Starting phenix.real_space_refine on Thu Mar 5 07:14:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nqd_0485/03_2026/6nqd_0485.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nqd_0485/03_2026/6nqd_0485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nqd_0485/03_2026/6nqd_0485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nqd_0485/03_2026/6nqd_0485.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nqd_0485/03_2026/6nqd_0485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nqd_0485/03_2026/6nqd_0485.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 12645 2.51 5 N 3273 2.21 5 O 4143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20175 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3399 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 23, 'TRANS': 415} Chain breaks: 5 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 976 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 793 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3399 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 23, 'TRANS': 415} Chain breaks: 5 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "F" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 976 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 793 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "I" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3399 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 23, 'TRANS': 415} Chain breaks: 5 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "J" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "K" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 976 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 793 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "M" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: 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: "X" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "Y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: 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: "i" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "j" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 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: "s" 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.05, per 1000 atoms: 0.25 Number of scatterers: 20175 At special positions: 0 Unit cell: (150, 145, 120, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4143 8.00 N 3273 7.00 C 12645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.11 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.01 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.05 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.11 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.05 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.01 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.05 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.11 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.05 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.04 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.02 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.02 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.01 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN M 5 " - " MAN M 6 " " MAN M 8 " - " MAN M 9 " " MAN N 4 " - " MAN N 5 " " MAN X 4 " - " MAN X 5 " " MAN X 5 " - " MAN X 6 " " MAN X 8 " - " MAN X 9 " " MAN Y 4 " - " MAN Y 5 " " MAN i 4 " - " MAN i 5 " " MAN i 5 " - " MAN i 6 " " MAN i 8 " - " MAN i 9 " " MAN j 4 " - " MAN j 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " MAN M 7 " - " MAN M 10 " " BMA N 3 " - " MAN N 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " MAN X 7 " - " MAN X 10 " " BMA Y 3 " - " MAN Y 4 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " " MAN i 7 " - " MAN i 10 " " BMA j 3 " - " MAN j 4 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA M 3 " - " MAN M 7 " " MAN M 7 " - " MAN M 8 " " BMA N 3 " - " MAN N 6 " " BMA X 3 " - " MAN X 7 " " MAN X 7 " - " MAN X 8 " " BMA Y 3 " - " MAN Y 6 " " BMA i 3 " - " MAN i 7 " " MAN i 7 " - " MAN i 8 " " BMA j 3 " - " MAN j 6 " BETA1-4 " 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG 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 a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG 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 l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-ASN " NAG A 619 " - " ASN A 160 " " NAG A 620 " - " ASN A 241 " " NAG A 623 " - " ASN A 295 " " NAG A 624 " - " ASN A 301 " " NAG A 627 " - " ASN A 355 " " NAG A 632 " - " ASN A 448 " " NAG B 705 " - " ASN B 611 " " NAG B 706 " - " ASN B 616 " " NAG B 707 " - " ASN B 625 " " NAG C 301 " - " ASN C 82B" " NAG E 619 " - " ASN E 160 " " NAG E 620 " - " ASN E 241 " " NAG E 623 " - " ASN E 295 " " NAG E 624 " - " ASN E 301 " " NAG E 627 " - " ASN E 355 " " NAG E 632 " - " ASN E 448 " " NAG F 705 " - " ASN F 611 " " NAG F 706 " - " ASN F 616 " " NAG F 707 " - " ASN F 625 " " NAG G 301 " - " ASN G 82B" " NAG I 619 " - " ASN I 160 " " NAG I 620 " - " ASN I 241 " " NAG I 623 " - " ASN I 295 " " NAG I 624 " - " ASN I 301 " " NAG I 627 " - " ASN I 355 " " NAG I 632 " - " ASN I 448 " " NAG J 705 " - " ASN J 611 " " NAG J 706 " - " ASN J 616 " " NAG J 707 " - " ASN J 625 " " NAG K 301 " - " ASN K 82B" " NAG M 1 " - " ASN A 234 " " NAG N 1 " - " ASN A 276 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 289 " " NAG Q 1 " - " ASN A 332 " " NAG R 1 " - " ASN A 386 " " NAG S 1 " - " ASN A 392 " " NAG T 1 " - " ASN A 197 " " NAG U 1 " - " ASN A 130 " " NAG V 1 " - " ASN A 262 " " NAG W 1 " - " ASN B 637 " " NAG X 1 " - " ASN E 234 " " NAG Y 1 " - " ASN E 276 " " NAG Z 1 " - " ASN E 156 " " NAG a 1 " - " ASN E 289 " " NAG b 1 " - " ASN E 332 " " NAG c 1 " - " ASN E 386 " " NAG d 1 " - " ASN E 392 " " NAG e 1 " - " ASN E 197 " " NAG f 1 " - " ASN E 130 " " NAG g 1 " - " ASN E 262 " " NAG h 1 " - " ASN F 637 " " NAG i 1 " - " ASN I 234 " " NAG j 1 " - " ASN I 276 " " NAG k 1 " - " ASN I 156 " " NAG l 1 " - " ASN I 289 " " NAG m 1 " - " ASN I 332 " " NAG n 1 " - " ASN I 386 " " NAG o 1 " - " ASN I 392 " " NAG p 1 " - " ASN I 197 " " NAG q 1 " - " ASN I 130 " " NAG r 1 " - " ASN I 262 " " NAG s 1 " - " ASN J 637 " Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 843.7 milliseconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 45 sheets defined 16.7% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 114 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 476 through 481 removed outlier: 4.043A pdb=" N ASN A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 548 removed outlier: 4.494A pdb=" N ILE B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 593 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 660 Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.004A pdb=" N PHE D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 114 Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 476 through 481 removed outlier: 4.043A pdb=" N ASN E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 548 removed outlier: 4.494A pdb=" N ILE F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER F 546 " --> pdb=" O ARG F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 593 Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 660 Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.004A pdb=" N PHE H 83 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 98 No H-bonds generated for 'chain 'I' and resid 96 through 98' Processing helix chain 'I' and resid 99 through 114 Processing helix chain 'I' and resid 335 through 353 Processing helix chain 'I' and resid 387 through 391 Processing helix chain 'I' and resid 476 through 481 removed outlier: 4.042A pdb=" N ASN I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 548 removed outlier: 4.494A pdb=" N ILE J 535 " --> pdb=" O GLY J 531 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER J 546 " --> pdb=" O ARG J 542 " (cutoff:3.500A) Processing helix chain 'J' and resid 573 through 593 Processing helix chain 'J' and resid 618 through 624 Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 660 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.004A pdb=" N PHE L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 496 removed outlier: 4.452A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 174 removed outlier: 3.688A pdb=" N GLN A 170 " --> pdb=" O MET A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.938A pdb=" N LYS A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER A 334 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 374 " --> pdb=" O CYS A 385 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.223A pdb=" N PHE A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.087A pdb=" N LEU A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 300 through 312 removed outlier: 6.631A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 393 through 395 Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AB3, first strand: chain 'C' and resid 58 through 59 removed outlier: 5.087A pdb=" N TYR C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ARG C 38 " --> pdb=" O TYR C 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 100E through 100F Processing sheet with id=AB5, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.872A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 494 through 496 removed outlier: 4.453A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR F 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AB9, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'E' and resid 93 through 94 Processing sheet with id=AC2, first strand: chain 'E' and resid 169 through 174 removed outlier: 3.688A pdb=" N GLN E 170 " --> pdb=" O MET E 161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.938A pdb=" N LYS E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER E 334 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN E 295 " --> pdb=" O ASN E 332 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS E 374 " --> pdb=" O CYS E 385 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 271 through 273 removed outlier: 12.223A pdb=" N PHE E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 12.088A pdb=" N LEU E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 300 through 312 removed outlier: 6.632A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 393 through 395 Processing sheet with id=AC7, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AC8, first strand: chain 'G' and resid 3 through 5 Processing sheet with id=AC9, first strand: chain 'G' and resid 58 through 59 removed outlier: 5.086A pdb=" N TYR G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ARG G 38 " --> pdb=" O TYR G 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 100E through 100F Processing sheet with id=AD2, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.872A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 494 through 496 removed outlier: 4.452A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR J 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 45 through 46 Processing sheet with id=AD6, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'I' and resid 93 through 94 Processing sheet with id=AD8, first strand: chain 'I' and resid 169 through 174 removed outlier: 3.688A pdb=" N GLN I 170 " --> pdb=" O MET I 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 271 through 273 removed outlier: 6.938A pdb=" N LYS I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER I 334 " --> pdb=" O LYS I 293 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS I 374 " --> pdb=" O CYS I 385 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 271 through 273 removed outlier: 12.223A pdb=" N PHE I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 12.088A pdb=" N LEU I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N GLU I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY I 451 " --> pdb=" O GLU I 290 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 300 through 312 removed outlier: 6.631A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 393 through 395 Processing sheet with id=AE4, first strand: chain 'I' and resid 423 through 424 Processing sheet with id=AE5, first strand: chain 'K' and resid 3 through 5 Processing sheet with id=AE6, first strand: chain 'K' and resid 58 through 59 removed outlier: 5.087A pdb=" N TYR K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ARG K 38 " --> pdb=" O TYR K 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 100E through 100F Processing sheet with id=AE8, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AE9, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.872A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) 681 hydrogen bonds defined for protein. 1782 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: 4.38 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6141 1.35 - 1.48: 5862 1.48 - 1.61: 8430 1.61 - 1.74: 0 1.74 - 1.87: 150 Bond restraints: 20583 Sorted by residual: bond pdb=" C1 NAG o 1 " pdb=" O5 NAG o 1 " ideal model delta sigma weight residual 1.406 1.499 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.499 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C1 NAG d 1 " pdb=" O5 NAG d 1 " ideal model delta sigma weight residual 1.406 1.498 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C1 NAG J 706 " pdb=" O5 NAG J 706 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C1 NAG F 706 " pdb=" O5 NAG F 706 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.06e+01 ... (remaining 20578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 25660 2.38 - 4.76: 2003 4.76 - 7.14: 268 7.14 - 9.52: 56 9.52 - 11.90: 18 Bond angle restraints: 28005 Sorted by residual: angle pdb=" N GLY B 516 " pdb=" CA GLY B 516 " pdb=" C GLY B 516 " ideal model delta sigma weight residual 112.51 124.41 -11.90 1.53e+00 4.27e-01 6.04e+01 angle pdb=" N GLY J 516 " pdb=" CA GLY J 516 " pdb=" C GLY J 516 " ideal model delta sigma weight residual 112.51 124.39 -11.88 1.53e+00 4.27e-01 6.03e+01 angle pdb=" N GLY F 516 " pdb=" CA GLY F 516 " pdb=" C GLY F 516 " ideal model delta sigma weight residual 112.51 124.39 -11.88 1.53e+00 4.27e-01 6.03e+01 angle pdb=" C ALA F 517 " pdb=" N MET F 518 " pdb=" CA MET F 518 " ideal model delta sigma weight residual 122.07 110.71 11.36 1.71e+00 3.42e-01 4.41e+01 angle pdb=" C ALA J 517 " pdb=" N MET J 518 " pdb=" CA MET J 518 " ideal model delta sigma weight residual 122.07 110.72 11.35 1.71e+00 3.42e-01 4.40e+01 ... (remaining 28000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.44: 12819 24.44 - 48.87: 816 48.87 - 73.31: 189 73.31 - 97.74: 96 97.74 - 122.18: 39 Dihedral angle restraints: 13959 sinusoidal: 7092 harmonic: 6867 Sorted by residual: dihedral pdb=" CB CYS I 501 " pdb=" SG CYS I 501 " pdb=" SG CYS J 605 " pdb=" CB CYS J 605 " ideal model delta sinusoidal sigma weight residual -86.00 -16.70 -69.30 1 1.00e+01 1.00e-02 6.21e+01 dihedral pdb=" CB CYS E 501 " pdb=" SG CYS E 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual -86.00 -16.70 -69.30 1 1.00e+01 1.00e-02 6.21e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual -86.00 -16.73 -69.27 1 1.00e+01 1.00e-02 6.20e+01 ... (remaining 13956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 3479 0.177 - 0.354: 106 0.354 - 0.531: 9 0.531 - 0.708: 6 0.708 - 0.885: 3 Chirality restraints: 3603 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 289 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN E 289 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" C1 NAG l 1 " pdb=" ND2 ASN I 289 " pdb=" C2 NAG l 1 " pdb=" O5 NAG l 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.96e+01 ... (remaining 3600 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 123 " -0.056 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO E 124 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO E 124 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 124 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 123 " 0.056 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO I 124 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO I 124 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 124 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 123 " -0.056 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO A 124 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " -0.049 5.00e-02 4.00e+02 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3185 2.75 - 3.29: 18917 3.29 - 3.83: 34025 3.83 - 4.36: 37626 4.36 - 4.90: 64547 Nonbonded interactions: 158300 Sorted by model distance: nonbonded pdb=" O ASN E 67 " pdb=" OG1 THR E 71 " model vdw 2.213 3.040 nonbonded pdb=" O ASN A 67 " pdb=" OG1 THR A 71 " model vdw 2.213 3.040 nonbonded pdb=" O ASN I 67 " pdb=" OG1 THR I 71 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR E 283 " pdb=" O GLY E 472 " model vdw 2.285 3.040 nonbonded pdb=" OG1 THR I 283 " pdb=" O GLY I 472 " model vdw 2.285 3.040 ... (remaining 158295 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'X' selection = chain 'i' } ncs_group { reference = chain 'N' selection = chain 'Y' selection = chain 'j' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' } ncs_group { reference = chain 'V' selection = chain 'g' selection = chain 'r' } ncs_group { reference = chain 'W' selection = chain 'h' selection = chain 's' } 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: 1.810 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.090 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 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:1.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 0.012 0.114 20763 Z= 0.552 Angle : 1.531 21.559 28506 Z= 0.766 Chirality : 0.085 0.885 3603 Planarity : 0.008 0.083 3342 Dihedral : 18.647 122.175 9426 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.77 % Allowed : 10.88 % Favored : 88.35 % Rotamer: Outliers : 8.15 % Allowed : 8.05 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.15), residues: 2343 helix: -3.03 (0.18), residues: 378 sheet: -1.65 (0.22), residues: 555 loop : -2.74 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG E 298 TYR 0.046 0.005 TYR L 91 PHE 0.043 0.005 PHE A 382 TRP 0.036 0.007 TRP L 35 HIS 0.010 0.002 HIS E 287 Details of bonding type rmsd covalent geometry : bond 0.01216 (20583) covalent geometry : angle 1.40406 (28005) SS BOND : bond 0.02528 ( 39) SS BOND : angle 4.65917 ( 78) hydrogen bonds : bond 0.16482 ( 669) hydrogen bonds : angle 8.65682 ( 1782) link_ALPHA1-2 : bond 0.00507 ( 12) link_ALPHA1-2 : angle 2.33128 ( 36) link_ALPHA1-3 : bond 0.00433 ( 12) link_ALPHA1-3 : angle 2.61612 ( 36) link_ALPHA1-6 : bond 0.00276 ( 9) link_ALPHA1-6 : angle 2.14664 ( 27) link_BETA1-4 : bond 0.00556 ( 45) link_BETA1-4 : angle 2.52544 ( 135) link_NAG-ASN : bond 0.01106 ( 63) link_NAG-ASN : angle 6.70330 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 545 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.7851 (p) cc_final: 0.7587 (t) REVERT: A 169 GLN cc_start: 0.7573 (tm-30) cc_final: 0.7097 (mp10) REVERT: A 207 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8292 (ptpp) REVERT: A 217 TYR cc_start: 0.8851 (m-80) cc_final: 0.8368 (m-10) REVERT: A 218 CYS cc_start: 0.6565 (OUTLIER) cc_final: 0.6364 (m) REVERT: A 362 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6880 (tmtt) REVERT: C 52 TRP cc_start: 0.8814 (t60) cc_final: 0.8530 (t60) REVERT: E 82 GLN cc_start: 0.6928 (pt0) cc_final: 0.6695 (mp10) REVERT: E 207 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8181 (ptpp) REVERT: E 305 THR cc_start: 0.8104 (t) cc_final: 0.7859 (m) REVERT: E 362 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6351 (tmtt) REVERT: H 92 ASP cc_start: 0.7861 (m-30) cc_final: 0.7326 (m-30) REVERT: I 133 SER cc_start: 0.7617 (p) cc_final: 0.7265 (t) REVERT: I 169 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7464 (mp10) REVERT: I 207 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8288 (ptpp) REVERT: I 218 CYS cc_start: 0.6589 (OUTLIER) cc_final: 0.6284 (m) REVERT: I 362 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6999 (tmtt) REVERT: L 24 ARG cc_start: 0.7968 (ttm110) cc_final: 0.7694 (mtp85) outliers start: 160 outliers final: 48 residues processed: 654 average time/residue: 0.1424 time to fit residues: 144.1645 Evaluate side-chains 482 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 426 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 485 LYS Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 362 LYS Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 469 ARG Chi-restraints excluded: chain I residue 485 LYS Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 249 HIS A 308 HIS A 354 ASN A 375 HIS B 590 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35AASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 249 HIS E 308 HIS E 354 ASN E 374 HIS E 375 HIS F 590 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35AASN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN I 249 HIS I 308 HIS I 354 ASN I 374 HIS I 375 HIS J 590 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35AASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.176028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.151969 restraints weight = 30763.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.154537 restraints weight = 18960.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.156749 restraints weight = 13897.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.157757 restraints weight = 10501.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.158157 restraints weight = 9665.020| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20763 Z= 0.175 Angle : 0.957 13.329 28506 Z= 0.440 Chirality : 0.055 0.557 3603 Planarity : 0.006 0.069 3342 Dihedral : 15.409 110.256 5511 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.13 % Favored : 92.74 % Rotamer: Outliers : 6.07 % Allowed : 14.78 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.16), residues: 2343 helix: -1.48 (0.22), residues: 396 sheet: -1.33 (0.22), residues: 558 loop : -2.31 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 20 TYR 0.030 0.002 TYR I 484 PHE 0.029 0.002 PHE E 382 TRP 0.038 0.003 TRP J 628 HIS 0.008 0.001 HIS G 3 Details of bonding type rmsd covalent geometry : bond 0.00382 (20583) covalent geometry : angle 0.86356 (28005) SS BOND : bond 0.00572 ( 39) SS BOND : angle 1.83071 ( 78) hydrogen bonds : bond 0.05020 ( 669) hydrogen bonds : angle 7.01978 ( 1782) link_ALPHA1-2 : bond 0.00849 ( 12) link_ALPHA1-2 : angle 1.65429 ( 36) link_ALPHA1-3 : bond 0.00860 ( 12) link_ALPHA1-3 : angle 1.97139 ( 36) link_ALPHA1-6 : bond 0.00471 ( 9) link_ALPHA1-6 : angle 1.86503 ( 27) link_BETA1-4 : bond 0.00503 ( 45) link_BETA1-4 : angle 1.88230 ( 135) link_NAG-ASN : bond 0.00985 ( 63) link_NAG-ASN : angle 4.69811 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 495 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.7304 (tm-30) cc_final: 0.6845 (mp10) REVERT: A 207 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8375 (ptpp) REVERT: A 217 TYR cc_start: 0.8651 (m-80) cc_final: 0.8261 (m-10) REVERT: A 227 ARG cc_start: 0.8758 (ttp-170) cc_final: 0.8554 (ttp80) REVERT: A 259 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8229 (pp) REVERT: A 305 THR cc_start: 0.8053 (t) cc_final: 0.7684 (m) REVERT: A 351 GLU cc_start: 0.7940 (tt0) cc_final: 0.7739 (tt0) REVERT: A 377 ASN cc_start: 0.7724 (t0) cc_final: 0.7450 (t0) REVERT: A 484 TYR cc_start: 0.9066 (p90) cc_final: 0.8833 (p90) REVERT: B 603 ILE cc_start: 0.8074 (mm) cc_final: 0.7549 (mt) REVERT: C 52 TRP cc_start: 0.8589 (t60) cc_final: 0.8083 (t60) REVERT: C 54 ARG cc_start: 0.8678 (mpp80) cc_final: 0.8080 (mtm180) REVERT: C 94 THR cc_start: 0.8434 (p) cc_final: 0.8199 (p) REVERT: E 82 GLN cc_start: 0.7187 (pt0) cc_final: 0.6974 (pm20) REVERT: E 207 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8338 (mttp) REVERT: E 290 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7927 (mt-10) REVERT: E 384 TYR cc_start: 0.6616 (m-10) cc_final: 0.6097 (m-10) REVERT: E 484 TYR cc_start: 0.8849 (p90) cc_final: 0.8577 (p90) REVERT: F 603 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7861 (mt) REVERT: G 73 ASP cc_start: 0.7628 (p0) cc_final: 0.7269 (p0) REVERT: H 47 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8132 (pt) REVERT: H 86 PHE cc_start: 0.6327 (m-10) cc_final: 0.6002 (m-10) REVERT: I 82 GLN cc_start: 0.7744 (mp10) cc_final: 0.7380 (pt0) REVERT: I 207 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8312 (ptpp) REVERT: I 298 ARG cc_start: 0.8283 (ttp80) cc_final: 0.8038 (ttp-110) REVERT: I 305 THR cc_start: 0.8148 (t) cc_final: 0.7826 (m) REVERT: I 370 GLU cc_start: 0.8258 (tt0) cc_final: 0.7733 (tt0) REVERT: I 384 TYR cc_start: 0.6874 (m-10) cc_final: 0.6486 (m-10) REVERT: J 603 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7619 (mt) REVERT: J 657 GLU cc_start: 0.7844 (tt0) cc_final: 0.7620 (tt0) REVERT: K 100 LEU cc_start: 0.8820 (mt) cc_final: 0.8598 (mt) REVERT: L 24 ARG cc_start: 0.7987 (ttm110) cc_final: 0.7537 (mtp85) outliers start: 119 outliers final: 60 residues processed: 573 average time/residue: 0.1371 time to fit residues: 123.1841 Evaluate side-chains 502 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 435 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 178 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 226 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 222 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 122 optimal weight: 0.0060 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35AASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35AASN K 43 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.173562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.149424 restraints weight = 30768.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.151858 restraints weight = 19506.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.153757 restraints weight = 13600.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.155435 restraints weight = 10579.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.155593 restraints weight = 9702.349| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20763 Z= 0.184 Angle : 0.922 13.085 28506 Z= 0.419 Chirality : 0.054 0.497 3603 Planarity : 0.005 0.048 3342 Dihedral : 13.048 107.880 5440 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.07 % Favored : 91.81 % Rotamer: Outliers : 5.45 % Allowed : 18.35 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.17), residues: 2343 helix: -0.69 (0.24), residues: 399 sheet: -1.00 (0.23), residues: 549 loop : -2.10 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 633 TYR 0.030 0.002 TYR B 586 PHE 0.028 0.002 PHE C 30 TRP 0.046 0.003 TRP J 628 HIS 0.006 0.001 HIS G 100F Details of bonding type rmsd covalent geometry : bond 0.00421 (20583) covalent geometry : angle 0.83047 (28005) SS BOND : bond 0.00476 ( 39) SS BOND : angle 1.71083 ( 78) hydrogen bonds : bond 0.04559 ( 669) hydrogen bonds : angle 6.59846 ( 1782) link_ALPHA1-2 : bond 0.00902 ( 12) link_ALPHA1-2 : angle 1.86218 ( 36) link_ALPHA1-3 : bond 0.01016 ( 12) link_ALPHA1-3 : angle 1.71470 ( 36) link_ALPHA1-6 : bond 0.00515 ( 9) link_ALPHA1-6 : angle 1.76339 ( 27) link_BETA1-4 : bond 0.00656 ( 45) link_BETA1-4 : angle 2.05563 ( 135) link_NAG-ASN : bond 0.00650 ( 63) link_NAG-ASN : angle 4.49134 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 471 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.7415 (tm-30) cc_final: 0.6846 (mp10) REVERT: A 207 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8364 (ptpp) REVERT: A 217 TYR cc_start: 0.8506 (m-80) cc_final: 0.8220 (m-80) REVERT: A 227 ARG cc_start: 0.8627 (ttp-170) cc_final: 0.8200 (ttp80) REVERT: A 259 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8087 (pp) REVERT: A 265 LEU cc_start: 0.8632 (mp) cc_final: 0.8366 (tp) REVERT: A 305 THR cc_start: 0.8014 (t) cc_final: 0.7749 (m) REVERT: A 456 ARG cc_start: 0.7533 (ttp80) cc_final: 0.7255 (ttp80) REVERT: B 591 LYS cc_start: 0.8762 (ptmt) cc_final: 0.8513 (pttt) REVERT: B 603 ILE cc_start: 0.8293 (mm) cc_final: 0.7887 (mt) REVERT: B 616 ASN cc_start: 0.6989 (p0) cc_final: 0.6683 (p0) REVERT: C 52 TRP cc_start: 0.8641 (t60) cc_final: 0.8284 (t60) REVERT: C 54 ARG cc_start: 0.8718 (mpp80) cc_final: 0.8045 (mpp80) REVERT: C 91 PHE cc_start: 0.7313 (m-80) cc_final: 0.6998 (m-80) REVERT: E 169 GLN cc_start: 0.7440 (tm-30) cc_final: 0.6834 (mp10) REVERT: E 207 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8350 (mttp) REVERT: E 217 TYR cc_start: 0.8512 (m-80) cc_final: 0.8233 (m-10) REVERT: E 377 ASN cc_start: 0.7613 (t0) cc_final: 0.7412 (t0) REVERT: E 484 TYR cc_start: 0.9002 (p90) cc_final: 0.8778 (p90) REVERT: F 530 MET cc_start: 0.6564 (mmt) cc_final: 0.6317 (mmt) REVERT: F 603 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8091 (mt) REVERT: F 628 TRP cc_start: 0.7726 (OUTLIER) cc_final: 0.7496 (m-10) REVERT: G 54 ARG cc_start: 0.8665 (mtm180) cc_final: 0.7984 (mtm180) REVERT: G 73 ASP cc_start: 0.7789 (p0) cc_final: 0.7554 (p0) REVERT: G 100 LEU cc_start: 0.9007 (mt) cc_final: 0.8770 (mt) REVERT: I 82 GLN cc_start: 0.7681 (mp10) cc_final: 0.7386 (pt0) REVERT: I 104 MET cc_start: 0.9067 (tmm) cc_final: 0.8468 (tmm) REVERT: I 181 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8512 (mp) REVERT: I 207 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8263 (ptpp) REVERT: I 209 SER cc_start: 0.8013 (t) cc_final: 0.7675 (m) REVERT: I 298 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7962 (ttp80) REVERT: I 305 THR cc_start: 0.8061 (t) cc_final: 0.7801 (m) REVERT: I 370 GLU cc_start: 0.8228 (tt0) cc_final: 0.7992 (tt0) REVERT: J 603 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7874 (mt) REVERT: J 616 ASN cc_start: 0.6844 (p0) cc_final: 0.6630 (p0) REVERT: J 657 GLU cc_start: 0.7880 (tt0) cc_final: 0.7575 (tt0) REVERT: K 54 ARG cc_start: 0.8739 (mtm180) cc_final: 0.8530 (mtm110) REVERT: K 100 LEU cc_start: 0.8904 (mt) cc_final: 0.8684 (mt) REVERT: L 24 ARG cc_start: 0.8013 (ttm110) cc_final: 0.7610 (mtp85) outliers start: 107 outliers final: 73 residues processed: 538 average time/residue: 0.1323 time to fit residues: 111.4014 Evaluate side-chains 504 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 423 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 583 VAL Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 646 LEU Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 163 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 87 optimal weight: 0.3980 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 478 ASN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100EHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.176312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.153460 restraints weight = 30654.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.156415 restraints weight = 18578.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.157901 restraints weight = 13116.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.158980 restraints weight = 10206.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.159169 restraints weight = 9276.651| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20763 Z= 0.164 Angle : 0.876 15.678 28506 Z= 0.399 Chirality : 0.053 0.468 3603 Planarity : 0.005 0.049 3342 Dihedral : 11.753 105.370 5437 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 6.63 % Allowed : 19.62 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.17), residues: 2343 helix: -0.02 (0.26), residues: 381 sheet: -0.97 (0.23), residues: 531 loop : -2.11 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 46 TYR 0.027 0.002 TYR A 484 PHE 0.030 0.002 PHE D 71 TRP 0.050 0.003 TRP B 628 HIS 0.006 0.001 HIS G 100E Details of bonding type rmsd covalent geometry : bond 0.00375 (20583) covalent geometry : angle 0.78584 (28005) SS BOND : bond 0.00466 ( 39) SS BOND : angle 1.87298 ( 78) hydrogen bonds : bond 0.04284 ( 669) hydrogen bonds : angle 6.32471 ( 1782) link_ALPHA1-2 : bond 0.00998 ( 12) link_ALPHA1-2 : angle 1.75419 ( 36) link_ALPHA1-3 : bond 0.01125 ( 12) link_ALPHA1-3 : angle 1.68029 ( 36) link_ALPHA1-6 : bond 0.00477 ( 9) link_ALPHA1-6 : angle 1.78288 ( 27) link_BETA1-4 : bond 0.00442 ( 45) link_BETA1-4 : angle 1.70597 ( 135) link_NAG-ASN : bond 0.00628 ( 63) link_NAG-ASN : angle 4.36062 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 458 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.6764 (mp10) REVERT: A 209 SER cc_start: 0.8266 (t) cc_final: 0.7861 (m) REVERT: A 217 TYR cc_start: 0.8468 (m-80) cc_final: 0.8193 (m-80) REVERT: A 227 ARG cc_start: 0.8653 (ttp-170) cc_final: 0.8396 (ttp80) REVERT: A 265 LEU cc_start: 0.8624 (mp) cc_final: 0.8395 (tp) REVERT: A 304 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7525 (ttp80) REVERT: A 305 THR cc_start: 0.8091 (t) cc_final: 0.7794 (m) REVERT: A 322 ILE cc_start: 0.5238 (OUTLIER) cc_final: 0.4959 (mp) REVERT: A 377 ASN cc_start: 0.7690 (t0) cc_final: 0.7430 (t0) REVERT: B 603 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7810 (mt) REVERT: B 616 ASN cc_start: 0.6709 (p0) cc_final: 0.6449 (p0) REVERT: C 32 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8083 (pp) REVERT: C 54 ARG cc_start: 0.8765 (mpp80) cc_final: 0.8110 (mpp80) REVERT: E 217 TYR cc_start: 0.8451 (m-80) cc_final: 0.8193 (m-10) REVERT: E 377 ASN cc_start: 0.7577 (t0) cc_final: 0.7370 (t0) REVERT: E 411 ASN cc_start: 0.7152 (p0) cc_final: 0.6863 (p0) REVERT: E 435 TYR cc_start: 0.7720 (t80) cc_final: 0.6966 (t80) REVERT: E 484 TYR cc_start: 0.9005 (p90) cc_final: 0.8794 (p90) REVERT: F 603 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7982 (mt) REVERT: F 628 TRP cc_start: 0.7851 (OUTLIER) cc_final: 0.7615 (m-10) REVERT: G 73 ASP cc_start: 0.7795 (p0) cc_final: 0.7578 (p0) REVERT: H 6 GLN cc_start: 0.6396 (pm20) cc_final: 0.6075 (mt0) REVERT: I 161 MET cc_start: 0.8333 (tpp) cc_final: 0.7873 (tpp) REVERT: I 181 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8440 (mp) REVERT: I 209 SER cc_start: 0.8089 (t) cc_final: 0.7583 (m) REVERT: I 305 THR cc_start: 0.8082 (t) cc_final: 0.7805 (m) REVERT: I 411 ASN cc_start: 0.7005 (p0) cc_final: 0.6726 (p0) REVERT: I 483 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8848 (mm) REVERT: J 603 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7916 (mt) REVERT: J 616 ASN cc_start: 0.6857 (p0) cc_final: 0.6642 (p0) REVERT: J 657 GLU cc_start: 0.7873 (tt0) cc_final: 0.7644 (tt0) REVERT: J 660 LEU cc_start: 0.6872 (tt) cc_final: 0.6350 (mp) REVERT: L 37 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7881 (pp30) outliers start: 130 outliers final: 76 residues processed: 536 average time/residue: 0.1269 time to fit residues: 109.0396 Evaluate side-chains 505 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 419 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 483 LEU Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 651 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 186 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 231 optimal weight: 7.9990 chunk 157 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.171701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.147295 restraints weight = 30687.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.150420 restraints weight = 19334.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.152050 restraints weight = 13100.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.152859 restraints weight = 10539.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.153159 restraints weight = 9943.230| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20763 Z= 0.183 Angle : 0.867 13.557 28506 Z= 0.397 Chirality : 0.052 0.451 3603 Planarity : 0.005 0.046 3342 Dihedral : 11.172 105.504 5424 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 6.73 % Allowed : 20.08 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.17), residues: 2343 helix: -0.36 (0.25), residues: 426 sheet: -1.08 (0.22), residues: 612 loop : -1.86 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 456 TYR 0.028 0.002 TYR I 484 PHE 0.025 0.002 PHE D 71 TRP 0.049 0.003 TRP B 628 HIS 0.006 0.001 HIS G 100E Details of bonding type rmsd covalent geometry : bond 0.00424 (20583) covalent geometry : angle 0.78551 (28005) SS BOND : bond 0.00476 ( 39) SS BOND : angle 1.77737 ( 78) hydrogen bonds : bond 0.04181 ( 669) hydrogen bonds : angle 6.22269 ( 1782) link_ALPHA1-2 : bond 0.00871 ( 12) link_ALPHA1-2 : angle 1.87167 ( 36) link_ALPHA1-3 : bond 0.01049 ( 12) link_ALPHA1-3 : angle 1.69725 ( 36) link_ALPHA1-6 : bond 0.00383 ( 9) link_ALPHA1-6 : angle 1.81074 ( 27) link_BETA1-4 : bond 0.00421 ( 45) link_BETA1-4 : angle 1.58815 ( 135) link_NAG-ASN : bond 0.00643 ( 63) link_NAG-ASN : angle 4.13015 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 436 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 SER cc_start: 0.8244 (t) cc_final: 0.7686 (m) REVERT: A 217 TYR cc_start: 0.8547 (m-80) cc_final: 0.8312 (m-80) REVERT: A 227 ARG cc_start: 0.8644 (ttp-170) cc_final: 0.8390 (ttp80) REVERT: A 265 LEU cc_start: 0.8614 (mp) cc_final: 0.8388 (tp) REVERT: A 322 ILE cc_start: 0.5169 (OUTLIER) cc_final: 0.4892 (mp) REVERT: A 483 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8772 (mm) REVERT: B 603 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7810 (mt) REVERT: B 616 ASN cc_start: 0.6726 (p0) cc_final: 0.6432 (p0) REVERT: C 32 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8089 (pp) REVERT: C 52 TRP cc_start: 0.8798 (t60) cc_final: 0.7942 (t60) REVERT: C 54 ARG cc_start: 0.8879 (mpp80) cc_final: 0.8146 (mpp80) REVERT: D 45 ARG cc_start: 0.8452 (ttp-170) cc_final: 0.8212 (ttp80) REVERT: E 217 TYR cc_start: 0.8468 (m-80) cc_final: 0.8075 (m-10) REVERT: E 376 PHE cc_start: 0.8329 (t80) cc_final: 0.8089 (t80) REVERT: E 411 ASN cc_start: 0.7109 (p0) cc_final: 0.6844 (p0) REVERT: E 435 TYR cc_start: 0.7784 (t80) cc_final: 0.7083 (t80) REVERT: E 484 TYR cc_start: 0.8960 (p90) cc_final: 0.8699 (p90) REVERT: E 492 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8315 (mt-10) REVERT: F 591 LYS cc_start: 0.8908 (ptmt) cc_final: 0.8422 (pttt) REVERT: F 603 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.8020 (mt) REVERT: F 628 TRP cc_start: 0.7982 (OUTLIER) cc_final: 0.7632 (m-10) REVERT: G 36 TRP cc_start: 0.7925 (m100) cc_final: 0.7181 (m100) REVERT: G 73 ASP cc_start: 0.8110 (p0) cc_final: 0.7862 (p0) REVERT: H 24 ARG cc_start: 0.8018 (ttm110) cc_final: 0.7754 (mtm110) REVERT: I 82 GLN cc_start: 0.7174 (pm20) cc_final: 0.6890 (pt0) REVERT: I 161 MET cc_start: 0.8385 (tpp) cc_final: 0.8082 (tpt) REVERT: I 181 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8520 (mp) REVERT: I 209 SER cc_start: 0.8085 (t) cc_final: 0.7616 (m) REVERT: I 411 ASN cc_start: 0.6993 (p0) cc_final: 0.6701 (p0) REVERT: I 483 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8873 (mm) REVERT: J 603 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8105 (mt) REVERT: J 624 ASN cc_start: 0.9017 (m-40) cc_final: 0.8537 (m-40) REVERT: J 660 LEU cc_start: 0.6953 (tt) cc_final: 0.6448 (mp) outliers start: 132 outliers final: 85 residues processed: 512 average time/residue: 0.1262 time to fit residues: 103.9173 Evaluate side-chains 520 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 426 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 483 LEU Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 583 VAL Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 651 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 173 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.168538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.143468 restraints weight = 30759.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.146768 restraints weight = 19315.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.148347 restraints weight = 13084.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.149672 restraints weight = 10432.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.149813 restraints weight = 9759.683| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20763 Z= 0.199 Angle : 0.872 13.562 28506 Z= 0.403 Chirality : 0.053 0.443 3603 Planarity : 0.005 0.063 3342 Dihedral : 10.863 106.729 5421 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 6.42 % Allowed : 20.95 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.17), residues: 2343 helix: -0.36 (0.25), residues: 429 sheet: -1.08 (0.22), residues: 612 loop : -1.81 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 46 TYR 0.031 0.002 TYR A 484 PHE 0.026 0.002 PHE D 71 TRP 0.049 0.003 TRP B 628 HIS 0.006 0.001 HIS G 100E Details of bonding type rmsd covalent geometry : bond 0.00468 (20583) covalent geometry : angle 0.79544 (28005) SS BOND : bond 0.00455 ( 39) SS BOND : angle 1.88892 ( 78) hydrogen bonds : bond 0.04132 ( 669) hydrogen bonds : angle 6.15475 ( 1782) link_ALPHA1-2 : bond 0.00802 ( 12) link_ALPHA1-2 : angle 1.95771 ( 36) link_ALPHA1-3 : bond 0.01013 ( 12) link_ALPHA1-3 : angle 1.69815 ( 36) link_ALPHA1-6 : bond 0.00310 ( 9) link_ALPHA1-6 : angle 1.87268 ( 27) link_BETA1-4 : bond 0.00335 ( 45) link_BETA1-4 : angle 1.56790 ( 135) link_NAG-ASN : bond 0.00650 ( 63) link_NAG-ASN : angle 3.98133 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 454 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 SER cc_start: 0.8130 (t) cc_final: 0.7601 (m) REVERT: A 217 TYR cc_start: 0.8602 (m-80) cc_final: 0.8398 (m-80) REVERT: A 227 ARG cc_start: 0.8677 (ttp-170) cc_final: 0.8400 (ttp80) REVERT: A 265 LEU cc_start: 0.8632 (mp) cc_final: 0.8368 (tp) REVERT: A 304 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7845 (ttp80) REVERT: A 322 ILE cc_start: 0.5292 (OUTLIER) cc_final: 0.4991 (mp) REVERT: A 483 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8834 (mm) REVERT: B 603 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7959 (mt) REVERT: B 616 ASN cc_start: 0.6614 (p0) cc_final: 0.6326 (p0) REVERT: C 32 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7566 (pp) REVERT: C 52 TRP cc_start: 0.8843 (t60) cc_final: 0.7931 (t60) REVERT: C 54 ARG cc_start: 0.8833 (mpp80) cc_final: 0.8091 (mpp80) REVERT: C 74 LEU cc_start: 0.8476 (tp) cc_final: 0.8108 (mp) REVERT: D 24 ARG cc_start: 0.7978 (mmt-90) cc_final: 0.7466 (mtp85) REVERT: E 169 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7064 (mp10) REVERT: E 209 SER cc_start: 0.8146 (t) cc_final: 0.7606 (m) REVERT: E 217 TYR cc_start: 0.8493 (m-80) cc_final: 0.8137 (m-10) REVERT: E 411 ASN cc_start: 0.7110 (p0) cc_final: 0.6846 (p0) REVERT: E 435 TYR cc_start: 0.7896 (t80) cc_final: 0.7096 (t80) REVERT: E 484 TYR cc_start: 0.9044 (p90) cc_final: 0.8797 (p90) REVERT: F 577 GLN cc_start: 0.8313 (tp-100) cc_final: 0.8090 (tp-100) REVERT: F 591 LYS cc_start: 0.8988 (ptmt) cc_final: 0.8517 (pttt) REVERT: F 628 TRP cc_start: 0.8062 (OUTLIER) cc_final: 0.7464 (m-10) REVERT: H 24 ARG cc_start: 0.8021 (ttm110) cc_final: 0.7746 (mtm110) REVERT: H 89 GLN cc_start: 0.7685 (tt0) cc_final: 0.7393 (tt0) REVERT: I 82 GLN cc_start: 0.7157 (pm20) cc_final: 0.6931 (pt0) REVERT: I 161 MET cc_start: 0.8447 (tpp) cc_final: 0.8050 (tpt) REVERT: I 181 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8604 (mp) REVERT: I 209 SER cc_start: 0.8044 (t) cc_final: 0.7607 (m) REVERT: I 411 ASN cc_start: 0.7133 (p0) cc_final: 0.6847 (p0) REVERT: I 483 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8932 (mm) REVERT: J 624 ASN cc_start: 0.9017 (m-40) cc_final: 0.8528 (m-40) REVERT: K 30 PHE cc_start: 0.8347 (m-80) cc_final: 0.7943 (m-80) outliers start: 126 outliers final: 93 residues processed: 523 average time/residue: 0.1266 time to fit residues: 106.7589 Evaluate side-chains 534 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 433 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 483 LEU Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 651 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 64 optimal weight: 0.0770 chunk 19 optimal weight: 0.4980 chunk 210 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 121 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN C 39 GLN C 100EHIS ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 GLN E 478 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.179119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.156276 restraints weight = 30420.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.158512 restraints weight = 18273.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.159879 restraints weight = 13498.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.160561 restraints weight = 11266.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.160814 restraints weight = 10746.815| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20763 Z= 0.150 Angle : 0.832 13.227 28506 Z= 0.382 Chirality : 0.051 0.428 3603 Planarity : 0.004 0.051 3342 Dihedral : 10.376 104.812 5421 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 5.05 % Allowed : 22.73 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.17), residues: 2343 helix: 0.04 (0.26), residues: 399 sheet: -1.18 (0.21), residues: 630 loop : -1.78 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 46 TYR 0.029 0.002 TYR I 484 PHE 0.022 0.002 PHE D 71 TRP 0.050 0.003 TRP J 628 HIS 0.004 0.001 HIS G 100E Details of bonding type rmsd covalent geometry : bond 0.00344 (20583) covalent geometry : angle 0.76010 (28005) SS BOND : bond 0.00581 ( 39) SS BOND : angle 1.76397 ( 78) hydrogen bonds : bond 0.03941 ( 669) hydrogen bonds : angle 6.00465 ( 1782) link_ALPHA1-2 : bond 0.00842 ( 12) link_ALPHA1-2 : angle 1.79656 ( 36) link_ALPHA1-3 : bond 0.01037 ( 12) link_ALPHA1-3 : angle 1.58229 ( 36) link_ALPHA1-6 : bond 0.00345 ( 9) link_ALPHA1-6 : angle 1.77773 ( 27) link_BETA1-4 : bond 0.00406 ( 45) link_BETA1-4 : angle 1.59366 ( 135) link_NAG-ASN : bond 0.00585 ( 63) link_NAG-ASN : angle 3.77127 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 454 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.6927 (mp10) REVERT: A 209 SER cc_start: 0.8040 (t) cc_final: 0.7575 (m) REVERT: A 227 ARG cc_start: 0.8678 (ttp-170) cc_final: 0.8398 (ttp80) REVERT: A 265 LEU cc_start: 0.8572 (mp) cc_final: 0.8335 (tp) REVERT: A 322 ILE cc_start: 0.5176 (OUTLIER) cc_final: 0.4926 (mp) REVERT: A 483 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8780 (mm) REVERT: B 591 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8399 (ttpt) REVERT: B 603 ILE cc_start: 0.8306 (mm) cc_final: 0.7932 (mt) REVERT: B 616 ASN cc_start: 0.6626 (p0) cc_final: 0.6301 (p0) REVERT: C 52 TRP cc_start: 0.8867 (t60) cc_final: 0.8171 (t60) REVERT: C 54 ARG cc_start: 0.8809 (mpp80) cc_final: 0.8192 (mpp80) REVERT: D 24 ARG cc_start: 0.7735 (mmt-90) cc_final: 0.7388 (mtp85) REVERT: E 35 TRP cc_start: 0.5964 (m-10) cc_final: 0.5764 (m-10) REVERT: E 82 GLN cc_start: 0.7452 (pm20) cc_final: 0.6806 (pt0) REVERT: E 169 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.6810 (mp10) REVERT: E 209 SER cc_start: 0.8084 (t) cc_final: 0.7593 (m) REVERT: E 217 TYR cc_start: 0.8398 (m-80) cc_final: 0.8072 (m-10) REVERT: E 411 ASN cc_start: 0.7038 (p0) cc_final: 0.6799 (p0) REVERT: E 435 TYR cc_start: 0.7766 (t80) cc_final: 0.7043 (t80) REVERT: E 484 TYR cc_start: 0.8961 (p90) cc_final: 0.8599 (p90) REVERT: F 591 LYS cc_start: 0.8799 (ptmt) cc_final: 0.8392 (pttt) REVERT: F 628 TRP cc_start: 0.8070 (OUTLIER) cc_final: 0.7608 (m-10) REVERT: H 24 ARG cc_start: 0.7943 (ttm110) cc_final: 0.7718 (mtm110) REVERT: H 32 TRP cc_start: 0.8723 (m100) cc_final: 0.8384 (m100) REVERT: H 89 GLN cc_start: 0.7388 (tt0) cc_final: 0.7147 (tt0) REVERT: I 161 MET cc_start: 0.8388 (tpp) cc_final: 0.8059 (tpt) REVERT: I 181 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8437 (mp) REVERT: I 209 SER cc_start: 0.7975 (t) cc_final: 0.7486 (m) REVERT: I 411 ASN cc_start: 0.7042 (p0) cc_final: 0.6773 (p0) REVERT: J 624 ASN cc_start: 0.9015 (m-40) cc_final: 0.8552 (m-40) outliers start: 99 outliers final: 71 residues processed: 505 average time/residue: 0.1267 time to fit residues: 102.9053 Evaluate side-chains 508 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 430 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 651 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 114 optimal weight: 0.9990 chunk 153 optimal weight: 0.0470 chunk 128 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 overall best weight: 1.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.172151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.147223 restraints weight = 31025.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.150213 restraints weight = 18709.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.151929 restraints weight = 12854.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.153570 restraints weight = 10212.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.153771 restraints weight = 9122.674| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20763 Z= 0.175 Angle : 0.878 18.282 28506 Z= 0.406 Chirality : 0.053 0.479 3603 Planarity : 0.005 0.057 3342 Dihedral : 10.275 104.067 5420 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 5.25 % Allowed : 22.94 % Favored : 71.81 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.17), residues: 2343 helix: 0.08 (0.25), residues: 408 sheet: -1.06 (0.21), residues: 618 loop : -1.80 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 50 TYR 0.029 0.002 TYR A 484 PHE 0.023 0.002 PHE D 71 TRP 0.050 0.003 TRP B 628 HIS 0.004 0.001 HIS E 339 Details of bonding type rmsd covalent geometry : bond 0.00408 (20583) covalent geometry : angle 0.79773 (28005) SS BOND : bond 0.00500 ( 39) SS BOND : angle 1.93656 ( 78) hydrogen bonds : bond 0.04196 ( 669) hydrogen bonds : angle 5.99416 ( 1782) link_ALPHA1-2 : bond 0.00757 ( 12) link_ALPHA1-2 : angle 1.92353 ( 36) link_ALPHA1-3 : bond 0.00998 ( 12) link_ALPHA1-3 : angle 1.63462 ( 36) link_ALPHA1-6 : bond 0.00285 ( 9) link_ALPHA1-6 : angle 1.83478 ( 27) link_BETA1-4 : bond 0.00390 ( 45) link_BETA1-4 : angle 1.68239 ( 135) link_NAG-ASN : bond 0.00694 ( 63) link_NAG-ASN : angle 4.09709 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 443 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 SER cc_start: 0.8033 (t) cc_final: 0.7559 (m) REVERT: A 227 ARG cc_start: 0.8628 (ttp-170) cc_final: 0.8365 (ttp80) REVERT: A 265 LEU cc_start: 0.8590 (mp) cc_final: 0.8310 (tp) REVERT: A 322 ILE cc_start: 0.5213 (OUTLIER) cc_final: 0.4918 (mp) REVERT: A 483 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.8842 (mm) REVERT: B 591 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8506 (ttpt) REVERT: B 603 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8129 (mt) REVERT: B 616 ASN cc_start: 0.6670 (p0) cc_final: 0.6312 (p0) REVERT: C 52 TRP cc_start: 0.8915 (t60) cc_final: 0.8157 (t60) REVERT: C 54 ARG cc_start: 0.8837 (mpp80) cc_final: 0.8142 (mpp80) REVERT: C 74 LEU cc_start: 0.8529 (tp) cc_final: 0.8248 (mp) REVERT: D 24 ARG cc_start: 0.7852 (mmt-90) cc_final: 0.7455 (mtp85) REVERT: E 82 GLN cc_start: 0.7464 (pm20) cc_final: 0.6951 (pt0) REVERT: E 169 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.6827 (mp10) REVERT: E 209 SER cc_start: 0.8110 (t) cc_final: 0.7581 (m) REVERT: E 217 TYR cc_start: 0.8508 (m-80) cc_final: 0.8171 (m-10) REVERT: E 218 CYS cc_start: 0.5855 (OUTLIER) cc_final: 0.5570 (m) REVERT: E 411 ASN cc_start: 0.7050 (p0) cc_final: 0.6795 (p0) REVERT: E 435 TYR cc_start: 0.7863 (t80) cc_final: 0.7015 (t80) REVERT: E 484 TYR cc_start: 0.9044 (p90) cc_final: 0.8671 (p90) REVERT: F 591 LYS cc_start: 0.8918 (ptmt) cc_final: 0.8507 (pttt) REVERT: F 628 TRP cc_start: 0.8138 (OUTLIER) cc_final: 0.7502 (m-10) REVERT: H 24 ARG cc_start: 0.7981 (ttm110) cc_final: 0.7753 (mtm110) REVERT: H 32 TRP cc_start: 0.8792 (m100) cc_final: 0.8020 (m100) REVERT: H 45 ARG cc_start: 0.8403 (ttp-170) cc_final: 0.8034 (ttp-170) REVERT: I 161 MET cc_start: 0.8399 (tpp) cc_final: 0.8097 (tpt) REVERT: I 181 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8436 (mp) REVERT: I 209 SER cc_start: 0.7970 (t) cc_final: 0.7476 (m) REVERT: I 411 ASN cc_start: 0.7029 (p0) cc_final: 0.6742 (p0) REVERT: I 483 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8974 (mm) REVERT: J 624 ASN cc_start: 0.9073 (m-40) cc_final: 0.8637 (m-40) outliers start: 103 outliers final: 82 residues processed: 497 average time/residue: 0.1233 time to fit residues: 99.0482 Evaluate side-chains 524 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 433 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 483 LEU Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 651 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 211 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 118 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 230 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 169 GLN B 624 ASN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 GLN E 375 HIS ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.172579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.147076 restraints weight = 31095.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.151218 restraints weight = 19702.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.152663 restraints weight = 13051.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.153032 restraints weight = 9769.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.153364 restraints weight = 9931.232| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 20763 Z= 0.173 Angle : 0.876 19.559 28506 Z= 0.406 Chirality : 0.055 1.031 3603 Planarity : 0.005 0.054 3342 Dihedral : 10.144 103.670 5420 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 5.35 % Allowed : 23.09 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.17), residues: 2343 helix: -0.15 (0.25), residues: 426 sheet: -1.17 (0.21), residues: 627 loop : -1.68 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 46 TYR 0.027 0.002 TYR A 484 PHE 0.024 0.002 PHE K 30 TRP 0.051 0.003 TRP B 628 HIS 0.003 0.001 HIS E 339 Details of bonding type rmsd covalent geometry : bond 0.00409 (20583) covalent geometry : angle 0.79994 (28005) SS BOND : bond 0.00477 ( 39) SS BOND : angle 2.27641 ( 78) hydrogen bonds : bond 0.04070 ( 669) hydrogen bonds : angle 5.92675 ( 1782) link_ALPHA1-2 : bond 0.00755 ( 12) link_ALPHA1-2 : angle 1.89478 ( 36) link_ALPHA1-3 : bond 0.00966 ( 12) link_ALPHA1-3 : angle 1.58747 ( 36) link_ALPHA1-6 : bond 0.00272 ( 9) link_ALPHA1-6 : angle 1.84899 ( 27) link_BETA1-4 : bond 0.00429 ( 45) link_BETA1-4 : angle 1.65115 ( 135) link_NAG-ASN : bond 0.00583 ( 63) link_NAG-ASN : angle 3.90665 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 448 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.6847 (mp10) REVERT: A 209 SER cc_start: 0.8019 (t) cc_final: 0.7543 (m) REVERT: A 217 TYR cc_start: 0.8289 (m-80) cc_final: 0.8074 (m-10) REVERT: A 227 ARG cc_start: 0.8585 (ttp-170) cc_final: 0.8318 (ttp80) REVERT: A 265 LEU cc_start: 0.8568 (mp) cc_final: 0.8288 (tp) REVERT: A 322 ILE cc_start: 0.5193 (OUTLIER) cc_final: 0.4938 (mp) REVERT: A 483 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.8875 (mm) REVERT: B 591 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8481 (ttpt) REVERT: B 603 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8141 (mt) REVERT: B 616 ASN cc_start: 0.6699 (p0) cc_final: 0.6243 (p0) REVERT: C 52 TRP cc_start: 0.8919 (t60) cc_final: 0.8122 (t60) REVERT: C 54 ARG cc_start: 0.8841 (mpp80) cc_final: 0.8124 (mpp80) REVERT: C 74 LEU cc_start: 0.8525 (tp) cc_final: 0.8286 (mp) REVERT: D 24 ARG cc_start: 0.7853 (mmt-90) cc_final: 0.7452 (mtp85) REVERT: E 82 GLN cc_start: 0.7484 (pm20) cc_final: 0.7026 (pt0) REVERT: E 169 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.6876 (mp10) REVERT: E 209 SER cc_start: 0.8065 (t) cc_final: 0.7534 (m) REVERT: E 218 CYS cc_start: 0.6066 (OUTLIER) cc_final: 0.5862 (m) REVERT: E 435 TYR cc_start: 0.7814 (t80) cc_final: 0.6987 (t80) REVERT: F 591 LYS cc_start: 0.8928 (ptmt) cc_final: 0.8536 (pttt) REVERT: F 628 TRP cc_start: 0.8165 (OUTLIER) cc_final: 0.7528 (m-10) REVERT: H 24 ARG cc_start: 0.7941 (ttm110) cc_final: 0.7735 (mtm110) REVERT: H 32 TRP cc_start: 0.8805 (m100) cc_final: 0.8322 (m100) REVERT: H 45 ARG cc_start: 0.8415 (ttp-170) cc_final: 0.8184 (ttp-170) REVERT: I 161 MET cc_start: 0.8400 (tpp) cc_final: 0.8084 (tpt) REVERT: I 181 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8400 (mp) REVERT: I 209 SER cc_start: 0.7955 (t) cc_final: 0.7479 (m) REVERT: I 411 ASN cc_start: 0.7036 (p0) cc_final: 0.6745 (p0) REVERT: I 483 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8959 (mm) REVERT: J 624 ASN cc_start: 0.9126 (m-40) cc_final: 0.8707 (m-40) outliers start: 105 outliers final: 88 residues processed: 504 average time/residue: 0.1283 time to fit residues: 103.7108 Evaluate side-chains 535 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 437 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 483 LEU Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 651 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 84 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 226 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 HIS ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.173282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.149073 restraints weight = 31114.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.151790 restraints weight = 20811.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.153391 restraints weight = 15397.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.154547 restraints weight = 11547.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.154851 restraints weight = 11001.903| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 20763 Z= 0.201 Angle : 0.895 17.223 28506 Z= 0.416 Chirality : 0.055 0.912 3603 Planarity : 0.005 0.056 3342 Dihedral : 10.140 104.084 5420 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 5.10 % Allowed : 23.65 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.17), residues: 2343 helix: -0.21 (0.25), residues: 426 sheet: -1.09 (0.21), residues: 642 loop : -1.72 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 50 TYR 0.034 0.002 TYR E 484 PHE 0.023 0.002 PHE D 71 TRP 0.051 0.003 TRP B 628 HIS 0.004 0.001 HIS E 339 Details of bonding type rmsd covalent geometry : bond 0.00475 (20583) covalent geometry : angle 0.82090 (28005) SS BOND : bond 0.00538 ( 39) SS BOND : angle 2.24637 ( 78) hydrogen bonds : bond 0.04081 ( 669) hydrogen bonds : angle 5.92396 ( 1782) link_ALPHA1-2 : bond 0.00708 ( 12) link_ALPHA1-2 : angle 1.99060 ( 36) link_ALPHA1-3 : bond 0.00911 ( 12) link_ALPHA1-3 : angle 1.60990 ( 36) link_ALPHA1-6 : bond 0.00224 ( 9) link_ALPHA1-6 : angle 1.94224 ( 27) link_BETA1-4 : bond 0.00390 ( 45) link_BETA1-4 : angle 1.63246 ( 135) link_NAG-ASN : bond 0.00594 ( 63) link_NAG-ASN : angle 3.88323 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 442 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 SER cc_start: 0.8040 (t) cc_final: 0.7520 (m) REVERT: A 227 ARG cc_start: 0.8653 (ttp-170) cc_final: 0.8417 (ttp80) REVERT: A 265 LEU cc_start: 0.8562 (mp) cc_final: 0.8283 (tp) REVERT: A 322 ILE cc_start: 0.5179 (OUTLIER) cc_final: 0.4926 (mp) REVERT: A 483 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.8937 (mm) REVERT: B 591 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8469 (ttpt) REVERT: B 603 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8203 (mt) REVERT: B 616 ASN cc_start: 0.6659 (p0) cc_final: 0.6297 (p0) REVERT: C 52 TRP cc_start: 0.8915 (t60) cc_final: 0.8121 (t60) REVERT: C 54 ARG cc_start: 0.8847 (mpp80) cc_final: 0.8170 (mpp80) REVERT: C 74 LEU cc_start: 0.8537 (tp) cc_final: 0.8264 (mp) REVERT: D 24 ARG cc_start: 0.7787 (mmt-90) cc_final: 0.7475 (mtp85) REVERT: E 82 GLN cc_start: 0.7392 (pm20) cc_final: 0.7012 (pt0) REVERT: E 100 MET cc_start: 0.8559 (ttt) cc_final: 0.8283 (ttt) REVERT: E 169 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.6970 (mp10) REVERT: E 181 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8360 (tp) REVERT: E 209 SER cc_start: 0.8109 (t) cc_final: 0.7621 (m) REVERT: E 218 CYS cc_start: 0.6116 (OUTLIER) cc_final: 0.5911 (m) REVERT: E 435 TYR cc_start: 0.7844 (t80) cc_final: 0.7019 (t80) REVERT: F 591 LYS cc_start: 0.8878 (ptmt) cc_final: 0.8485 (pttt) REVERT: F 628 TRP cc_start: 0.8146 (OUTLIER) cc_final: 0.7235 (m-10) REVERT: H 86 PHE cc_start: 0.6599 (m-10) cc_final: 0.6267 (m-80) REVERT: I 161 MET cc_start: 0.8528 (tpp) cc_final: 0.8189 (tpt) REVERT: I 181 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8462 (mp) REVERT: I 209 SER cc_start: 0.7968 (t) cc_final: 0.7492 (m) REVERT: I 411 ASN cc_start: 0.7092 (p0) cc_final: 0.6807 (p0) REVERT: I 483 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9011 (mm) REVERT: J 624 ASN cc_start: 0.9121 (m-40) cc_final: 0.8832 (m-40) REVERT: K 36 TRP cc_start: 0.7424 (m100) cc_final: 0.7214 (m100) REVERT: K 54 ARG cc_start: 0.8839 (mtm180) cc_final: 0.8287 (mtm180) outliers start: 100 outliers final: 88 residues processed: 497 average time/residue: 0.1286 time to fit residues: 103.3263 Evaluate side-chains 529 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 431 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 483 LEU Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 651 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 215 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 222 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 206 optimal weight: 0.3980 chunk 18 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 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 169 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 HIS ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 ASN ** I 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 HIS K 43 GLN ** K 100EHIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.177496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.153637 restraints weight = 30835.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.156488 restraints weight = 19779.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.157895 restraints weight = 14232.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.158414 restraints weight = 11189.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.158747 restraints weight = 11087.849| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20763 Z= 0.153 Angle : 0.857 16.248 28506 Z= 0.396 Chirality : 0.053 0.777 3603 Planarity : 0.004 0.054 3342 Dihedral : 9.831 101.124 5420 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 5.10 % Allowed : 23.65 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.17), residues: 2343 helix: -0.10 (0.25), residues: 420 sheet: -1.06 (0.21), residues: 651 loop : -1.66 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 46 TYR 0.029 0.002 TYR E 484 PHE 0.021 0.002 PHE D 71 TRP 0.050 0.003 TRP B 628 HIS 0.004 0.001 HIS K 100E Details of bonding type rmsd covalent geometry : bond 0.00356 (20583) covalent geometry : angle 0.78499 (28005) SS BOND : bond 0.00662 ( 39) SS BOND : angle 2.11889 ( 78) hydrogen bonds : bond 0.03974 ( 669) hydrogen bonds : angle 5.80572 ( 1782) link_ALPHA1-2 : bond 0.00790 ( 12) link_ALPHA1-2 : angle 1.82190 ( 36) link_ALPHA1-3 : bond 0.00981 ( 12) link_ALPHA1-3 : angle 1.49783 ( 36) link_ALPHA1-6 : bond 0.00277 ( 9) link_ALPHA1-6 : angle 1.83734 ( 27) link_BETA1-4 : bond 0.00443 ( 45) link_BETA1-4 : angle 1.65013 ( 135) link_NAG-ASN : bond 0.00579 ( 63) link_NAG-ASN : angle 3.74941 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3257.56 seconds wall clock time: 57 minutes 24.77 seconds (3444.77 seconds total)