Starting phenix.real_space_refine on Wed Mar 20 01:21:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nb6_0403/03_2024/6nb6_0403.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nb6_0403/03_2024/6nb6_0403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nb6_0403/03_2024/6nb6_0403.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nb6_0403/03_2024/6nb6_0403.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nb6_0403/03_2024/6nb6_0403.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nb6_0403/03_2024/6nb6_0403.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.046 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 132 5.16 5 C 16099 2.51 5 N 4307 2.21 5 O 5245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 613": "OD1" <-> "OD2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 761": "NH1" <-> "NH2" Residue "A PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 790": "OD1" <-> "OD2" Residue "A PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 899": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 977": "NH1" <-> "NH2" Residue "A TYR 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 613": "OD1" <-> "OD2" Residue "B PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 761": "NH1" <-> "NH2" Residue "B PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 899": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 976": "OD1" <-> "OD2" Residue "B ARG 977": "NH1" <-> "NH2" Residue "B TYR 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 569": "OE1" <-> "OE2" Residue "C PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 593": "OE1" <-> "OE2" Residue "C TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 613": "OD1" <-> "OD2" Residue "C TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 761": "NH1" <-> "NH2" Residue "C TYR 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 899": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25783 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 7515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 7515 Classifications: {'peptide': 1052} Incomplete info: {'truncation_to_alanine': 212} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 998} Chain breaks: 7 Unresolved non-hydrogen bonds: 728 Unresolved non-hydrogen angles: 931 Unresolved non-hydrogen dihedrals: 571 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 30, 'TYR:plan': 2, 'ASN:plan1': 13, 'HIS:plan': 4, 'PHE:plan': 16, 'GLU:plan': 21, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 420 Chain: "B" Number of atoms: 6925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 6925 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 311} Link IDs: {'PCIS': 2, 'PTRANS': 50, 'TRANS': 973} Chain breaks: 8 Unresolved non-hydrogen bonds: 1165 Unresolved non-hydrogen angles: 1511 Unresolved non-hydrogen dihedrals: 960 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 6, 'TYR:plan': 15, 'ASN:plan1': 24, 'TRP:plan': 4, 'ASP:plan': 36, 'PHE:plan': 28, 'GLU:plan': 23, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 715 Chain: "C" Number of atoms: 7085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1055, 7085 Classifications: {'peptide': 1055} Incomplete info: {'truncation_to_alanine': 335} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1001} Chain breaks: 7 Unresolved non-hydrogen bonds: 1206 Unresolved non-hydrogen angles: 1559 Unresolved non-hydrogen dihedrals: 979 Unresolved non-hydrogen chiralities: 113 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 6, 'TYR:plan': 16, 'ASN:plan1': 27, 'TRP:plan': 2, 'ASP:plan': 43, 'PHE:plan': 26, 'GLU:plan': 22, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 732 Chain: "H" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 613 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 388 Unresolved non-hydrogen angles: 504 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 9, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 256 Chain: "I" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 618 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 120} Unresolved non-hydrogen bonds: 392 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 9, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 260 Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 557 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 189 Chain: "M" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 552 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 305 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 254 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 189 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 14.33, per 1000 atoms: 0.56 Number of scatterers: 25783 At special positions: 0 Unit cell: (141.11, 149.33, 221.94, 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 132 16.00 O 5245 8.00 N 4307 7.00 C 16099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 133 " distance=2.04 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.02 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.07 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.14 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.02 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.09 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.05 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.05 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.05 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.02 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.09 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.05 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.06 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 133 " distance=2.04 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.01 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.02 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.02 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.04 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.04 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.02 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.09 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 93 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA b 3 " - " MAN b 4 " " BMA e 3 " - " MAN e 4 " " BMA p 3 " - " MAN p 4 " " BMA r 3 " - " MAN r 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA O 3 " - " MAN O 5 " " BMA P 3 " - " MAN P 5 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 5 " " BMA b 3 " - " MAN b 5 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 5 " " BMA p 3 " - " MAN p 5 " " BMA r 3 " - " MAN r 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-ASN " NAG A1301 " - " ASN A 357 " " NAG A1302 " - " ASN A 65 " " NAG A1303 " - " ASN A 73 " " NAG A1310 " - " ASN A 158 " " NAG A1311 " - " ASN A 227 " " NAG A1315 " - " ASN A 318 " " NAG A1319 " - " ASN A 589 " " NAG B1301 " - " ASN B 357 " " NAG B1302 " - " ASN B 29 " " NAG B1303 " - " ASN B 65 " " NAG B1312 " - " ASN B 227 " " NAG B1322 " - " ASN B 589 " " NAG C1301 " - " ASN C 357 " " NAG C1302 " - " ASN C 29 " " NAG C1303 " - " ASN C 65 " " NAG C1304 " - " ASN C 73 " " NAG C1326 " - " ASN C 589 " " NAG D 1 " - " ASN A 109 " " NAG E 1 " - " ASN A 119 " " NAG F 1 " - " ASN A 269 " " NAG G 1 " - " ASN A 330 " " NAG J 1 " - " ASN A 602 " " NAG K 1 " - " ASN A 691 " " NAG N 1 " - " ASN A 699 " " NAG O 1 " - " ASN A 783 " " NAG P 1 " - " ASN A1056 " " NAG Q 1 " - " ASN A1080 " " NAG R 1 " - " ASN A1116 " " NAG S 1 " - " ASN B 109 " " NAG T 1 " - " ASN B 119 " " NAG U 1 " - " ASN B 158 " " NAG V 1 " - " ASN B 269 " " NAG W 1 " - " ASN B 318 " " NAG X 1 " - " ASN B 330 " " NAG Y 1 " - " ASN B 602 " " NAG Z 1 " - " ASN B 691 " " NAG a 1 " - " ASN B 699 " " NAG b 1 " - " ASN B 783 " " NAG c 1 " - " ASN B1056 " " NAG d 1 " - " ASN B1080 " " NAG e 1 " - " ASN B1116 " " NAG f 1 " - " ASN C 109 " " NAG g 1 " - " ASN C 119 " " NAG h 1 " - " ASN C 158 " " NAG i 1 " - " ASN C 227 " " NAG j 1 " - " ASN C 269 " " NAG k 1 " - " ASN C 318 " " NAG l 1 " - " ASN C 330 " " NAG m 1 " - " ASN C 602 " " NAG n 1 " - " ASN C 691 " " NAG o 1 " - " ASN C 699 " " NAG p 1 " - " ASN C 783 " " NAG q 1 " - " ASN C1056 " " NAG r 1 " - " ASN C1080 " " NAG s 1 " - " ASN C1116 " Time building additional restraints: 12.07 Conformation dependent library (CDL) restraints added in 5.3 seconds 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6732 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 62 sheets defined 23.1% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.671A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 397 removed outlier: 4.006A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 602 through 612 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.746A pdb=" N ILE A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU A 755 " --> pdb=" O GLY A 751 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 756 " --> pdb=" O ILE A 752 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 787 No H-bonds generated for 'chain 'A' and resid 785 through 787' Processing helix chain 'A' and resid 798 through 806 Processing helix chain 'A' and resid 848 through 867 removed outlier: 3.958A pdb=" N THR A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY A 867 " --> pdb=" O THR A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 895 through 901 removed outlier: 4.047A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 Processing helix chain 'A' and resid 927 through 947 Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 959 through 964 Processing helix chain 'A' and resid 967 through 1015 Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1122 through 1127 Processing helix chain 'B' and resid 281 through 290 Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 370 through 377 removed outlier: 4.933A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 removed outlier: 4.252A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 602 through 612 Processing helix chain 'B' and resid 719 through 725 Processing helix chain 'B' and resid 728 through 737 removed outlier: 3.524A pdb=" N GLN B 737 " --> pdb=" O ASN B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 765 removed outlier: 3.641A pdb=" N THR B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL B 763 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 805 Processing helix chain 'B' and resid 848 through 866 Processing helix chain 'B' and resid 867 through 870 removed outlier: 3.846A pdb=" N PHE B 870 " --> pdb=" O GLY B 867 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 867 through 870' Processing helix chain 'B' and resid 879 through 892 Processing helix chain 'B' and resid 895 through 901 removed outlier: 4.008A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 Processing helix chain 'B' and resid 927 through 947 Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 959 through 964 Processing helix chain 'B' and resid 967 through 1015 Processing helix chain 'B' and resid 1098 through 1100 No H-bonds generated for 'chain 'B' and resid 1098 through 1100' Processing helix chain 'B' and resid 1122 through 1127 Processing helix chain 'C' and resid 281 through 290 Processing helix chain 'C' and resid 325 through 330 removed outlier: 3.612A pdb=" N PHE C 329 " --> pdb=" O PHE C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 340 Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 370 through 377 removed outlier: 3.827A pdb=" N LEU C 374 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASN C 375 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 397 removed outlier: 3.950A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 602 through 612 Processing helix chain 'C' and resid 719 through 725 removed outlier: 4.045A pdb=" N ILE C 724 " --> pdb=" O CYS C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 736 Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 740 through 765 Processing helix chain 'C' and resid 798 through 806 Processing helix chain 'C' and resid 848 through 867 removed outlier: 3.570A pdb=" N THR C 865 " --> pdb=" O SER C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 870 No H-bonds generated for 'chain 'C' and resid 868 through 870' Processing helix chain 'C' and resid 879 through 892 Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.222A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 922 Processing helix chain 'C' and resid 927 through 947 Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 959 through 964 Processing helix chain 'C' and resid 967 through 1015 removed outlier: 4.052A pdb=" N VAL C 973 " --> pdb=" O PRO C 969 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 108 through 112 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 108 through 112 Processing helix chain 'L' and resid 84 through 88 Processing helix chain 'M' and resid 84 through 88 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 8.407A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N HIS A 181 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE A 203 " --> pdb=" O HIS A 181 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ARG A 183 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLN A 201 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N PHE A 185 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLY A 199 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N PHE A 187 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N TYR A 197 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ASN A 189 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TYR A 195 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.702A pdb=" N GLY B 552 " --> pdb=" O ASP B 560 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 59 removed outlier: 7.526A pdb=" N THR A 261 " --> pdb=" O ASP A 277 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ASP A 277 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET A 263 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA A 275 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS A 265 " --> pdb=" O THR A 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.536A pdb=" N GLY A 100 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 161 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 131 through 138 removed outlier: 6.867A pdb=" N GLU A 131 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE A 152 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 11.367A pdb=" N ASN A 135 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 10.623A pdb=" N THR A 150 " --> pdb=" O ASN A 135 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 615 through 616 removed outlier: 5.305A pdb=" N ILE A 299 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR A 585 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLN A 301 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A 583 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 303 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS A 635 " --> pdb=" O TYR A 598 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 631 " --> pdb=" O GLY A 634 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 314 removed outlier: 5.998A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY A 552 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 341 through 345 Processing sheet with id=AB1, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.551A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AB3, first strand: chain 'A' and resid 640 through 646 removed outlier: 5.715A pdb=" N THR A 678 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A 644 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 683 through 684 removed outlier: 5.966A pdb=" N ALA A 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 693 through 697 Processing sheet with id=AB6, first strand: chain 'A' and resid 700 through 710 removed outlier: 3.587A pdb=" N ALA A1038 " --> pdb=" O GLY A1041 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.317A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AB9, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AC1, first strand: chain 'A' and resid 821 through 823 Processing sheet with id=AC2, first strand: chain 'A' and resid 1102 through 1107 removed outlier: 4.664A pdb=" N ALA A1069 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 31 through 34 removed outlier: 7.550A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N PHE B 213 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG B 38 " --> pdb=" O ASN B 214 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N LEU B 216 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 31 through 34 Processing sheet with id=AC5, first strand: chain 'B' and resid 46 through 47 removed outlier: 6.716A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 51 through 59 removed outlier: 7.612A pdb=" N THR B 261 " --> pdb=" O ASP B 277 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASP B 277 " --> pdb=" O THR B 261 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N MET B 263 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA B 275 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS B 265 " --> pdb=" O THR B 273 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 80 through 82 removed outlier: 6.203A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 123 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TYR B 163 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE B 125 " --> pdb=" O PHE B 161 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE B 161 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ALA B 127 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N CYS B 159 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN B 155 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N CYS B 133 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE B 153 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN B 135 " --> pdb=" O MET B 151 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N MET B 151 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 615 through 616 removed outlier: 5.291A pdb=" N ILE B 299 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N THR B 585 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLN B 301 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 583 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 303 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 341 through 345 removed outlier: 6.281A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 341 through 345 removed outlier: 6.997A pdb=" N GLU B 502 " --> pdb=" O SER B 380 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 382 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N SER B 500 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA B 384 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL B 498 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER B 386 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL B 496 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL B 388 " --> pdb=" O TYR B 494 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TYR B 494 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE B 501 " --> pdb=" O MET B 417 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N MET B 417 " --> pdb=" O PHE B 501 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLY B 418 " --> pdb=" O TYR B 367 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AD3, first strand: chain 'B' and resid 640 through 646 removed outlier: 5.058A pdb=" N THR B 678 " --> pdb=" O VAL B 642 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR B 644 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 693 through 697 removed outlier: 3.941A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B1083 " --> pdb=" O ASN B1080 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 700 through 710 removed outlier: 3.540A pdb=" N ALA B1038 " --> pdb=" O GLY B1041 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.396A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 769 through 770 Processing sheet with id=AD8, first strand: chain 'B' and resid 1102 through 1107 removed outlier: 4.863A pdb=" N ALA B1069 " --> pdb=" O SER B1105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 31 through 34 removed outlier: 7.768A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 51 through 59 removed outlier: 7.509A pdb=" N THR C 261 " --> pdb=" O ASP C 277 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASP C 277 " --> pdb=" O THR C 261 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N MET C 263 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA C 275 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS C 265 " --> pdb=" O THR C 273 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 81 through 82 removed outlier: 13.451A pdb=" N PHE C 231 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 12.074A pdb=" N ASP C 134 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N ALA C 233 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU C 235 " --> pdb=" O PRO C 136 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE C 152 " --> pdb=" O CYS C 133 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 81 through 82 Processing sheet with id=AE4, first strand: chain 'C' and resid 615 through 616 removed outlier: 5.294A pdb=" N ILE C 299 " --> pdb=" O THR C 585 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR C 585 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLN C 301 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL C 583 " --> pdb=" O GLN C 301 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER C 303 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.653A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS C 419 " --> pdb=" O LEU C 499 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.047A pdb=" N CYS C 348 " --> pdb=" O CYS C 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE8, first strand: chain 'C' and resid 640 through 646 removed outlier: 5.185A pdb=" N THR C 678 " --> pdb=" O VAL C 642 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR C 644 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 693 through 697 Processing sheet with id=AF1, first strand: chain 'C' and resid 700 through 710 removed outlier: 3.629A pdb=" N ALA C1038 " --> pdb=" O GLY C1041 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.305A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AF4, first strand: chain 'C' and resid 821 through 822 Processing sheet with id=AF5, first strand: chain 'C' and resid 1102 through 1107 removed outlier: 4.582A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF7, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.695A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.695A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.643A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.643A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.002A pdb=" N GLN L 42 " --> pdb=" O ARG L 51 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG L 51 " --> pdb=" O GLN L 42 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 10 through 14 Processing sheet with id=AG6, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AG7, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.090A pdb=" N GLN M 42 " --> pdb=" O ARG M 51 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ARG M 51 " --> pdb=" O GLN M 42 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 10 through 12 1260 hydrogen bonds defined for protein. 3345 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: 13.82 Time building geometry restraints manager: 12.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7089 1.33 - 1.46: 7552 1.46 - 1.59: 11437 1.59 - 1.73: 1 1.73 - 1.86: 168 Bond restraints: 26247 Sorted by residual: bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.559 -0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" C1 NAG k 2 " pdb=" O5 NAG k 2 " ideal model delta sigma weight residual 1.406 1.558 -0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.553 -0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" C1 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.406 1.551 -0.145 2.00e-02 2.50e+03 5.29e+01 bond pdb=" C1 NAG j 2 " pdb=" O5 NAG j 2 " ideal model delta sigma weight residual 1.406 1.551 -0.145 2.00e-02 2.50e+03 5.28e+01 ... (remaining 26242 not shown) Histogram of bond angle deviations from ideal: 91.02 - 100.49: 9 100.49 - 109.96: 6190 109.96 - 119.43: 15724 119.43 - 128.90: 14009 128.90 - 138.37: 67 Bond angle restraints: 35999 Sorted by residual: angle pdb=" N LEU B 927 " pdb=" CA LEU B 927 " pdb=" CB LEU B 927 " ideal model delta sigma weight residual 111.43 91.02 20.41 1.48e+00 4.57e-01 1.90e+02 angle pdb=" N ALA C 926 " pdb=" CA ALA C 926 " pdb=" C ALA C 926 " ideal model delta sigma weight residual 110.80 138.37 -27.57 2.13e+00 2.20e-01 1.68e+02 angle pdb=" N ALA B 926 " pdb=" CA ALA B 926 " pdb=" C ALA B 926 " ideal model delta sigma weight residual 110.80 138.18 -27.38 2.13e+00 2.20e-01 1.65e+02 angle pdb=" N LEU C 927 " pdb=" CA LEU C 927 " pdb=" CB LEU C 927 " ideal model delta sigma weight residual 111.43 92.53 18.90 1.48e+00 4.57e-01 1.63e+02 angle pdb=" CG1 VAL B 808 " pdb=" CB VAL B 808 " pdb=" CG2 VAL B 808 " ideal model delta sigma weight residual 110.80 131.78 -20.98 2.20e+00 2.07e-01 9.10e+01 ... (remaining 35994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.83: 16471 21.83 - 43.65: 537 43.65 - 65.48: 122 65.48 - 87.31: 208 87.31 - 109.13: 149 Dihedral angle restraints: 17487 sinusoidal: 7075 harmonic: 10412 Sorted by residual: dihedral pdb=" C ALA C 926 " pdb=" N ALA C 926 " pdb=" CA ALA C 926 " pdb=" CB ALA C 926 " ideal model delta harmonic sigma weight residual -122.60 -160.02 37.42 0 2.50e+00 1.60e-01 2.24e+02 dihedral pdb=" N ALA C 926 " pdb=" C ALA C 926 " pdb=" CA ALA C 926 " pdb=" CB ALA C 926 " ideal model delta harmonic sigma weight residual 122.90 160.30 -37.40 0 2.50e+00 1.60e-01 2.24e+02 dihedral pdb=" N ALA B 926 " pdb=" C ALA B 926 " pdb=" CA ALA B 926 " pdb=" CB ALA B 926 " ideal model delta harmonic sigma weight residual 122.90 158.18 -35.28 0 2.50e+00 1.60e-01 1.99e+02 ... (remaining 17484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.356: 4678 0.356 - 0.713: 48 0.713 - 1.069: 0 1.069 - 1.426: 0 1.426 - 1.782: 2 Chirality restraints: 4728 Sorted by residual: chirality pdb=" C1 NAG i 2 " pdb=" O4 NAG i 1 " pdb=" C2 NAG i 2 " pdb=" O5 NAG i 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-02 2.50e+03 2.32e+02 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-02 2.50e+03 2.19e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-02 2.50e+03 2.18e+02 ... (remaining 4725 not shown) Planarity restraints: 4624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 269 " 0.065 2.00e-02 2.50e+03 6.61e-02 5.46e+01 pdb=" CG ASN B 269 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN B 269 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 269 " -0.098 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 269 " 0.057 2.00e-02 2.50e+03 5.95e-02 4.42e+01 pdb=" CG ASN A 269 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 269 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 269 " -0.090 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 65 " 0.033 2.00e-02 2.50e+03 3.37e-02 1.42e+01 pdb=" CG ASN A 65 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN A 65 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 65 " -0.051 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.041 2.00e-02 2.50e+03 ... (remaining 4621 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7113 2.79 - 3.32: 22433 3.32 - 3.85: 39920 3.85 - 4.37: 43173 4.37 - 4.90: 74127 Nonbonded interactions: 186766 Sorted by model distance: nonbonded pdb=" O PHE C1071 " pdb=" OG1 THR C1102 " model vdw 2.264 2.440 nonbonded pdb=" NZ LYS A 793 " pdb=" OG1 THR A 795 " model vdw 2.285 2.520 nonbonded pdb=" O PHE B1071 " pdb=" OG1 THR B1102 " model vdw 2.291 2.440 nonbonded pdb=" O PHE A1071 " pdb=" OG1 THR A1102 " model vdw 2.296 2.440 nonbonded pdb=" N ASN A 109 " pdb=" OD1 ASN A 109 " model vdw 2.351 2.520 ... (remaining 186761 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 18 through 31 or (resid 32 through 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 39 or (resid 40 and (na \ me N or name CA or name C or name O or name CB )) or resid 41 through 54 or (res \ id 55 through 58 and (name N or name CA or name C or name O or name CB )) or res \ id 59 through 65 or (resid 66 through 67 and (name N or name CA or name C or nam \ e O or name CB )) or resid 68 or (resid 69 through 78 and (name N or name CA or \ name C or name O or name CB )) or resid 79 through 100 or (resid 101 through 103 \ and (name N or name CA or name C or name O or name CB )) or resid 104 through 1 \ 37 or resid 149 through 160 or (resid 161 through 168 and (name N or name CA or \ name C or name O or name CB )) or resid 180 through 197 or (resid 198 and (name \ N or name CA or name C or name O or name CB )) or resid 199 through 237 or resid \ 250 through 260 or (resid 261 and (name N or name CA or name C or name O or nam \ e CB )) or resid 262 through 271 or (resid 272 through 277 and (name N or name C \ A or name C or name O or name CB )) or resid 278 through 295 or (resid 296 and ( \ name N or name CA or name C or name O or name CB )) or resid 297 through 300 or \ (resid 301 and (name N or name CA or name C or name O or name CB )) or resid 302 \ through 306 or (resid 307 through 308 and (name N or name CA or name C or name \ O or name CB )) or resid 309 through 324 or (resid 325 and (name N or name CA or \ name C or name O or name CB )) or (resid 326 through 329 and (name N or name CA \ or name C or name O or name CB )) or resid 330 through 331 or (resid 332 throug \ h 334 and (name N or name CA or name C or name O or name CB )) or resid 335 thro \ ugh 336 or (resid 337 through 347 and (name N or name CA or name C or name O or \ name CB )) or resid 348 or (resid 349 through 356 and (name N or name CA or name \ C or name O or name CB )) or resid 357 or (resid 358 through 365 and (name N or \ name CA or name C or name O or name CB )) or resid 366 or (resid 367 and (name \ N or name CA or name C or name O or name CB )) or resid 368 or (resid 369 throug \ h 377 and (name N or name CA or name C or name O or name CB )) or resid 378 or ( \ resid 379 through 390 and (name N or name CA or name C or name O or name CB )) o \ r (resid 391 through 398 and (name N or name CA or name C or name O or name CB ) \ ) or resid 399 through 404 or (resid 405 through 412 and (name N or name CA or n \ ame C or name O or name CB )) or resid 413 through 415 or (resid 416 through 417 \ and (name N or name CA or name C or name O or name CB )) or resid 418 through 4 \ 19 or (resid 420 through 433 and (name N or name CA or name C or name O or name \ CB )) or resid 434 or (resid 435 through 445 and (name N or name CA or name C or \ name O or name CB )) or (resid 446 through 449 and (name N or name CA or name C \ or name O or name CB )) or resid 450 or (resid 451 through 458 and (name N or n \ ame CA or name C or name O or name CB )) or resid 459 or (resid 460 through 461 \ and (name N or name CA or name C or name O or name CB )) or resid 462 through 47 \ 2 or (resid 473 and (name N or name CA or name C or name O or name CB )) or resi \ d 474 or (resid 475 through 476 and (name N or name CA or name C or name O or na \ me CB )) or resid 477 through 478 or (resid 479 through 481 and (name N or name \ CA or name C or name O or name CB )) or resid 482 or (resid 483 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 492 and (name N or name CA or \ name C or name O or name CB )) or resid 493 or (resid 494 through 502 and (name \ N or name CA or name C or name O or name CB )) or (resid 509 through 510 and (n \ ame N or name CA or name C or name O or name CB )) or resid 511 through 513 or ( \ resid 514 through 520 and (name N or name CA or name C or name O or name CB )) o \ r resid 521 or (resid 522 and (name N or name CA or name C or name O or name CB \ )) or resid 523 through 548 or (resid 549 through 550 and (name N or name CA or \ name C or name O or name CB )) or resid 551 through 559 or (resid 560 and (name \ N or name CA or name C or name O or name CB )) or resid 561 through 565 or (resi \ d 566 and (name N or name CA or name C or name O or name CB )) or resid 567 thro \ ugh 592 or (resid 593 and (name N or name CA or name C or name O or name CB )) o \ r resid 594 through 604 or (resid 605 and (name N or name CA or name C or name O \ or name CB )) or resid 606 through 610 or (resid 611 through 612 and (name N or \ name CA or name C or name O or name CB )) or resid 613 through 625 or (resid 62 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 627 through \ 661 or (resid 662 through 671 and (name N or name CA or name C or name O or name \ CB )) or resid 672 through 683 or (resid 684 and (name N or name CA or name C o \ r name O or name CB )) or resid 685 through 740 or (resid 741 and (name N or nam \ e CA or name C or name O or name CB )) or resid 742 through 756 or (resid 757 an \ d (name N or name CA or name C or name O or name CB )) or resid 758 through 761 \ or (resid 762 and (name N or name CA or name C or name O or name CB )) or resid \ 763 through 767 or (resid 768 and (name N or name CA or name C or name O or name \ CB )) or resid 769 through 808 or resid 836 through 837 or (resid 838 and (name \ N or name CA or name C or name O or name CB )) or resid 839 through 848 or (res \ id 849 and (name N or name CA or name C or name O or name CB )) or resid 850 thr \ ough 899 or (resid 900 and (name N or name CA or name C or name O or name CB )) \ or resid 901 through 902 or (resid 903 and (name N or name CA or name C or name \ O or name CB )) or resid 904 through 931 or (resid 932 and (name N or name CA or \ name C or name O or name CB )) or resid 933 through 971 or (resid 972 and (name \ N or name CA or name C or name O or name CB )) or resid 973 through 975 or (res \ id 976 and (name N or name CA or name C or name O or name CB )) or resid 977 thr \ ough 1012 or (resid 1013 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1014 through 1022 or (resid 1023 and (name N or name CA or name C or \ name O or name CB )) or resid 1024 through 1072 or (resid 1073 through 1074 and \ (name N or name CA or name C or name O or name CB )) or resid 1075 through 1099 \ or (resid 1100 and (name N or name CA or name C or name O or name CB )) or resid \ 1101 through 1108 or (resid 1109 and (name N or name CA or name C or name O or \ name CB )) or resid 1110 through 1116 or (resid 1117 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1118 through 1127 or resid 1301 through 1 \ 311)) selection = (chain 'B' and (resid 18 through 21 or (resid 31 through 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 45 or (resid 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 48 or (res \ id 49 through 52 and (name N or name CA or name C or name O or name CB )) or res \ id 53 through 54 or (resid 55 through 58 and (name N or name CA or name C or nam \ e O or name CB )) or resid 59 through 63 or (resid 64 and (name N or name CA or \ name C or name O or name CB )) or resid 65 through 137 or resid 149 through 168 \ or resid 180 through 199 or (resid 200 through 201 and (name N or name CA or nam \ e C or name O or name CB )) or resid 202 through 212 or (resid 213 through 217 a \ nd (name N or name CA or name C or name O or name CB )) or resid 218 through 259 \ or (resid 260 through 261 and (name N or name CA or name C or name O or name CB \ )) or resid 262 or (resid 263 and (name N or name CA or name C or name O or nam \ e CB )) or resid 264 or (resid 265 and (name N or name CA or name C or name O or \ name CB )) or resid 266 through 284 or (resid 285 and (name N or name CA or nam \ e C or name O or name CB )) or resid 286 through 295 or (resid 296 and (name N o \ r name CA or name C or name O or name CB )) or resid 297 through 300 or (resid 3 \ 01 and (name N or name CA or name C or name O or name CB )) or resid 302 through \ 306 or (resid 307 through 308 and (name N or name CA or name C or name O or nam \ e CB )) or resid 309 through 437 or (resid 438 through 445 and (name N or name C \ A or name C or name O or name CB )) or resid 446 through 515 or (resid 516 throu \ gh 520 and (name N or name CA or name C or name O or name CB )) or resid 521 or \ (resid 522 and (name N or name CA or name C or name O or name CB )) or resid 523 \ through 548 or (resid 549 through 550 and (name N or name CA or name C or name \ O or name CB )) or resid 551 through 553 or (resid 554 and (name N or name CA or \ name C or name O or name CB )) or resid 555 through 559 or (resid 560 and (name \ N or name CA or name C or name O or name CB )) or resid 561 through 565 or (res \ id 566 and (name N or name CA or name C or name O or name CB )) or resid 567 thr \ ough 598 or (resid 599 through 600 and (name N or name CA or name C or name O or \ name CB )) or resid 601 through 604 or (resid 605 and (name N or name CA or nam \ e C or name O or name CB )) or resid 606 through 610 or (resid 611 through 612 a \ nd (name N or name CA or name C or name O or name CB )) or resid 613 through 625 \ or (resid 626 and (name N or name CA or name C or name O or name CB )) or resid \ 627 through 639 or (resid 640 and (name N or name CA or name C or name O or nam \ e CB )) or resid 641 through 642 or (resid 643 and (name N or name CA or name C \ or name O or name CB )) or resid 644 through 661 or (resid 662 through 671 and ( \ name N or name CA or name C or name O or name CB )) or resid 672 through 740 or \ (resid 741 and (name N or name CA or name C or name O or name CB )) or resid 742 \ through 756 or (resid 757 and (name N or name CA or name C or name O or name CB \ )) or resid 758 through 767 or (resid 768 and (name N or name CA or name C or n \ ame O or name CB )) or resid 769 through 808 or (resid 836 and (name N or name C \ A or name C or name O or name CB )) or resid 837 or (resid 838 and (name N or na \ me CA or name C or name O or name CB )) or resid 839 through 848 or (resid 849 a \ nd (name N or name CA or name C or name O or name CB )) or resid 850 through 899 \ or (resid 900 and (name N or name CA or name C or name O or name CB )) or resid \ 901 through 902 or (resid 903 and (name N or name CA or name C or name O or nam \ e CB )) or resid 904 through 931 or (resid 932 and (name N or name CA or name C \ or name O or name CB )) or resid 933 through 966 or (resid 967 and (name N or na \ me CA or name C or name O or name CB )) or resid 968 through 975 or (resid 976 a \ nd (name N or name CA or name C or name O or name CB )) or resid 977 through 101 \ 2 or (resid 1013 and (name N or name CA or name C or name O or name CB )) or res \ id 1014 through 1116 or (resid 1117 and (name N or name CA or name C or name O o \ r name CB )) or resid 1118 through 1122 or (resid 1123 through 1124 and (name N \ or name CA or name C or name O or name CB )) or resid 1125 through 1127 or resid \ 1301 through 1322)) selection = (chain 'C' and (resid 18 through 21 or resid 31 through 37 or (resid 38 and (nam \ e N or name CA or name C or name O or name CB )) or resid 39 or (resid 40 and (n \ ame N or name CA or name C or name O or name CB )) or resid 41 through 51 or (re \ sid 52 and (name N or name CA or name C or name O or name CB )) or resid 53 thro \ ugh 55 or (resid 56 through 58 and (name N or name CA or name C or name O or nam \ e CB )) or resid 59 or (resid 60 and (name N or name CA or name C or name O or n \ ame CB )) or resid 61 through 66 or (resid 67 and (name N or name CA or name C o \ r name O or name CB )) or resid 68 or (resid 69 through 78 and (name N or name C \ A or name C or name O or name CB )) or resid 79 through 82 or (resid 83 through \ 85 and (name N or name CA or name C or name O or name CB )) or resid 86 through \ 100 or (resid 101 through 103 and (name N or name CA or name C or name O or name \ CB )) or resid 104 through 137 or resid 149 through 160 or (resid 161 through 1 \ 91 and (name N or name CA or name C or name O or name CB )) or resid 192 through \ 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or r \ esid 197 through 208 or (resid 209 and (name N or name CA or name C or name O or \ name CB )) or resid 210 through 212 or (resid 213 through 217 and (name N or na \ me CA or name C or name O or name CB )) or resid 218 through 219 or (resid 220 t \ hrough 222 and (name N or name CA or name C or name O or name CB )) or resid 223 \ through 237 or resid 250 through 260 or (resid 261 and (name N or name CA or na \ me C or name O or name CB )) or resid 262 or (resid 263 and (name N or name CA o \ r name C or name O or name CB )) or resid 264 through 270 or (resid 271 through \ 277 and (name N or name CA or name C or name O or name CB )) or resid 278 throug \ h 284 or (resid 285 and (name N or name CA or name C or name O or name CB )) or \ resid 286 through 337 or (resid 338 through 347 and (name N or name CA or name C \ or name O or name CB )) or resid 348 through 409 or (resid 410 through 412 and \ (name N or name CA or name C or name O or name CB )) or resid 413 through 474 or \ (resid 475 through 476 and (name N or name CA or name C or name O or name CB )) \ or resid 477 through 483 or resid 492 through 502 or resid 509 through 518 or ( \ resid 519 through 520 and (name N or name CA or name C or name O or name CB )) o \ r resid 521 through 568 or (resid 569 and (name N or name CA or name C or name O \ or name CB )) or resid 570 through 592 or (resid 593 and (name N or name CA or \ name C or name O or name CB )) or resid 594 through 598 or (resid 599 through 60 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 601 through \ 663 or resid 671 through 706 or (resid 707 and (name N or name CA or name C or n \ ame O or name CB )) or resid 708 through 808 or resid 836 through 917 or (resid \ 918 and (name N or name CA or name C or name O or name CB )) or resid 919 throug \ h 971 or (resid 972 and (name N or name CA or name C or name O or name CB )) or \ resid 973 through 1022 or (resid 1023 and (name N or name CA or name C or name O \ or name CB )) or resid 1024 through 1072 or (resid 1073 through 1074 and (name \ N or name CA or name C or name O or name CB )) or resid 1075 through 1099 or (re \ sid 1100 and (name N or name CA or name C or name O or name CB )) or resid 1101 \ through 1108 or (resid 1109 and (name N or name CA or name C or name O or name C \ B )) or resid 1110 through 1122 or (resid 1123 through 1124 and (name N or name \ CA or name C or name O or name CB )) or resid 1125 through 1127 or resid 1301 th \ rough 1326)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'N' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'q' selection = chain 's' } ncs_group { reference = chain 'H' selection = (chain 'I' and resid 2 through 124) } ncs_group { reference = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'b' selection = chain 'e' selection = chain 'p' selection = chain 'r' } ncs_group { reference = (chain 'L' and resid 3 through 111) selection = chain 'M' } 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: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.790 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 75.840 Find NCS groups from input model: 2.560 Set up NCS constraints: 0.530 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 : 0.017 0.153 26247 Z= 1.098 Angle : 1.499 27.568 35999 Z= 0.922 Chirality : 0.105 1.782 4728 Planarity : 0.006 0.029 4569 Dihedral : 19.893 109.135 10611 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.33 % Favored : 96.44 % Rotamer: Outliers : 0.42 % Allowed : 1.90 % Favored : 97.68 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 6.67 % 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: 0.22 (0.14), residues: 3541 helix: 0.45 (0.18), residues: 702 sheet: 0.81 (0.17), residues: 849 loop : -0.19 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.005 TRP C1084 HIS 0.007 0.001 HIS B 661 PHE 0.024 0.004 PHE A 629 TYR 0.037 0.005 TYR C 677 ARG 0.004 0.001 ARG B1089 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 310 time to evaluate : 2.975 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: A 538 LEU cc_start: 0.9093 (tp) cc_final: 0.8806 (mt) REVERT: A 868 TRP cc_start: 0.5301 (m100) cc_final: 0.4295 (m100) REVERT: B 263 MET cc_start: 0.8442 (ttp) cc_final: 0.7672 (tpp) REVERT: B 285 GLU cc_start: 0.9038 (tt0) cc_final: 0.8611 (tt0) REVERT: B 302 THR cc_start: 0.8805 (p) cc_final: 0.8532 (p) REVERT: B 894 THR cc_start: 0.8070 (m) cc_final: 0.7609 (p) REVERT: C 263 MET cc_start: 0.8590 (ttp) cc_final: 0.8340 (ttp) REVERT: C 679 MET cc_start: 0.8644 (ptm) cc_final: 0.8410 (ptm) REVERT: C 759 ASN cc_start: 0.9046 (m-40) cc_final: 0.8653 (m-40) REVERT: C 770 MET cc_start: 0.7697 (mmm) cc_final: 0.7336 (mmm) outliers start: 8 outliers final: 6 residues processed: 318 average time/residue: 0.3557 time to fit residues: 180.1164 Evaluate side-chains 148 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 142 time to evaluate : 2.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 182 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 279 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 170 optimal weight: 0.5980 chunk 208 optimal weight: 0.9980 chunk 324 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 GLN A 661 HIS A 733 ASN A 786 GLN A 984 GLN A1095 GLN B 661 HIS B 917 GLN ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN C 661 HIS ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 786 GLN C1095 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26247 Z= 0.227 Angle : 0.733 19.792 35999 Z= 0.355 Chirality : 0.054 0.821 4728 Planarity : 0.005 0.067 4569 Dihedral : 13.851 81.830 6766 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.60 % Favored : 97.37 % Rotamer: Outliers : 0.16 % Allowed : 1.74 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.65 (0.14), residues: 3541 helix: 1.73 (0.20), residues: 702 sheet: 0.87 (0.18), residues: 808 loop : -0.17 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1084 HIS 0.005 0.001 HIS B 661 PHE 0.019 0.002 PHE A 329 TYR 0.019 0.001 TYR A1049 ARG 0.029 0.001 ARG C1001 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 198 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 397 ILE cc_start: 0.9146 (mp) cc_final: 0.8772 (mm) REVERT: A 622 TYR cc_start: 0.7317 (t80) cc_final: 0.6946 (t80) REVERT: A 722 MET cc_start: 0.9359 (tpp) cc_final: 0.8976 (tpt) REVERT: A 868 TRP cc_start: 0.5444 (m100) cc_final: 0.4614 (m100) REVERT: B 263 MET cc_start: 0.8502 (ttp) cc_final: 0.7466 (tpp) REVERT: B 285 GLU cc_start: 0.9081 (tt0) cc_final: 0.8869 (tt0) REVERT: B 302 THR cc_start: 0.9037 (p) cc_final: 0.8801 (p) REVERT: B 528 ASN cc_start: 0.8578 (t0) cc_final: 0.8141 (m-40) REVERT: B 722 MET cc_start: 0.8395 (tpt) cc_final: 0.8070 (tpp) REVERT: B 804 LEU cc_start: 0.9365 (mp) cc_final: 0.9102 (mt) REVERT: B 894 THR cc_start: 0.8165 (m) cc_final: 0.7789 (p) REVERT: C 264 LEU cc_start: 0.9370 (mp) cc_final: 0.9153 (mt) REVERT: C 558 PHE cc_start: 0.8601 (m-80) cc_final: 0.8113 (m-80) REVERT: C 679 MET cc_start: 0.8541 (ptm) cc_final: 0.8269 (ptm) REVERT: C 770 MET cc_start: 0.7780 (mmm) cc_final: 0.7396 (mmm) REVERT: C 851 MET cc_start: 0.8662 (mtp) cc_final: 0.8282 (mtp) outliers start: 3 outliers final: 1 residues processed: 201 average time/residue: 0.3454 time to fit residues: 118.3006 Evaluate side-chains 126 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 180 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 269 optimal weight: 0.9990 chunk 220 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 324 optimal weight: 50.0000 chunk 350 optimal weight: 50.0000 chunk 289 optimal weight: 2.9990 chunk 322 optimal weight: 0.0970 chunk 110 optimal weight: 9.9990 chunk 260 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 786 GLN B1095 GLN C 759 ASN ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1030 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26247 Z= 0.239 Angle : 0.669 16.710 35999 Z= 0.326 Chirality : 0.050 0.562 4728 Planarity : 0.004 0.060 4569 Dihedral : 9.632 71.900 6766 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.11 % Allowed : 3.37 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.61 (0.14), residues: 3541 helix: 1.95 (0.20), residues: 700 sheet: 0.71 (0.17), residues: 879 loop : -0.27 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 868 HIS 0.006 0.002 HIS A1030 PHE 0.023 0.001 PHE A 364 TYR 0.016 0.001 TYR B1049 ARG 0.011 0.001 ARG C1001 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 160 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 622 TYR cc_start: 0.7384 (t80) cc_final: 0.6833 (t80) REVERT: B 263 MET cc_start: 0.8496 (ttp) cc_final: 0.7540 (tpp) REVERT: B 528 ASN cc_start: 0.8604 (t0) cc_final: 0.8019 (m-40) REVERT: B 894 THR cc_start: 0.8335 (m) cc_final: 0.7963 (p) REVERT: C 263 MET cc_start: 0.8393 (tpp) cc_final: 0.7951 (mmm) REVERT: C 558 PHE cc_start: 0.8671 (m-80) cc_final: 0.8073 (m-80) REVERT: C 679 MET cc_start: 0.8672 (ptm) cc_final: 0.8320 (ptm) REVERT: C 692 ASN cc_start: 0.8131 (p0) cc_final: 0.7830 (p0) REVERT: C 723 TYR cc_start: 0.9342 (t80) cc_final: 0.8967 (t80) REVERT: C 770 MET cc_start: 0.7693 (mmm) cc_final: 0.7459 (mmm) REVERT: C 851 MET cc_start: 0.8632 (mtp) cc_final: 0.8257 (mtp) REVERT: C 972 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8855 (mm-30) outliers start: 2 outliers final: 1 residues processed: 162 average time/residue: 0.3409 time to fit residues: 93.5751 Evaluate side-chains 111 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 320 optimal weight: 30.0000 chunk 244 optimal weight: 20.0000 chunk 168 optimal weight: 0.1980 chunk 35 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 325 optimal weight: 8.9990 chunk 345 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 308 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 744 GLN A1030 HIS B 280 GLN B 939 GLN B1030 HIS ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 786 GLN C 917 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26247 Z= 0.234 Angle : 0.645 14.919 35999 Z= 0.311 Chirality : 0.050 0.527 4728 Planarity : 0.004 0.065 4569 Dihedral : 8.573 65.707 6766 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.64 (0.14), residues: 3541 helix: 1.98 (0.20), residues: 695 sheet: 0.80 (0.17), residues: 869 loop : -0.29 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 868 HIS 0.007 0.001 HIS C1030 PHE 0.016 0.001 PHE A 629 TYR 0.019 0.001 TYR A 367 ARG 0.006 0.001 ARG C 758 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 3.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 622 TYR cc_start: 0.7433 (t80) cc_final: 0.6834 (t80) REVERT: B 263 MET cc_start: 0.8412 (ttp) cc_final: 0.7542 (tpp) REVERT: B 528 ASN cc_start: 0.8840 (t0) cc_final: 0.8192 (m-40) REVERT: C 558 PHE cc_start: 0.8641 (m-80) cc_final: 0.8041 (m-80) REVERT: C 679 MET cc_start: 0.8616 (ptm) cc_final: 0.8258 (ptm) REVERT: C 709 MET cc_start: 0.8648 (mtp) cc_final: 0.8238 (ptp) REVERT: C 851 MET cc_start: 0.8788 (mtp) cc_final: 0.8379 (mtp) REVERT: C 972 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8883 (mm-30) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.3285 time to fit residues: 87.1272 Evaluate side-chains 103 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.5485 > 50: distance: 65 - 74: 21.287 distance: 74 - 75: 22.042 distance: 75 - 76: 29.731 distance: 75 - 78: 26.565 distance: 76 - 77: 16.797 distance: 76 - 85: 48.132 distance: 78 - 79: 6.163 distance: 79 - 80: 9.498 distance: 79 - 81: 42.263 distance: 81 - 83: 10.339 distance: 82 - 84: 44.329 distance: 83 - 84: 17.591 distance: 85 - 86: 11.559 distance: 86 - 89: 39.076 distance: 87 - 88: 30.505 distance: 87 - 91: 8.370 distance: 91 - 92: 18.306 distance: 91 - 97: 40.866 distance: 92 - 93: 12.435 distance: 92 - 95: 35.533 distance: 93 - 94: 4.084 distance: 93 - 98: 7.840 distance: 95 - 96: 50.160 distance: 96 - 97: 5.310 distance: 98 - 99: 31.419 distance: 99 - 100: 21.653 distance: 99 - 102: 22.773 distance: 100 - 101: 44.499 distance: 100 - 107: 20.387 distance: 102 - 103: 34.408 distance: 103 - 104: 8.725 distance: 104 - 105: 7.653 distance: 104 - 106: 4.759 distance: 107 - 108: 5.108 distance: 108 - 109: 26.450 distance: 108 - 111: 4.910 distance: 109 - 110: 13.646 distance: 109 - 115: 26.806 distance: 111 - 112: 12.000 distance: 111 - 113: 39.861 distance: 112 - 114: 9.353 distance: 115 - 116: 28.434 distance: 116 - 117: 37.666 distance: 116 - 119: 29.145 distance: 117 - 118: 37.310 distance: 117 - 123: 37.738 distance: 119 - 120: 15.549 distance: 119 - 121: 18.667 distance: 120 - 122: 24.453 distance: 123 - 124: 24.436 distance: 124 - 127: 5.875 distance: 125 - 126: 26.194 distance: 125 - 130: 20.762 distance: 127 - 128: 17.016 distance: 127 - 129: 17.844 distance: 130 - 131: 10.675 distance: 131 - 132: 7.746 distance: 131 - 134: 32.703 distance: 132 - 133: 29.555 distance: 132 - 137: 15.307 distance: 134 - 135: 32.814 distance: 134 - 136: 42.198 distance: 137 - 138: 20.978 distance: 138 - 139: 14.216 distance: 138 - 141: 33.933 distance: 139 - 140: 21.721 distance: 139 - 145: 9.316 distance: 141 - 142: 18.443 distance: 145 - 146: 20.086 distance: 146 - 147: 6.538 distance: 146 - 149: 16.890 distance: 147 - 148: 16.171 distance: 147 - 153: 19.615 distance: 149 - 150: 13.567 distance: 150 - 151: 12.152 distance: 150 - 152: 6.931