Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 20:43:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us6_26727/04_2023/7us6_26727.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us6_26727/04_2023/7us6_26727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us6_26727/04_2023/7us6_26727.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us6_26727/04_2023/7us6_26727.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us6_26727/04_2023/7us6_26727.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us6_26727/04_2023/7us6_26727.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 0.066 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 124 5.16 5 C 15235 2.51 5 N 3932 2.21 5 O 4456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 737": "OD1" <-> "OD2" Residue "A PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "A PHE 1244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1257": "NH1" <-> "NH2" Residue "A PHE 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 737": "OD1" <-> "OD2" Residue "B PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1137": "NH1" <-> "NH2" Residue "B PHE 1244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1257": "NH1" <-> "NH2" Residue "B PHE 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 737": "OD1" <-> "OD2" Residue "C PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1137": "NH1" <-> "NH2" Residue "C ASP 1181": "OD1" <-> "OD2" Residue "C PHE 1244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1257": "NH1" <-> "NH2" Residue "C PHE 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1281": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 23747 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 7464 Classifications: {'peptide': 1053} Incomplete info: {'truncation_to_alanine': 237} Link IDs: {'PTRANS': 40, 'TRANS': 1012} Chain breaks: 8 Unresolved non-hydrogen bonds: 651 Unresolved non-hydrogen angles: 828 Unresolved non-hydrogen dihedrals: 501 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 18, 'TRP:plan': 2, 'ASP:plan': 44, 'GLU:plan': 23, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 400 Chain: "B" Number of atoms: 7409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 7409 Classifications: {'peptide': 1053} Incomplete info: {'truncation_to_alanine': 259} Link IDs: {'PTRANS': 40, 'TRANS': 1012} Chain breaks: 8 Unresolved non-hydrogen bonds: 708 Unresolved non-hydrogen angles: 900 Unresolved non-hydrogen dihedrals: 548 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 16, 'TRP:plan': 2, 'ASP:plan': 48, 'PHE:plan': 1, 'GLU:plan': 24, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 431 Chain: "C" Number of atoms: 7430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 7430 Classifications: {'peptide': 1053} Incomplete info: {'truncation_to_alanine': 249} Link IDs: {'PTRANS': 40, 'TRANS': 1012} Chain breaks: 8 Unresolved non-hydrogen bonds: 687 Unresolved non-hydrogen angles: 877 Unresolved non-hydrogen dihedrals: 529 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 45, 'PHE:plan': 1, 'GLU:plan': 24, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 413 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 chiralities: 2 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 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 chiralities: 2 Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'BMA': 1, 'MAN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 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 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 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 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 chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 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 chiralities: 2 Chain: "Q" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'BMA': 1, 'MAN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 chiralities: 2 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 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 chiralities: 2 Chain: "Y" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'BMA': 1, 'MAN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 chiralities: 2 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 12.67, per 1000 atoms: 0.53 Number of scatterers: 23747 At special positions: 0 Unit cell: (144.996, 155.955, 157.641, 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 124 16.00 O 4456 8.00 N 3932 7.00 C 15235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 250 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 327 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 444 " distance=2.13 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 399 " distance=2.03 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 492 " distance=2.09 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 626 " distance=2.09 Simple disulfide: pdb=" SG CYS A 581 " - pdb=" SG CYS A 594 " distance=2.03 Simple disulfide: pdb=" SG CYS A 609 " - pdb=" SG CYS A 636 " distance=2.03 Simple disulfide: pdb=" SG CYS A 685 " - pdb=" SG CYS A 736 " distance=2.04 Simple disulfide: pdb=" SG CYS A 797 " - pdb=" SG CYS A 809 " distance=2.03 Simple disulfide: pdb=" SG CYS A 860 " - pdb=" SG CYS A 882 " distance=2.10 Simple disulfide: pdb=" SG CYS A 865 " - pdb=" SG CYS A 871 " distance=2.04 Simple disulfide: pdb=" SG CYS A 983 " - pdb=" SG CYS A 994 " distance=2.04 Simple disulfide: pdb=" SG CYS A1186 " - pdb=" SG CYS A1197 " distance=2.02 Simple disulfide: pdb=" SG CYS A1236 " - pdb=" SG CYS A1287 " distance=2.13 Simple disulfide: pdb=" SG CYS B 250 " - pdb=" SG CYS B 254 " distance=2.03 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 327 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 444 " distance=2.13 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 399 " distance=2.03 Simple disulfide: pdb=" SG CYS B 483 " - pdb=" SG CYS B 492 " distance=2.09 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 626 " distance=2.09 Simple disulfide: pdb=" SG CYS B 581 " - pdb=" SG CYS B 594 " distance=2.03 Simple disulfide: pdb=" SG CYS B 609 " - pdb=" SG CYS B 636 " distance=2.03 Simple disulfide: pdb=" SG CYS B 685 " - pdb=" SG CYS B 736 " distance=2.04 Simple disulfide: pdb=" SG CYS B 797 " - pdb=" SG CYS B 809 " distance=2.03 Simple disulfide: pdb=" SG CYS B 860 " - pdb=" SG CYS B 882 " distance=2.10 Simple disulfide: pdb=" SG CYS B 865 " - pdb=" SG CYS B 871 " distance=2.04 Simple disulfide: pdb=" SG CYS B 983 " - pdb=" SG CYS B 994 " distance=2.04 Simple disulfide: pdb=" SG CYS B1186 " - pdb=" SG CYS B1197 " distance=2.02 Simple disulfide: pdb=" SG CYS B1236 " - pdb=" SG CYS B1287 " distance=2.13 Simple disulfide: pdb=" SG CYS C 250 " - pdb=" SG CYS C 254 " distance=2.03 Simple disulfide: pdb=" SG CYS C 303 " - pdb=" SG CYS C 327 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 444 " distance=2.13 Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 399 " distance=2.03 Simple disulfide: pdb=" SG CYS C 483 " - pdb=" SG CYS C 492 " distance=2.09 Simple disulfide: pdb=" SG CYS C 567 " - pdb=" SG CYS C 626 " distance=2.09 Simple disulfide: pdb=" SG CYS C 581 " - pdb=" SG CYS C 594 " distance=2.03 Simple disulfide: pdb=" SG CYS C 609 " - pdb=" SG CYS C 636 " distance=2.03 Simple disulfide: pdb=" SG CYS C 685 " - pdb=" SG CYS C 736 " distance=2.04 Simple disulfide: pdb=" SG CYS C 797 " - pdb=" SG CYS C 809 " distance=2.03 Simple disulfide: pdb=" SG CYS C 860 " - pdb=" SG CYS C 882 " distance=2.11 Simple disulfide: pdb=" SG CYS C 865 " - pdb=" SG CYS C 871 " distance=2.04 Simple disulfide: pdb=" SG CYS C 983 " - pdb=" SG CYS C 994 " distance=2.04 Simple disulfide: pdb=" SG CYS C1186 " - pdb=" SG CYS C1197 " distance=2.02 Simple disulfide: pdb=" SG CYS C1236 " - pdb=" SG CYS C1287 " distance=2.13 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA H 1 " - " MAN H 2 " " BMA N 3 " - " MAN N 4 " " BMA Q 1 " - " MAN Q 2 " " BMA V 3 " - " MAN V 4 " " BMA Y 1 " - " MAN Y 2 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA H 1 " - " MAN H 3 " " BMA N 3 " - " MAN N 5 " " BMA Q 1 " - " MAN Q 3 " " BMA V 3 " - " MAN V 5 " " BMA Y 1 " - " MAN Y 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA H 1 " " 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 N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA Q 1 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA Y 1 " " 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-ASN " NAG A1501 " - " ASN A 531 " " NAG A1502 " - " ASN A 42 " " NAG A1503 " - " ASN A 242 " " NAG A1504 " - " ASN A 448 " " NAG A1505 " - " ASN A 779 " " NAG A1506 " - " ASN A 553 " " NAG A1507 " - " ASN A 703 " " NAG A1508 " - " ASN A 818 " " NAG A1509 " - " ASN A 920 " " NAG A1510 " - " ASN A1293 " " NAG A1511 " - " ASN A 561 " " NAG A1512 " - " ASN A 404 " " NAG A1513 " - " ASN A 361 " " NAG A1514 " - " ASN A 515 " " NAG B1501 " - " ASN B 531 " " NAG B1502 " - " ASN B 42 " " NAG B1503 " - " ASN B 242 " " NAG B1504 " - " ASN B 448 " " NAG B1505 " - " ASN B 779 " " NAG B1506 " - " ASN B 553 " " NAG B1507 " - " ASN B 703 " " NAG B1508 " - " ASN B 818 " " NAG B1509 " - " ASN B 920 " " NAG B1510 " - " ASN B1293 " " NAG B1511 " - " ASN B 344 " " NAG B1512 " - " ASN B 561 " " NAG B1513 " - " ASN B 404 " " NAG B1514 " - " ASN B 361 " " NAG B1515 " - " ASN B 515 " " NAG C1501 " - " ASN C 531 " " NAG C1502 " - " ASN C 42 " " NAG C1503 " - " ASN C 242 " " NAG C1504 " - " ASN C 448 " " NAG C1505 " - " ASN C 779 " " NAG C1506 " - " ASN C 553 " " NAG C1507 " - " ASN C 703 " " NAG C1508 " - " ASN C 818 " " NAG C1509 " - " ASN C 920 " " NAG C1510 " - " ASN C1293 " " NAG C1511 " - " ASN C 561 " " NAG C1512 " - " ASN C 404 " " NAG C1513 " - " ASN C 361 " " NAG C1514 " - " ASN C 515 " " NAG D 1 " - " ASN A 249 " " NAG E 1 " - " ASN A1199 " " NAG F 1 " - " ASN A 839 " " NAG G 1 " - " ASN A 284 " " NAG I 1 " - " ASN A 724 " " NAG J 1 " - " ASN A 833 " " NAG K 1 " - " ASN A1073 " " NAG L 1 " - " ASN A 344 " " NAG M 1 " - " ASN B 249 " " NAG N 1 " - " ASN B1199 " " NAG O 1 " - " ASN B 839 " " NAG P 1 " - " ASN B 284 " " NAG R 1 " - " ASN B 724 " " NAG S 1 " - " ASN B 833 " " NAG T 1 " - " ASN B1073 " " NAG U 1 " - " ASN C 249 " " NAG V 1 " - " ASN C1199 " " NAG W 1 " - " ASN C 839 " " NAG X 1 " - " ASN C 284 " " NAG Z 1 " - " ASN C 724 " " NAG a 1 " - " ASN C 833 " " NAG b 1 " - " ASN C1073 " " NAG c 1 " - " ASN C 344 " Time building additional restraints: 10.66 Conformation dependent library (CDL) restraints added in 3.8 seconds 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5898 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 45 sheets defined 26.6% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 32 through 44 removed outlier: 4.150A pdb=" N ILE A 36 " --> pdb=" O HIS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 261 Processing helix chain 'A' and resid 485 through 495 Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 859 through 865 Processing helix chain 'A' and resid 868 through 875 removed outlier: 3.662A pdb=" N LYS A 873 " --> pdb=" O PRO A 869 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU A 874 " --> pdb=" O ARG A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 904 Processing helix chain 'A' and resid 907 through 912 Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 926 through 930 removed outlier: 3.519A pdb=" N LYS A 930 " --> pdb=" O PRO A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 938 No H-bonds generated for 'chain 'A' and resid 936 through 938' Processing helix chain 'A' and resid 939 through 944 Processing helix chain 'A' and resid 958 through 967 Processing helix chain 'A' and resid 980 through 985 Processing helix chain 'A' and resid 991 through 998 Processing helix chain 'A' and resid 1009 through 1022 Processing helix chain 'A' and resid 1037 through 1050 removed outlier: 3.743A pdb=" N TYR A1048 " --> pdb=" O ALA A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1080 Processing helix chain 'A' and resid 1093 through 1118 Processing helix chain 'A' and resid 1119 through 1122 Processing helix chain 'A' and resid 1130 through 1138 Processing helix chain 'A' and resid 1139 through 1187 removed outlier: 4.867A pdb=" N ALA A1145 " --> pdb=" O PRO A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1279 No H-bonds generated for 'chain 'A' and resid 1277 through 1279' Processing helix chain 'A' and resid 1298 through 1303 Processing helix chain 'B' and resid 33 through 44 Processing helix chain 'B' and resid 253 through 261 Processing helix chain 'B' and resid 485 through 495 Processing helix chain 'B' and resid 595 through 598 Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 859 through 865 Processing helix chain 'B' and resid 868 through 875 removed outlier: 3.661A pdb=" N LYS B 873 " --> pdb=" O PRO B 869 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B 874 " --> pdb=" O ARG B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 904 Processing helix chain 'B' and resid 907 through 912 Processing helix chain 'B' and resid 915 through 920 Processing helix chain 'B' and resid 926 through 930 removed outlier: 3.519A pdb=" N LYS B 930 " --> pdb=" O PRO B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 938 No H-bonds generated for 'chain 'B' and resid 936 through 938' Processing helix chain 'B' and resid 939 through 944 Processing helix chain 'B' and resid 958 through 967 Processing helix chain 'B' and resid 980 through 985 Processing helix chain 'B' and resid 991 through 998 Processing helix chain 'B' and resid 1009 through 1022 Processing helix chain 'B' and resid 1037 through 1050 removed outlier: 3.743A pdb=" N TYR B1048 " --> pdb=" O ALA B1044 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1080 Processing helix chain 'B' and resid 1093 through 1118 Processing helix chain 'B' and resid 1119 through 1122 Processing helix chain 'B' and resid 1130 through 1138 Processing helix chain 'B' and resid 1139 through 1187 removed outlier: 4.867A pdb=" N ALA B1145 " --> pdb=" O PRO B1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 1277 through 1279 No H-bonds generated for 'chain 'B' and resid 1277 through 1279' Processing helix chain 'B' and resid 1298 through 1303 Processing helix chain 'C' and resid 33 through 44 Processing helix chain 'C' and resid 253 through 261 Processing helix chain 'C' and resid 485 through 495 Processing helix chain 'C' and resid 595 through 598 Processing helix chain 'C' and resid 612 through 616 Processing helix chain 'C' and resid 859 through 865 Processing helix chain 'C' and resid 868 through 875 removed outlier: 3.661A pdb=" N LYS C 873 " --> pdb=" O PRO C 869 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU C 874 " --> pdb=" O ARG C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 904 Processing helix chain 'C' and resid 907 through 912 Processing helix chain 'C' and resid 915 through 920 Processing helix chain 'C' and resid 926 through 930 removed outlier: 3.519A pdb=" N LYS C 930 " --> pdb=" O PRO C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 938 No H-bonds generated for 'chain 'C' and resid 936 through 938' Processing helix chain 'C' and resid 939 through 944 Processing helix chain 'C' and resid 958 through 967 Processing helix chain 'C' and resid 980 through 985 Processing helix chain 'C' and resid 991 through 998 Processing helix chain 'C' and resid 1009 through 1022 Processing helix chain 'C' and resid 1037 through 1050 removed outlier: 3.744A pdb=" N TYR C1048 " --> pdb=" O ALA C1044 " (cutoff:3.500A) Processing helix chain 'C' and resid 1059 through 1080 Processing helix chain 'C' and resid 1093 through 1118 Processing helix chain 'C' and resid 1119 through 1122 Processing helix chain 'C' and resid 1130 through 1138 Processing helix chain 'C' and resid 1139 through 1187 removed outlier: 4.867A pdb=" N ALA C1145 " --> pdb=" O PRO C1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 1277 through 1279 No H-bonds generated for 'chain 'C' and resid 1277 through 1279' Processing helix chain 'C' and resid 1298 through 1303 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 57 Processing sheet with id=AA2, first strand: chain 'A' and resid 291 through 306 removed outlier: 3.522A pdb=" N LEU A 299 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER A 464 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL A 301 " --> pdb=" O TYR A 462 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR A 462 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS A 303 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE A 460 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TRP A 305 " --> pdb=" O TRP A 458 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TRP A 458 " --> pdb=" O TRP A 305 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN A 342 " --> pdb=" O TRP A 458 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE A 460 " --> pdb=" O ARG A 340 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG A 340 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TYR A 462 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL A 338 " --> pdb=" O TYR A 462 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A 431 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASN A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 306 removed outlier: 3.522A pdb=" N LEU A 299 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER A 464 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL A 301 " --> pdb=" O TYR A 462 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR A 462 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS A 303 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE A 460 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TRP A 305 " --> pdb=" O TRP A 458 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TRP A 458 " --> pdb=" O TRP A 305 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLU A 467 " --> pdb=" O TYR A 482 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TYR A 482 " --> pdb=" O GLU A 467 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU A 469 " --> pdb=" O VAL A 480 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL A 480 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN A 471 " --> pdb=" O LYS A 478 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 314 through 318 removed outlier: 3.642A pdb=" N VAL A 357 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 314 through 318 removed outlier: 3.642A pdb=" N VAL A 357 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR A 356 " --> pdb=" O CYS A 372 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N CYS A 372 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N CYS A 399 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR A 410 " --> pdb=" O CYS A 399 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL A 401 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA7, first strand: chain 'A' and resid 502 through 507 removed outlier: 3.504A pdb=" N GLY A 751 " --> pdb=" O ALA A 743 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE A 745 " --> pdb=" O ILE A 749 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE A 749 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS A 765 " --> pdb=" O SER A 776 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 515 through 519 removed outlier: 6.683A pdb=" N ASN A 515 " --> pdb=" O ASP A 687 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ASN A 689 " --> pdb=" O ASN A 515 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER A 517 " --> pdb=" O ASN A 689 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 730 " --> pdb=" O THR A 702 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU A 720 " --> pdb=" O VAL A 733 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR A 712 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 553 through 555 removed outlier: 6.732A pdb=" N THR A 528 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TYR A 576 " --> pdb=" O THR A 528 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A 530 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N HIS A 578 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A 532 " --> pdb=" O HIS A 578 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR A 580 " --> pdb=" O ILE A 532 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE A 534 " --> pdb=" O THR A 580 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LYS A 582 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU A 536 " --> pdb=" O LYS A 582 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 567 removed outlier: 4.445A pdb=" N GLY A 661 " --> pdb=" O PHE A 622 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 572 through 583 current: chain 'A' and resid 600 through 605 Processing sheet with id=AB2, first strand: chain 'A' and resid 801 through 803 Processing sheet with id=AB3, first strand: chain 'A' and resid 832 through 850 removed outlier: 6.561A pdb=" N ASN A 833 " --> pdb=" O THR A1230 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR A1230 " --> pdb=" O ASN A 833 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR A 835 " --> pdb=" O THR A1228 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR A1228 " --> pdb=" O THR A 835 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR A1226 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN A 839 " --> pdb=" O THR A1224 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY A1213 " --> pdb=" O ALA A1209 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ALA A1209 " --> pdb=" O GLY A1213 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A1215 " --> pdb=" O ALA A1207 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ALA A1207 " --> pdb=" O ILE A1215 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE A1217 " --> pdb=" O SER A1205 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER A1205 " --> pdb=" O PHE A1217 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N THR A1219 " --> pdb=" O LEU A1203 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 856 through 858 Processing sheet with id=AB5, first strand: chain 'A' and resid 1281 through 1284 Processing sheet with id=AB6, first strand: chain 'A' and resid 1253 through 1257 Processing sheet with id=AB7, first strand: chain 'B' and resid 52 through 57 Processing sheet with id=AB8, first strand: chain 'B' and resid 291 through 306 removed outlier: 3.522A pdb=" N LEU B 299 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER B 464 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL B 301 " --> pdb=" O TYR B 462 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR B 462 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS B 303 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE B 460 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TRP B 305 " --> pdb=" O TRP B 458 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TRP B 458 " --> pdb=" O TRP B 305 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN B 342 " --> pdb=" O TRP B 458 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE B 460 " --> pdb=" O ARG B 340 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG B 340 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TYR B 462 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 338 " --> pdb=" O TYR B 462 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B 431 " --> pdb=" O ASN B 435 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASN B 435 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 291 through 306 removed outlier: 3.522A pdb=" N LEU B 299 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER B 464 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL B 301 " --> pdb=" O TYR B 462 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR B 462 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS B 303 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE B 460 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TRP B 305 " --> pdb=" O TRP B 458 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TRP B 458 " --> pdb=" O TRP B 305 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLU B 467 " --> pdb=" O TYR B 482 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TYR B 482 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU B 469 " --> pdb=" O VAL B 480 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL B 480 " --> pdb=" O LEU B 469 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN B 471 " --> pdb=" O LYS B 478 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 314 through 318 removed outlier: 3.643A pdb=" N VAL B 357 " --> pdb=" O ASN B 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 314 through 318 removed outlier: 3.643A pdb=" N VAL B 357 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR B 356 " --> pdb=" O CYS B 372 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N CYS B 372 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N CYS B 399 " --> pdb=" O TYR B 410 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TYR B 410 " --> pdb=" O CYS B 399 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 401 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC4, first strand: chain 'B' and resid 502 through 507 removed outlier: 3.504A pdb=" N GLY B 751 " --> pdb=" O ALA B 743 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE B 745 " --> pdb=" O ILE B 749 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE B 749 " --> pdb=" O ILE B 745 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS B 765 " --> pdb=" O SER B 776 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 515 through 519 removed outlier: 6.683A pdb=" N ASN B 515 " --> pdb=" O ASP B 687 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ASN B 689 " --> pdb=" O ASN B 515 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER B 517 " --> pdb=" O ASN B 689 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE B 730 " --> pdb=" O THR B 702 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU B 720 " --> pdb=" O VAL B 733 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR B 712 " --> pdb=" O LEU B 720 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 553 through 555 removed outlier: 6.732A pdb=" N THR B 528 " --> pdb=" O SER B 574 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TYR B 576 " --> pdb=" O THR B 528 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 530 " --> pdb=" O TYR B 576 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N HIS B 578 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE B 532 " --> pdb=" O HIS B 578 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR B 580 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE B 534 " --> pdb=" O THR B 580 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LYS B 582 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU B 536 " --> pdb=" O LYS B 582 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 565 through 567 removed outlier: 4.445A pdb=" N GLY B 661 " --> pdb=" O PHE B 622 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 572 through 583 current: chain 'B' and resid 600 through 605 Processing sheet with id=AC8, first strand: chain 'B' and resid 801 through 803 Processing sheet with id=AC9, first strand: chain 'B' and resid 832 through 850 removed outlier: 6.561A pdb=" N ASN B 833 " --> pdb=" O THR B1230 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR B1230 " --> pdb=" O ASN B 833 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR B 835 " --> pdb=" O THR B1228 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR B1228 " --> pdb=" O THR B 835 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR B1226 " --> pdb=" O PRO B 837 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN B 839 " --> pdb=" O THR B1224 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY B1213 " --> pdb=" O ALA B1209 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ALA B1209 " --> pdb=" O GLY B1213 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE B1215 " --> pdb=" O ALA B1207 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ALA B1207 " --> pdb=" O ILE B1215 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE B1217 " --> pdb=" O SER B1205 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER B1205 " --> pdb=" O PHE B1217 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N THR B1219 " --> pdb=" O LEU B1203 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 856 through 858 Processing sheet with id=AD2, first strand: chain 'B' and resid 1281 through 1284 Processing sheet with id=AD3, first strand: chain 'B' and resid 1253 through 1257 Processing sheet with id=AD4, first strand: chain 'C' and resid 52 through 57 Processing sheet with id=AD5, first strand: chain 'C' and resid 291 through 306 removed outlier: 3.522A pdb=" N LEU C 299 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER C 464 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL C 301 " --> pdb=" O TYR C 462 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR C 462 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS C 303 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE C 460 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TRP C 305 " --> pdb=" O TRP C 458 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TRP C 458 " --> pdb=" O TRP C 305 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN C 342 " --> pdb=" O TRP C 458 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE C 460 " --> pdb=" O ARG C 340 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG C 340 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TYR C 462 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 338 " --> pdb=" O TYR C 462 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE C 431 " --> pdb=" O ASN C 435 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASN C 435 " --> pdb=" O ILE C 431 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 291 through 306 removed outlier: 3.522A pdb=" N LEU C 299 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER C 464 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL C 301 " --> pdb=" O TYR C 462 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR C 462 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS C 303 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE C 460 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TRP C 305 " --> pdb=" O TRP C 458 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TRP C 458 " --> pdb=" O TRP C 305 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLU C 467 " --> pdb=" O TYR C 482 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TYR C 482 " --> pdb=" O GLU C 467 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU C 469 " --> pdb=" O VAL C 480 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL C 480 " --> pdb=" O LEU C 469 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN C 471 " --> pdb=" O LYS C 478 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 314 through 318 removed outlier: 3.643A pdb=" N VAL C 357 " --> pdb=" O ASN C 448 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 314 through 318 removed outlier: 3.643A pdb=" N VAL C 357 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR C 356 " --> pdb=" O CYS C 372 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N CYS C 372 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N CYS C 399 " --> pdb=" O TYR C 410 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR C 410 " --> pdb=" O CYS C 399 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL C 401 " --> pdb=" O LEU C 408 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE1, first strand: chain 'C' and resid 502 through 507 removed outlier: 3.504A pdb=" N GLY C 751 " --> pdb=" O ALA C 743 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE C 745 " --> pdb=" O ILE C 749 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE C 749 " --> pdb=" O ILE C 745 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS C 765 " --> pdb=" O SER C 776 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 515 through 519 removed outlier: 6.683A pdb=" N ASN C 515 " --> pdb=" O ASP C 687 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ASN C 689 " --> pdb=" O ASN C 515 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER C 517 " --> pdb=" O ASN C 689 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE C 730 " --> pdb=" O THR C 702 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU C 720 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR C 712 " --> pdb=" O LEU C 720 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 553 through 555 removed outlier: 6.733A pdb=" N THR C 528 " --> pdb=" O SER C 574 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TYR C 576 " --> pdb=" O THR C 528 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL C 530 " --> pdb=" O TYR C 576 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N HIS C 578 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE C 532 " --> pdb=" O HIS C 578 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR C 580 " --> pdb=" O ILE C 532 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE C 534 " --> pdb=" O THR C 580 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LYS C 582 " --> pdb=" O ILE C 534 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU C 536 " --> pdb=" O LYS C 582 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 565 through 567 removed outlier: 4.445A pdb=" N GLY C 661 " --> pdb=" O PHE C 622 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 572 through 583 current: chain 'C' and resid 600 through 605 Processing sheet with id=AE5, first strand: chain 'C' and resid 801 through 803 Processing sheet with id=AE6, first strand: chain 'C' and resid 832 through 850 removed outlier: 6.560A pdb=" N ASN C 833 " --> pdb=" O THR C1230 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR C1230 " --> pdb=" O ASN C 833 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR C 835 " --> pdb=" O THR C1228 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR C1228 " --> pdb=" O THR C 835 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR C1226 " --> pdb=" O PRO C 837 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN C 839 " --> pdb=" O THR C1224 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY C1213 " --> pdb=" O ALA C1209 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ALA C1209 " --> pdb=" O GLY C1213 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE C1215 " --> pdb=" O ALA C1207 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ALA C1207 " --> pdb=" O ILE C1215 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE C1217 " --> pdb=" O SER C1205 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER C1205 " --> pdb=" O PHE C1217 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N THR C1219 " --> pdb=" O LEU C1203 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 856 through 858 Processing sheet with id=AE8, first strand: chain 'C' and resid 1281 through 1284 Processing sheet with id=AE9, first strand: chain 'C' and resid 1253 through 1257 1017 hydrogen bonds defined for protein. 2808 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: 11.71 Time building geometry restraints manager: 11.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3846 1.31 - 1.45: 7384 1.45 - 1.59: 12805 1.59 - 1.73: 18 1.73 - 1.86: 155 Bond restraints: 24208 Sorted by residual: bond pdb=" C CYS A 865 " pdb=" O CYS A 865 " ideal model delta sigma weight residual 1.234 1.334 -0.100 1.16e-02 7.43e+03 7.36e+01 bond pdb=" C CYS C 865 " pdb=" O CYS C 865 " ideal model delta sigma weight residual 1.234 1.334 -0.099 1.16e-02 7.43e+03 7.34e+01 bond pdb=" C CYS B 865 " pdb=" O CYS B 865 " ideal model delta sigma weight residual 1.234 1.334 -0.099 1.16e-02 7.43e+03 7.34e+01 bond pdb=" C CYS C 581 " pdb=" O CYS C 581 " ideal model delta sigma weight residual 1.236 1.176 0.060 1.19e-02 7.06e+03 2.54e+01 bond pdb=" C CYS B 581 " pdb=" O CYS B 581 " ideal model delta sigma weight residual 1.236 1.176 0.060 1.19e-02 7.06e+03 2.51e+01 ... (remaining 24203 not shown) Histogram of bond angle deviations from ideal: 91.35 - 99.87: 9 99.87 - 108.38: 1667 108.38 - 116.89: 16151 116.89 - 125.41: 15133 125.41 - 133.92: 230 Bond angle restraints: 33190 Sorted by residual: angle pdb=" CG1 VAL B 349 " pdb=" CB VAL B 349 " pdb=" CG2 VAL B 349 " ideal model delta sigma weight residual 110.80 131.31 -20.51 2.20e+00 2.07e-01 8.69e+01 angle pdb=" CG1 VAL C 349 " pdb=" CB VAL C 349 " pdb=" CG2 VAL C 349 " ideal model delta sigma weight residual 110.80 131.29 -20.49 2.20e+00 2.07e-01 8.67e+01 angle pdb=" CG1 VAL A 349 " pdb=" CB VAL A 349 " pdb=" CG2 VAL A 349 " ideal model delta sigma weight residual 110.80 131.28 -20.48 2.20e+00 2.07e-01 8.67e+01 angle pdb=" CD1 LEU C 598 " pdb=" CG LEU C 598 " pdb=" CD2 LEU C 598 " ideal model delta sigma weight residual 110.80 129.53 -18.73 2.20e+00 2.07e-01 7.25e+01 angle pdb=" CD1 LEU B 598 " pdb=" CG LEU B 598 " pdb=" CD2 LEU B 598 " ideal model delta sigma weight residual 110.80 129.49 -18.69 2.20e+00 2.07e-01 7.22e+01 ... (remaining 33185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 12831 17.75 - 35.50: 366 35.50 - 53.24: 71 53.24 - 70.99: 35 70.99 - 88.74: 7 Dihedral angle restraints: 13310 sinusoidal: 4141 harmonic: 9169 Sorted by residual: dihedral pdb=" C CYS A 865 " pdb=" N CYS A 865 " pdb=" CA CYS A 865 " pdb=" CB CYS A 865 " ideal model delta harmonic sigma weight residual -122.60 -137.27 14.67 0 2.50e+00 1.60e-01 3.45e+01 dihedral pdb=" C CYS B 865 " pdb=" N CYS B 865 " pdb=" CA CYS B 865 " pdb=" CB CYS B 865 " ideal model delta harmonic sigma weight residual -122.60 -137.26 14.66 0 2.50e+00 1.60e-01 3.44e+01 dihedral pdb=" C CYS C 865 " pdb=" N CYS C 865 " pdb=" CA CYS C 865 " pdb=" CB CYS C 865 " ideal model delta harmonic sigma weight residual -122.60 -137.24 14.64 0 2.50e+00 1.60e-01 3.43e+01 ... (remaining 13307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 3855 0.165 - 0.331: 424 0.331 - 0.496: 62 0.496 - 0.662: 3 0.662 - 0.827: 6 Chirality restraints: 4350 Sorted by residual: chirality pdb=" C1 NAG b 2 " pdb=" O4 NAG b 1 " pdb=" C2 NAG b 2 " pdb=" O5 NAG b 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.87e+02 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.84e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.83e+02 ... (remaining 4347 not shown) Planarity restraints: 4163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 2 " 0.150 2.00e-02 2.50e+03 1.27e-01 2.01e+02 pdb=" C7 NAG W 2 " -0.030 2.00e-02 2.50e+03 pdb=" C8 NAG W 2 " -0.037 2.00e-02 2.50e+03 pdb=" N2 NAG W 2 " -0.203 2.00e-02 2.50e+03 pdb=" O7 NAG W 2 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 2 " -0.150 2.00e-02 2.50e+03 1.27e-01 2.01e+02 pdb=" C7 NAG O 2 " 0.031 2.00e-02 2.50e+03 pdb=" C8 NAG O 2 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG O 2 " 0.203 2.00e-02 2.50e+03 pdb=" O7 NAG O 2 " -0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.150 2.00e-02 2.50e+03 1.27e-01 2.01e+02 pdb=" C7 NAG F 2 " 0.030 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.203 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.120 2.00e-02 2.50e+03 ... (remaining 4160 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 325 2.66 - 3.22: 21547 3.22 - 3.78: 34497 3.78 - 4.34: 48565 4.34 - 4.90: 77722 Nonbonded interactions: 182656 Sorted by model distance: nonbonded pdb=" O ASN A 866 " pdb=" OD1 ASN A 866 " model vdw 2.101 3.040 nonbonded pdb=" O ASN C 866 " pdb=" OD1 ASN C 866 " model vdw 2.101 3.040 nonbonded pdb=" O ASN B 866 " pdb=" OD1 ASN B 866 " model vdw 2.102 3.040 nonbonded pdb=" NZ LYS A1249 " pdb=" OD1 ASP C1280 " model vdw 2.476 2.520 nonbonded pdb=" C ASN B 866 " pdb=" OD1 ASN B 866 " model vdw 2.487 3.270 ... (remaining 182651 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 32 through 43 or (resid 44 through 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 49 or (resid 50 through \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or (resid 57 and (name N or name CA or name C or name O or name CB )) or res \ id 58 through 60 or (resid 61 through 234 and (name N or name CA or name C or na \ me O or name CB )) or resid 235 through 238 or (resid 239 through 240 and (name \ N or name CA or name C or name O or name CB )) or resid 241 through 258 or (resi \ d 259 and (name N or name CA or name C or name O or name CB )) or resid 260 thro \ ugh 314 or (resid 315 and (name N or name CA or name C or name O or name CB )) o \ r resid 316 through 352 or (resid 353 and (name N or name CA or name C or name O \ or name CB )) or resid 354 through 358 or (resid 359 and (name N or name CA or \ name C or name O or name CB )) or resid 360 through 362 or (resid 363 and (name \ N or name CA or name C or name O or name CB )) or resid 364 through 368 or (resi \ d 369 and (name N or name CA or name C or name O or name CB )) or resid 370 or ( \ resid 371 and (name N or name CA or name C or name O or name CB )) or resid 372 \ through 391 or (resid 392 and (name N or name CA or name C or name O or name CB \ )) or resid 393 through 405 or (resid 406 and (name N or name CA or name C or na \ me O or name CB )) or resid 407 through 473 or (resid 474 and (name N or name CA \ or name C or name O or name CB )) or resid 475 through 478 or (resid 479 and (n \ ame N or name CA or name C or name O or name CB )) or resid 480 through 495 or ( \ resid 496 through 498 and (name N or name CA or name C or name O or name CB )) o \ r resid 499 through 520 or (resid 521 and (name N or name CA or name C or name O \ or name CB )) or resid 522 through 524 or (resid 525 through 526 and (name N or \ name CA or name C or name O or name CB )) or resid 527 through 548 or (resid 54 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 550 through \ 554 or (resid 555 and (name N or name CA or name C or name O or name CB )) or re \ sid 556 through 562 or (resid 563 through 564 and (name N or name CA or name C o \ r name O or name CB )) or resid 565 through 620 or (resid 621 and (name N or nam \ e CA or name C or name O or name CB )) or resid 622 through 731 or (resid 732 an \ d (name N or name CA or name C or name O or name CB )) or resid 733 through 757 \ or (resid 758 through 759 and (name N or name CA or name C or name O or name CB \ )) or resid 760 through 780 or (resid 781 through 796 and (name N or name CA or \ name C or name O or name CB )) or resid 797 through 821 or (resid 822 through 82 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 824 through \ 842 or (resid 843 and (name N or name CA or name C or name O or name CB )) or re \ sid 844 through 856 or (resid 857 through 858 and (name N or name CA or name C o \ r name O or name CB )) or resid 859 through 901 or (resid 902 and (name N or nam \ e CA or name C or name O or name CB )) or resid 903 through 906 or (resid 907 th \ rough 908 and (name N or name CA or name C or name O or name CB )) or resid 909 \ through 914 or (resid 915 and (name N or name CA or name C or name O or name CB \ )) or resid 916 through 937 or (resid 938 and (name N or name CA or name C or na \ me O or name CB )) or resid 939 through 955 or (resid 956 and (name N or name CA \ or name C or name O or name CB )) or resid 957 through 978 or (resid 979 and (n \ ame N or name CA or name C or name O or name CB )) or resid 980 through 1103 or \ (resid 1104 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 05 through 1163 or (resid 1164 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1165 through 1174 or (resid 1175 and (name N or name CA or name \ C or name O or name CB )) or resid 1176 through 1188 or (resid 1189 and (name N \ or name CA or name C or name O or name CB )) or resid 1190 or (resid 1191 throu \ gh 1192 and (name N or name CA or name C or name O or name CB )) or resid 1193 t \ hrough 1204 or (resid 1205 and (name N or name CA or name C or name O or name CB \ )) or resid 1206 through 1251 or (resid 1252 and (name N or name CA or name C o \ r name O or name CB )) or resid 1253 through 1289 or (resid 1290 and (name N or \ name CA or name C or name O or name CB )) or resid 1291 through 1303 or resid 15 \ 01 through 1514)) selection = (chain 'B' and (resid 32 through 46 or (resid 47 and (name N or name CA or name \ C or name O or name CB )) or resid 48 through 49 or (resid 50 through 53 and (na \ me N or name CA or name C or name O or name CB )) or resid 54 through 246 or (re \ sid 247 through 248 and (name N or name CA or name C or name O or name CB )) or \ resid 249 through 308 or (resid 309 and (name N or name CA or name C or name O o \ r name CB )) or resid 310 through 350 or (resid 351 and (name N or name CA or na \ me C or name O or name CB )) or resid 352 through 362 or (resid 363 and (name N \ or name CA or name C or name O or name CB )) or resid 364 through 405 or (resid \ 406 and (name N or name CA or name C or name O or name CB )) or resid 407 throug \ h 484 or (resid 485 and (name N or name CA or name C or name O or name CB )) or \ resid 486 through 573 or (resid 574 and (name N or name CA or name C or name O o \ r name CB )) or resid 575 through 600 or (resid 601 through 602 and (name N or n \ ame CA or name C or name O or name CB )) or resid 603 through 620 or (resid 621 \ and (name N or name CA or name C or name O or name CB )) or resid 622 through 65 \ 6 or (resid 657 and (name N or name CA or name C or name O or name CB )) or resi \ d 658 through 662 or (resid 663 and (name N or name CA or name C or name O or na \ me CB )) or resid 664 through 709 or (resid 710 and (name N or name CA or name C \ or name O or name CB )) or resid 711 through 731 or (resid 732 and (name N or n \ ame CA or name C or name O or name CB )) or resid 733 through 770 or (resid 771 \ and (name N or name CA or name C or name O or name CB )) or resid 772 through 77 \ 5 or (resid 776 and (name N or name CA or name C or name O or name CB )) or resi \ d 777 through 780 or (resid 781 through 796 and (name N or name CA or name C or \ name O or name CB )) or resid 797 through 809 or (resid 810 and (name N or name \ CA or name C or name O or name CB )) or resid 811 through 842 or (resid 843 and \ (name N or name CA or name C or name O or name CB )) or resid 844 through 923 or \ (resid 924 and (name N or name CA or name C or name O or name CB )) or resid 92 \ 5 through 1008 or (resid 1009 through 1011 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1012 through 1018 or (resid 1019 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1020 through 1054 or (resid 1055 \ through 1059 and (name N or name CA or name C or name O or name CB )) or resid \ 1060 through 1102 or (resid 1103 through 1104 and (name N or name CA or name C o \ r name O or name CB )) or resid 1105 through 1106 or (resid 1107 and (name N or \ name CA or name C or name O or name CB )) or resid 1108 through 1174 or (resid 1 \ 175 and (name N or name CA or name C or name O or name CB )) or resid 1176 throu \ gh 1232 or (resid 1233 and (name N or name CA or name C or name O or name CB )) \ or resid 1234 through 1289 or (resid 1290 and (name N or name CA or name C or na \ me O or name CB )) or resid 1291 through 1303 or resid 1501 through 1514)) selection = (chain 'C' and (resid 32 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 238 or (resid 239 through 240 and \ (name N or name CA or name C or name O or name CB )) or resid 241 through 258 or \ (resid 259 and (name N or name CA or name C or name O or name CB )) or resid 26 \ 0 through 289 or (resid 290 and (name N or name CA or name C or name O or name C \ B )) or resid 291 through 314 or (resid 315 and (name N or name CA or name C or \ name O or name CB )) or resid 316 through 350 or (resid 351 and (name N or name \ CA or name C or name O or name CB )) or resid 352 through 391 or (resid 392 and \ (name N or name CA or name C or name O or name CB )) or resid 393 through 423 or \ (resid 424 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 5 through 473 or (resid 474 and (name N or name CA or name C or name O or name C \ B )) or resid 475 through 484 or (resid 485 and (name N or name CA or name C or \ name O or name CB )) or resid 486 through 554 or (resid 555 and (name N or name \ CA or name C or name O or name CB )) or resid 556 through 573 or (resid 574 and \ (name N or name CA or name C or name O or name CB )) or resid 575 through 600 or \ (resid 601 through 602 and (name N or name CA or name C or name O or name CB )) \ or resid 603 through 638 or (resid 639 and (name N or name CA or name C or name \ O or name CB )) or resid 640 through 662 or (resid 663 and (name N or name CA o \ r name C or name O or name CB )) or resid 664 through 669 or (resid 678 and (nam \ e N or name CA or name C or name O or name CB )) or resid 679 through 754 or (re \ sid 755 and (name N or name CA or name C or name O or name CB )) or resid 756 th \ rough 763 or (resid 764 and (name N or name CA or name C or name O or name CB )) \ or resid 765 through 803 or (resid 804 and (name N or name CA or name C or name \ O or name CB )) or resid 805 through 809 or (resid 810 and (name N or name CA o \ r name C or name O or name CB )) or resid 811 through 857 or (resid 858 and (nam \ e N or name CA or name C or name O or name CB )) or resid 859 through 876 or (re \ sid 877 and (name N or name CA or name C or name O or name CB )) or resid 878 or \ (resid 879 through 881 and (name N or name CA or name C or name O or name CB )) \ or resid 882 through 914 or (resid 915 and (name N or name CA or name C or name \ O or name CB )) or resid 916 through 937 or (resid 938 and (name N or name CA o \ r name C or name O or name CB )) or resid 939 through 1008 or (resid 1009 throug \ h 1011 and (name N or name CA or name C or name O or name CB )) or resid 1012 th \ rough 1054 or (resid 1055 through 1059 and (name N or name CA or name C or name \ O or name CB )) or resid 1060 through 1127 or (resid 1128 through 1130 and (name \ N or name CA or name C or name O or name CB )) or resid 1131 or (resid 1132 thr \ ough 1133 and (name N or name CA or name C or name O or name CB )) or resid 1134 \ through 1162 or (resid 1163 through 1164 and (name N or name CA or name C or na \ me O or name CB )) or resid 1165 through 1180 or (resid 1181 and (name N or name \ CA or name C or name O or name CB )) or resid 1182 through 1191 or (resid 1192 \ and (name N or name CA or name C or name O or name CB )) or resid 1193 through 1 \ 204 or (resid 1205 and (name N or name CA or name C or name O or name CB )) or r \ esid 1206 through 1251 or (resid 1252 and (name N or name CA or name C or name O \ or name CB )) or resid 1253 through 1261 or (resid 1262 and (name N or name CA \ or name C or name O or name CB )) or resid 1263 through 1279 or (resid 1280 and \ (name N or name CA or name C or name O or name CB )) or resid 1281 through 1303 \ or resid 1501 through 1514)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'E' selection = chain 'N' selection = chain 'V' } ncs_group { reference = chain 'H' selection = chain 'Q' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 29.630 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 66.970 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.380 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.015 0.134 24208 Z= 0.975 Angle : 1.490 20.507 33190 Z= 0.956 Chirality : 0.111 0.827 4350 Planarity : 0.008 0.127 4097 Dihedral : 9.614 88.741 7277 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.39 % Allowed : 2.71 % Favored : 96.91 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.41 % 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: 0.23 (0.14), residues: 3105 helix: 0.51 (0.17), residues: 729 sheet: 0.61 (0.18), residues: 756 loop : -0.14 (0.15), residues: 1620 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 311 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 320 average time/residue: 0.4316 time to fit residues: 209.5273 Evaluate side-chains 162 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 156 time to evaluate : 3.504 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 6 average time/residue: 0.2123 time to fit residues: 6.3605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 0.7980 chunk 238 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 246 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 286 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN A 619 HIS A 701 GLN A 999 ASN A1164 GLN B 619 HIS B 701 GLN B 999 ASN C 474 ASN C 619 HIS C 701 GLN C 999 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 24208 Z= 0.238 Angle : 0.604 10.482 33190 Z= 0.319 Chirality : 0.046 0.257 4350 Planarity : 0.004 0.040 4097 Dihedral : 4.555 25.115 3349 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 2.02 % 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: 0.60 (0.14), residues: 3105 helix: 1.76 (0.19), residues: 720 sheet: 0.33 (0.17), residues: 792 loop : -0.11 (0.15), residues: 1593 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 208 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 20 residues processed: 235 average time/residue: 0.3590 time to fit residues: 135.8396 Evaluate side-chains 175 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 155 time to evaluate : 2.880 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 2 residues processed: 20 average time/residue: 0.2419 time to fit residues: 12.4694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 158 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 238 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 286 optimal weight: 0.9980 chunk 309 optimal weight: 0.0770 chunk 255 optimal weight: 6.9990 chunk 284 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A 527 HIS B 265 GLN C 265 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 24208 Z= 0.251 Angle : 0.557 13.931 33190 Z= 0.289 Chirality : 0.046 0.451 4350 Planarity : 0.004 0.037 4097 Dihedral : 4.377 35.717 3349 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.32 % Favored : 98.58 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 3105 helix: 1.91 (0.19), residues: 744 sheet: 0.39 (0.18), residues: 774 loop : -0.19 (0.15), residues: 1587 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 19 residues processed: 211 average time/residue: 0.3647 time to fit residues: 121.2948 Evaluate side-chains 178 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 2.524 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 3 residues processed: 19 average time/residue: 0.2328 time to fit residues: 11.7787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 283 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 148 optimal weight: 7.9990 chunk 31 optimal weight: 0.0970 chunk 136 optimal weight: 0.6980 chunk 192 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 chunk 304 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 272 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 HIS B 765 HIS B1052 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 24208 Z= 0.201 Angle : 0.499 7.064 33190 Z= 0.261 Chirality : 0.044 0.409 4350 Planarity : 0.004 0.038 4097 Dihedral : 4.146 26.545 3349 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.67 % Favored : 98.23 % Rotamer Outliers : 1.46 % 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: 0.70 (0.15), residues: 3105 helix: 2.08 (0.19), residues: 744 sheet: 0.38 (0.18), residues: 759 loop : -0.20 (0.15), residues: 1602 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 183 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 9 residues processed: 206 average time/residue: 0.3388 time to fit residues: 113.8261 Evaluate side-chains 164 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 155 time to evaluate : 2.573 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 9 average time/residue: 0.2613 time to fit residues: 7.6224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 253 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 226 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 259 optimal weight: 7.9990 chunk 210 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 273 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1052 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.062 24208 Z= 0.568 Angle : 0.691 8.528 33190 Z= 0.349 Chirality : 0.050 0.390 4350 Planarity : 0.005 0.041 4097 Dihedral : 4.796 25.784 3349 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.48 % Favored : 97.42 % Rotamer Outliers : 2.47 % 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: 0.08 (0.14), residues: 3105 helix: 1.32 (0.19), residues: 753 sheet: 0.24 (0.18), residues: 735 loop : -0.61 (0.14), residues: 1617 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 141 time to evaluate : 2.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 27 residues processed: 181 average time/residue: 0.3456 time to fit residues: 102.9640 Evaluate side-chains 160 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 3.010 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 3 residues processed: 27 average time/residue: 0.2435 time to fit residues: 15.9977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 102 optimal weight: 0.9980 chunk 274 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 178 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 304 optimal weight: 0.9990 chunk 253 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 160 optimal weight: 0.4980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1060 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 24208 Z= 0.208 Angle : 0.509 6.346 33190 Z= 0.264 Chirality : 0.044 0.355 4350 Planarity : 0.004 0.042 4097 Dihedral : 4.313 27.772 3349 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.77 % Favored : 98.13 % Rotamer Outliers : 1.31 % 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: 0.27 (0.15), residues: 3105 helix: 1.64 (0.19), residues: 768 sheet: 0.27 (0.18), residues: 732 loop : -0.55 (0.14), residues: 1605 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 161 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 185 average time/residue: 0.3369 time to fit residues: 103.6966 Evaluate side-chains 154 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 2.697 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 10 average time/residue: 0.2132 time to fit residues: 7.6088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 293 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 222 optimal weight: 0.9990 chunk 172 optimal weight: 0.5980 chunk 256 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 303 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 185 optimal weight: 0.6980 chunk 140 optimal weight: 0.0000 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1060 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 24208 Z= 0.177 Angle : 0.487 6.766 33190 Z= 0.250 Chirality : 0.044 0.342 4350 Planarity : 0.004 0.044 4097 Dihedral : 4.069 29.811 3349 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.96 % Favored : 97.94 % Rotamer Outliers : 0.81 % 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: 0.41 (0.15), residues: 3105 helix: 1.87 (0.19), residues: 768 sheet: 0.31 (0.18), residues: 729 loop : -0.51 (0.15), residues: 1608 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 159 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 170 average time/residue: 0.3417 time to fit residues: 96.0558 Evaluate side-chains 159 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 2.730 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 10 average time/residue: 0.2172 time to fit residues: 7.6045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 187 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 193 optimal weight: 0.5980 chunk 206 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 238 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1060 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 24208 Z= 0.171 Angle : 0.484 12.517 33190 Z= 0.250 Chirality : 0.044 0.337 4350 Planarity : 0.004 0.043 4097 Dihedral : 3.966 26.469 3349 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.61 % Favored : 98.29 % Rotamer Outliers : 0.86 % 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: 0.53 (0.15), residues: 3105 helix: 2.12 (0.19), residues: 747 sheet: 0.21 (0.18), residues: 759 loop : -0.39 (0.15), residues: 1599 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 165 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 181 average time/residue: 0.3570 time to fit residues: 105.9920 Evaluate side-chains 157 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 2.696 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 8 average time/residue: 0.2333 time to fit residues: 7.2080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 276 optimal weight: 0.9980 chunk 290 optimal weight: 0.8980 chunk 265 optimal weight: 0.6980 chunk 282 optimal weight: 10.0000 chunk 170 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 222 optimal weight: 0.3980 chunk 86 optimal weight: 0.9980 chunk 255 optimal weight: 0.9980 chunk 267 optimal weight: 0.9980 chunk 281 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1060 GLN C1060 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 24208 Z= 0.164 Angle : 0.476 12.099 33190 Z= 0.245 Chirality : 0.043 0.333 4350 Planarity : 0.004 0.043 4097 Dihedral : 3.879 24.051 3349 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.93 % Favored : 97.97 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 3105 helix: 2.18 (0.19), residues: 747 sheet: 0.24 (0.18), residues: 759 loop : -0.36 (0.15), residues: 1599 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 156 time to evaluate : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 163 average time/residue: 0.3270 time to fit residues: 89.0988 Evaluate side-chains 150 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 2.717 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 4 average time/residue: 0.2165 time to fit residues: 5.2282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 185 optimal weight: 0.8980 chunk 299 optimal weight: 0.9980 chunk 182 optimal weight: 0.0970 chunk 141 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 313 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 249 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1060 GLN C1060 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 24208 Z= 0.199 Angle : 0.499 17.752 33190 Z= 0.255 Chirality : 0.044 0.333 4350 Planarity : 0.004 0.043 4097 Dihedral : 3.944 40.831 3349 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.80 % Favored : 98.10 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.15), residues: 3105 helix: 2.14 (0.19), residues: 747 sheet: 0.24 (0.18), residues: 759 loop : -0.36 (0.15), residues: 1599 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 157 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 160 average time/residue: 0.3454 time to fit residues: 91.2562 Evaluate side-chains 152 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 2.837 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.2131 time to fit residues: 4.7855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 198 optimal weight: 0.9980 chunk 266 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 250 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 257 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1060 GLN C1060 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.107679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.095867 restraints weight = 33743.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.090113 restraints weight = 59620.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.089022 restraints weight = 48787.914| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 24208 Z= 0.243 Angle : 0.529 14.511 33190 Z= 0.270 Chirality : 0.045 0.336 4350 Planarity : 0.004 0.043 4097 Dihedral : 4.042 37.213 3349 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.16 % Favored : 97.75 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3105 helix: 1.91 (0.19), residues: 768 sheet: 0.28 (0.19), residues: 729 loop : -0.44 (0.15), residues: 1608 =============================================================================== Job complete usr+sys time: 3904.47 seconds wall clock time: 72 minutes 41.43 seconds (4361.43 seconds total)