14), residues: 3270 helix: 1.38 (0.20), residues: 708 sheet: 0.78 (0.18), residues: 774 loop : -1.77 (0.13), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 152 HIS 0.003 0.001 HIS A 146 PHE 0.016 0.001 PHE C 133 TYR 0.018 0.001 TYR B 265 ARG 0.004 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 260 time to evaluate : 3.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 33 residues processed: 292 average time/residue: 1.3380 time to fit residues: 462.9866 Evaluate side-chains 276 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 243 time to evaluate : 3.245 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 25 residues processed: 8 average time/residue: 1.0396 time to fit residues: 14.0802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 305 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 231 optimal weight: 5.9990 chunk 179 optimal weight: 0.9980 chunk 266 optimal weight: 0.2980 chunk 176 optimal weight: 0.9990 chunk 315 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN B 99 ASN C 99 ASN C 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 27552 Z= 0.238 Angle : 0.652 19.372 37494 Z= 0.339 Chirality : 0.049 0.412 4458 Planarity : 0.004 0.046 4755 Dihedral : 6.549 59.399 5256 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.11 % Favored : 95.83 % Rotamer: Outliers : 1.81 % Allowed : 12.32 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3270 helix: 1.40 (0.20), residues: 708 sheet: 0.78 (0.18), residues: 777 loop : -1.78 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 152 HIS 0.003 0.001 HIS A 146 PHE 0.014 0.002 PHE B1121 TYR 0.038 0.002 TYR A 904 ARG 0.003 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 255 time to evaluate : 2.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 35 residues processed: 289 average time/residue: 1.2905 time to fit residues: 442.8489 Evaluate side-chains 280 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 245 time to evaluate : 2.780 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 25 residues processed: 10 average time/residue: 0.8816 time to fit residues: 14.9311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 194 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 188 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 214 optimal weight: 0.6980 chunk 155 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 563 GLN A 613 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A1005 GLN B 99 ASN B 690 GLN C 99 ASN C 207 HIS C 901 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 27552 Z= 0.277 Angle : 0.678 19.769 37494 Z= 0.354 Chirality : 0.050 0.436 4458 Planarity : 0.004 0.047 4755 Dihedral : 6.600 59.051 5256 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.35 % Favored : 95.56 % Rotamer: Outliers : 1.74 % Allowed : 12.46 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: -0.65 (0.14), residues: 3270 helix: 1.30 (0.20), residues: 708 sheet: 0.73 (0.18), residues: 774 loop : -1.79 (0.13), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 152 HIS 0.003 0.001 HIS C1064 PHE 0.015 0.002 PHE C 133 TYR 0.043 0.002 TYR A 904 ARG 0.005 0.000 ARG B1000 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 251 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 37 residues processed: 288 average time/residue: 1.3000 time to fit residues: 443.2585 Evaluate side-chains 284 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 247 time to evaluate : 2.901 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 27 residues processed: 10 average time/residue: 0.8405 time to fit residues: 14.7764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 301 optimal weight: 0.9980 chunk 275 optimal weight: 0.7980 chunk 293 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 230 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 265 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 292 optimal weight: 0.0030 chunk 192 optimal weight: 2.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 563 GLN A 658 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN B 99 ASN B 690 GLN C 99 ASN C 207 HIS C 901 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 27552 Z= 0.217 Angle : 0.629 18.555 37494 Z= 0.326 Chirality : 0.048 0.433 4458 Planarity : 0.004 0.049 4755 Dihedral : 6.462 58.817 5256 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.07 % Favored : 95.86 % Rotamer: Outliers : 1.29 % Allowed : 12.77 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: -0.56 (0.14), residues: 3270 helix: 1.45 (0.20), residues: 708 sheet: 0.75 (0.18), residues: 777 loop : -1.75 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 152 HIS 0.003 0.001 HIS B 66 PHE 0.014 0.001 PHE A 643 TYR 0.029 0.001 TYR A 904 ARG 0.003 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 248 time to evaluate : 3.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 32 residues processed: 278 average time/residue: 1.2790 time to fit residues: 421.8200 Evaluate side-chains 271 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 239 time to evaluate : 2.950 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 27 residues processed: 5 average time/residue: 0.7877 time to fit residues: 9.2917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 310 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 325 optimal weight: 0.7980 chunk 299 optimal weight: 2.9990 chunk 259 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 159 optimal weight: 0.0870 chunk 206 optimal weight: 0.5980 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 563 GLN A 658 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN B 99 ASN B 690 GLN C 99 ASN C 207 HIS C 901 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 27552 Z= 0.232 Angle : 0.639 18.373 37494 Z= 0.332 Chirality : 0.048 0.432 4458 Planarity : 0.004 0.045 4755 Dihedral : 6.458 58.486 5256 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.35 % Favored : 95.59 % Rotamer: Outliers : 1.22 % Allowed : 12.84 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: -0.57 (0.14), residues: 3270 helix: 1.44 (0.20), residues: 708 sheet: 0.74 (0.18), residues: 777 loop : -1.76 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 152 HIS 0.003 0.001 HIS B 66 PHE 0.016 0.002 PHE A 643 TYR 0.027 0.002 TYR A 904 ARG 0.006 0.000 ARG C 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 246 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 31 residues processed: 274 average time/residue: 1.3343 time to fit residues: 437.6803 Evaluate side-chains 276 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 245 time to evaluate : 2.909 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 27 residues processed: 4 average time/residue: 0.8599 time to fit residues: 8.4036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 239 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 259 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 266 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 563 GLN A 658 ASN A 954 GLN B 99 ASN B 690 GLN C 99 ASN C 207 HIS C 901 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.146103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.113415 restraints weight = 48680.978| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.72 r_work: 0.3006 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 27552 Z= 0.239 Angle : 0.641 18.229 37494 Z= 0.334 Chirality : 0.049 0.433 4458 Planarity : 0.004 0.046 4755 Dihedral : 6.461 58.386 5256 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.23 % Favored : 95.71 % Rotamer: Outliers : 1.15 % Allowed : 13.05 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: -0.58 (0.14), residues: 3270 helix: 1.42 (0.20), residues: 708 sheet: 0.74 (0.18), residues: 777 loop : -1.76 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 152 HIS 0.003 0.001 HIS B 66 PHE 0.017 0.002 PHE A 643 TYR 0.027 0.002 TYR A 904 ARG 0.005 0.000 ARG C 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9378.91 seconds wall clock time: 169 minutes 19.61 seconds (10159.61 seconds total)