Starting phenix.real_space_refine on Wed May 6 14:37:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8apx_15578/05_2026/8apx_15578.cif Found real_map, /net/cci-nas-00/data/ceres_data/8apx_15578/05_2026/8apx_15578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8apx_15578/05_2026/8apx_15578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8apx_15578/05_2026/8apx_15578.map" model { file = "/net/cci-nas-00/data/ceres_data/8apx_15578/05_2026/8apx_15578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8apx_15578/05_2026/8apx_15578.cif" } resolution = 3.2 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= 0.004 sd= 0.049 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: 6 Type Number sf(0) Gaussians Zn 12 6.06 5 P 12 5.49 5 S 324 5.16 5 C 26196 2.51 5 N 7272 2.21 5 O 7800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 183 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41616 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 271 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 30} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PJ3:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3136 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 271 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 30} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PJ3:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3136 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 271 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 30} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PJ3:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3136 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 271 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 30} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PJ3:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3136 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 271 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 30} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PJ3:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3136 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 271 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 30} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PJ3:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3136 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 271 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 30} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PJ3:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3136 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 271 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 30} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PJ3:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3136 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "I" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 271 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 30} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PJ3:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3136 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 271 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 30} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PJ3:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3136 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "K" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 271 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 30} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PJ3:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3136 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "L" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 271 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 30} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PJ3:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3136 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1036 SG CYS A 134 45.723 164.976 30.277 1.00139.66 S ATOM 1088 SG CYS A 141 43.256 162.169 30.655 1.00114.07 S ATOM 4477 SG CYS B 134 21.722 128.098 28.918 1.00140.48 S ATOM 4529 SG CYS B 141 19.712 125.219 30.722 1.00105.16 S ATOM 7918 SG CYS C 134 16.574 85.563 30.217 1.00137.95 S ATOM 7970 SG CYS C 141 17.812 82.003 30.646 1.00 99.47 S ATOM 11359 SG CYS D 134 36.691 46.336 28.990 1.00143.96 S ATOM 11411 SG CYS D 141 38.155 43.017 30.708 1.00112.38 S ATOM 14800 SG CYS E 134 71.008 20.351 30.350 1.00136.88 S ATOM 14852 SG CYS E 141 74.635 19.805 30.715 1.00111.98 S ATOM 18241 SG CYS F 134 114.678 18.133 28.838 1.00142.75 S ATOM 18293 SG CYS F 141 118.363 17.829 30.727 1.00109.17 S ATOM 21682 SG CYS G 134 154.395 35.145 30.290 1.00132.31 S ATOM 21734 SG CYS G 141 156.881 37.998 30.657 1.00112.21 S ATOM 25123 SG CYS H 134 179.804 71.018 30.371 1.00139.92 S ATOM 25175 SG CYS H 141 180.301 74.659 30.682 1.00108.89 S ATOM 28564 SG CYS I 134 183.786 114.626 30.076 1.00143.71 S ATOM 28616 SG CYS I 141 182.348 118.070 30.610 1.00105.56 S ATOM 32005 SG CYS J 134 165.025 154.332 30.304 1.00138.88 S ATOM 32057 SG CYS J 141 162.176 156.838 30.684 1.00120.23 S ATOM 35446 SG CYS K 134 128.111 178.352 29.033 1.00150.83 S ATOM 35498 SG CYS K 141 125.153 180.347 30.715 1.00118.88 S ATOM 38887 SG CYS L 134 85.502 183.551 30.226 1.00139.20 S ATOM 38939 SG CYS L 141 82.013 182.311 30.640 1.00106.65 S Time building chain proxies: 9.62, per 1000 atoms: 0.23 Number of scatterers: 41616 At special positions: 0 Unit cell: (200.925, 200.925, 88.065, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 12 29.99 S 324 16.00 P 12 15.00 O 7800 8.00 N 7272 7.00 C 26196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=24, symmetry=0 Number of additional bonds: simple=24, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 134 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 134 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 79 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 141 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 79 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 141 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 134 " pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 134 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 141 " pdb="ZN ZN D1001 " - pdb=" NE2 HIS D 79 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 141 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 79 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 134 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 134 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 79 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 141 " pdb=" ZN G1001 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 141 " pdb="ZN ZN G1001 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 134 " pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 141 " pdb="ZN ZN H1001 " - pdb=" NE2 HIS H 79 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 134 " pdb=" ZN I1001 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 141 " pdb="ZN ZN I1001 " - pdb=" NE2 HIS I 79 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 134 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 141 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 134 " pdb="ZN ZN J1001 " - pdb=" NE2 HIS J 79 " pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 134 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 141 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 141 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 134 " pdb="ZN ZN L1001 " - pdb=" NE2 HIS L 79 " 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10056 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 61 sheets defined 32.2% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 removed outlier: 3.743A pdb=" N ALA A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 55 Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.919A pdb=" N MET A 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N MET A 73 " --> pdb=" O ARG A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 69 through 73' Processing helix chain 'A' and resid 88 through 101 Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.665A pdb=" N LYS A 115 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 169 removed outlier: 3.871A pdb=" N LYS A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 351 through 363 Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.533A pdb=" N MET A 383 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 384 " --> pdb=" O ASN A 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 380 through 384' Processing helix chain 'A' and resid 385 through 403 Processing helix chain 'A' and resid 461 through 468 removed outlier: 3.591A pdb=" N THR A 466 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.771A pdb=" N ALA B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 55 Processing helix chain 'B' and resid 69 through 73 removed outlier: 3.860A pdb=" N MET B 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET B 73 " --> pdb=" O ARG B 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 69 through 73' Processing helix chain 'B' and resid 88 through 101 Processing helix chain 'B' and resid 111 through 125 removed outlier: 3.823A pdb=" N LYS B 115 " --> pdb=" O ASN B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 169 removed outlier: 4.072A pdb=" N LYS B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 335 through 342 Processing helix chain 'B' and resid 351 through 363 Processing helix chain 'B' and resid 380 through 384 removed outlier: 3.535A pdb=" N MET B 383 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B 384 " --> pdb=" O ASN B 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 380 through 384' Processing helix chain 'B' and resid 385 through 403 Processing helix chain 'B' and resid 461 through 468 removed outlier: 3.587A pdb=" N THR B 466 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.773A pdb=" N ALA C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 55 Processing helix chain 'C' and resid 69 through 73 removed outlier: 3.919A pdb=" N MET C 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET C 73 " --> pdb=" O ARG C 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 69 through 73' Processing helix chain 'C' and resid 88 through 101 Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.540A pdb=" N LYS C 115 " --> pdb=" O ASN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 169 removed outlier: 3.973A pdb=" N LYS C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 351 through 363 Processing helix chain 'C' and resid 380 through 384 removed outlier: 3.616A pdb=" N ILE C 384 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 403 removed outlier: 3.635A pdb=" N GLU C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 468 removed outlier: 3.611A pdb=" N THR C 466 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 22 removed outlier: 3.748A pdb=" N ALA D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 55 Processing helix chain 'D' and resid 69 through 73 removed outlier: 3.912A pdb=" N MET D 72 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET D 73 " --> pdb=" O ARG D 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 69 through 73' Processing helix chain 'D' and resid 88 through 101 Processing helix chain 'D' and resid 111 through 125 removed outlier: 3.528A pdb=" N LYS D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 169 removed outlier: 3.860A pdb=" N LYS D 168 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 351 through 363 Processing helix chain 'D' and resid 380 through 384 removed outlier: 3.547A pdb=" N MET D 383 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE D 384 " --> pdb=" O ASN D 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 380 through 384' Processing helix chain 'D' and resid 385 through 403 Processing helix chain 'D' and resid 461 through 468 removed outlier: 3.586A pdb=" N THR D 466 " --> pdb=" O ILE D 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 22 removed outlier: 3.739A pdb=" N ALA E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 55 Processing helix chain 'E' and resid 69 through 73 removed outlier: 3.869A pdb=" N MET E 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET E 73 " --> pdb=" O ARG E 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 69 through 73' Processing helix chain 'E' and resid 88 through 101 Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.649A pdb=" N LYS E 115 " --> pdb=" O ASN E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 141 removed outlier: 4.043A pdb=" N CYS E 141 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 169 removed outlier: 4.065A pdb=" N LYS E 168 " --> pdb=" O HIS E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 185 Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 335 through 342 Processing helix chain 'E' and resid 351 through 363 Processing helix chain 'E' and resid 380 through 384 removed outlier: 3.538A pdb=" N MET E 383 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE E 384 " --> pdb=" O ASN E 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 380 through 384' Processing helix chain 'E' and resid 385 through 403 removed outlier: 3.511A pdb=" N GLN E 389 " --> pdb=" O PRO E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 468 removed outlier: 3.595A pdb=" N THR E 466 " --> pdb=" O ILE E 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 22 removed outlier: 3.784A pdb=" N ALA F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 55 Processing helix chain 'F' and resid 69 through 73 removed outlier: 3.920A pdb=" N MET F 72 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N MET F 73 " --> pdb=" O ARG F 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 69 through 73' Processing helix chain 'F' and resid 88 through 101 Processing helix chain 'F' and resid 111 through 125 removed outlier: 3.675A pdb=" N LYS F 115 " --> pdb=" O ASN F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 141 removed outlier: 4.028A pdb=" N CYS F 141 " --> pdb=" O ASP F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 169 removed outlier: 3.868A pdb=" N LYS F 168 " --> pdb=" O HIS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 185 Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 335 through 342 Processing helix chain 'F' and resid 351 through 363 Processing helix chain 'F' and resid 380 through 384 removed outlier: 3.532A pdb=" N MET F 383 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE F 384 " --> pdb=" O ASN F 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 380 through 384' Processing helix chain 'F' and resid 385 through 403 removed outlier: 3.778A pdb=" N GLU F 403 " --> pdb=" O ARG F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 468 removed outlier: 3.560A pdb=" N THR F 466 " --> pdb=" O ILE F 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 22 removed outlier: 3.716A pdb=" N ALA G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 55 Processing helix chain 'G' and resid 69 through 73 removed outlier: 3.867A pdb=" N MET G 72 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N MET G 73 " --> pdb=" O ARG G 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 69 through 73' Processing helix chain 'G' and resid 88 through 101 Processing helix chain 'G' and resid 111 through 125 removed outlier: 3.872A pdb=" N LYS G 115 " --> pdb=" O ASN G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 169 removed outlier: 3.866A pdb=" N LYS G 168 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 185 Processing helix chain 'G' and resid 192 through 195 Processing helix chain 'G' and resid 252 through 257 Processing helix chain 'G' and resid 335 through 342 Processing helix chain 'G' and resid 351 through 363 Processing helix chain 'G' and resid 380 through 384 removed outlier: 3.568A pdb=" N MET G 383 " --> pdb=" O LYS G 380 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE G 384 " --> pdb=" O ASN G 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 380 through 384' Processing helix chain 'G' and resid 385 through 403 Processing helix chain 'G' and resid 461 through 468 removed outlier: 3.558A pdb=" N THR G 466 " --> pdb=" O ILE G 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 22 removed outlier: 3.774A pdb=" N ALA H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 55 Processing helix chain 'H' and resid 69 through 73 removed outlier: 3.903A pdb=" N MET H 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET H 73 " --> pdb=" O ARG H 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 69 through 73' Processing helix chain 'H' and resid 88 through 101 Processing helix chain 'H' and resid 111 through 125 removed outlier: 3.820A pdb=" N LYS H 115 " --> pdb=" O ASN H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 167 Processing helix chain 'H' and resid 180 through 185 Processing helix chain 'H' and resid 192 through 195 Processing helix chain 'H' and resid 252 through 257 Processing helix chain 'H' and resid 335 through 342 Processing helix chain 'H' and resid 351 through 363 Processing helix chain 'H' and resid 380 through 384 removed outlier: 3.540A pdb=" N MET H 383 " --> pdb=" O LYS H 380 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE H 384 " --> pdb=" O ASN H 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 380 through 384' Processing helix chain 'H' and resid 385 through 403 Processing helix chain 'H' and resid 461 through 468 removed outlier: 3.570A pdb=" N THR H 466 " --> pdb=" O ILE H 462 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 22 removed outlier: 3.758A pdb=" N ALA I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 55 Processing helix chain 'I' and resid 69 through 73 removed outlier: 3.910A pdb=" N MET I 72 " --> pdb=" O ALA I 69 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET I 73 " --> pdb=" O ARG I 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 69 through 73' Processing helix chain 'I' and resid 88 through 101 Processing helix chain 'I' and resid 111 through 125 removed outlier: 3.721A pdb=" N LYS I 115 " --> pdb=" O ASN I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 169 removed outlier: 3.825A pdb=" N LYS I 168 " --> pdb=" O HIS I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 185 Processing helix chain 'I' and resid 252 through 257 Processing helix chain 'I' and resid 335 through 342 Processing helix chain 'I' and resid 351 through 363 Processing helix chain 'I' and resid 380 through 384 removed outlier: 3.519A pdb=" N MET I 383 " --> pdb=" O LYS I 380 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE I 384 " --> pdb=" O ASN I 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 380 through 384' Processing helix chain 'I' and resid 385 through 403 removed outlier: 3.672A pdb=" N GLU I 403 " --> pdb=" O ARG I 399 " (cutoff:3.500A) Processing helix chain 'I' and resid 461 through 468 removed outlier: 3.568A pdb=" N THR I 466 " --> pdb=" O ILE I 462 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 22 removed outlier: 3.750A pdb=" N ALA J 17 " --> pdb=" O ALA J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 55 Processing helix chain 'J' and resid 69 through 73 removed outlier: 3.786A pdb=" N MET J 72 " --> pdb=" O ALA J 69 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N MET J 73 " --> pdb=" O ARG J 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 69 through 73' Processing helix chain 'J' and resid 88 through 101 Processing helix chain 'J' and resid 111 through 125 removed outlier: 3.697A pdb=" N LYS J 115 " --> pdb=" O ASN J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 169 removed outlier: 3.843A pdb=" N LYS J 168 " --> pdb=" O HIS J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 252 through 257 Processing helix chain 'J' and resid 335 through 342 Processing helix chain 'J' and resid 351 through 363 Processing helix chain 'J' and resid 380 through 384 removed outlier: 3.617A pdb=" N MET J 383 " --> pdb=" O LYS J 380 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE J 384 " --> pdb=" O ASN J 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 380 through 384' Processing helix chain 'J' and resid 385 through 403 Processing helix chain 'J' and resid 461 through 468 removed outlier: 3.583A pdb=" N THR J 466 " --> pdb=" O ILE J 462 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 22 removed outlier: 3.766A pdb=" N ALA K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 55 Processing helix chain 'K' and resid 69 through 73 removed outlier: 3.841A pdb=" N MET K 72 " --> pdb=" O ALA K 69 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N MET K 73 " --> pdb=" O ARG K 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 69 through 73' Processing helix chain 'K' and resid 88 through 101 Processing helix chain 'K' and resid 111 through 125 removed outlier: 3.616A pdb=" N LYS K 115 " --> pdb=" O ASN K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 169 removed outlier: 4.067A pdb=" N LYS K 168 " --> pdb=" O HIS K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 185 Processing helix chain 'K' and resid 252 through 257 Processing helix chain 'K' and resid 335 through 342 Processing helix chain 'K' and resid 351 through 363 Processing helix chain 'K' and resid 380 through 384 removed outlier: 3.531A pdb=" N MET K 383 " --> pdb=" O LYS K 380 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE K 384 " --> pdb=" O ASN K 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 380 through 384' Processing helix chain 'K' and resid 385 through 403 removed outlier: 3.512A pdb=" N GLN K 389 " --> pdb=" O PRO K 385 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU K 403 " --> pdb=" O ARG K 399 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 468 removed outlier: 3.571A pdb=" N THR K 466 " --> pdb=" O ILE K 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 22 removed outlier: 3.776A pdb=" N ALA L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 55 Processing helix chain 'L' and resid 69 through 73 removed outlier: 3.910A pdb=" N MET L 72 " --> pdb=" O ALA L 69 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET L 73 " --> pdb=" O ARG L 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 69 through 73' Processing helix chain 'L' and resid 88 through 101 Processing helix chain 'L' and resid 111 through 125 Processing helix chain 'L' and resid 157 through 169 removed outlier: 3.898A pdb=" N LYS L 168 " --> pdb=" O HIS L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 185 Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 252 through 257 Processing helix chain 'L' and resid 335 through 342 Processing helix chain 'L' and resid 351 through 363 Processing helix chain 'L' and resid 380 through 384 removed outlier: 3.617A pdb=" N ILE L 384 " --> pdb=" O ASN L 381 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 403 removed outlier: 3.649A pdb=" N GLU L 403 " --> pdb=" O ARG L 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 461 through 468 removed outlier: 3.587A pdb=" N THR L 466 " --> pdb=" O ILE L 462 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 removed outlier: 8.166A pdb=" N CYS A 134 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS A 80 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE A 61 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL A 81 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP A 63 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN A 151 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA A 148 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL A 176 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR A 150 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N PHE A 178 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER A 281 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A 287 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 275 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N PHE A 447 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N HIS A 265 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 197 through 201 Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 307 Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 334 Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'B' and resid 133 through 134 removed outlier: 8.398A pdb=" N CYS B 134 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N CYS B 80 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 61 " --> pdb=" O HIS B 79 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL B 81 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASP B 63 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN B 151 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA B 148 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL B 176 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR B 150 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N PHE B 178 " --> pdb=" O TYR B 150 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 280 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG B 289 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR B 278 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR B 291 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS B 276 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N PHE B 447 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N HIS B 265 " --> pdb=" O PHE B 447 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 197 through 201 Processing sheet with id=AA9, first strand: chain 'B' and resid 303 through 307 Processing sheet with id=AB1, first strand: chain 'B' and resid 324 through 334 Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'C' and resid 133 through 134 removed outlier: 8.203A pdb=" N CYS C 134 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS C 80 " --> pdb=" O CYS C 134 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE C 61 " --> pdb=" O HIS C 79 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL C 81 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASP C 63 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 147 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN C 151 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA C 148 " --> pdb=" O TYR C 174 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N VAL C 176 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR C 150 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N PHE C 178 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL C 280 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ARG C 289 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR C 278 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N THR C 291 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N CYS C 276 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N PHE C 447 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N HIS C 265 " --> pdb=" O PHE C 447 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 197 through 201 Processing sheet with id=AB5, first strand: chain 'C' and resid 303 through 307 Processing sheet with id=AB6, first strand: chain 'C' and resid 324 through 334 Processing sheet with id=AB7, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'D' and resid 133 through 134 removed outlier: 8.414A pdb=" N CYS D 134 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N CYS D 80 " --> pdb=" O CYS D 134 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE D 61 " --> pdb=" O HIS D 79 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL D 81 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP D 63 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN D 151 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA D 148 " --> pdb=" O TYR D 174 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL D 176 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR D 150 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N PHE D 178 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL D 280 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARG D 289 " --> pdb=" O THR D 278 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THR D 278 " --> pdb=" O ARG D 289 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 197 through 201 Processing sheet with id=AC1, first strand: chain 'D' and resid 272 through 275 removed outlier: 8.602A pdb=" N PHE D 447 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N HIS D 265 " --> pdb=" O PHE D 447 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 303 through 307 Processing sheet with id=AC3, first strand: chain 'D' and resid 324 through 334 Processing sheet with id=AC4, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AC5, first strand: chain 'E' and resid 133 through 134 removed outlier: 8.178A pdb=" N CYS E 134 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS E 80 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE E 61 " --> pdb=" O HIS E 79 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL E 81 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP E 63 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN E 151 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA E 148 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL E 176 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR E 150 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N PHE E 178 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL E 280 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG E 289 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR E 278 " --> pdb=" O ARG E 289 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR E 291 " --> pdb=" O CYS E 276 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N CYS E 276 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N PHE E 447 " --> pdb=" O VAL E 263 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N HIS E 265 " --> pdb=" O PHE E 447 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 197 through 201 Processing sheet with id=AC7, first strand: chain 'E' and resid 303 through 307 Processing sheet with id=AC8, first strand: chain 'E' and resid 324 through 334 Processing sheet with id=AC9, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AD1, first strand: chain 'F' and resid 133 through 134 removed outlier: 8.470A pdb=" N CYS F 134 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS F 80 " --> pdb=" O CYS F 134 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLN F 151 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA F 148 " --> pdb=" O TYR F 174 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL F 176 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR F 150 " --> pdb=" O VAL F 176 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N PHE F 178 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL F 280 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ARG F 289 " --> pdb=" O THR F 278 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR F 278 " --> pdb=" O ARG F 289 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N THR F 291 " --> pdb=" O CYS F 276 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N CYS F 276 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N PHE F 447 " --> pdb=" O VAL F 263 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N HIS F 265 " --> pdb=" O PHE F 447 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 197 through 201 Processing sheet with id=AD3, first strand: chain 'F' and resid 303 through 307 Processing sheet with id=AD4, first strand: chain 'F' and resid 324 through 334 Processing sheet with id=AD5, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AD6, first strand: chain 'G' and resid 133 through 134 removed outlier: 8.081A pdb=" N CYS G 134 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N CYS G 80 " --> pdb=" O CYS G 134 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE G 61 " --> pdb=" O HIS G 79 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL G 81 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASP G 63 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN G 151 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA G 148 " --> pdb=" O TYR G 174 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N VAL G 176 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR G 150 " --> pdb=" O VAL G 176 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N PHE G 178 " --> pdb=" O TYR G 150 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL G 280 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG G 289 " --> pdb=" O THR G 278 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N THR G 278 " --> pdb=" O ARG G 289 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N THR G 291 " --> pdb=" O CYS G 276 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N CYS G 276 " --> pdb=" O THR G 291 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N PHE G 447 " --> pdb=" O VAL G 263 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N HIS G 265 " --> pdb=" O PHE G 447 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 197 through 201 Processing sheet with id=AD8, first strand: chain 'G' and resid 303 through 307 Processing sheet with id=AD9, first strand: chain 'G' and resid 324 through 334 Processing sheet with id=AE1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'H' and resid 133 through 134 removed outlier: 8.168A pdb=" N CYS H 134 " --> pdb=" O TYR H 78 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N CYS H 80 " --> pdb=" O CYS H 134 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE H 61 " --> pdb=" O HIS H 79 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL H 81 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP H 63 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN H 151 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA H 148 " --> pdb=" O TYR H 174 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL H 176 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR H 150 " --> pdb=" O VAL H 176 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N PHE H 178 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL H 280 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG H 289 " --> pdb=" O THR H 278 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N THR H 278 " --> pdb=" O ARG H 289 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR H 291 " --> pdb=" O CYS H 276 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N CYS H 276 " --> pdb=" O THR H 291 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N PHE H 447 " --> pdb=" O VAL H 263 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N HIS H 265 " --> pdb=" O PHE H 447 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 197 through 201 Processing sheet with id=AE4, first strand: chain 'H' and resid 303 through 307 Processing sheet with id=AE5, first strand: chain 'H' and resid 324 through 334 Processing sheet with id=AE6, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AE7, first strand: chain 'I' and resid 133 through 134 removed outlier: 8.317A pdb=" N CYS I 134 " --> pdb=" O TYR I 78 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS I 80 " --> pdb=" O CYS I 134 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE I 61 " --> pdb=" O HIS I 79 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL I 81 " --> pdb=" O ILE I 61 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASP I 63 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLN I 151 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA I 148 " --> pdb=" O TYR I 174 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N VAL I 176 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR I 150 " --> pdb=" O VAL I 176 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N PHE I 178 " --> pdb=" O TYR I 150 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL I 280 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG I 289 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR I 278 " --> pdb=" O ARG I 289 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR I 291 " --> pdb=" O CYS I 276 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N CYS I 276 " --> pdb=" O THR I 291 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N PHE I 447 " --> pdb=" O VAL I 263 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N HIS I 265 " --> pdb=" O PHE I 447 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 197 through 201 Processing sheet with id=AE9, first strand: chain 'I' and resid 303 through 307 Processing sheet with id=AF1, first strand: chain 'I' and resid 324 through 334 Processing sheet with id=AF2, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AF3, first strand: chain 'J' and resid 133 through 134 removed outlier: 8.209A pdb=" N CYS J 134 " --> pdb=" O TYR J 78 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N CYS J 80 " --> pdb=" O CYS J 134 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE J 61 " --> pdb=" O HIS J 79 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL J 81 " --> pdb=" O ILE J 61 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASP J 63 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN J 151 " --> pdb=" O ILE J 64 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA J 148 " --> pdb=" O TYR J 174 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL J 176 " --> pdb=" O ALA J 148 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TYR J 150 " --> pdb=" O VAL J 176 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N PHE J 178 " --> pdb=" O TYR J 150 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TYR J 285 " --> pdb=" O SER J 281 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER J 281 " --> pdb=" O TYR J 285 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL J 287 " --> pdb=" O VAL J 279 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N PHE J 447 " --> pdb=" O VAL J 263 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N HIS J 265 " --> pdb=" O PHE J 447 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 197 through 201 Processing sheet with id=AF5, first strand: chain 'J' and resid 303 through 307 Processing sheet with id=AF6, first strand: chain 'J' and resid 324 through 334 Processing sheet with id=AF7, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AF8, first strand: chain 'K' and resid 133 through 134 removed outlier: 8.408A pdb=" N CYS K 134 " --> pdb=" O TYR K 78 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N CYS K 80 " --> pdb=" O CYS K 134 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE K 61 " --> pdb=" O HIS K 79 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL K 81 " --> pdb=" O ILE K 61 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP K 63 " --> pdb=" O VAL K 81 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLN K 151 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA K 148 " --> pdb=" O TYR K 174 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N VAL K 176 " --> pdb=" O ALA K 148 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TYR K 150 " --> pdb=" O VAL K 176 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N PHE K 178 " --> pdb=" O TYR K 150 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TYR K 285 " --> pdb=" O SER K 281 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER K 281 " --> pdb=" O TYR K 285 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL K 287 " --> pdb=" O VAL K 279 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP K 277 " --> pdb=" O ARG K 289 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG K 275 " --> pdb=" O THR K 291 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N PHE K 447 " --> pdb=" O VAL K 263 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS K 265 " --> pdb=" O PHE K 447 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 197 through 201 Processing sheet with id=AG1, first strand: chain 'K' and resid 303 through 307 Processing sheet with id=AG2, first strand: chain 'K' and resid 324 through 334 Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AG4, first strand: chain 'L' and resid 133 through 134 removed outlier: 8.283A pdb=" N CYS L 134 " --> pdb=" O TYR L 78 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N CYS L 80 " --> pdb=" O CYS L 134 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE L 61 " --> pdb=" O HIS L 79 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL L 81 " --> pdb=" O ILE L 61 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP L 63 " --> pdb=" O VAL L 81 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLN L 151 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA L 148 " --> pdb=" O TYR L 174 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL L 176 " --> pdb=" O ALA L 148 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TYR L 150 " --> pdb=" O VAL L 176 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N PHE L 178 " --> pdb=" O TYR L 150 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL L 280 " --> pdb=" O VAL L 287 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG L 289 " --> pdb=" O THR L 278 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N THR L 278 " --> pdb=" O ARG L 289 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR L 291 " --> pdb=" O CYS L 276 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N CYS L 276 " --> pdb=" O THR L 291 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N PHE L 447 " --> pdb=" O VAL L 263 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N HIS L 265 " --> pdb=" O PHE L 447 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 197 through 201 Processing sheet with id=AG6, first strand: chain 'L' and resid 303 through 307 Processing sheet with id=AG7, first strand: chain 'L' and resid 324 through 334 1577 hydrogen bonds defined for protein. 4476 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: 8.72 Time building geometry restraints manager: 4.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.28: 6732 1.28 - 1.43: 10762 1.43 - 1.58: 24446 1.58 - 1.73: 24 1.73 - 1.89: 516 Bond restraints: 42480 Sorted by residual: bond pdb=" CA PJ3 A 37 " pdb=" C PJ3 A 37 " ideal model delta sigma weight residual 1.525 1.864 -0.339 2.10e-02 2.27e+03 2.60e+02 bond pdb=" CA PJ3 G 37 " pdb=" C PJ3 G 37 " ideal model delta sigma weight residual 1.525 1.864 -0.339 2.10e-02 2.27e+03 2.60e+02 bond pdb=" CA PJ3 I 37 " pdb=" C PJ3 I 37 " ideal model delta sigma weight residual 1.525 1.863 -0.338 2.10e-02 2.27e+03 2.59e+02 bond pdb=" CA PJ3 L 37 " pdb=" C PJ3 L 37 " ideal model delta sigma weight residual 1.525 1.863 -0.338 2.10e-02 2.27e+03 2.59e+02 bond pdb=" CA PJ3 K 37 " pdb=" C PJ3 K 37 " ideal model delta sigma weight residual 1.525 1.863 -0.338 2.10e-02 2.27e+03 2.59e+02 ... (remaining 42475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 56879 3.75 - 7.51: 618 7.51 - 11.26: 66 11.26 - 15.02: 25 15.02 - 18.77: 24 Bond angle restraints: 57612 Sorted by residual: angle pdb=" N PJ3 H 37 " pdb=" CA PJ3 H 37 " pdb=" CB PJ3 H 37 " ideal model delta sigma weight residual 110.50 123.68 -13.18 1.70e+00 3.46e-01 6.01e+01 angle pdb=" N PJ3 B 37 " pdb=" CA PJ3 B 37 " pdb=" CB PJ3 B 37 " ideal model delta sigma weight residual 110.50 123.59 -13.09 1.70e+00 3.46e-01 5.93e+01 angle pdb=" N PJ3 E 37 " pdb=" CA PJ3 E 37 " pdb=" CB PJ3 E 37 " ideal model delta sigma weight residual 110.50 123.58 -13.08 1.70e+00 3.46e-01 5.92e+01 angle pdb=" N PJ3 F 37 " pdb=" CA PJ3 F 37 " pdb=" CB PJ3 F 37 " ideal model delta sigma weight residual 110.50 123.55 -13.05 1.70e+00 3.46e-01 5.89e+01 angle pdb=" N PJ3 D 37 " pdb=" CA PJ3 D 37 " pdb=" CB PJ3 D 37 " ideal model delta sigma weight residual 110.50 123.48 -12.98 1.70e+00 3.46e-01 5.83e+01 ... (remaining 57607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 24735 35.98 - 71.97: 1226 71.97 - 107.95: 91 107.95 - 143.94: 0 143.94 - 179.92: 24 Dihedral angle restraints: 26076 sinusoidal: 10596 harmonic: 15480 Sorted by residual: dihedral pdb=" CA ILE J 384 " pdb=" C ILE J 384 " pdb=" N PRO J 385 " pdb=" CA PRO J 385 " ideal model delta harmonic sigma weight residual 180.00 144.02 35.98 0 5.00e+00 4.00e-02 5.18e+01 dihedral pdb=" CA ILE G 384 " pdb=" C ILE G 384 " pdb=" N PRO G 385 " pdb=" CA PRO G 385 " ideal model delta harmonic sigma weight residual 180.00 144.34 35.66 0 5.00e+00 4.00e-02 5.09e+01 dihedral pdb=" CA ILE D 384 " pdb=" C ILE D 384 " pdb=" N PRO D 385 " pdb=" CA PRO D 385 " ideal model delta harmonic sigma weight residual 180.00 145.12 34.88 0 5.00e+00 4.00e-02 4.87e+01 ... (remaining 26073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 5356 0.058 - 0.116: 1082 0.116 - 0.174: 88 0.174 - 0.232: 14 0.232 - 0.290: 24 Chirality restraints: 6564 Sorted by residual: chirality pdb=" C1' PJ3 G 37 " pdb=" C2' PJ3 G 37 " pdb=" N9 PJ3 G 37 " pdb=" O4' PJ3 G 37 " both_signs ideal model delta sigma weight residual False 2.20 2.49 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C1' PJ3 D 37 " pdb=" C2' PJ3 D 37 " pdb=" N9 PJ3 D 37 " pdb=" O4' PJ3 D 37 " both_signs ideal model delta sigma weight residual False 2.20 2.48 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C1' PJ3 J 37 " pdb=" C2' PJ3 J 37 " pdb=" N9 PJ3 J 37 " pdb=" O4' PJ3 J 37 " both_signs ideal model delta sigma weight residual False 2.20 2.48 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 6561 not shown) Planarity restraints: 7248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5 PJ3 B 37 " 0.105 2.00e-02 2.50e+03 1.62e-01 2.63e+02 pdb=" C8 PJ3 B 37 " 0.071 2.00e-02 2.50e+03 pdb=" CM7 PJ3 B 37 " 0.105 2.00e-02 2.50e+03 pdb=" N7 PJ3 B 37 " -0.280 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5 PJ3 H 37 " -0.105 2.00e-02 2.50e+03 1.62e-01 2.62e+02 pdb=" C8 PJ3 H 37 " -0.070 2.00e-02 2.50e+03 pdb=" CM7 PJ3 H 37 " -0.104 2.00e-02 2.50e+03 pdb=" N7 PJ3 H 37 " 0.279 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5 PJ3 D 37 " 0.105 2.00e-02 2.50e+03 1.61e-01 2.59e+02 pdb=" C8 PJ3 D 37 " 0.069 2.00e-02 2.50e+03 pdb=" CM7 PJ3 D 37 " 0.103 2.00e-02 2.50e+03 pdb=" N7 PJ3 D 37 " -0.278 2.00e-02 2.50e+03 ... (remaining 7245 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 803 2.65 - 3.21: 38672 3.21 - 3.77: 65972 3.77 - 4.34: 89715 4.34 - 4.90: 145293 Nonbonded interactions: 340455 Sorted by model distance: nonbonded pdb=" OH TYR F 150 " pdb=" OE1 GLN F 165 " model vdw 2.086 3.040 nonbonded pdb=" OD2 ASP D 152 " pdb=" OH TYR D 285 " model vdw 2.089 3.040 nonbonded pdb=" OH TYR C 150 " pdb=" OE1 GLN C 165 " model vdw 2.100 3.040 nonbonded pdb=" OH TYR K 150 " pdb=" OE1 GLN K 165 " model vdw 2.110 3.040 nonbonded pdb=" OH TYR I 150 " pdb=" OE1 GLN I 165 " model vdw 2.112 3.040 ... (remaining 340450 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 44.300 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.339 42540 Z= 0.512 Angle : 0.987 18.773 57612 Z= 0.463 Chirality : 0.048 0.290 6564 Planarity : 0.010 0.164 7248 Dihedral : 20.474 179.922 16020 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.66 % Allowed : 34.99 % Favored : 64.36 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.06 % 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: -1.55 (0.11), residues: 5148 helix: 0.49 (0.13), residues: 1524 sheet: -1.10 (0.13), residues: 1308 loop : -2.01 (0.11), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 325 TYR 0.029 0.002 TYR I 285 PHE 0.035 0.002 PHE I 43 TRP 0.025 0.002 TRP F 258 HIS 0.003 0.000 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00927 (42480) covalent geometry : angle 0.98716 (57612) hydrogen bonds : bond 0.12290 ( 1577) hydrogen bonds : angle 5.59495 ( 4476) metal coordination : bond 0.00677 ( 36) Misc. bond : bond 0.10218 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1863 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 1834 time to evaluate : 1.524 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8433 (mmtt) cc_final: 0.8137 (mmtt) REVERT: A 88 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6422 (tm-30) REVERT: A 133 PHE cc_start: 0.7948 (t80) cc_final: 0.7662 (t80) REVERT: A 185 TYR cc_start: 0.8756 (m-80) cc_final: 0.8402 (m-80) REVERT: A 267 LYS cc_start: 0.8244 (mtmt) cc_final: 0.7878 (mtmt) REVERT: A 345 ILE cc_start: 0.9041 (mm) cc_final: 0.8821 (mm) REVERT: A 399 ARG cc_start: 0.7877 (tpp80) cc_final: 0.7664 (tpp80) REVERT: A 443 VAL cc_start: 0.8692 (t) cc_final: 0.8425 (p) REVERT: B 179 ASP cc_start: 0.8157 (t0) cc_final: 0.7699 (t0) REVERT: B 247 LEU cc_start: 0.8512 (tp) cc_final: 0.8294 (tt) REVERT: B 263 VAL cc_start: 0.8938 (m) cc_final: 0.8736 (t) REVERT: B 267 LYS cc_start: 0.8342 (mtpt) cc_final: 0.8082 (mtmm) REVERT: B 436 ASP cc_start: 0.8051 (t0) cc_final: 0.7767 (t70) REVERT: C 179 ASP cc_start: 0.8325 (t0) cc_final: 0.8100 (t0) REVERT: C 427 LYS cc_start: 0.7421 (mmmm) cc_final: 0.7189 (mmtm) REVERT: D 168 LYS cc_start: 0.8689 (mtmt) cc_final: 0.8231 (mtpp) REVERT: D 180 THR cc_start: 0.8285 (p) cc_final: 0.8031 (m) REVERT: D 197 THR cc_start: 0.8594 (p) cc_final: 0.8294 (t) REVERT: D 232 LYS cc_start: 0.8254 (ptmt) cc_final: 0.7940 (ptmt) REVERT: D 234 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7210 (mm-30) REVERT: D 272 PHE cc_start: 0.7664 (m-80) cc_final: 0.7393 (m-10) REVERT: D 274 CYS cc_start: 0.8189 (m) cc_final: 0.7879 (m) REVERT: D 345 ILE cc_start: 0.8951 (mm) cc_final: 0.8723 (mm) REVERT: E 20 ARG cc_start: 0.7969 (ttm-80) cc_final: 0.7723 (mtm-85) REVERT: E 28 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7349 (mm-30) REVERT: E 144 ARG cc_start: 0.8052 (ttm110) cc_final: 0.7651 (ttm110) REVERT: E 171 ARG cc_start: 0.7048 (mtm-85) cc_final: 0.6523 (mtm-85) REVERT: E 180 THR cc_start: 0.8413 (m) cc_final: 0.8131 (m) REVERT: E 195 TYR cc_start: 0.7831 (m-80) cc_final: 0.7573 (m-10) REVERT: E 219 GLU cc_start: 0.4760 (OUTLIER) cc_final: 0.4504 (pp20) REVERT: E 297 TYR cc_start: 0.7759 (m-10) cc_final: 0.7432 (m-10) REVERT: E 303 TYR cc_start: 0.7899 (m-80) cc_final: 0.7659 (m-10) REVERT: E 405 GLU cc_start: 0.7153 (tp30) cc_final: 0.6855 (tp30) REVERT: E 438 GLN cc_start: 0.7582 (mp10) cc_final: 0.7202 (mp10) REVERT: F 20 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7529 (mtm-85) REVERT: F 43 PHE cc_start: 0.8889 (t80) cc_final: 0.8627 (t80) REVERT: F 314 MET cc_start: 0.7813 (mtp) cc_final: 0.7533 (ttp) REVERT: F 436 ASP cc_start: 0.7839 (t0) cc_final: 0.7380 (t0) REVERT: G 16 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8154 (mmtt) REVERT: G 71 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7278 (ptp-110) REVERT: G 76 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7549 (mtt90) REVERT: G 88 GLU cc_start: 0.7135 (tt0) cc_final: 0.6893 (tm-30) REVERT: G 150 TYR cc_start: 0.8621 (m-80) cc_final: 0.8419 (m-80) REVERT: G 183 PHE cc_start: 0.8497 (m-80) cc_final: 0.8188 (m-80) REVERT: G 274 CYS cc_start: 0.8246 (m) cc_final: 0.7589 (m) REVERT: G 400 LYS cc_start: 0.8448 (tppt) cc_final: 0.7871 (tppt) REVERT: G 438 GLN cc_start: 0.8036 (mp10) cc_final: 0.7351 (mp10) REVERT: G 442 LYS cc_start: 0.8352 (mttt) cc_final: 0.8043 (tttt) REVERT: H 16 LYS cc_start: 0.8422 (mmtt) cc_final: 0.8186 (mmtt) REVERT: H 28 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7372 (mm-30) REVERT: H 30 ARG cc_start: 0.7284 (ptp-170) cc_final: 0.7049 (mtm110) REVERT: H 106 LYS cc_start: 0.7920 (mtmm) cc_final: 0.7672 (mtmm) REVERT: H 171 ARG cc_start: 0.7098 (mtm-85) cc_final: 0.6620 (mtm-85) REVERT: H 176 VAL cc_start: 0.8668 (p) cc_final: 0.8397 (m) REVERT: H 180 THR cc_start: 0.8379 (m) cc_final: 0.8086 (m) REVERT: H 400 LYS cc_start: 0.8097 (tppt) cc_final: 0.7885 (tppt) REVERT: H 436 ASP cc_start: 0.8279 (t0) cc_final: 0.8046 (t70) REVERT: I 70 ARG cc_start: 0.7700 (ttm110) cc_final: 0.7339 (ttm110) REVERT: I 75 ASP cc_start: 0.8140 (p0) cc_final: 0.7864 (p0) REVERT: I 188 MET cc_start: 0.8420 (mmt) cc_final: 0.8018 (mmt) REVERT: I 204 VAL cc_start: 0.8879 (m) cc_final: 0.8669 (t) REVERT: I 255 LEU cc_start: 0.8686 (tp) cc_final: 0.8485 (tt) REVERT: I 289 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7561 (mtp-110) REVERT: I 319 ASP cc_start: 0.7546 (m-30) cc_final: 0.7201 (m-30) REVERT: I 400 LYS cc_start: 0.8116 (tppt) cc_final: 0.7835 (tppt) REVERT: I 434 ARG cc_start: 0.8394 (mpp80) cc_final: 0.6828 (mpp80) REVERT: J 99 LYS cc_start: 0.8948 (mmmm) cc_final: 0.8700 (mmmm) REVERT: J 154 TYR cc_start: 0.8626 (m-80) cc_final: 0.8396 (m-80) REVERT: J 183 PHE cc_start: 0.8508 (m-80) cc_final: 0.8197 (m-80) REVERT: J 245 SER cc_start: 0.8476 (p) cc_final: 0.8267 (p) REVERT: J 314 MET cc_start: 0.8319 (mtp) cc_final: 0.8083 (ttp) REVERT: J 378 THR cc_start: 0.8044 (m) cc_final: 0.7733 (p) REVERT: J 400 LYS cc_start: 0.8364 (tppt) cc_final: 0.7785 (tppt) REVERT: K 76 ARG cc_start: 0.8292 (mtt90) cc_final: 0.7886 (mtt90) REVERT: K 204 VAL cc_start: 0.8620 (m) cc_final: 0.8418 (p) REVERT: K 264 PHE cc_start: 0.8121 (p90) cc_final: 0.7825 (p90) REVERT: K 313 LEU cc_start: 0.8430 (mt) cc_final: 0.8083 (mm) REVERT: K 340 ASP cc_start: 0.7670 (t0) cc_final: 0.7296 (t0) REVERT: K 341 GLN cc_start: 0.7753 (mt0) cc_final: 0.7273 (mt0) REVERT: L 71 ARG cc_start: 0.7744 (mtm-85) cc_final: 0.7152 (ptp-110) REVERT: L 245 SER cc_start: 0.8470 (t) cc_final: 0.8249 (p) outliers start: 29 outliers final: 10 residues processed: 1843 average time/residue: 0.2879 time to fit residues: 823.6239 Evaluate side-chains 1810 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1798 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain E residue 219 GLU Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 403 GLU Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 20 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 6.9990 chunk 41 optimal weight: 0.0770 chunk 265 optimal weight: 2.9990 chunk 497 optimal weight: 3.9990 chunk 414 optimal weight: 3.9990 chunk 310 optimal weight: 0.9980 chunk 488 optimal weight: 0.4980 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 0.9980 chunk 142 optimal weight: 0.6980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.137656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.122408 restraints weight = 65043.476| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.72 r_work: 0.3453 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 42540 Z= 0.134 Angle : 0.719 13.945 57612 Z= 0.341 Chirality : 0.044 0.141 6564 Planarity : 0.006 0.129 7248 Dihedral : 15.465 179.851 6379 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.83 % Favored : 94.15 % Rotamer: Outliers : 4.62 % Allowed : 30.03 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.37 % 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: -1.29 (0.11), residues: 5148 helix: 1.01 (0.13), residues: 1596 sheet: -1.21 (0.13), residues: 1332 loop : -2.01 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 411 TYR 0.018 0.001 TYR G 5 PHE 0.027 0.002 PHE A 264 TRP 0.018 0.002 TRP F 258 HIS 0.004 0.001 HIS F 79 Details of bonding type rmsd covalent geometry : bond 0.00317 (42480) covalent geometry : angle 0.71935 (57612) hydrogen bonds : bond 0.03414 ( 1577) hydrogen bonds : angle 4.73993 ( 4476) metal coordination : bond 0.00654 ( 36) Misc. bond : bond 0.00048 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2055 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 1851 time to evaluate : 1.322 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7803 (ttm110) cc_final: 0.7583 (ttm110) REVERT: A 76 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8228 (mtp85) REVERT: A 88 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6638 (tm-30) REVERT: A 92 ARG cc_start: 0.7439 (mmp80) cc_final: 0.7089 (mmp80) REVERT: A 106 LYS cc_start: 0.7987 (mtmm) cc_final: 0.7661 (mtmm) REVERT: A 115 LYS cc_start: 0.8776 (mptp) cc_final: 0.8339 (mptp) REVERT: A 118 ASP cc_start: 0.7760 (m-30) cc_final: 0.7530 (m-30) REVERT: A 133 PHE cc_start: 0.8018 (t80) cc_final: 0.7740 (t80) REVERT: A 135 LEU cc_start: 0.8543 (mt) cc_final: 0.8229 (mm) REVERT: A 142 ARG cc_start: 0.7627 (tpp80) cc_final: 0.7330 (ttm-80) REVERT: A 150 TYR cc_start: 0.8711 (m-80) cc_final: 0.8498 (m-80) REVERT: A 184 MET cc_start: 0.8408 (mmm) cc_final: 0.8182 (mmm) REVERT: A 208 LYS cc_start: 0.8796 (ttpp) cc_final: 0.8590 (ttpp) REVERT: A 228 MET cc_start: 0.0925 (tpp) cc_final: 0.0590 (tpp) REVERT: A 243 VAL cc_start: 0.7800 (t) cc_final: 0.7470 (t) REVERT: A 248 TYR cc_start: 0.8026 (m-10) cc_final: 0.7770 (m-10) REVERT: A 325 ARG cc_start: 0.7905 (ptp-110) cc_final: 0.7528 (ttm-80) REVERT: A 399 ARG cc_start: 0.7908 (tpp80) cc_final: 0.7307 (tpp80) REVERT: A 403 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: A 443 VAL cc_start: 0.8617 (t) cc_final: 0.8339 (p) REVERT: B 24 MET cc_start: 0.8365 (pmm) cc_final: 0.8013 (pmm) REVERT: B 63 ASP cc_start: 0.7502 (t0) cc_final: 0.7277 (t0) REVERT: B 115 LYS cc_start: 0.8720 (mptp) cc_final: 0.8316 (mptp) REVERT: B 144 ARG cc_start: 0.8266 (ttm110) cc_final: 0.8059 (ttm110) REVERT: B 176 VAL cc_start: 0.8568 (p) cc_final: 0.8300 (m) REVERT: B 184 MET cc_start: 0.8320 (mmm) cc_final: 0.7904 (tpp) REVERT: B 274 CYS cc_start: 0.8178 (m) cc_final: 0.7883 (m) REVERT: B 313 LEU cc_start: 0.8243 (mt) cc_final: 0.7926 (mm) REVERT: B 396 LYS cc_start: 0.8456 (mmmm) cc_final: 0.7919 (mmtm) REVERT: B 434 ARG cc_start: 0.8502 (mpp80) cc_final: 0.7240 (mpp80) REVERT: C 16 LYS cc_start: 0.8520 (mptt) cc_final: 0.8212 (mptt) REVERT: C 76 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7614 (mtt90) REVERT: C 115 LYS cc_start: 0.8678 (mptp) cc_final: 0.8454 (mptp) REVERT: C 195 TYR cc_start: 0.8257 (m-80) cc_final: 0.8010 (m-80) REVERT: C 219 GLU cc_start: 0.5498 (OUTLIER) cc_final: 0.5061 (pp20) REVERT: C 436 ASP cc_start: 0.8102 (t0) cc_final: 0.7847 (t0) REVERT: D 115 LYS cc_start: 0.8741 (mptp) cc_final: 0.8476 (mptp) REVERT: D 118 ASP cc_start: 0.7790 (m-30) cc_final: 0.7468 (m-30) REVERT: D 150 TYR cc_start: 0.8810 (m-80) cc_final: 0.8579 (m-80) REVERT: D 163 TYR cc_start: 0.8499 (t80) cc_final: 0.8258 (t80) REVERT: D 232 LYS cc_start: 0.8270 (ptmt) cc_final: 0.7979 (ptmt) REVERT: D 234 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7402 (mm-30) REVERT: D 272 PHE cc_start: 0.7552 (m-80) cc_final: 0.7304 (m-10) REVERT: D 274 CYS cc_start: 0.8112 (m) cc_final: 0.7886 (m) REVERT: D 285 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7163 (t80) REVERT: D 345 ILE cc_start: 0.8995 (mm) cc_final: 0.8763 (mm) REVERT: E 16 LYS cc_start: 0.8444 (mmtt) cc_final: 0.8146 (mmmt) REVERT: E 20 ARG cc_start: 0.8166 (ttm-80) cc_final: 0.7957 (mtm-85) REVERT: E 115 LYS cc_start: 0.8721 (mptp) cc_final: 0.8342 (mptp) REVERT: E 144 ARG cc_start: 0.8044 (ttm110) cc_final: 0.7672 (ttm110) REVERT: E 275 ARG cc_start: 0.7862 (ttt180) cc_final: 0.7588 (ptt180) REVERT: E 291 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8479 (p) REVERT: E 297 TYR cc_start: 0.8013 (m-10) cc_final: 0.7693 (m-10) REVERT: E 436 ASP cc_start: 0.8209 (t0) cc_final: 0.7865 (t70) REVERT: F 30 ARG cc_start: 0.7170 (ptp-110) cc_final: 0.6373 (ttm110) REVERT: F 43 PHE cc_start: 0.8792 (t80) cc_final: 0.8496 (t80) REVERT: F 115 LYS cc_start: 0.8735 (mptp) cc_final: 0.8374 (mptp) REVERT: F 133 PHE cc_start: 0.8246 (t80) cc_final: 0.7982 (t80) REVERT: F 135 LEU cc_start: 0.8544 (mt) cc_final: 0.8263 (mm) REVERT: F 314 MET cc_start: 0.7876 (mtp) cc_final: 0.7652 (ttp) REVERT: F 325 ARG cc_start: 0.7640 (ptp-110) cc_final: 0.7187 (ttp-170) REVERT: F 433 LYS cc_start: 0.8375 (mmmt) cc_final: 0.8062 (mmmt) REVERT: F 434 ARG cc_start: 0.8247 (mpp80) cc_final: 0.6852 (mpp80) REVERT: F 436 ASP cc_start: 0.7837 (t0) cc_final: 0.7569 (t0) REVERT: F 441 GLN cc_start: 0.7817 (mt0) cc_final: 0.7539 (mt0) REVERT: G 16 LYS cc_start: 0.8389 (mmtt) cc_final: 0.7945 (mmtt) REVERT: G 76 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7588 (mtt90) REVERT: G 88 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6764 (tm-30) REVERT: G 92 ARG cc_start: 0.7585 (mmp80) cc_final: 0.7290 (mmp80) REVERT: G 115 LYS cc_start: 0.8813 (mptp) cc_final: 0.8446 (mptp) REVERT: G 118 ASP cc_start: 0.7852 (m-30) cc_final: 0.7635 (m-30) REVERT: G 179 ASP cc_start: 0.7991 (t0) cc_final: 0.7741 (t0) REVERT: G 184 MET cc_start: 0.8146 (mmm) cc_final: 0.7929 (mmm) REVERT: G 250 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7093 (mm-30) REVERT: G 274 CYS cc_start: 0.8134 (m) cc_final: 0.7507 (m) REVERT: G 380 LYS cc_start: 0.8381 (mmmm) cc_final: 0.8146 (mmmm) REVERT: G 399 ARG cc_start: 0.7888 (tpp80) cc_final: 0.6948 (tpp80) REVERT: G 400 LYS cc_start: 0.8396 (tppt) cc_final: 0.7984 (tppt) REVERT: G 403 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: G 442 LYS cc_start: 0.8382 (mttt) cc_final: 0.8159 (tttm) REVERT: G 448 ASP cc_start: 0.7659 (t0) cc_final: 0.7442 (t0) REVERT: H 71 ARG cc_start: 0.7979 (mtm-85) cc_final: 0.7248 (ptp90) REVERT: H 76 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7652 (mtt90) REVERT: H 115 LYS cc_start: 0.8814 (mptp) cc_final: 0.8345 (mptp) REVERT: H 171 ARG cc_start: 0.7244 (mtm-85) cc_final: 0.6574 (mtm-85) REVERT: H 248 TYR cc_start: 0.7675 (m-10) cc_final: 0.7446 (m-10) REVERT: H 291 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8394 (p) REVERT: H 360 VAL cc_start: 0.8738 (p) cc_final: 0.8399 (m) REVERT: H 399 ARG cc_start: 0.7663 (tpp80) cc_final: 0.6993 (tpp80) REVERT: H 403 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: H 436 ASP cc_start: 0.8245 (t0) cc_final: 0.8006 (t70) REVERT: H 447 PHE cc_start: 0.8595 (m-80) cc_final: 0.8111 (m-80) REVERT: I 63 ASP cc_start: 0.7774 (t0) cc_final: 0.6455 (t0) REVERT: I 71 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7193 (mtm110) REVERT: I 72 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7609 (tmm) REVERT: I 75 ASP cc_start: 0.8073 (p0) cc_final: 0.7853 (p0) REVERT: I 115 LYS cc_start: 0.8779 (mptp) cc_final: 0.8467 (mptp) REVERT: I 135 LEU cc_start: 0.8501 (mt) cc_final: 0.8273 (mm) REVERT: I 184 MET cc_start: 0.8382 (tpp) cc_final: 0.7931 (tpp) REVERT: I 204 VAL cc_start: 0.8820 (m) cc_final: 0.8615 (t) REVERT: I 232 LYS cc_start: 0.7818 (ptmt) cc_final: 0.7496 (ptmt) REVERT: I 319 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.7061 (m-30) REVERT: I 357 LYS cc_start: 0.8638 (ttmm) cc_final: 0.8432 (ttmt) REVERT: I 400 LYS cc_start: 0.8089 (tppt) cc_final: 0.7687 (tppt) REVERT: I 403 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: I 434 ARG cc_start: 0.8346 (mpp80) cc_final: 0.6845 (mpp80) REVERT: I 438 GLN cc_start: 0.8043 (mp10) cc_final: 0.7338 (mt0) REVERT: J 71 ARG cc_start: 0.7882 (mtm110) cc_final: 0.7536 (ptp90) REVERT: J 99 LYS cc_start: 0.8980 (mmmm) cc_final: 0.8682 (mmmm) REVERT: J 115 LYS cc_start: 0.8783 (mptp) cc_final: 0.8377 (mptp) REVERT: J 154 TYR cc_start: 0.8699 (m-80) cc_final: 0.8320 (m-80) REVERT: J 183 PHE cc_start: 0.8555 (m-80) cc_final: 0.8210 (m-80) REVERT: J 240 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7863 (mp) REVERT: J 245 SER cc_start: 0.8469 (p) cc_final: 0.8246 (p) REVERT: J 314 MET cc_start: 0.8286 (mtp) cc_final: 0.8073 (ttp) REVERT: J 378 THR cc_start: 0.8055 (m) cc_final: 0.7802 (p) REVERT: J 383 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8042 (ppp) REVERT: J 403 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: K 63 ASP cc_start: 0.7252 (t0) cc_final: 0.6928 (t0) REVERT: K 76 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8016 (mtt90) REVERT: K 88 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6776 (tt0) REVERT: K 115 LYS cc_start: 0.8780 (mptp) cc_final: 0.8462 (mptp) REVERT: K 171 ARG cc_start: 0.7068 (mtm-85) cc_final: 0.6847 (mtm-85) REVERT: K 204 VAL cc_start: 0.8597 (m) cc_final: 0.8380 (p) REVERT: K 283 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: K 313 LEU cc_start: 0.8370 (mt) cc_final: 0.8029 (mm) REVERT: L 24 MET cc_start: 0.8407 (pmm) cc_final: 0.7995 (pmm) REVERT: L 71 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7385 (ptp-110) REVERT: L 115 LYS cc_start: 0.8814 (mptp) cc_final: 0.8314 (mptp) REVERT: L 154 TYR cc_start: 0.8524 (m-80) cc_final: 0.8187 (m-80) REVERT: L 171 ARG cc_start: 0.6847 (mtm-85) cc_final: 0.6363 (mtm-85) REVERT: L 179 ASP cc_start: 0.8058 (t0) cc_final: 0.7589 (t0) REVERT: L 195 TYR cc_start: 0.8339 (m-80) cc_final: 0.8027 (m-80) REVERT: L 202 GLU cc_start: 0.8170 (tp30) cc_final: 0.7693 (tp30) REVERT: L 238 ARG cc_start: 0.7719 (ttm110) cc_final: 0.7268 (mtm110) REVERT: L 271 SER cc_start: 0.7494 (p) cc_final: 0.7206 (m) REVERT: L 283 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: L 383 MET cc_start: 0.8626 (ttp) cc_final: 0.8178 (ttp) REVERT: L 427 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6660 (mmtm) REVERT: L 434 ARG cc_start: 0.8384 (mpp80) cc_final: 0.7220 (tpp80) REVERT: L 446 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7327 (mm-30) outliers start: 204 outliers final: 115 residues processed: 1936 average time/residue: 0.2830 time to fit residues: 852.1873 Evaluate side-chains 1949 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 1810 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 238 ARG Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 275 ARG Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 236 CYS Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 305 VAL Chi-restraints excluded: chain H residue 342 MET Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 403 GLU Chi-restraints excluded: chain H residue 429 HIS Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 238 ARG Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 314 MET Chi-restraints excluded: chain I residue 319 ASP Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 403 GLU Chi-restraints excluded: chain J residue 72 MET Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 236 CYS Chi-restraints excluded: chain J residue 240 LEU Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 383 MET Chi-restraints excluded: chain J residue 403 GLU Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 236 CYS Chi-restraints excluded: chain K residue 283 GLU Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 397 GLU Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 194 SER Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 283 GLU Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 314 MET Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain L residue 342 MET Chi-restraints excluded: chain L residue 348 THR Chi-restraints excluded: chain L residue 358 LEU Chi-restraints excluded: chain L residue 405 GLU Chi-restraints excluded: chain L residue 427 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 175 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 348 optimal weight: 4.9990 chunk 307 optimal weight: 4.9990 chunk 326 optimal weight: 1.9990 chunk 299 optimal weight: 0.9990 chunk 212 optimal weight: 0.6980 chunk 204 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 291 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.133623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.117514 restraints weight = 65125.885| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.79 r_work: 0.3417 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 42540 Z= 0.161 Angle : 0.696 14.618 57612 Z= 0.331 Chirality : 0.044 0.145 6564 Planarity : 0.005 0.106 7248 Dihedral : 14.628 176.354 6354 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.39 % Allowed : 29.71 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.37 % 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: -1.17 (0.11), residues: 5148 helix: 1.22 (0.14), residues: 1608 sheet: -1.24 (0.13), residues: 1332 loop : -2.00 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG D 92 TYR 0.023 0.002 TYR I 5 PHE 0.028 0.002 PHE D 183 TRP 0.016 0.002 TRP C 258 HIS 0.003 0.001 HIS J 308 Details of bonding type rmsd covalent geometry : bond 0.00372 (42480) covalent geometry : angle 0.69552 (57612) hydrogen bonds : bond 0.03242 ( 1577) hydrogen bonds : angle 4.58509 ( 4476) metal coordination : bond 0.00650 ( 36) Misc. bond : bond 0.00071 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2105 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 1867 time to evaluate : 1.642 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: 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: 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 30 ARG cc_start: 0.6058 (ptt-90) cc_final: 0.5761 (ptt-90) REVERT: A 76 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8301 (mtt90) REVERT: A 88 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6595 (tm-30) REVERT: A 92 ARG cc_start: 0.7553 (mmp80) cc_final: 0.7205 (mmp80) REVERT: A 115 LYS cc_start: 0.8842 (mptp) cc_final: 0.8351 (mptp) REVERT: A 118 ASP cc_start: 0.7797 (m-30) cc_final: 0.7529 (m-30) REVERT: A 133 PHE cc_start: 0.7911 (t80) cc_final: 0.7703 (t80) REVERT: A 135 LEU cc_start: 0.8579 (mt) cc_final: 0.8192 (mm) REVERT: A 171 ARG cc_start: 0.7300 (mtm-85) cc_final: 0.7094 (mtm-85) REVERT: A 188 MET cc_start: 0.8307 (mmt) cc_final: 0.7729 (mmt) REVERT: A 214 SER cc_start: 0.8483 (t) cc_final: 0.7928 (p) REVERT: A 228 MET cc_start: 0.0945 (tpp) cc_final: 0.0590 (tpp) REVERT: A 232 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.7146 (ptmt) REVERT: A 242 SER cc_start: 0.7990 (t) cc_final: 0.7517 (p) REVERT: A 243 VAL cc_start: 0.7956 (t) cc_final: 0.7664 (t) REVERT: A 248 TYR cc_start: 0.8165 (m-10) cc_final: 0.7884 (m-10) REVERT: A 258 TRP cc_start: 0.8597 (m100) cc_final: 0.7481 (m100) REVERT: A 267 LYS cc_start: 0.8316 (mtmt) cc_final: 0.8113 (mtmt) REVERT: A 325 ARG cc_start: 0.7960 (ptp-110) cc_final: 0.7624 (ttm-80) REVERT: A 396 LYS cc_start: 0.8506 (mmmm) cc_final: 0.7972 (mmtm) REVERT: A 399 ARG cc_start: 0.8036 (tpp80) cc_final: 0.7816 (tpp80) REVERT: A 403 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7467 (mt-10) REVERT: A 443 VAL cc_start: 0.8596 (t) cc_final: 0.8301 (p) REVERT: B 56 ASP cc_start: 0.7403 (t0) cc_final: 0.7118 (t70) REVERT: B 63 ASP cc_start: 0.7349 (t0) cc_final: 0.7088 (t0) REVERT: B 71 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7925 (mtm-85) REVERT: B 115 LYS cc_start: 0.8732 (mptp) cc_final: 0.8226 (mptp) REVERT: B 179 ASP cc_start: 0.8082 (t0) cc_final: 0.7746 (t0) REVERT: B 184 MET cc_start: 0.8468 (mmm) cc_final: 0.7906 (mmm) REVERT: B 195 TYR cc_start: 0.8452 (m-80) cc_final: 0.8228 (m-80) REVERT: B 234 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7474 (mm-30) REVERT: B 236 CYS cc_start: 0.8191 (p) cc_final: 0.7958 (p) REVERT: B 283 GLU cc_start: 0.7836 (tp30) cc_final: 0.7630 (tp30) REVERT: B 313 LEU cc_start: 0.8287 (mt) cc_final: 0.7960 (mm) REVERT: B 396 LYS cc_start: 0.8437 (mmmm) cc_final: 0.7862 (mmtm) REVERT: B 434 ARG cc_start: 0.8587 (mpp80) cc_final: 0.7381 (mpp80) REVERT: B 436 ASP cc_start: 0.8341 (t0) cc_final: 0.7865 (t70) REVERT: C 16 LYS cc_start: 0.8515 (mptt) cc_final: 0.8138 (mppt) REVERT: C 51 ILE cc_start: 0.8258 (mm) cc_final: 0.7996 (mm) REVERT: C 115 LYS cc_start: 0.8718 (mptp) cc_final: 0.8399 (mptp) REVERT: C 195 TYR cc_start: 0.8371 (m-80) cc_final: 0.8135 (m-80) REVERT: C 219 GLU cc_start: 0.5732 (OUTLIER) cc_final: 0.5357 (pp20) REVERT: C 283 GLU cc_start: 0.7874 (tp30) cc_final: 0.7586 (tp30) REVERT: C 427 LYS cc_start: 0.7722 (mmmm) cc_final: 0.7325 (mmmm) REVERT: C 436 ASP cc_start: 0.8157 (t0) cc_final: 0.7901 (t0) REVERT: D 28 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7305 (mm-30) REVERT: D 88 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6837 (tm-30) REVERT: D 115 LYS cc_start: 0.8781 (mptp) cc_final: 0.8381 (mptp) REVERT: D 150 TYR cc_start: 0.8778 (m-80) cc_final: 0.8575 (m-80) REVERT: D 163 TYR cc_start: 0.8550 (t80) cc_final: 0.8271 (t80) REVERT: D 165 GLN cc_start: 0.8111 (mt0) cc_final: 0.7902 (mt0) REVERT: D 168 LYS cc_start: 0.8883 (mtmt) cc_final: 0.8408 (mtpp) REVERT: D 171 ARG cc_start: 0.7341 (mtm-85) cc_final: 0.6912 (mtm-85) REVERT: D 197 THR cc_start: 0.8386 (p) cc_final: 0.8071 (t) REVERT: D 232 LYS cc_start: 0.8351 (ptmt) cc_final: 0.8076 (ptmt) REVERT: D 234 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7440 (mm-30) REVERT: D 274 CYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7869 (m) REVERT: D 285 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.7247 (t80) REVERT: D 345 ILE cc_start: 0.9002 (mm) cc_final: 0.8779 (mm) REVERT: D 448 ASP cc_start: 0.7735 (t0) cc_final: 0.7496 (t0) REVERT: E 16 LYS cc_start: 0.8480 (mmtt) cc_final: 0.8139 (mmmt) REVERT: E 20 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7987 (mtm-85) REVERT: E 24 MET cc_start: 0.8698 (pmm) cc_final: 0.8265 (pmm) REVERT: E 115 LYS cc_start: 0.8774 (mptp) cc_final: 0.8325 (mptp) REVERT: E 144 ARG cc_start: 0.8181 (ttm110) cc_final: 0.7956 (ttm110) REVERT: E 201 ASP cc_start: 0.8080 (t0) cc_final: 0.7796 (t0) REVERT: E 275 ARG cc_start: 0.7893 (ttt180) cc_final: 0.7624 (ptt180) REVERT: E 291 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8479 (p) REVERT: E 297 TYR cc_start: 0.8112 (m-10) cc_final: 0.7771 (m-10) REVERT: E 396 LYS cc_start: 0.8368 (tppt) cc_final: 0.8037 (mmtt) REVERT: E 399 ARG cc_start: 0.7859 (tpp80) cc_final: 0.7592 (tpp80) REVERT: E 436 ASP cc_start: 0.8328 (t0) cc_final: 0.7793 (t70) REVERT: F 30 ARG cc_start: 0.7252 (ptp-110) cc_final: 0.6551 (ttm110) REVERT: F 85 ARG cc_start: 0.7529 (mmp80) cc_final: 0.7210 (mmp80) REVERT: F 115 LYS cc_start: 0.8747 (mptp) cc_final: 0.8215 (mptp) REVERT: F 135 LEU cc_start: 0.8541 (mt) cc_final: 0.8308 (mm) REVERT: F 184 MET cc_start: 0.8319 (tpp) cc_final: 0.7801 (tpp) REVERT: F 258 TRP cc_start: 0.8540 (m100) cc_final: 0.7441 (m100) REVERT: F 275 ARG cc_start: 0.7867 (ttt90) cc_final: 0.7611 (ttt90) REVERT: F 285 TYR cc_start: 0.8135 (OUTLIER) cc_final: 0.7331 (t80) REVERT: F 316 LYS cc_start: 0.8183 (tppp) cc_final: 0.7752 (tppp) REVERT: F 434 ARG cc_start: 0.8349 (mpp80) cc_final: 0.6896 (mpp80) REVERT: F 436 ASP cc_start: 0.7959 (t0) cc_final: 0.7734 (t0) REVERT: F 441 GLN cc_start: 0.7719 (mt0) cc_final: 0.7497 (mt0) REVERT: G 30 ARG cc_start: 0.6333 (pmt170) cc_final: 0.5977 (pmt170) REVERT: G 63 ASP cc_start: 0.7406 (t0) cc_final: 0.7199 (t0) REVERT: G 76 ARG cc_start: 0.8170 (mtt90) cc_final: 0.7781 (mtt90) REVERT: G 88 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6902 (tm-30) REVERT: G 111 ASN cc_start: 0.8654 (t0) cc_final: 0.8365 (t0) REVERT: G 115 LYS cc_start: 0.8828 (mptp) cc_final: 0.8346 (mptp) REVERT: G 118 ASP cc_start: 0.7809 (m-30) cc_final: 0.7545 (m-30) REVERT: G 179 ASP cc_start: 0.8126 (t0) cc_final: 0.7891 (t0) REVERT: G 184 MET cc_start: 0.8337 (mmm) cc_final: 0.7988 (mmm) REVERT: G 248 TYR cc_start: 0.8029 (m-10) cc_final: 0.7561 (m-10) REVERT: G 274 CYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7243 (m) REVERT: G 275 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7461 (ptt180) REVERT: G 285 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.6938 (t80) REVERT: G 293 SER cc_start: 0.8241 (m) cc_final: 0.7734 (p) REVERT: G 380 LYS cc_start: 0.8446 (mmmm) cc_final: 0.8204 (mmmm) REVERT: G 399 ARG cc_start: 0.7925 (tpp80) cc_final: 0.6975 (tpp80) REVERT: G 403 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: G 448 ASP cc_start: 0.7688 (t0) cc_final: 0.7443 (t0) REVERT: H 71 ARG cc_start: 0.8053 (mtm-85) cc_final: 0.7378 (ptp90) REVERT: H 76 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8129 (mtt90) REVERT: H 85 ARG cc_start: 0.7509 (mmp80) cc_final: 0.7249 (mmp80) REVERT: H 115 LYS cc_start: 0.8816 (mptp) cc_final: 0.8332 (mptp) REVERT: H 171 ARG cc_start: 0.7229 (mtm-85) cc_final: 0.6944 (mtm-85) REVERT: H 184 MET cc_start: 0.8435 (mmm) cc_final: 0.8088 (tmm) REVERT: H 219 GLU cc_start: 0.5194 (OUTLIER) cc_final: 0.4765 (pp20) REVERT: H 291 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8396 (p) REVERT: H 313 LEU cc_start: 0.8293 (mt) cc_final: 0.7936 (mm) REVERT: H 396 LYS cc_start: 0.8279 (tppt) cc_final: 0.8057 (mmtm) REVERT: H 399 ARG cc_start: 0.7783 (tpp80) cc_final: 0.7376 (tpp-160) REVERT: H 400 LYS cc_start: 0.8113 (tppt) cc_final: 0.7803 (tppt) REVERT: H 436 ASP cc_start: 0.8349 (t0) cc_final: 0.8081 (t70) REVERT: H 447 PHE cc_start: 0.8563 (m-80) cc_final: 0.8143 (m-80) REVERT: I 5 TYR cc_start: 0.8144 (m-10) cc_final: 0.7696 (m-10) REVERT: I 16 LYS cc_start: 0.8471 (mppt) cc_final: 0.8226 (mtpt) REVERT: I 30 ARG cc_start: 0.6513 (ptp90) cc_final: 0.5687 (ptp90) REVERT: I 63 ASP cc_start: 0.7888 (t0) cc_final: 0.7144 (t0) REVERT: I 72 MET cc_start: 0.7899 (tmm) cc_final: 0.7599 (tmm) REVERT: I 106 LYS cc_start: 0.7987 (mtmm) cc_final: 0.7780 (mtmm) REVERT: I 115 LYS cc_start: 0.8784 (mptp) cc_final: 0.8262 (mptp) REVERT: I 184 MET cc_start: 0.8552 (tpp) cc_final: 0.8343 (tpp) REVERT: I 204 VAL cc_start: 0.8832 (m) cc_final: 0.8606 (t) REVERT: I 232 LYS cc_start: 0.8083 (ptmt) cc_final: 0.7728 (ptmt) REVERT: I 285 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.7443 (t80) REVERT: I 319 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7119 (m-30) REVERT: I 357 LYS cc_start: 0.8669 (ttmm) cc_final: 0.8451 (ttmt) REVERT: I 400 LYS cc_start: 0.8150 (tppt) cc_final: 0.7746 (tppt) REVERT: I 403 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: I 405 GLU cc_start: 0.7829 (mp0) cc_final: 0.7273 (mp0) REVERT: I 436 ASP cc_start: 0.8223 (t0) cc_final: 0.7896 (t0) REVERT: I 438 GLN cc_start: 0.8098 (mp10) cc_final: 0.7350 (mt0) REVERT: J 30 ARG cc_start: 0.7500 (ptp-170) cc_final: 0.7263 (ptp-170) REVERT: J 41 ARG cc_start: 0.7844 (tpp-160) cc_final: 0.7464 (tpp-160) REVERT: J 92 ARG cc_start: 0.7573 (mmp80) cc_final: 0.7130 (mmp80) REVERT: J 99 LYS cc_start: 0.8978 (mmmm) cc_final: 0.8682 (mmmm) REVERT: J 111 ASN cc_start: 0.8585 (t0) cc_final: 0.8232 (t0) REVERT: J 115 LYS cc_start: 0.8799 (mptp) cc_final: 0.8293 (mptp) REVERT: J 171 ARG cc_start: 0.7612 (mtm-85) cc_final: 0.7031 (mtm-85) REVERT: J 183 PHE cc_start: 0.8630 (m-80) cc_final: 0.8282 (m-80) REVERT: J 240 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7999 (mt) REVERT: J 248 TYR cc_start: 0.8047 (m-10) cc_final: 0.7622 (m-10) REVERT: J 285 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.6730 (t80) REVERT: J 288 LYS cc_start: 0.8671 (mttm) cc_final: 0.8448 (mttp) REVERT: J 378 THR cc_start: 0.8054 (m) cc_final: 0.7828 (p) REVERT: J 383 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8142 (ppp) REVERT: J 400 LYS cc_start: 0.8322 (tppt) cc_final: 0.7598 (tmtt) REVERT: J 403 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: J 426 GLN cc_start: 0.5794 (mt0) cc_final: 0.4885 (mt0) REVERT: J 446 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7510 (mm-30) REVERT: K 24 MET cc_start: 0.8424 (pmm) cc_final: 0.8084 (pmm) REVERT: K 63 ASP cc_start: 0.7402 (t0) cc_final: 0.7026 (t0) REVERT: K 76 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8091 (mtt90) REVERT: K 88 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6650 (tt0) REVERT: K 115 LYS cc_start: 0.8779 (mptp) cc_final: 0.8380 (mptp) REVERT: K 171 ARG cc_start: 0.7179 (mtm-85) cc_final: 0.6902 (mtm-85) REVERT: K 195 TYR cc_start: 0.8482 (m-80) cc_final: 0.8281 (m-80) REVERT: K 201 ASP cc_start: 0.7801 (t0) cc_final: 0.7583 (t0) REVERT: K 313 LEU cc_start: 0.8368 (mt) cc_final: 0.8009 (mm) REVERT: K 325 ARG cc_start: 0.7266 (ttm110) cc_final: 0.6920 (ttm170) REVERT: K 433 LYS cc_start: 0.8461 (mmmt) cc_final: 0.8247 (mmtt) REVERT: K 441 GLN cc_start: 0.7516 (mt0) cc_final: 0.7306 (mt0) REVERT: L 71 ARG cc_start: 0.7914 (mtm-85) cc_final: 0.7377 (ptp-110) REVERT: L 92 ARG cc_start: 0.7721 (mmp80) cc_final: 0.7317 (mmp80) REVERT: L 106 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7945 (mtmm) REVERT: L 115 LYS cc_start: 0.8841 (mptp) cc_final: 0.8362 (mptp) REVERT: L 168 LYS cc_start: 0.8880 (mtmt) cc_final: 0.8441 (mtpp) REVERT: L 171 ARG cc_start: 0.6937 (mtm-85) cc_final: 0.6506 (mtm-85) REVERT: L 184 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.8046 (tpp) REVERT: L 195 TYR cc_start: 0.8445 (m-80) cc_final: 0.8177 (m-80) REVERT: L 202 GLU cc_start: 0.8123 (tp30) cc_final: 0.7826 (tp30) REVERT: L 238 ARG cc_start: 0.7719 (ttm110) cc_final: 0.7356 (mtm110) REVERT: L 266 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8379 (mt) REVERT: L 271 SER cc_start: 0.7560 (p) cc_final: 0.7266 (m) REVERT: L 283 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: L 403 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: L 427 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6826 (mmtm) REVERT: L 434 ARG cc_start: 0.8456 (mpp80) cc_final: 0.7296 (tpp80) REVERT: L 446 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7320 (mm-30) outliers start: 238 outliers final: 150 residues processed: 1965 average time/residue: 0.2812 time to fit residues: 855.3969 Evaluate side-chains 2005 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 1824 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 398 CYS Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 238 ARG Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 425 LYS Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 275 ARG Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 411 ARG Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 342 MET Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 403 GLU Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 238 ARG Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 314 MET Chi-restraints excluded: chain I residue 319 ASP Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 403 GLU Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 236 CYS Chi-restraints excluded: chain J residue 240 LEU Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 383 MET Chi-restraints excluded: chain J residue 403 GLU Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 283 GLU Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 342 MET Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain K residue 408 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 53 GLN Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 120 GLN Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain L residue 194 SER Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 283 GLU Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain L residue 342 MET Chi-restraints excluded: chain L residue 348 THR Chi-restraints excluded: chain L residue 358 LEU Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 405 GLU Chi-restraints excluded: chain L residue 426 GLN Chi-restraints excluded: chain L residue 427 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 313 optimal weight: 0.5980 chunk 455 optimal weight: 0.9980 chunk 265 optimal weight: 1.9990 chunk 226 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 410 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 405 optimal weight: 0.8980 chunk 460 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.134248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.118078 restraints weight = 64842.567| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.81 r_work: 0.3426 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 42540 Z= 0.133 Angle : 0.673 14.380 57612 Z= 0.320 Chirality : 0.043 0.145 6564 Planarity : 0.005 0.090 7248 Dihedral : 14.116 175.773 6351 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.77 % Allowed : 30.50 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.37 % 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: -1.07 (0.11), residues: 5148 helix: 1.37 (0.14), residues: 1608 sheet: -1.22 (0.13), residues: 1296 loop : -1.96 (0.11), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 289 TYR 0.017 0.002 TYR K 174 PHE 0.030 0.002 PHE A 264 TRP 0.017 0.002 TRP C 258 HIS 0.003 0.001 HIS J 308 Details of bonding type rmsd covalent geometry : bond 0.00314 (42480) covalent geometry : angle 0.67263 (57612) hydrogen bonds : bond 0.02950 ( 1577) hydrogen bonds : angle 4.47831 ( 4476) metal coordination : bond 0.00545 ( 36) Misc. bond : bond 0.00044 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2089 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 255 poor density : 1834 time to evaluate : 1.570 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.6103 (ptt-90) cc_final: 0.5860 (ptt-90) REVERT: A 76 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8273 (mtt90) REVERT: A 88 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6445 (tm-30) REVERT: A 92 ARG cc_start: 0.7557 (mmp80) cc_final: 0.7118 (mmp80) REVERT: A 111 ASN cc_start: 0.8565 (t0) cc_final: 0.8275 (t0) REVERT: A 115 LYS cc_start: 0.8798 (mptp) cc_final: 0.8206 (mptp) REVERT: A 133 PHE cc_start: 0.7868 (t80) cc_final: 0.7660 (t80) REVERT: A 135 LEU cc_start: 0.8596 (mt) cc_final: 0.8208 (mm) REVERT: A 171 ARG cc_start: 0.7232 (mtm-85) cc_final: 0.7017 (mtm-85) REVERT: A 188 MET cc_start: 0.8302 (mmt) cc_final: 0.7792 (mmt) REVERT: A 214 SER cc_start: 0.8469 (t) cc_final: 0.7925 (p) REVERT: A 228 MET cc_start: 0.1051 (tpp) cc_final: 0.0682 (tpp) REVERT: A 242 SER cc_start: 0.8057 (t) cc_final: 0.7619 (p) REVERT: A 243 VAL cc_start: 0.7916 (t) cc_final: 0.7626 (t) REVERT: A 248 TYR cc_start: 0.8167 (m-10) cc_final: 0.7854 (m-10) REVERT: A 258 TRP cc_start: 0.8601 (m100) cc_final: 0.7517 (m100) REVERT: A 267 LYS cc_start: 0.8358 (mtmt) cc_final: 0.8141 (mtmt) REVERT: A 278 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8579 (p) REVERT: A 285 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.7051 (t80) REVERT: A 325 ARG cc_start: 0.7911 (ptp-110) cc_final: 0.7604 (ttm-80) REVERT: A 396 LYS cc_start: 0.8502 (mmmm) cc_final: 0.7881 (mmtm) REVERT: A 399 ARG cc_start: 0.8025 (tpp80) cc_final: 0.7270 (tpp80) REVERT: A 403 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7221 (mt-10) REVERT: A 443 VAL cc_start: 0.8593 (t) cc_final: 0.8296 (p) REVERT: B 63 ASP cc_start: 0.7479 (t0) cc_final: 0.7255 (t0) REVERT: B 115 LYS cc_start: 0.8729 (mptp) cc_final: 0.8175 (mptp) REVERT: B 184 MET cc_start: 0.8473 (mmm) cc_final: 0.7914 (mmm) REVERT: B 236 CYS cc_start: 0.8195 (p) cc_final: 0.7925 (p) REVERT: B 245 SER cc_start: 0.8587 (p) cc_final: 0.8294 (t) REVERT: B 313 LEU cc_start: 0.8318 (mt) cc_final: 0.7979 (mm) REVERT: B 396 LYS cc_start: 0.8423 (mmmm) cc_final: 0.7829 (mmtm) REVERT: B 426 GLN cc_start: 0.6457 (mt0) cc_final: 0.6215 (mt0) REVERT: B 436 ASP cc_start: 0.8338 (t0) cc_final: 0.7889 (t70) REVERT: C 16 LYS cc_start: 0.8521 (mptt) cc_final: 0.8142 (mppt) REVERT: C 51 ILE cc_start: 0.8370 (mm) cc_final: 0.8114 (mm) REVERT: C 92 ARG cc_start: 0.7892 (mmp80) cc_final: 0.7449 (mmp80) REVERT: C 115 LYS cc_start: 0.8725 (mptp) cc_final: 0.8361 (mptp) REVERT: C 135 LEU cc_start: 0.8615 (mt) cc_final: 0.8248 (mm) REVERT: C 144 ARG cc_start: 0.8315 (ttm110) cc_final: 0.8079 (ttm110) REVERT: C 195 TYR cc_start: 0.8324 (m-80) cc_final: 0.8066 (m-80) REVERT: C 219 GLU cc_start: 0.5631 (OUTLIER) cc_final: 0.5350 (pp20) REVERT: C 403 GLU cc_start: 0.7662 (mp0) cc_final: 0.7381 (mp0) REVERT: D 88 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6823 (tm-30) REVERT: D 115 LYS cc_start: 0.8777 (mptp) cc_final: 0.8363 (mptp) REVERT: D 163 TYR cc_start: 0.8551 (t80) cc_final: 0.8268 (t80) REVERT: D 165 GLN cc_start: 0.8061 (mt0) cc_final: 0.7859 (mt0) REVERT: D 168 LYS cc_start: 0.8915 (mtmt) cc_final: 0.8435 (mtpp) REVERT: D 171 ARG cc_start: 0.7345 (mtm-85) cc_final: 0.6885 (mtm-85) REVERT: D 197 THR cc_start: 0.8347 (p) cc_final: 0.8015 (t) REVERT: D 234 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7385 (mm-30) REVERT: D 274 CYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7538 (m) REVERT: D 285 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7358 (t80) REVERT: D 345 ILE cc_start: 0.9011 (mm) cc_final: 0.8778 (mm) REVERT: D 448 ASP cc_start: 0.7714 (t0) cc_final: 0.7460 (t0) REVERT: E 16 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8069 (mmmt) REVERT: E 20 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.8010 (mtm-85) REVERT: E 24 MET cc_start: 0.8660 (pmm) cc_final: 0.8304 (pmm) REVERT: E 71 ARG cc_start: 0.8039 (mtm-85) cc_final: 0.7821 (mtm-85) REVERT: E 115 LYS cc_start: 0.8779 (mptp) cc_final: 0.8219 (mptp) REVERT: E 144 ARG cc_start: 0.8117 (ttm110) cc_final: 0.7762 (mmm-85) REVERT: E 150 TYR cc_start: 0.8551 (m-80) cc_final: 0.8192 (m-80) REVERT: E 197 THR cc_start: 0.8309 (p) cc_final: 0.7938 (t) REVERT: E 275 ARG cc_start: 0.7858 (ttt180) cc_final: 0.7508 (ttp80) REVERT: E 291 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8481 (p) REVERT: E 297 TYR cc_start: 0.7955 (m-10) cc_final: 0.7751 (m-10) REVERT: E 396 LYS cc_start: 0.8432 (tppt) cc_final: 0.8102 (mmtm) REVERT: E 399 ARG cc_start: 0.7847 (tpp80) cc_final: 0.7525 (tpp80) REVERT: E 405 GLU cc_start: 0.7403 (tp30) cc_final: 0.6989 (tp30) REVERT: E 436 ASP cc_start: 0.8353 (t0) cc_final: 0.7680 (t70) REVERT: F 30 ARG cc_start: 0.7269 (ptp-110) cc_final: 0.6701 (ttm110) REVERT: F 43 PHE cc_start: 0.8811 (t80) cc_final: 0.8327 (t80) REVERT: F 111 ASN cc_start: 0.8590 (t0) cc_final: 0.8334 (t0) REVERT: F 115 LYS cc_start: 0.8752 (mptp) cc_final: 0.8159 (mptp) REVERT: F 135 LEU cc_start: 0.8453 (mt) cc_final: 0.8218 (mm) REVERT: F 144 ARG cc_start: 0.8102 (ttm110) cc_final: 0.7840 (ttm110) REVERT: F 184 MET cc_start: 0.8359 (tpp) cc_final: 0.7835 (tpp) REVERT: F 258 TRP cc_start: 0.8540 (m100) cc_final: 0.7463 (m100) REVERT: F 275 ARG cc_start: 0.7883 (ttt90) cc_final: 0.7659 (ttt90) REVERT: F 285 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7240 (t80) REVERT: F 433 LYS cc_start: 0.8456 (mmmt) cc_final: 0.8225 (mmmt) REVERT: F 441 GLN cc_start: 0.7736 (mt0) cc_final: 0.7487 (mt0) REVERT: G 16 LYS cc_start: 0.8387 (mmtt) cc_final: 0.7940 (mmtt) REVERT: G 30 ARG cc_start: 0.6612 (pmt170) cc_final: 0.6205 (pmt170) REVERT: G 43 PHE cc_start: 0.8847 (t80) cc_final: 0.8264 (t80) REVERT: G 76 ARG cc_start: 0.8176 (mtt90) cc_final: 0.7854 (mtt90) REVERT: G 88 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6512 (tm-30) REVERT: G 92 ARG cc_start: 0.7712 (mmp80) cc_final: 0.7089 (mmp80) REVERT: G 111 ASN cc_start: 0.8678 (t0) cc_final: 0.8282 (t0) REVERT: G 115 LYS cc_start: 0.8813 (mptp) cc_final: 0.8291 (mptp) REVERT: G 150 TYR cc_start: 0.8802 (m-80) cc_final: 0.8342 (m-80) REVERT: G 184 MET cc_start: 0.8329 (mmm) cc_final: 0.7934 (mmm) REVERT: G 248 TYR cc_start: 0.8088 (m-10) cc_final: 0.7643 (m-10) REVERT: G 274 CYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7576 (m) REVERT: G 285 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.6795 (t80) REVERT: G 293 SER cc_start: 0.8220 (m) cc_final: 0.7721 (p) REVERT: G 397 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7952 (mm-30) REVERT: G 406 LYS cc_start: 0.8886 (mmmm) cc_final: 0.8552 (mmtp) REVERT: G 433 LYS cc_start: 0.8420 (mmmt) cc_final: 0.8121 (mmtt) REVERT: G 448 ASP cc_start: 0.7663 (t0) cc_final: 0.7384 (t0) REVERT: H 56 ASP cc_start: 0.7634 (t0) cc_final: 0.7345 (t70) REVERT: H 76 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7614 (mtt90) REVERT: H 88 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6729 (tm-30) REVERT: H 111 ASN cc_start: 0.8609 (t0) cc_final: 0.8176 (t0) REVERT: H 115 LYS cc_start: 0.8773 (mptp) cc_final: 0.8137 (mptp) REVERT: H 171 ARG cc_start: 0.7209 (mtm-85) cc_final: 0.6915 (mtm-85) REVERT: H 176 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8247 (m) REVERT: H 219 GLU cc_start: 0.5009 (OUTLIER) cc_final: 0.4601 (pp20) REVERT: H 258 TRP cc_start: 0.8431 (m100) cc_final: 0.8181 (m100) REVERT: H 273 THR cc_start: 0.8472 (p) cc_final: 0.8269 (p) REVERT: H 291 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8398 (p) REVERT: H 313 LEU cc_start: 0.8290 (mt) cc_final: 0.7948 (mm) REVERT: H 396 LYS cc_start: 0.8287 (tppt) cc_final: 0.8036 (mmtm) REVERT: H 399 ARG cc_start: 0.7709 (tpp80) cc_final: 0.7310 (tpp-160) REVERT: H 400 LYS cc_start: 0.8115 (tppt) cc_final: 0.7753 (tppt) REVERT: H 405 GLU cc_start: 0.7600 (tp30) cc_final: 0.7221 (tp30) REVERT: H 436 ASP cc_start: 0.8337 (t0) cc_final: 0.8066 (t70) REVERT: H 447 PHE cc_start: 0.8549 (m-80) cc_final: 0.8162 (m-80) REVERT: I 16 LYS cc_start: 0.8481 (mppt) cc_final: 0.8214 (mtpt) REVERT: I 22 TYR cc_start: 0.8358 (m-80) cc_final: 0.7995 (m-80) REVERT: I 30 ARG cc_start: 0.6499 (ptp90) cc_final: 0.5767 (ptp90) REVERT: I 72 MET cc_start: 0.7798 (tmm) cc_final: 0.7459 (tmm) REVERT: I 106 LYS cc_start: 0.8029 (mtmm) cc_final: 0.7755 (mtmm) REVERT: I 115 LYS cc_start: 0.8773 (mptp) cc_final: 0.8184 (mptp) REVERT: I 184 MET cc_start: 0.8592 (tpp) cc_final: 0.8158 (tpp) REVERT: I 204 VAL cc_start: 0.8836 (m) cc_final: 0.8612 (t) REVERT: I 285 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.7325 (t80) REVERT: I 319 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7143 (m-30) REVERT: I 357 LYS cc_start: 0.8667 (ttmm) cc_final: 0.8393 (ttmt) REVERT: I 400 LYS cc_start: 0.8162 (tppt) cc_final: 0.7955 (tppt) REVERT: I 405 GLU cc_start: 0.7853 (mp0) cc_final: 0.7336 (mp0) REVERT: I 438 GLN cc_start: 0.8095 (mp10) cc_final: 0.7300 (mt0) REVERT: J 28 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7368 (mm-30) REVERT: J 41 ARG cc_start: 0.7856 (tpp-160) cc_final: 0.7372 (tpp-160) REVERT: J 76 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8225 (mtt90) REVERT: J 88 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6144 (tm-30) REVERT: J 92 ARG cc_start: 0.7529 (mmp80) cc_final: 0.6883 (mmp80) REVERT: J 99 LYS cc_start: 0.8974 (mmmm) cc_final: 0.8676 (mmmm) REVERT: J 111 ASN cc_start: 0.8603 (t0) cc_final: 0.8157 (t0) REVERT: J 115 LYS cc_start: 0.8829 (mptp) cc_final: 0.8227 (mptp) REVERT: J 140 SER cc_start: 0.8035 (p) cc_final: 0.7804 (p) REVERT: J 171 ARG cc_start: 0.7601 (mtm-85) cc_final: 0.7041 (mtm-85) REVERT: J 183 PHE cc_start: 0.8610 (m-80) cc_final: 0.8242 (m-80) REVERT: J 240 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7965 (mt) REVERT: J 274 CYS cc_start: 0.8007 (m) cc_final: 0.7507 (m) REVERT: J 278 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8498 (p) REVERT: J 285 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.6702 (t80) REVERT: J 288 LYS cc_start: 0.8675 (mttm) cc_final: 0.8464 (mttp) REVERT: J 380 LYS cc_start: 0.8481 (mmmm) cc_final: 0.8203 (mmmm) REVERT: J 383 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7992 (ppp) REVERT: J 400 LYS cc_start: 0.8344 (tppt) cc_final: 0.7794 (tmtt) REVERT: J 403 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: J 426 GLN cc_start: 0.5938 (mt0) cc_final: 0.5678 (mt0) REVERT: J 446 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7573 (mm-30) REVERT: K 30 ARG cc_start: 0.7300 (mtm110) cc_final: 0.6964 (ttm110) REVERT: K 63 ASP cc_start: 0.7412 (t0) cc_final: 0.7107 (t0) REVERT: K 76 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8070 (mtt90) REVERT: K 88 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6749 (tt0) REVERT: K 115 LYS cc_start: 0.8780 (mptp) cc_final: 0.8176 (mptp) REVERT: K 171 ARG cc_start: 0.7170 (mtm-85) cc_final: 0.6856 (mtm-85) REVERT: K 224 LYS cc_start: 0.1451 (OUTLIER) cc_final: 0.0747 (pttm) REVERT: K 274 CYS cc_start: 0.8053 (m) cc_final: 0.7670 (m) REVERT: K 313 LEU cc_start: 0.8375 (mt) cc_final: 0.8031 (mm) REVERT: K 434 ARG cc_start: 0.8650 (mpp80) cc_final: 0.7331 (tpp80) REVERT: K 441 GLN cc_start: 0.7502 (mt0) cc_final: 0.7273 (mt0) REVERT: L 20 ARG cc_start: 0.8033 (ttm-80) cc_final: 0.7707 (mtm-85) REVERT: L 71 ARG cc_start: 0.7856 (mtm-85) cc_final: 0.7360 (ptp-110) REVERT: L 92 ARG cc_start: 0.7726 (mmp80) cc_final: 0.7306 (mmp80) REVERT: L 106 LYS cc_start: 0.8190 (mtmm) cc_final: 0.7901 (mtmm) REVERT: L 115 LYS cc_start: 0.8887 (mptp) cc_final: 0.8372 (mptp) REVERT: L 168 LYS cc_start: 0.8889 (mtmt) cc_final: 0.8446 (mtpp) REVERT: L 171 ARG cc_start: 0.6920 (mtm-85) cc_final: 0.6427 (mtm-85) REVERT: L 195 TYR cc_start: 0.8417 (m-80) cc_final: 0.8116 (m-80) REVERT: L 202 GLU cc_start: 0.8114 (tp30) cc_final: 0.7590 (tp30) REVERT: L 238 ARG cc_start: 0.7703 (ttm110) cc_final: 0.7445 (mtm110) REVERT: L 266 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8394 (mt) REVERT: L 271 SER cc_start: 0.7572 (p) cc_final: 0.7272 (m) REVERT: L 283 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: L 427 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6883 (mmtp) REVERT: L 446 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7296 (mm-30) outliers start: 255 outliers final: 159 residues processed: 1937 average time/residue: 0.2844 time to fit residues: 853.1920 Evaluate side-chains 2019 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 1827 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 236 CYS Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 292 MET Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 398 CYS Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 238 ARG Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 411 ARG Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain H residue 19 GLN Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 292 MET Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain H residue 342 MET Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 403 GLU Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain I residue 20 ARG Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 238 ARG Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 314 MET Chi-restraints excluded: chain I residue 319 ASP Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 76 ARG Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 236 CYS Chi-restraints excluded: chain J residue 240 LEU Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 383 MET Chi-restraints excluded: chain J residue 403 GLU Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 224 LYS Chi-restraints excluded: chain K residue 283 GLU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 342 MET Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 398 CYS Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain K residue 408 LEU Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 53 GLN Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 194 SER Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 283 GLU Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain L residue 342 MET Chi-restraints excluded: chain L residue 348 THR Chi-restraints excluded: chain L residue 358 LEU Chi-restraints excluded: chain L residue 405 GLU Chi-restraints excluded: chain L residue 426 GLN Chi-restraints excluded: chain L residue 427 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 147 optimal weight: 0.0670 chunk 104 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 361 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 451 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 228 optimal weight: 6.9990 chunk 334 optimal weight: 6.9990 overall best weight: 2.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 GLN L 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.131772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.115615 restraints weight = 64617.268| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.76 r_work: 0.3343 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 42540 Z= 0.278 Angle : 0.742 14.864 57612 Z= 0.359 Chirality : 0.047 0.178 6564 Planarity : 0.005 0.083 7248 Dihedral : 13.998 178.249 6348 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 6.39 % Allowed : 30.23 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.37 % 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: -1.27 (0.11), residues: 5148 helix: 1.10 (0.13), residues: 1680 sheet: -1.29 (0.14), residues: 1140 loop : -2.11 (0.11), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 30 TYR 0.029 0.002 TYR G 5 PHE 0.034 0.002 PHE H 264 TRP 0.015 0.003 TRP C 258 HIS 0.004 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00609 (42480) covalent geometry : angle 0.74196 (57612) hydrogen bonds : bond 0.03633 ( 1577) hydrogen bonds : angle 4.64206 ( 4476) metal coordination : bond 0.00618 ( 36) Misc. bond : bond 0.00125 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2237 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 282 poor density : 1955 time to evaluate : 1.555 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: 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: 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 41 ARG cc_start: 0.8045 (tpp-160) cc_final: 0.7454 (tpp-160) REVERT: A 52 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7466 (mt-10) REVERT: A 63 ASP cc_start: 0.7651 (t0) cc_final: 0.7410 (t0) REVERT: A 85 ARG cc_start: 0.7682 (mmp80) cc_final: 0.7423 (mmp80) REVERT: A 88 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6530 (tm-30) REVERT: A 92 ARG cc_start: 0.7609 (mmp80) cc_final: 0.7187 (mmp80) REVERT: A 133 PHE cc_start: 0.7811 (t80) cc_final: 0.7566 (t80) REVERT: A 135 LEU cc_start: 0.8669 (mt) cc_final: 0.8320 (mt) REVERT: A 165 GLN cc_start: 0.8388 (mt0) cc_final: 0.8173 (mt0) REVERT: A 171 ARG cc_start: 0.7375 (mtm-85) cc_final: 0.7006 (mtm-85) REVERT: A 176 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8246 (t) REVERT: A 188 MET cc_start: 0.8428 (mmt) cc_final: 0.7943 (mmt) REVERT: A 228 MET cc_start: 0.1080 (tpp) cc_final: 0.0751 (tpp) REVERT: A 234 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7491 (mm-30) REVERT: A 242 SER cc_start: 0.8215 (t) cc_final: 0.7647 (p) REVERT: A 243 VAL cc_start: 0.8209 (t) cc_final: 0.7908 (t) REVERT: A 247 LEU cc_start: 0.8478 (tp) cc_final: 0.8106 (tt) REVERT: A 248 TYR cc_start: 0.8186 (m-10) cc_final: 0.7782 (m-10) REVERT: A 267 LYS cc_start: 0.8308 (mtmt) cc_final: 0.7992 (mtmt) REVERT: A 278 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8624 (p) REVERT: A 285 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.6879 (t80) REVERT: A 349 GLU cc_start: 0.7322 (tt0) cc_final: 0.6901 (tt0) REVERT: A 362 LEU cc_start: 0.8807 (mm) cc_final: 0.8583 (mp) REVERT: A 396 LYS cc_start: 0.8537 (mmmm) cc_final: 0.8101 (tppt) REVERT: A 399 ARG cc_start: 0.8136 (tpp80) cc_final: 0.7836 (tpp80) REVERT: A 403 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7326 (mt-10) REVERT: A 443 VAL cc_start: 0.8617 (t) cc_final: 0.8323 (p) REVERT: B 24 MET cc_start: 0.8516 (pmm) cc_final: 0.8174 (pmm) REVERT: B 41 ARG cc_start: 0.8038 (tpp-160) cc_final: 0.7523 (tpp-160) REVERT: B 63 ASP cc_start: 0.7682 (t0) cc_final: 0.7407 (t0) REVERT: B 71 ARG cc_start: 0.8327 (mtm-85) cc_final: 0.8123 (mtm-85) REVERT: B 111 ASN cc_start: 0.8663 (t0) cc_final: 0.8243 (t0) REVERT: B 115 LYS cc_start: 0.8788 (mptp) cc_final: 0.8100 (mptp) REVERT: B 184 MET cc_start: 0.8572 (mmm) cc_final: 0.7900 (tpp) REVERT: B 219 GLU cc_start: 0.6284 (OUTLIER) cc_final: 0.5951 (pp20) REVERT: B 234 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7498 (mm-30) REVERT: B 245 SER cc_start: 0.8746 (p) cc_final: 0.8480 (t) REVERT: B 313 LEU cc_start: 0.8362 (mt) cc_final: 0.8024 (mm) REVERT: B 396 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7843 (mmtm) REVERT: C 16 LYS cc_start: 0.8549 (mptt) cc_final: 0.8162 (mppt) REVERT: C 24 MET cc_start: 0.8667 (pmm) cc_final: 0.8088 (pmm) REVERT: C 115 LYS cc_start: 0.8736 (mptp) cc_final: 0.8284 (mptp) REVERT: C 135 LEU cc_start: 0.8646 (mt) cc_final: 0.8293 (mm) REVERT: C 144 ARG cc_start: 0.8365 (ttm110) cc_final: 0.8120 (ttm110) REVERT: C 171 ARG cc_start: 0.7370 (mtm-85) cc_final: 0.6777 (mtm-85) REVERT: C 179 ASP cc_start: 0.8115 (t0) cc_final: 0.7859 (t0) REVERT: C 184 MET cc_start: 0.8602 (mmm) cc_final: 0.8179 (mmm) REVERT: C 258 TRP cc_start: 0.8538 (m100) cc_final: 0.7564 (m100) REVERT: C 285 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7288 (t80) REVERT: C 297 TYR cc_start: 0.8143 (m-80) cc_final: 0.7926 (m-80) REVERT: C 325 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7753 (ttm-80) REVERT: C 383 MET cc_start: 0.8506 (ttp) cc_final: 0.8267 (ttm) REVERT: C 399 ARG cc_start: 0.8097 (tpp80) cc_final: 0.7506 (tpp80) REVERT: C 403 GLU cc_start: 0.7704 (mp0) cc_final: 0.7351 (mp0) REVERT: C 427 LYS cc_start: 0.7916 (mmmm) cc_final: 0.7471 (mmmm) REVERT: C 436 ASP cc_start: 0.8366 (t0) cc_final: 0.7917 (t0) REVERT: D 28 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7445 (mm-30) REVERT: D 76 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8206 (mtt90) REVERT: D 88 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6965 (tm-30) REVERT: D 115 LYS cc_start: 0.8805 (mptp) cc_final: 0.8317 (mptp) REVERT: D 163 TYR cc_start: 0.8671 (t80) cc_final: 0.8369 (t80) REVERT: D 165 GLN cc_start: 0.8122 (mt0) cc_final: 0.7862 (mt0) REVERT: D 171 ARG cc_start: 0.7527 (mtm-85) cc_final: 0.7073 (mtm-85) REVERT: D 179 ASP cc_start: 0.8037 (t0) cc_final: 0.7665 (t0) REVERT: D 184 MET cc_start: 0.8550 (mmm) cc_final: 0.8052 (tpp) REVERT: D 197 THR cc_start: 0.8388 (p) cc_final: 0.8137 (t) REVERT: D 234 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7510 (mm-30) REVERT: D 243 VAL cc_start: 0.8376 (m) cc_final: 0.8099 (p) REVERT: D 274 CYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7831 (m) REVERT: D 285 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7442 (t80) REVERT: D 324 GLU cc_start: 0.7285 (tt0) cc_final: 0.6947 (tt0) REVERT: D 325 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7849 (ttm170) REVERT: D 426 GLN cc_start: 0.7447 (mt0) cc_final: 0.7156 (mt0) REVERT: D 448 ASP cc_start: 0.7730 (t0) cc_final: 0.7485 (t0) REVERT: E 16 LYS cc_start: 0.8489 (mmtt) cc_final: 0.8119 (mmmt) REVERT: E 20 ARG cc_start: 0.8244 (ttm-80) cc_final: 0.7997 (mtm-85) REVERT: E 24 MET cc_start: 0.8693 (pmm) cc_final: 0.8471 (pmm) REVERT: E 63 ASP cc_start: 0.7593 (t0) cc_final: 0.7148 (t0) REVERT: E 71 ARG cc_start: 0.8165 (mtm-85) cc_final: 0.7789 (mtm-85) REVERT: E 115 LYS cc_start: 0.8781 (mptp) cc_final: 0.8206 (mptp) REVERT: E 144 ARG cc_start: 0.8224 (ttm110) cc_final: 0.7813 (mmm-85) REVERT: E 151 GLN cc_start: 0.8217 (tp40) cc_final: 0.7990 (tp40) REVERT: E 171 ARG cc_start: 0.7555 (mtm-85) cc_final: 0.7026 (mtm-85) REVERT: E 180 THR cc_start: 0.8292 (m) cc_final: 0.7992 (p) REVERT: E 197 THR cc_start: 0.8415 (p) cc_final: 0.8095 (t) REVERT: E 236 CYS cc_start: 0.8270 (p) cc_final: 0.8018 (p) REVERT: E 243 VAL cc_start: 0.8354 (m) cc_final: 0.8076 (p) REVERT: E 275 ARG cc_start: 0.7840 (ttt180) cc_final: 0.7495 (ttp80) REVERT: E 297 TYR cc_start: 0.8113 (m-10) cc_final: 0.7617 (m-10) REVERT: E 399 ARG cc_start: 0.7914 (tpp80) cc_final: 0.7570 (tpp80) REVERT: E 436 ASP cc_start: 0.8466 (t0) cc_final: 0.7673 (t70) REVERT: E 447 PHE cc_start: 0.8506 (m-80) cc_final: 0.8094 (m-10) REVERT: F 92 ARG cc_start: 0.7912 (mmp80) cc_final: 0.7478 (mmp80) REVERT: F 115 LYS cc_start: 0.8775 (mptp) cc_final: 0.8208 (mptp) REVERT: F 135 LEU cc_start: 0.8621 (mt) cc_final: 0.8407 (mt) REVERT: F 184 MET cc_start: 0.8621 (tpp) cc_final: 0.8232 (tpp) REVERT: F 188 MET cc_start: 0.8299 (mmt) cc_final: 0.8001 (mmt) REVERT: F 232 LYS cc_start: 0.8189 (ptmt) cc_final: 0.7759 (ptmt) REVERT: F 346 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8359 (tt) REVERT: F 405 GLU cc_start: 0.7618 (tp30) cc_final: 0.7413 (tp30) REVERT: F 436 ASP cc_start: 0.8241 (t0) cc_final: 0.8027 (t0) REVERT: F 438 GLN cc_start: 0.8057 (mp10) cc_final: 0.7454 (mt0) REVERT: F 441 GLN cc_start: 0.7733 (mt0) cc_final: 0.7442 (mt0) REVERT: G 16 LYS cc_start: 0.8398 (mmtt) cc_final: 0.7977 (mmtt) REVERT: G 41 ARG cc_start: 0.8010 (tpp-160) cc_final: 0.7409 (tpp-160) REVERT: G 76 ARG cc_start: 0.8280 (mtt90) cc_final: 0.7990 (mtt90) REVERT: G 88 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6595 (tm-30) REVERT: G 92 ARG cc_start: 0.7747 (mmp80) cc_final: 0.7057 (mmp80) REVERT: G 106 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7897 (mtmm) REVERT: G 111 ASN cc_start: 0.8743 (t0) cc_final: 0.8110 (t0) REVERT: G 115 LYS cc_start: 0.8823 (mptp) cc_final: 0.8255 (mptp) REVERT: G 135 LEU cc_start: 0.8822 (mt) cc_final: 0.8357 (mt) REVERT: G 150 TYR cc_start: 0.8830 (m-80) cc_final: 0.8558 (m-10) REVERT: G 163 TYR cc_start: 0.8623 (t80) cc_final: 0.8321 (t80) REVERT: G 165 GLN cc_start: 0.8370 (mt0) cc_final: 0.8139 (mt0) REVERT: G 179 ASP cc_start: 0.8230 (t0) cc_final: 0.7678 (t0) REVERT: G 188 MET cc_start: 0.8295 (mmt) cc_final: 0.7593 (mmt) REVERT: G 234 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7340 (mm-30) REVERT: G 274 CYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7678 (m) REVERT: G 275 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7452 (ptt180) REVERT: G 285 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.6956 (t80) REVERT: G 324 GLU cc_start: 0.7171 (tt0) cc_final: 0.6765 (tt0) REVERT: G 383 MET cc_start: 0.8601 (ttp) cc_final: 0.8176 (ttp) REVERT: G 397 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7909 (mm-30) REVERT: G 399 ARG cc_start: 0.7988 (tpp80) cc_final: 0.7095 (tpp80) REVERT: G 403 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: G 448 ASP cc_start: 0.7618 (t0) cc_final: 0.7376 (t0) REVERT: H 28 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7473 (mm-30) REVERT: H 56 ASP cc_start: 0.7715 (t70) cc_final: 0.7440 (t70) REVERT: H 63 ASP cc_start: 0.7691 (t0) cc_final: 0.7457 (t0) REVERT: H 76 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8195 (mtt90) REVERT: H 88 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6786 (tm-30) REVERT: H 99 LYS cc_start: 0.8937 (mmmm) cc_final: 0.8729 (mmmm) REVERT: H 111 ASN cc_start: 0.8699 (t0) cc_final: 0.7986 (t0) REVERT: H 115 LYS cc_start: 0.8856 (mptp) cc_final: 0.8069 (mptp) REVERT: H 171 ARG cc_start: 0.7532 (mtm-85) cc_final: 0.7122 (mtm-85) REVERT: H 179 ASP cc_start: 0.8151 (t0) cc_final: 0.7567 (t0) REVERT: H 243 VAL cc_start: 0.8178 (m) cc_final: 0.7934 (p) REVERT: H 399 ARG cc_start: 0.7863 (tpp80) cc_final: 0.7413 (tpp-160) REVERT: H 400 LYS cc_start: 0.8137 (tppt) cc_final: 0.7766 (tppt) REVERT: H 436 ASP cc_start: 0.8519 (t0) cc_final: 0.8163 (t70) REVERT: H 447 PHE cc_start: 0.8519 (m-80) cc_final: 0.8094 (m-80) REVERT: I 16 LYS cc_start: 0.8491 (mppt) cc_final: 0.8218 (mtpt) REVERT: I 22 TYR cc_start: 0.8448 (m-80) cc_final: 0.8131 (m-80) REVERT: I 52 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7437 (mt-10) REVERT: I 72 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7653 (tmm) REVERT: I 106 LYS cc_start: 0.8212 (mtmm) cc_final: 0.7828 (mtmm) REVERT: I 111 ASN cc_start: 0.8629 (t0) cc_final: 0.8290 (t0) REVERT: I 115 LYS cc_start: 0.8810 (mptp) cc_final: 0.8177 (mptp) REVERT: I 184 MET cc_start: 0.8664 (tpp) cc_final: 0.8132 (tpp) REVERT: I 188 MET cc_start: 0.8426 (mmt) cc_final: 0.8034 (mmt) REVERT: I 204 VAL cc_start: 0.8865 (m) cc_final: 0.8588 (t) REVERT: I 357 LYS cc_start: 0.8712 (ttmm) cc_final: 0.8510 (ttmt) REVERT: I 405 GLU cc_start: 0.7818 (mp0) cc_final: 0.7300 (mp0) REVERT: I 436 ASP cc_start: 0.8389 (t0) cc_final: 0.8017 (t70) REVERT: I 441 GLN cc_start: 0.7664 (mt0) cc_final: 0.7440 (mt0) REVERT: J 28 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7315 (mm-30) REVERT: J 41 ARG cc_start: 0.8060 (tpp-160) cc_final: 0.7443 (tpp-160) REVERT: J 63 ASP cc_start: 0.7829 (t0) cc_final: 0.6949 (t0) REVERT: J 76 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8263 (mtt90) REVERT: J 88 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.5850 (tm-30) REVERT: J 92 ARG cc_start: 0.7690 (mmp80) cc_final: 0.6986 (mmp80) REVERT: J 99 LYS cc_start: 0.8951 (mmmm) cc_final: 0.8646 (mmmm) REVERT: J 111 ASN cc_start: 0.8688 (t0) cc_final: 0.8001 (t0) REVERT: J 115 LYS cc_start: 0.8811 (mptp) cc_final: 0.8116 (mptp) REVERT: J 140 SER cc_start: 0.8171 (p) cc_final: 0.7943 (p) REVERT: J 171 ARG cc_start: 0.7710 (mtm-85) cc_final: 0.7098 (mtm-85) REVERT: J 240 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8055 (mt) REVERT: J 275 ARG cc_start: 0.7618 (ttt180) cc_final: 0.7183 (ptt180) REVERT: J 277 ASP cc_start: 0.7918 (p0) cc_final: 0.7547 (p0) REVERT: J 278 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8613 (p) REVERT: J 285 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.7018 (t80) REVERT: J 288 LYS cc_start: 0.8681 (mttm) cc_final: 0.8462 (mttp) REVERT: J 378 THR cc_start: 0.8060 (m) cc_final: 0.7791 (p) REVERT: J 397 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7893 (mm-30) REVERT: J 400 LYS cc_start: 0.8298 (tppt) cc_final: 0.7574 (tppt) REVERT: J 401 ASP cc_start: 0.7881 (t0) cc_final: 0.6982 (t0) REVERT: J 403 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: J 404 ASP cc_start: 0.7974 (m-30) cc_final: 0.7692 (m-30) REVERT: J 406 LYS cc_start: 0.8837 (mmtp) cc_final: 0.8615 (mmtp) REVERT: J 446 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7726 (mm-30) REVERT: K 28 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7478 (mm-30) REVERT: K 63 ASP cc_start: 0.7658 (t0) cc_final: 0.7429 (t0) REVERT: K 76 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8106 (mtt90) REVERT: K 115 LYS cc_start: 0.8792 (mptp) cc_final: 0.8226 (mptp) REVERT: K 171 ARG cc_start: 0.7402 (mtm-85) cc_final: 0.7009 (mtm-85) REVERT: K 238 ARG cc_start: 0.7788 (ttm110) cc_final: 0.7411 (mtm110) REVERT: K 274 CYS cc_start: 0.8160 (m) cc_final: 0.7717 (m) REVERT: K 283 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: K 313 LEU cc_start: 0.8375 (mt) cc_final: 0.7998 (mm) REVERT: K 341 GLN cc_start: 0.8227 (tt0) cc_final: 0.7945 (tt0) REVERT: K 362 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8460 (mt) REVERT: L 20 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7786 (ttm-80) REVERT: L 52 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7588 (mt-10) REVERT: L 63 ASP cc_start: 0.7610 (t0) cc_final: 0.6711 (t0) REVERT: L 71 ARG cc_start: 0.7989 (mtm-85) cc_final: 0.7438 (ptp-110) REVERT: L 92 ARG cc_start: 0.7807 (mmp80) cc_final: 0.7396 (mmp80) REVERT: L 106 LYS cc_start: 0.8398 (mtmm) cc_final: 0.8093 (mtmm) REVERT: L 115 LYS cc_start: 0.8852 (mptp) cc_final: 0.8193 (mptp) REVERT: L 168 LYS cc_start: 0.8945 (mtmt) cc_final: 0.8537 (mtpp) REVERT: L 171 ARG cc_start: 0.7224 (mtm-85) cc_final: 0.6936 (mtm-85) REVERT: L 195 TYR cc_start: 0.8555 (m-80) cc_final: 0.8327 (m-80) REVERT: L 202 GLU cc_start: 0.8147 (tp30) cc_final: 0.7858 (tp30) REVERT: L 232 LYS cc_start: 0.8300 (ptmt) cc_final: 0.7833 (ptmt) REVERT: L 238 ARG cc_start: 0.7729 (ttm110) cc_final: 0.7381 (mtm110) REVERT: L 266 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8517 (mt) REVERT: L 283 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: L 285 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.7553 (t80) REVERT: L 324 GLU cc_start: 0.7270 (tt0) cc_final: 0.7034 (tt0) REVERT: L 403 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7176 (mp0) REVERT: L 427 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.7005 (mmtt) REVERT: L 446 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7304 (mm-30) outliers start: 282 outliers final: 167 residues processed: 2069 average time/residue: 0.2874 time to fit residues: 916.5742 Evaluate side-chains 2131 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 1929 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 396 LYS Chi-restraints excluded: chain B residue 398 CYS Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 292 MET Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 316 LYS Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 398 CYS Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 275 ARG Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 340 ASP Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 411 ARG Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain H residue 19 GLN Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 292 MET Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 342 MET Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 398 CYS Chi-restraints excluded: chain H residue 403 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 319 ASP Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 76 ARG Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 236 CYS Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 240 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 383 MET Chi-restraints excluded: chain J residue 403 GLU Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 232 LYS Chi-restraints excluded: chain K residue 283 GLU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 398 CYS Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain K residue 408 LEU Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 120 GLN Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 152 ASP Chi-restraints excluded: chain L residue 194 SER Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 283 GLU Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain L residue 327 SER Chi-restraints excluded: chain L residue 342 MET Chi-restraints excluded: chain L residue 348 THR Chi-restraints excluded: chain L residue 358 LEU Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 405 GLU Chi-restraints excluded: chain L residue 426 GLN Chi-restraints excluded: chain L residue 427 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 54 optimal weight: 0.0570 chunk 279 optimal weight: 6.9990 chunk 445 optimal weight: 0.5980 chunk 491 optimal weight: 1.9990 chunk 278 optimal weight: 0.8980 chunk 292 optimal weight: 0.4980 chunk 84 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 475 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.133486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.117214 restraints weight = 64466.264| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.79 r_work: 0.3411 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 42540 Z= 0.125 Angle : 0.682 14.361 57612 Z= 0.327 Chirality : 0.043 0.145 6564 Planarity : 0.005 0.097 7248 Dihedral : 13.759 179.707 6348 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 5.39 % Allowed : 32.38 % Favored : 62.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.97 % 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: -1.08 (0.11), residues: 5148 helix: 1.26 (0.13), residues: 1680 sheet: -1.12 (0.14), residues: 1272 loop : -2.05 (0.11), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 30 TYR 0.025 0.001 TYR G 5 PHE 0.035 0.002 PHE C 264 TRP 0.019 0.002 TRP C 258 HIS 0.003 0.000 HIS J 308 Details of bonding type rmsd covalent geometry : bond 0.00298 (42480) covalent geometry : angle 0.68181 (57612) hydrogen bonds : bond 0.02845 ( 1577) hydrogen bonds : angle 4.50042 ( 4476) metal coordination : bond 0.00508 ( 36) Misc. bond : bond 0.00033 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2101 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 1863 time to evaluate : 1.610 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: 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: 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 41 ARG cc_start: 0.7875 (tpp-160) cc_final: 0.7338 (tpp-160) REVERT: A 43 PHE cc_start: 0.8779 (t80) cc_final: 0.8403 (t80) REVERT: A 76 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7835 (mtt90) REVERT: A 88 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6377 (tm-30) REVERT: A 92 ARG cc_start: 0.7551 (mmp80) cc_final: 0.7115 (mmp80) REVERT: A 133 PHE cc_start: 0.7879 (t80) cc_final: 0.7623 (t80) REVERT: A 135 LEU cc_start: 0.8570 (mt) cc_final: 0.8104 (mm) REVERT: A 150 TYR cc_start: 0.8641 (m-80) cc_final: 0.8415 (m-80) REVERT: A 163 TYR cc_start: 0.8589 (t80) cc_final: 0.8308 (t80) REVERT: A 171 ARG cc_start: 0.7242 (mtm-85) cc_final: 0.7023 (mtm-85) REVERT: A 188 MET cc_start: 0.8372 (mmt) cc_final: 0.7953 (mmt) REVERT: A 202 GLU cc_start: 0.8193 (tp30) cc_final: 0.7796 (mp0) REVERT: A 214 SER cc_start: 0.8495 (t) cc_final: 0.7935 (p) REVERT: A 234 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7395 (mm-30) REVERT: A 242 SER cc_start: 0.8178 (t) cc_final: 0.7700 (p) REVERT: A 243 VAL cc_start: 0.8010 (t) cc_final: 0.7711 (t) REVERT: A 248 TYR cc_start: 0.8125 (m-10) cc_final: 0.7851 (m-10) REVERT: A 278 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8618 (p) REVERT: A 285 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.6946 (t80) REVERT: A 363 ASN cc_start: 0.8422 (t0) cc_final: 0.8101 (t0) REVERT: A 396 LYS cc_start: 0.8493 (mmmm) cc_final: 0.8058 (tppt) REVERT: A 399 ARG cc_start: 0.8013 (tpp80) cc_final: 0.7266 (tpp80) REVERT: A 403 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7145 (mt-10) REVERT: B 24 MET cc_start: 0.8489 (pmm) cc_final: 0.8189 (pmm) REVERT: B 111 ASN cc_start: 0.8633 (t0) cc_final: 0.8170 (t0) REVERT: B 115 LYS cc_start: 0.8721 (mptp) cc_final: 0.8010 (mptp) REVERT: B 171 ARG cc_start: 0.7449 (mtm-85) cc_final: 0.7204 (mtm-85) REVERT: B 184 MET cc_start: 0.8510 (mmm) cc_final: 0.7957 (mmm) REVERT: B 219 GLU cc_start: 0.6145 (OUTLIER) cc_final: 0.5783 (pp20) REVERT: B 236 CYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7851 (p) REVERT: B 245 SER cc_start: 0.8645 (p) cc_final: 0.8378 (t) REVERT: B 313 LEU cc_start: 0.8347 (mt) cc_final: 0.8002 (mm) REVERT: B 396 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7935 (mmtm) REVERT: B 400 LYS cc_start: 0.8435 (tppt) cc_final: 0.8130 (tppt) REVERT: B 427 LYS cc_start: 0.6333 (mmpt) cc_final: 0.6114 (mmtm) REVERT: C 16 LYS cc_start: 0.8550 (mptt) cc_final: 0.8157 (mppt) REVERT: C 24 MET cc_start: 0.8591 (pmm) cc_final: 0.7983 (pmm) REVERT: C 111 ASN cc_start: 0.8519 (t0) cc_final: 0.8280 (t0) REVERT: C 115 LYS cc_start: 0.8700 (mptp) cc_final: 0.8134 (mptp) REVERT: C 135 LEU cc_start: 0.8498 (mt) cc_final: 0.8269 (mm) REVERT: C 184 MET cc_start: 0.8569 (mmm) cc_final: 0.8096 (mmm) REVERT: C 203 GLN cc_start: 0.8683 (mt0) cc_final: 0.8450 (mt0) REVERT: C 285 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7203 (t80) REVERT: C 297 TYR cc_start: 0.8003 (m-80) cc_final: 0.7751 (m-80) REVERT: C 362 LEU cc_start: 0.8682 (mm) cc_final: 0.8395 (tt) REVERT: C 403 GLU cc_start: 0.7719 (mp0) cc_final: 0.7335 (mp0) REVERT: C 427 LYS cc_start: 0.7907 (mmmm) cc_final: 0.7470 (mmmm) REVERT: C 436 ASP cc_start: 0.8245 (t0) cc_final: 0.7651 (t0) REVERT: D 28 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7350 (mm-30) REVERT: D 76 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8177 (mtp85) REVERT: D 88 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6849 (tm-30) REVERT: D 115 LYS cc_start: 0.8763 (mptp) cc_final: 0.8262 (mptp) REVERT: D 146 ASP cc_start: 0.6975 (p0) cc_final: 0.5989 (p0) REVERT: D 163 TYR cc_start: 0.8604 (t80) cc_final: 0.8255 (t80) REVERT: D 165 GLN cc_start: 0.8037 (mt0) cc_final: 0.7747 (mt0) REVERT: D 171 ARG cc_start: 0.7382 (mtm-85) cc_final: 0.6806 (mtm-85) REVERT: D 179 ASP cc_start: 0.7911 (t0) cc_final: 0.7463 (t0) REVERT: D 197 THR cc_start: 0.8288 (p) cc_final: 0.8010 (t) REVERT: D 234 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7446 (mm-30) REVERT: D 236 CYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7788 (p) REVERT: D 243 VAL cc_start: 0.8376 (m) cc_final: 0.8013 (p) REVERT: D 274 CYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7851 (m) REVERT: D 285 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7506 (t80) REVERT: D 324 GLU cc_start: 0.7189 (tt0) cc_final: 0.6894 (tt0) REVERT: D 362 LEU cc_start: 0.8655 (mp) cc_final: 0.8375 (tt) REVERT: D 426 GLN cc_start: 0.7239 (mt0) cc_final: 0.6975 (mt0) REVERT: D 448 ASP cc_start: 0.7679 (t0) cc_final: 0.7407 (t0) REVERT: E 16 LYS cc_start: 0.8453 (mmtt) cc_final: 0.8082 (mmmt) REVERT: E 20 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7974 (mtm-85) REVERT: E 24 MET cc_start: 0.8580 (pmm) cc_final: 0.8284 (pmm) REVERT: E 111 ASN cc_start: 0.8630 (t0) cc_final: 0.8236 (t0) REVERT: E 115 LYS cc_start: 0.8748 (mptp) cc_final: 0.8102 (mptp) REVERT: E 151 GLN cc_start: 0.8174 (tp40) cc_final: 0.7931 (tp40) REVERT: E 197 THR cc_start: 0.8379 (p) cc_final: 0.8057 (t) REVERT: E 236 CYS cc_start: 0.8300 (p) cc_final: 0.8001 (p) REVERT: E 243 VAL cc_start: 0.8221 (m) cc_final: 0.7927 (p) REVERT: E 275 ARG cc_start: 0.7871 (ttt180) cc_final: 0.7545 (ptt180) REVERT: E 297 TYR cc_start: 0.7971 (m-10) cc_final: 0.7741 (m-10) REVERT: E 325 ARG cc_start: 0.7882 (ttm-80) cc_final: 0.7490 (ttm170) REVERT: E 405 GLU cc_start: 0.7452 (tp30) cc_final: 0.7044 (tp30) REVERT: E 436 ASP cc_start: 0.8363 (t0) cc_final: 0.7644 (t70) REVERT: E 447 PHE cc_start: 0.8457 (m-80) cc_final: 0.8034 (m-10) REVERT: F 16 LYS cc_start: 0.8588 (mptt) cc_final: 0.8258 (mppt) REVERT: F 30 ARG cc_start: 0.7393 (ptp-170) cc_final: 0.6989 (ttm110) REVERT: F 92 ARG cc_start: 0.7889 (mmp80) cc_final: 0.7480 (mmp80) REVERT: F 115 LYS cc_start: 0.8755 (mptp) cc_final: 0.8200 (mptp) REVERT: F 184 MET cc_start: 0.8492 (tpp) cc_final: 0.7903 (tpp) REVERT: F 188 MET cc_start: 0.8190 (mmt) cc_final: 0.7944 (mmt) REVERT: F 232 LYS cc_start: 0.8152 (ptmt) cc_final: 0.7727 (ptmt) REVERT: F 240 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7846 (mt) REVERT: F 258 TRP cc_start: 0.8571 (m100) cc_final: 0.7575 (m100) REVERT: F 275 ARG cc_start: 0.8014 (ttt180) cc_final: 0.7714 (ttt180) REVERT: F 325 ARG cc_start: 0.7681 (ptp-110) cc_final: 0.7466 (ttm-80) REVERT: F 340 ASP cc_start: 0.7654 (t0) cc_final: 0.7401 (t0) REVERT: F 436 ASP cc_start: 0.8029 (t0) cc_final: 0.7823 (t0) REVERT: F 441 GLN cc_start: 0.7687 (mt0) cc_final: 0.7462 (mt0) REVERT: G 41 ARG cc_start: 0.7874 (tpp-160) cc_final: 0.7303 (tpp-160) REVERT: G 76 ARG cc_start: 0.8197 (mtt90) cc_final: 0.7911 (mtt90) REVERT: G 92 ARG cc_start: 0.7670 (mmp80) cc_final: 0.7049 (mmp80) REVERT: G 106 LYS cc_start: 0.8050 (mtmm) cc_final: 0.7816 (mtmm) REVERT: G 111 ASN cc_start: 0.8702 (t0) cc_final: 0.8123 (t0) REVERT: G 115 LYS cc_start: 0.8780 (mptp) cc_final: 0.8199 (mptp) REVERT: G 150 TYR cc_start: 0.8782 (m-80) cc_final: 0.8284 (m-80) REVERT: G 163 TYR cc_start: 0.8573 (t80) cc_final: 0.8212 (t80) REVERT: G 171 ARG cc_start: 0.7520 (mtm-85) cc_final: 0.7236 (mtm-85) REVERT: G 179 ASP cc_start: 0.8162 (t0) cc_final: 0.7736 (t70) REVERT: G 275 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7518 (ptt180) REVERT: G 285 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.7058 (t80) REVERT: G 293 SER cc_start: 0.8185 (m) cc_final: 0.7638 (p) REVERT: G 324 GLU cc_start: 0.7054 (tt0) cc_final: 0.6656 (tt0) REVERT: G 397 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7951 (mm-30) REVERT: G 399 ARG cc_start: 0.7855 (tpp80) cc_final: 0.6938 (tpp80) REVERT: G 400 LYS cc_start: 0.8301 (tppt) cc_final: 0.7799 (tppt) REVERT: G 403 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: G 430 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8321 (p) REVERT: G 448 ASP cc_start: 0.7569 (t0) cc_final: 0.7301 (t0) REVERT: H 56 ASP cc_start: 0.7684 (t70) cc_final: 0.7375 (t70) REVERT: H 76 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7662 (mtt90) REVERT: H 88 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6696 (tm-30) REVERT: H 111 ASN cc_start: 0.8684 (t0) cc_final: 0.8113 (t0) REVERT: H 115 LYS cc_start: 0.8830 (mptp) cc_final: 0.8100 (mptp) REVERT: H 171 ARG cc_start: 0.7260 (mtm-85) cc_final: 0.6905 (mtm-85) REVERT: H 179 ASP cc_start: 0.8099 (t0) cc_final: 0.7549 (t0) REVERT: H 258 TRP cc_start: 0.8505 (m100) cc_final: 0.8273 (m100) REVERT: H 399 ARG cc_start: 0.7745 (tpp80) cc_final: 0.7319 (tpp-160) REVERT: H 400 LYS cc_start: 0.8134 (tppt) cc_final: 0.7737 (tppt) REVERT: H 436 ASP cc_start: 0.8424 (t0) cc_final: 0.8067 (t70) REVERT: H 447 PHE cc_start: 0.8489 (m-80) cc_final: 0.8053 (m-80) REVERT: I 16 LYS cc_start: 0.8488 (mppt) cc_final: 0.8211 (mtpt) REVERT: I 22 TYR cc_start: 0.8388 (m-80) cc_final: 0.8025 (m-80) REVERT: I 72 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7570 (tmm) REVERT: I 106 LYS cc_start: 0.8166 (mtmm) cc_final: 0.7762 (mtmm) REVERT: I 111 ASN cc_start: 0.8570 (t0) cc_final: 0.8242 (t0) REVERT: I 115 LYS cc_start: 0.8755 (mptp) cc_final: 0.8119 (mptp) REVERT: I 184 MET cc_start: 0.8559 (tpp) cc_final: 0.7846 (mmm) REVERT: I 204 VAL cc_start: 0.8825 (m) cc_final: 0.8622 (t) REVERT: I 357 LYS cc_start: 0.8696 (ttmm) cc_final: 0.8463 (ttmt) REVERT: I 362 LEU cc_start: 0.8805 (mm) cc_final: 0.8534 (tt) REVERT: I 400 LYS cc_start: 0.8309 (tppt) cc_final: 0.7819 (ttpt) REVERT: I 405 GLU cc_start: 0.7803 (mp0) cc_final: 0.7276 (mp0) REVERT: I 436 ASP cc_start: 0.8330 (t0) cc_final: 0.8011 (t70) REVERT: I 441 GLN cc_start: 0.7615 (mt0) cc_final: 0.7163 (mt0) REVERT: J 72 MET cc_start: 0.8306 (tmm) cc_final: 0.8037 (tmm) REVERT: J 92 ARG cc_start: 0.7604 (mmp80) cc_final: 0.7151 (mmp80) REVERT: J 111 ASN cc_start: 0.8635 (t0) cc_final: 0.8006 (t0) REVERT: J 115 LYS cc_start: 0.8764 (mptp) cc_final: 0.8122 (mptp) REVERT: J 140 SER cc_start: 0.8165 (p) cc_final: 0.7917 (p) REVERT: J 171 ARG cc_start: 0.7664 (mtm-85) cc_final: 0.7082 (mtm-85) REVERT: J 195 TYR cc_start: 0.8489 (m-80) cc_final: 0.8270 (m-80) REVERT: J 240 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7928 (mt) REVERT: J 274 CYS cc_start: 0.8066 (m) cc_final: 0.7308 (m) REVERT: J 275 ARG cc_start: 0.7615 (ttt180) cc_final: 0.7184 (ptt180) REVERT: J 277 ASP cc_start: 0.7998 (p0) cc_final: 0.7743 (p0) REVERT: J 278 THR cc_start: 0.8920 (m) cc_final: 0.8582 (p) REVERT: J 285 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.6766 (t80) REVERT: J 324 GLU cc_start: 0.7282 (tt0) cc_final: 0.7000 (tt0) REVERT: J 393 LYS cc_start: 0.8565 (mttp) cc_final: 0.8244 (mttp) REVERT: J 397 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7856 (mm-30) REVERT: J 400 LYS cc_start: 0.8267 (tppt) cc_final: 0.7455 (tppt) REVERT: J 401 ASP cc_start: 0.7798 (t0) cc_final: 0.7021 (t0) REVERT: J 404 ASP cc_start: 0.7887 (m-30) cc_final: 0.7575 (m-30) REVERT: J 406 LYS cc_start: 0.8800 (mmtp) cc_final: 0.8589 (mmtp) REVERT: K 63 ASP cc_start: 0.7070 (t0) cc_final: 0.6728 (t0) REVERT: K 76 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7896 (mtt90) REVERT: K 115 LYS cc_start: 0.8772 (mptp) cc_final: 0.8196 (mptp) REVERT: K 171 ARG cc_start: 0.7305 (mtm-85) cc_final: 0.6905 (mtm-85) REVERT: K 238 ARG cc_start: 0.7767 (ttm110) cc_final: 0.7390 (mtm110) REVERT: K 274 CYS cc_start: 0.8127 (m) cc_final: 0.7753 (m) REVERT: K 289 ARG cc_start: 0.7671 (ttp80) cc_final: 0.7337 (mtp-110) REVERT: K 313 LEU cc_start: 0.8344 (mt) cc_final: 0.7968 (mm) REVERT: K 340 ASP cc_start: 0.7761 (t0) cc_final: 0.7365 (t0) REVERT: K 341 GLN cc_start: 0.8226 (tt0) cc_final: 0.8009 (tt0) REVERT: L 20 ARG cc_start: 0.8049 (ttm-80) cc_final: 0.7711 (ttm-80) REVERT: L 43 PHE cc_start: 0.8904 (t80) cc_final: 0.8191 (t80) REVERT: L 51 ILE cc_start: 0.8475 (mm) cc_final: 0.8219 (mm) REVERT: L 71 ARG cc_start: 0.7838 (mtm-85) cc_final: 0.7381 (ptp-110) REVERT: L 92 ARG cc_start: 0.7791 (mmp80) cc_final: 0.7311 (mmp80) REVERT: L 106 LYS cc_start: 0.8338 (mtmm) cc_final: 0.8066 (mtmm) REVERT: L 115 LYS cc_start: 0.8823 (mptp) cc_final: 0.8171 (mptp) REVERT: L 168 LYS cc_start: 0.8859 (mtmt) cc_final: 0.8410 (mtpp) REVERT: L 171 ARG cc_start: 0.7146 (mtm-85) cc_final: 0.6656 (mtm-85) REVERT: L 184 MET cc_start: 0.8249 (mtp) cc_final: 0.8019 (tpp) REVERT: L 195 TYR cc_start: 0.8457 (m-80) cc_final: 0.8157 (m-80) REVERT: L 202 GLU cc_start: 0.8092 (tp30) cc_final: 0.7611 (tp30) REVERT: L 232 LYS cc_start: 0.8281 (ptmt) cc_final: 0.7825 (ptmt) REVERT: L 238 ARG cc_start: 0.7662 (ttm110) cc_final: 0.7410 (mtm110) REVERT: L 258 TRP cc_start: 0.8645 (m100) cc_final: 0.7608 (m100) REVERT: L 266 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8474 (mt) REVERT: L 283 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: L 285 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7286 (t80) REVERT: L 324 GLU cc_start: 0.7120 (tt0) cc_final: 0.6908 (tt0) REVERT: L 400 LYS cc_start: 0.8160 (tppt) cc_final: 0.7928 (tppt) REVERT: L 403 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: L 427 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7251 (mmtt) REVERT: L 446 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7288 (mm-30) outliers start: 238 outliers final: 170 residues processed: 1947 average time/residue: 0.2861 time to fit residues: 859.6774 Evaluate side-chains 2058 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 1859 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 396 LYS Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 53 GLN Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 292 MET Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 398 CYS Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 238 ARG Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 275 ARG Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 411 ARG Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain H residue 19 GLN Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 292 MET Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 342 MET Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 379 MET Chi-restraints excluded: chain H residue 398 CYS Chi-restraints excluded: chain H residue 403 GLU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 319 ASP Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 53 GLN Chi-restraints excluded: chain J residue 76 ARG Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 202 GLU Chi-restraints excluded: chain J residue 240 LEU Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain J residue 301 THR Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 403 GLU Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 283 GLU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 342 MET Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain K residue 408 LEU Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 53 GLN Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 120 GLN Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 152 ASP Chi-restraints excluded: chain L residue 194 SER Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 237 ASP Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 283 GLU Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain L residue 342 MET Chi-restraints excluded: chain L residue 348 THR Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 405 GLU Chi-restraints excluded: chain L residue 427 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 280 optimal weight: 7.9990 chunk 239 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 362 optimal weight: 3.9990 chunk 447 optimal weight: 0.6980 chunk 397 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 82 optimal weight: 10.0000 chunk 211 optimal weight: 20.0000 chunk 25 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: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.133293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.117103 restraints weight = 64505.026| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.77 r_work: 0.3407 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 42540 Z= 0.137 Angle : 0.682 14.411 57612 Z= 0.326 Chirality : 0.043 0.156 6564 Planarity : 0.005 0.070 7248 Dihedral : 13.687 179.651 6348 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 5.39 % Allowed : 32.72 % Favored : 61.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.97 % 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: -0.99 (0.11), residues: 5148 helix: 1.36 (0.14), residues: 1680 sheet: -1.15 (0.13), residues: 1296 loop : -1.98 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 30 TYR 0.026 0.001 TYR G 5 PHE 0.036 0.002 PHE B 264 TRP 0.020 0.002 TRP F 258 HIS 0.002 0.001 HIS J 308 Details of bonding type rmsd covalent geometry : bond 0.00323 (42480) covalent geometry : angle 0.68220 (57612) hydrogen bonds : bond 0.02856 ( 1577) hydrogen bonds : angle 4.44438 ( 4476) metal coordination : bond 0.00512 ( 36) Misc. bond : bond 0.00041 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2073 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 1835 time to evaluate : 1.216 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: 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: 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 41 ARG cc_start: 0.7886 (tpp-160) cc_final: 0.7341 (tpp-160) REVERT: A 43 PHE cc_start: 0.8800 (t80) cc_final: 0.8407 (t80) REVERT: A 76 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7835 (mtt90) REVERT: A 88 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6304 (tm-30) REVERT: A 92 ARG cc_start: 0.7583 (mmp80) cc_final: 0.7107 (mmp80) REVERT: A 135 LEU cc_start: 0.8570 (mt) cc_final: 0.8364 (mt) REVERT: A 163 TYR cc_start: 0.8547 (t80) cc_final: 0.8247 (t80) REVERT: A 171 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.6976 (mtm-85) REVERT: A 188 MET cc_start: 0.8402 (mmt) cc_final: 0.7949 (mmt) REVERT: A 214 SER cc_start: 0.8504 (t) cc_final: 0.7947 (p) REVERT: A 234 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7422 (mm-30) REVERT: A 242 SER cc_start: 0.8199 (t) cc_final: 0.7673 (p) REVERT: A 243 VAL cc_start: 0.8063 (t) cc_final: 0.7770 (t) REVERT: A 248 TYR cc_start: 0.8127 (m-10) cc_final: 0.7811 (m-10) REVERT: A 278 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8631 (p) REVERT: A 285 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.6879 (t80) REVERT: A 363 ASN cc_start: 0.8445 (t0) cc_final: 0.8141 (t0) REVERT: A 396 LYS cc_start: 0.8510 (mmmm) cc_final: 0.8046 (tppt) REVERT: A 399 ARG cc_start: 0.8007 (tpp80) cc_final: 0.7231 (tpp80) REVERT: A 403 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7114 (mt-10) REVERT: B 24 MET cc_start: 0.8490 (pmm) cc_final: 0.8226 (pmm) REVERT: B 86 SER cc_start: 0.7209 (p) cc_final: 0.6839 (p) REVERT: B 111 ASN cc_start: 0.8659 (t0) cc_final: 0.8064 (t0) REVERT: B 115 LYS cc_start: 0.8756 (mptp) cc_final: 0.8002 (mptp) REVERT: B 140 SER cc_start: 0.8262 (p) cc_final: 0.8011 (p) REVERT: B 171 ARG cc_start: 0.7429 (mtm-85) cc_final: 0.7200 (mtm-85) REVERT: B 184 MET cc_start: 0.8523 (mmm) cc_final: 0.7968 (mmm) REVERT: B 236 CYS cc_start: 0.8068 (p) cc_final: 0.7742 (p) REVERT: B 245 SER cc_start: 0.8616 (p) cc_final: 0.8348 (t) REVERT: B 313 LEU cc_start: 0.8348 (mt) cc_final: 0.8002 (mm) REVERT: B 396 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7891 (mmtm) REVERT: B 400 LYS cc_start: 0.8403 (tppt) cc_final: 0.8037 (mppt) REVERT: B 433 LYS cc_start: 0.8554 (mmmt) cc_final: 0.8264 (mmtt) REVERT: B 436 ASP cc_start: 0.8333 (t0) cc_final: 0.7431 (t0) REVERT: C 16 LYS cc_start: 0.8541 (mptt) cc_final: 0.8133 (mppt) REVERT: C 24 MET cc_start: 0.8624 (pmm) cc_final: 0.8024 (pmm) REVERT: C 92 ARG cc_start: 0.7902 (mmp80) cc_final: 0.7533 (mmp80) REVERT: C 111 ASN cc_start: 0.8538 (t0) cc_final: 0.8275 (t0) REVERT: C 115 LYS cc_start: 0.8715 (mptp) cc_final: 0.8100 (mptp) REVERT: C 135 LEU cc_start: 0.8514 (mt) cc_final: 0.8084 (mm) REVERT: C 179 ASP cc_start: 0.7955 (t0) cc_final: 0.7735 (t0) REVERT: C 195 TYR cc_start: 0.8407 (m-80) cc_final: 0.8171 (m-80) REVERT: C 203 GLN cc_start: 0.8713 (mt0) cc_final: 0.8489 (mt0) REVERT: C 256 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8197 (ttmt) REVERT: C 285 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7192 (t80) REVERT: C 297 TYR cc_start: 0.8005 (m-80) cc_final: 0.7794 (m-80) REVERT: C 403 GLU cc_start: 0.7731 (mp0) cc_final: 0.7292 (mp0) REVERT: C 427 LYS cc_start: 0.7915 (mmmm) cc_final: 0.7465 (mmmm) REVERT: C 436 ASP cc_start: 0.8203 (t0) cc_final: 0.7613 (t0) REVERT: D 28 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7352 (mm-30) REVERT: D 76 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8175 (mtp85) REVERT: D 88 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6839 (tm-30) REVERT: D 115 LYS cc_start: 0.8797 (mptp) cc_final: 0.8271 (mptp) REVERT: D 163 TYR cc_start: 0.8613 (t80) cc_final: 0.8260 (t80) REVERT: D 165 GLN cc_start: 0.8012 (mt0) cc_final: 0.7729 (mt0) REVERT: D 171 ARG cc_start: 0.7409 (mtm-85) cc_final: 0.6944 (mtm-85) REVERT: D 197 THR cc_start: 0.8309 (p) cc_final: 0.8022 (t) REVERT: D 234 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7427 (mm-30) REVERT: D 236 CYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7735 (p) REVERT: D 243 VAL cc_start: 0.8385 (m) cc_final: 0.8024 (p) REVERT: D 274 CYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7181 (m) REVERT: D 285 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.7515 (t80) REVERT: D 292 MET cc_start: 0.7754 (mmt) cc_final: 0.7550 (mmt) REVERT: D 293 SER cc_start: 0.8182 (m) cc_final: 0.7613 (p) REVERT: D 324 GLU cc_start: 0.7200 (tt0) cc_final: 0.6898 (tt0) REVERT: D 340 ASP cc_start: 0.7606 (m-30) cc_final: 0.7336 (t0) REVERT: D 400 LYS cc_start: 0.8451 (tppt) cc_final: 0.8222 (tppt) REVERT: D 426 GLN cc_start: 0.7306 (mt0) cc_final: 0.7034 (mt0) REVERT: D 448 ASP cc_start: 0.7660 (t0) cc_final: 0.7366 (t0) REVERT: E 16 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8233 (mmmt) REVERT: E 24 MET cc_start: 0.8579 (pmm) cc_final: 0.8300 (pmm) REVERT: E 76 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8095 (mtp85) REVERT: E 115 LYS cc_start: 0.8781 (mptp) cc_final: 0.8199 (mptp) REVERT: E 144 ARG cc_start: 0.8188 (ttm110) cc_final: 0.7677 (ttm110) REVERT: E 150 TYR cc_start: 0.8498 (m-80) cc_final: 0.8179 (m-80) REVERT: E 168 LYS cc_start: 0.8876 (mtmt) cc_final: 0.8289 (mtpt) REVERT: E 184 MET cc_start: 0.8241 (mmm) cc_final: 0.7757 (mmm) REVERT: E 197 THR cc_start: 0.8389 (p) cc_final: 0.7984 (t) REVERT: E 236 CYS cc_start: 0.8242 (p) cc_final: 0.7942 (p) REVERT: E 275 ARG cc_start: 0.7896 (ttt180) cc_final: 0.7549 (ptt180) REVERT: E 297 TYR cc_start: 0.7959 (m-10) cc_final: 0.7753 (m-10) REVERT: E 396 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7979 (mmtm) REVERT: E 405 GLU cc_start: 0.7489 (tp30) cc_final: 0.7111 (tp30) REVERT: E 436 ASP cc_start: 0.8419 (t0) cc_final: 0.7649 (t70) REVERT: E 447 PHE cc_start: 0.8425 (m-80) cc_final: 0.7984 (m-10) REVERT: F 16 LYS cc_start: 0.8589 (mptt) cc_final: 0.8251 (mppt) REVERT: F 30 ARG cc_start: 0.7297 (ptp-170) cc_final: 0.6863 (ttm110) REVERT: F 115 LYS cc_start: 0.8750 (mptp) cc_final: 0.8174 (mptp) REVERT: F 135 LEU cc_start: 0.8506 (mt) cc_final: 0.8292 (mm) REVERT: F 184 MET cc_start: 0.8510 (tpp) cc_final: 0.8169 (tpp) REVERT: F 188 MET cc_start: 0.8204 (mmt) cc_final: 0.7907 (mmt) REVERT: F 232 LYS cc_start: 0.8178 (ptmt) cc_final: 0.7762 (ptmt) REVERT: F 240 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7839 (mt) REVERT: F 258 TRP cc_start: 0.8460 (m100) cc_final: 0.7359 (m100) REVERT: F 325 ARG cc_start: 0.7646 (ptp-110) cc_final: 0.7426 (ttm-80) REVERT: F 340 ASP cc_start: 0.7669 (t0) cc_final: 0.7422 (t0) REVERT: F 345 ILE cc_start: 0.8978 (mm) cc_final: 0.8732 (mm) REVERT: F 396 LYS cc_start: 0.8284 (mmtm) cc_final: 0.7784 (mmmm) REVERT: F 441 GLN cc_start: 0.7647 (mt0) cc_final: 0.7409 (mt0) REVERT: G 41 ARG cc_start: 0.7929 (tpp-160) cc_final: 0.7341 (tpp-160) REVERT: G 43 PHE cc_start: 0.8842 (t80) cc_final: 0.8414 (t80) REVERT: G 76 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7885 (mtt90) REVERT: G 92 ARG cc_start: 0.7693 (mmp80) cc_final: 0.7268 (mmp80) REVERT: G 106 LYS cc_start: 0.8114 (mtmm) cc_final: 0.7889 (mtmm) REVERT: G 111 ASN cc_start: 0.8703 (t0) cc_final: 0.8079 (t0) REVERT: G 115 LYS cc_start: 0.8805 (mptp) cc_final: 0.8173 (mptp) REVERT: G 163 TYR cc_start: 0.8576 (t80) cc_final: 0.8182 (t80) REVERT: G 171 ARG cc_start: 0.7526 (mtm-85) cc_final: 0.7225 (mtm-85) REVERT: G 179 ASP cc_start: 0.8185 (t0) cc_final: 0.7732 (t70) REVERT: G 234 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7318 (mm-30) REVERT: G 274 CYS cc_start: 0.8149 (m) cc_final: 0.7764 (m) REVERT: G 275 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7584 (ptt180) REVERT: G 285 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.6978 (t80) REVERT: G 293 SER cc_start: 0.8163 (m) cc_final: 0.7605 (p) REVERT: G 324 GLU cc_start: 0.7055 (tt0) cc_final: 0.6639 (tt0) REVERT: G 397 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7951 (mm-30) REVERT: G 399 ARG cc_start: 0.7830 (tpp80) cc_final: 0.6940 (tpp80) REVERT: G 400 LYS cc_start: 0.8289 (tppt) cc_final: 0.7782 (tppt) REVERT: G 403 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: G 427 LYS cc_start: 0.6658 (mmtt) cc_final: 0.6359 (mmtt) REVERT: G 430 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8335 (p) REVERT: G 448 ASP cc_start: 0.7558 (t0) cc_final: 0.7295 (t0) REVERT: H 28 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7406 (mm-30) REVERT: H 56 ASP cc_start: 0.7719 (t70) cc_final: 0.7413 (t70) REVERT: H 76 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7617 (mtt90) REVERT: H 88 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6714 (tm-30) REVERT: H 111 ASN cc_start: 0.8706 (t0) cc_final: 0.8131 (t0) REVERT: H 115 LYS cc_start: 0.8841 (mptp) cc_final: 0.8148 (mptp) REVERT: H 150 TYR cc_start: 0.8565 (m-80) cc_final: 0.8272 (m-80) REVERT: H 171 ARG cc_start: 0.7253 (mtm-85) cc_final: 0.6901 (mtm-85) REVERT: H 179 ASP cc_start: 0.8117 (t0) cc_final: 0.7453 (t0) REVERT: H 258 TRP cc_start: 0.8528 (m100) cc_final: 0.8317 (m100) REVERT: H 275 ARG cc_start: 0.7829 (ttt180) cc_final: 0.7402 (ptt180) REVERT: H 399 ARG cc_start: 0.7748 (tpp80) cc_final: 0.7290 (tpp-160) REVERT: H 400 LYS cc_start: 0.8124 (tppt) cc_final: 0.7710 (tppt) REVERT: H 436 ASP cc_start: 0.8443 (t0) cc_final: 0.7861 (t70) REVERT: H 447 PHE cc_start: 0.8470 (m-80) cc_final: 0.8067 (m-80) REVERT: I 16 LYS cc_start: 0.8502 (mppt) cc_final: 0.8223 (mtpt) REVERT: I 22 TYR cc_start: 0.8404 (m-80) cc_final: 0.8083 (m-80) REVERT: I 30 ARG cc_start: 0.6544 (ptp90) cc_final: 0.6067 (ptp90) REVERT: I 72 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7592 (tmm) REVERT: I 106 LYS cc_start: 0.8196 (mtmm) cc_final: 0.7799 (mtmm) REVERT: I 111 ASN cc_start: 0.8595 (t0) cc_final: 0.8204 (t0) REVERT: I 115 LYS cc_start: 0.8791 (mptp) cc_final: 0.8118 (mptp) REVERT: I 184 MET cc_start: 0.8584 (tpp) cc_final: 0.7877 (mmm) REVERT: I 204 VAL cc_start: 0.8785 (m) cc_final: 0.8574 (t) REVERT: I 357 LYS cc_start: 0.8705 (ttmm) cc_final: 0.8436 (ttmt) REVERT: I 362 LEU cc_start: 0.8785 (mm) cc_final: 0.8515 (tt) REVERT: I 400 LYS cc_start: 0.8289 (tppt) cc_final: 0.7798 (ttpt) REVERT: I 405 GLU cc_start: 0.7821 (mp0) cc_final: 0.7337 (mp0) REVERT: I 436 ASP cc_start: 0.8332 (t0) cc_final: 0.8108 (t0) REVERT: I 441 GLN cc_start: 0.7668 (mt0) cc_final: 0.7218 (mt0) REVERT: I 446 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7413 (mm-30) REVERT: J 28 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7408 (mm-30) REVERT: J 43 PHE cc_start: 0.8801 (t80) cc_final: 0.8513 (t80) REVERT: J 76 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8095 (mtt90) REVERT: J 92 ARG cc_start: 0.7644 (mmp80) cc_final: 0.7170 (mmp80) REVERT: J 99 LYS cc_start: 0.8944 (mmmm) cc_final: 0.8718 (mmmm) REVERT: J 115 LYS cc_start: 0.8777 (mptp) cc_final: 0.8184 (mptp) REVERT: J 140 SER cc_start: 0.8175 (p) cc_final: 0.7924 (p) REVERT: J 171 ARG cc_start: 0.7641 (mtm-85) cc_final: 0.7070 (mtm-85) REVERT: J 195 TYR cc_start: 0.8496 (m-80) cc_final: 0.8245 (m-80) REVERT: J 240 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7954 (mt) REVERT: J 274 CYS cc_start: 0.8099 (m) cc_final: 0.7883 (m) REVERT: J 275 ARG cc_start: 0.7695 (ttt180) cc_final: 0.7333 (ptt180) REVERT: J 278 THR cc_start: 0.8897 (m) cc_final: 0.8553 (p) REVERT: J 283 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: J 285 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.6736 (t80) REVERT: J 324 GLU cc_start: 0.7289 (tt0) cc_final: 0.6986 (tt0) REVERT: J 357 LYS cc_start: 0.8636 (ttmm) cc_final: 0.8429 (ttmt) REVERT: J 393 LYS cc_start: 0.8549 (mttp) cc_final: 0.8296 (mttp) REVERT: J 397 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7799 (mm-30) REVERT: J 400 LYS cc_start: 0.8243 (tppt) cc_final: 0.7428 (tppt) REVERT: J 404 ASP cc_start: 0.7940 (m-30) cc_final: 0.7617 (m-30) REVERT: K 28 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7475 (mm-30) REVERT: K 76 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7962 (mtt90) REVERT: K 115 LYS cc_start: 0.8788 (mptp) cc_final: 0.8194 (mptp) REVERT: K 171 ARG cc_start: 0.7320 (mtm-85) cc_final: 0.6945 (mtm-85) REVERT: K 195 TYR cc_start: 0.8553 (m-80) cc_final: 0.8307 (m-80) REVERT: K 238 ARG cc_start: 0.7758 (ttm110) cc_final: 0.7396 (mtm110) REVERT: K 274 CYS cc_start: 0.8132 (m) cc_final: 0.7674 (m) REVERT: K 289 ARG cc_start: 0.7707 (ttp80) cc_final: 0.7413 (mtp-110) REVERT: K 313 LEU cc_start: 0.8331 (mt) cc_final: 0.7947 (mm) REVERT: K 340 ASP cc_start: 0.7775 (t0) cc_final: 0.7394 (t0) REVERT: K 341 GLN cc_start: 0.8259 (tt0) cc_final: 0.8018 (tt0) REVERT: L 20 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7680 (mtm-85) REVERT: L 43 PHE cc_start: 0.8915 (t80) cc_final: 0.8140 (t80) REVERT: L 51 ILE cc_start: 0.8578 (mm) cc_final: 0.8322 (mm) REVERT: L 71 ARG cc_start: 0.7880 (mtm-85) cc_final: 0.7457 (ptp-110) REVERT: L 92 ARG cc_start: 0.7815 (mmp80) cc_final: 0.7320 (mmp80) REVERT: L 106 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8185 (mtmm) REVERT: L 115 LYS cc_start: 0.8825 (mptp) cc_final: 0.8167 (mptp) REVERT: L 168 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8421 (mtpp) REVERT: L 171 ARG cc_start: 0.7107 (mtm-85) cc_final: 0.6634 (mtm-85) REVERT: L 184 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.8062 (tpp) REVERT: L 195 TYR cc_start: 0.8487 (m-80) cc_final: 0.8211 (m-80) REVERT: L 202 GLU cc_start: 0.8084 (tp30) cc_final: 0.7599 (tp30) REVERT: L 232 LYS cc_start: 0.8297 (ptmt) cc_final: 0.7832 (ptmt) REVERT: L 238 ARG cc_start: 0.7672 (ttm110) cc_final: 0.7398 (mtm110) REVERT: L 258 TRP cc_start: 0.8624 (m100) cc_final: 0.7496 (m100) REVERT: L 266 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8481 (mt) REVERT: L 283 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: L 285 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7210 (t80) REVERT: L 400 LYS cc_start: 0.8118 (tppt) cc_final: 0.7906 (tppt) REVERT: L 402 MET cc_start: 0.7507 (tpp) cc_final: 0.7116 (tpp) REVERT: L 403 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: L 405 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: L 427 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7249 (mmtt) REVERT: L 429 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.8140 (m-70) REVERT: L 446 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7306 (mm-30) outliers start: 238 outliers final: 172 residues processed: 1922 average time/residue: 0.2930 time to fit residues: 872.8294 Evaluate side-chains 2044 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 1837 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 396 LYS Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 53 GLN Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 292 MET Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 275 ARG Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 411 ARG Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain H residue 19 GLN Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 292 MET Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 342 MET Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 398 CYS Chi-restraints excluded: chain H residue 403 GLU Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 238 ARG Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 314 MET Chi-restraints excluded: chain I residue 319 ASP Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 53 GLN Chi-restraints excluded: chain J residue 76 ARG Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 240 LEU Chi-restraints excluded: chain J residue 283 GLU Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain J residue 301 THR Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 403 GLU Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 283 GLU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain K residue 349 GLU Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain K residue 408 LEU Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 53 GLN Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain L residue 120 GLN Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 152 ASP Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain L residue 194 SER Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 283 GLU Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain L residue 348 THR Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 405 GLU Chi-restraints excluded: chain L residue 427 LYS Chi-restraints excluded: chain L residue 429 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 204 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 437 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 299 optimal weight: 3.9990 chunk 303 optimal weight: 1.9990 chunk 373 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 225 optimal weight: 2.9990 chunk 455 optimal weight: 2.9990 chunk 272 optimal weight: 0.0870 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.133694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.117472 restraints weight = 64283.334| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.77 r_work: 0.3415 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 42540 Z= 0.131 Angle : 0.679 14.395 57612 Z= 0.325 Chirality : 0.043 0.144 6564 Planarity : 0.005 0.089 7248 Dihedral : 13.630 178.980 6348 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.48 % Allowed : 32.86 % Favored : 61.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.97 % 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: -1.00 (0.11), residues: 5148 helix: 1.39 (0.13), residues: 1692 sheet: -0.87 (0.15), residues: 1056 loop : -2.16 (0.11), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG J 71 TYR 0.024 0.001 TYR G 5 PHE 0.033 0.002 PHE B 264 TRP 0.018 0.002 TRP C 258 HIS 0.003 0.000 HIS J 308 Details of bonding type rmsd covalent geometry : bond 0.00311 (42480) covalent geometry : angle 0.67914 (57612) hydrogen bonds : bond 0.02778 ( 1577) hydrogen bonds : angle 4.39666 ( 4476) metal coordination : bond 0.00491 ( 36) Misc. bond : bond 0.00038 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2094 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 1852 time to evaluate : 1.496 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7880 (tpp-160) cc_final: 0.7344 (tpp-160) REVERT: A 43 PHE cc_start: 0.8800 (t80) cc_final: 0.8417 (t80) REVERT: A 76 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7837 (mtt90) REVERT: A 88 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6250 (tm-30) REVERT: A 92 ARG cc_start: 0.7578 (mmp80) cc_final: 0.7078 (mmp80) REVERT: A 133 PHE cc_start: 0.7841 (t80) cc_final: 0.7572 (t80) REVERT: A 135 LEU cc_start: 0.8588 (mt) cc_final: 0.8281 (mm) REVERT: A 163 TYR cc_start: 0.8515 (t80) cc_final: 0.8256 (t80) REVERT: A 171 ARG cc_start: 0.7228 (mtm-85) cc_final: 0.6982 (mtm-85) REVERT: A 185 TYR cc_start: 0.8794 (m-80) cc_final: 0.8461 (m-80) REVERT: A 188 MET cc_start: 0.8387 (mmt) cc_final: 0.7957 (mmt) REVERT: A 214 SER cc_start: 0.8496 (t) cc_final: 0.7911 (p) REVERT: A 242 SER cc_start: 0.8203 (t) cc_final: 0.7699 (p) REVERT: A 243 VAL cc_start: 0.8057 (t) cc_final: 0.7796 (t) REVERT: A 266 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8497 (mt) REVERT: A 278 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8629 (p) REVERT: A 285 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.6912 (t80) REVERT: A 363 ASN cc_start: 0.8452 (t0) cc_final: 0.8155 (t0) REVERT: A 396 LYS cc_start: 0.8494 (mmmm) cc_final: 0.8019 (tppt) REVERT: A 399 ARG cc_start: 0.8008 (tpp80) cc_final: 0.7220 (tpp80) REVERT: A 403 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7072 (mt-10) REVERT: A 427 LYS cc_start: 0.8061 (tptt) cc_final: 0.7528 (mmtm) REVERT: B 24 MET cc_start: 0.8484 (pmm) cc_final: 0.8232 (pmm) REVERT: B 86 SER cc_start: 0.7204 (p) cc_final: 0.6838 (p) REVERT: B 111 ASN cc_start: 0.8651 (t0) cc_final: 0.8102 (t0) REVERT: B 115 LYS cc_start: 0.8769 (mptp) cc_final: 0.8017 (mptp) REVERT: B 140 SER cc_start: 0.8261 (p) cc_final: 0.8003 (p) REVERT: B 171 ARG cc_start: 0.7409 (mtm-85) cc_final: 0.7181 (mtm-85) REVERT: B 184 MET cc_start: 0.8493 (mmm) cc_final: 0.7813 (tpp) REVERT: B 236 CYS cc_start: 0.8103 (p) cc_final: 0.7849 (p) REVERT: B 245 SER cc_start: 0.8586 (p) cc_final: 0.8306 (t) REVERT: B 260 LEU cc_start: 0.8472 (mt) cc_final: 0.8227 (mt) REVERT: B 313 LEU cc_start: 0.8327 (mt) cc_final: 0.7964 (mm) REVERT: B 396 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7881 (mmtm) REVERT: B 400 LYS cc_start: 0.8396 (tppt) cc_final: 0.7982 (mppt) REVERT: B 433 LYS cc_start: 0.8562 (mmmt) cc_final: 0.8268 (mmtt) REVERT: B 436 ASP cc_start: 0.8346 (t0) cc_final: 0.7422 (t0) REVERT: C 24 MET cc_start: 0.8623 (pmm) cc_final: 0.8029 (pmm) REVERT: C 30 ARG cc_start: 0.7243 (ptp-170) cc_final: 0.7022 (ptp-170) REVERT: C 111 ASN cc_start: 0.8559 (t0) cc_final: 0.8287 (t0) REVERT: C 115 LYS cc_start: 0.8713 (mptp) cc_final: 0.8113 (mptp) REVERT: C 135 LEU cc_start: 0.8493 (mt) cc_final: 0.8070 (mm) REVERT: C 179 ASP cc_start: 0.7966 (t0) cc_final: 0.7750 (t0) REVERT: C 195 TYR cc_start: 0.8407 (m-80) cc_final: 0.8173 (m-80) REVERT: C 203 GLN cc_start: 0.8704 (mt0) cc_final: 0.8456 (mt0) REVERT: C 256 LYS cc_start: 0.8484 (ttpt) cc_final: 0.8153 (ttmt) REVERT: C 285 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7183 (t80) REVERT: C 324 GLU cc_start: 0.7239 (tt0) cc_final: 0.6951 (tt0) REVERT: C 358 LEU cc_start: 0.8893 (tp) cc_final: 0.8654 (tp) REVERT: C 403 GLU cc_start: 0.7741 (mp0) cc_final: 0.7293 (mp0) REVERT: C 427 LYS cc_start: 0.7917 (mmmm) cc_final: 0.7470 (mmmm) REVERT: C 436 ASP cc_start: 0.8215 (t0) cc_final: 0.7544 (t0) REVERT: D 28 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7350 (mm-30) REVERT: D 63 ASP cc_start: 0.7346 (t0) cc_final: 0.7008 (t0) REVERT: D 76 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8140 (mtp85) REVERT: D 88 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6891 (tm-30) REVERT: D 92 ARG cc_start: 0.8022 (mtp85) cc_final: 0.7256 (mtp85) REVERT: D 115 LYS cc_start: 0.8804 (mptp) cc_final: 0.8277 (mptp) REVERT: D 146 ASP cc_start: 0.6970 (p0) cc_final: 0.6060 (p0) REVERT: D 163 TYR cc_start: 0.8603 (t80) cc_final: 0.8256 (t80) REVERT: D 165 GLN cc_start: 0.8010 (mt0) cc_final: 0.7733 (mt0) REVERT: D 171 ARG cc_start: 0.7394 (mtm-85) cc_final: 0.6817 (mtm-85) REVERT: D 184 MET cc_start: 0.8312 (mmm) cc_final: 0.7993 (tpp) REVERT: D 197 THR cc_start: 0.8294 (p) cc_final: 0.8006 (t) REVERT: D 243 VAL cc_start: 0.8382 (m) cc_final: 0.8044 (p) REVERT: D 274 CYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7142 (m) REVERT: D 285 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.7542 (t80) REVERT: D 293 SER cc_start: 0.8160 (m) cc_final: 0.7587 (p) REVERT: D 340 ASP cc_start: 0.7617 (m-30) cc_final: 0.7126 (t0) REVERT: D 362 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8385 (tt) REVERT: D 380 LYS cc_start: 0.8519 (mmmm) cc_final: 0.8097 (mmtp) REVERT: D 426 GLN cc_start: 0.7248 (mt0) cc_final: 0.6948 (mt0) REVERT: D 448 ASP cc_start: 0.7630 (t0) cc_final: 0.7343 (t0) REVERT: E 16 LYS cc_start: 0.8510 (mmtt) cc_final: 0.8217 (mmmt) REVERT: E 24 MET cc_start: 0.8567 (pmm) cc_final: 0.8297 (pmm) REVERT: E 28 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7467 (mm-30) REVERT: E 76 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8180 (mtp85) REVERT: E 115 LYS cc_start: 0.8794 (mptp) cc_final: 0.8196 (mptp) REVERT: E 144 ARG cc_start: 0.8194 (ttm110) cc_final: 0.7704 (ttm110) REVERT: E 150 TYR cc_start: 0.8469 (m-80) cc_final: 0.8138 (m-80) REVERT: E 168 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8274 (mtpt) REVERT: E 184 MET cc_start: 0.8203 (mmm) cc_final: 0.7733 (mmm) REVERT: E 197 THR cc_start: 0.8389 (p) cc_final: 0.7976 (t) REVERT: E 236 CYS cc_start: 0.8252 (p) cc_final: 0.7941 (p) REVERT: E 275 ARG cc_start: 0.7884 (ttt180) cc_final: 0.7609 (ptt180) REVERT: E 405 GLU cc_start: 0.7515 (tp30) cc_final: 0.7167 (tp30) REVERT: E 406 LYS cc_start: 0.8491 (mmtp) cc_final: 0.7770 (mmtp) REVERT: E 436 ASP cc_start: 0.8431 (t0) cc_final: 0.7683 (t70) REVERT: E 447 PHE cc_start: 0.8453 (m-80) cc_final: 0.8007 (m-10) REVERT: F 16 LYS cc_start: 0.8606 (mptt) cc_final: 0.8252 (mppt) REVERT: F 30 ARG cc_start: 0.7262 (ptp-170) cc_final: 0.6802 (ttm110) REVERT: F 115 LYS cc_start: 0.8727 (mptp) cc_final: 0.8150 (mptp) REVERT: F 135 LEU cc_start: 0.8423 (mt) cc_final: 0.8192 (mm) REVERT: F 179 ASP cc_start: 0.8058 (t0) cc_final: 0.7751 (t70) REVERT: F 184 MET cc_start: 0.8495 (tpp) cc_final: 0.8175 (tpp) REVERT: F 188 MET cc_start: 0.8206 (mmt) cc_final: 0.7913 (mmt) REVERT: F 232 LYS cc_start: 0.8170 (ptmt) cc_final: 0.7769 (ptmt) REVERT: F 240 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7898 (mt) REVERT: F 258 TRP cc_start: 0.8441 (m100) cc_final: 0.7261 (m100) REVERT: F 325 ARG cc_start: 0.7639 (ptp-110) cc_final: 0.7405 (ttm170) REVERT: F 340 ASP cc_start: 0.7684 (t0) cc_final: 0.7431 (t0) REVERT: F 345 ILE cc_start: 0.8980 (mm) cc_final: 0.8752 (mm) REVERT: F 396 LYS cc_start: 0.8250 (mmtm) cc_final: 0.7849 (mmmm) REVERT: F 441 GLN cc_start: 0.7617 (mt0) cc_final: 0.7377 (mt0) REVERT: G 16 LYS cc_start: 0.8333 (mmtt) cc_final: 0.7985 (mmtt) REVERT: G 41 ARG cc_start: 0.7902 (tpp-160) cc_final: 0.7338 (tpp-160) REVERT: G 43 PHE cc_start: 0.8831 (t80) cc_final: 0.8382 (t80) REVERT: G 71 ARG cc_start: 0.8019 (mtm-85) cc_final: 0.7759 (mtm-85) REVERT: G 76 ARG cc_start: 0.8223 (mtt90) cc_final: 0.7903 (mtt90) REVERT: G 92 ARG cc_start: 0.7679 (mmp80) cc_final: 0.7344 (mmp80) REVERT: G 106 LYS cc_start: 0.8112 (mtmm) cc_final: 0.7870 (mtmm) REVERT: G 111 ASN cc_start: 0.8695 (t0) cc_final: 0.8072 (t0) REVERT: G 115 LYS cc_start: 0.8796 (mptp) cc_final: 0.8146 (mptp) REVERT: G 151 GLN cc_start: 0.8393 (tp40) cc_final: 0.8150 (tp40) REVERT: G 163 TYR cc_start: 0.8566 (t80) cc_final: 0.8174 (t80) REVERT: G 171 ARG cc_start: 0.7522 (mtm-85) cc_final: 0.7272 (mtm-85) REVERT: G 179 ASP cc_start: 0.8209 (t0) cc_final: 0.7758 (t70) REVERT: G 274 CYS cc_start: 0.8119 (m) cc_final: 0.7744 (m) REVERT: G 275 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7586 (ptt180) REVERT: G 285 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.6928 (t80) REVERT: G 293 SER cc_start: 0.8162 (m) cc_final: 0.7551 (p) REVERT: G 324 GLU cc_start: 0.7042 (tt0) cc_final: 0.6642 (tt0) REVERT: G 363 ASN cc_start: 0.8283 (t0) cc_final: 0.7845 (t0) REVERT: G 380 LYS cc_start: 0.8413 (mmmm) cc_final: 0.8171 (mmtp) REVERT: G 397 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7963 (mm-30) REVERT: G 399 ARG cc_start: 0.7817 (tpp80) cc_final: 0.7003 (tpp80) REVERT: G 400 LYS cc_start: 0.8293 (tppt) cc_final: 0.7806 (tppt) REVERT: G 403 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: G 406 LYS cc_start: 0.8849 (mmmm) cc_final: 0.8545 (mmtp) REVERT: G 430 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8323 (p) REVERT: G 448 ASP cc_start: 0.7504 (t0) cc_final: 0.7299 (t0) REVERT: H 28 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7361 (mm-30) REVERT: H 56 ASP cc_start: 0.7739 (t70) cc_final: 0.7439 (t70) REVERT: H 76 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7551 (mtt90) REVERT: H 88 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6672 (tm-30) REVERT: H 111 ASN cc_start: 0.8670 (t0) cc_final: 0.8092 (t0) REVERT: H 115 LYS cc_start: 0.8824 (mptp) cc_final: 0.8143 (mptp) REVERT: H 171 ARG cc_start: 0.7201 (mtm-85) cc_final: 0.6849 (mtm-85) REVERT: H 258 TRP cc_start: 0.8500 (m100) cc_final: 0.8252 (m100) REVERT: H 275 ARG cc_start: 0.7829 (ttt180) cc_final: 0.7421 (ptt180) REVERT: H 399 ARG cc_start: 0.7769 (tpp80) cc_final: 0.7315 (tpp-160) REVERT: H 400 LYS cc_start: 0.8141 (tppt) cc_final: 0.7749 (tppt) REVERT: H 436 ASP cc_start: 0.8407 (t0) cc_final: 0.8046 (t70) REVERT: H 447 PHE cc_start: 0.8485 (m-80) cc_final: 0.8117 (m-80) REVERT: I 16 LYS cc_start: 0.8495 (mppt) cc_final: 0.8225 (mtpt) REVERT: I 22 TYR cc_start: 0.8405 (m-80) cc_final: 0.8090 (m-80) REVERT: I 72 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7668 (tmm) REVERT: I 106 LYS cc_start: 0.8202 (mtmm) cc_final: 0.7826 (mtmm) REVERT: I 111 ASN cc_start: 0.8570 (t0) cc_final: 0.8153 (t0) REVERT: I 115 LYS cc_start: 0.8757 (mptp) cc_final: 0.8106 (mptp) REVERT: I 184 MET cc_start: 0.8572 (tpp) cc_final: 0.8044 (tpp) REVERT: I 204 VAL cc_start: 0.8812 (m) cc_final: 0.8609 (t) REVERT: I 289 ARG cc_start: 0.8011 (ttp80) cc_final: 0.7538 (mtp-110) REVERT: I 357 LYS cc_start: 0.8707 (ttmm) cc_final: 0.8430 (ttmt) REVERT: I 362 LEU cc_start: 0.8755 (mm) cc_final: 0.8538 (tt) REVERT: I 400 LYS cc_start: 0.8240 (tppt) cc_final: 0.7778 (ttpt) REVERT: I 405 GLU cc_start: 0.7819 (mp0) cc_final: 0.7360 (mp0) REVERT: I 441 GLN cc_start: 0.7668 (mt0) cc_final: 0.7403 (mt0) REVERT: I 446 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7308 (mm-30) REVERT: J 20 ARG cc_start: 0.8091 (mtp-110) cc_final: 0.7846 (mtp-110) REVERT: J 28 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7350 (mm-30) REVERT: J 76 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8138 (mtt90) REVERT: J 92 ARG cc_start: 0.7643 (mmp80) cc_final: 0.7179 (mmp80) REVERT: J 111 ASN cc_start: 0.8671 (t0) cc_final: 0.7975 (t0) REVERT: J 115 LYS cc_start: 0.8773 (mptp) cc_final: 0.8089 (mptp) REVERT: J 140 SER cc_start: 0.8183 (p) cc_final: 0.7931 (p) REVERT: J 163 TYR cc_start: 0.8601 (t80) cc_final: 0.8341 (t80) REVERT: J 171 ARG cc_start: 0.7650 (mtm-85) cc_final: 0.7065 (mtm-85) REVERT: J 195 TYR cc_start: 0.8472 (m-80) cc_final: 0.8208 (m-80) REVERT: J 274 CYS cc_start: 0.8093 (m) cc_final: 0.7802 (m) REVERT: J 275 ARG cc_start: 0.7733 (ttt180) cc_final: 0.7296 (ptt180) REVERT: J 278 THR cc_start: 0.8889 (m) cc_final: 0.8551 (p) REVERT: J 283 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: J 285 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.6844 (t80) REVERT: J 313 LEU cc_start: 0.8316 (mt) cc_final: 0.7936 (mp) REVERT: J 324 GLU cc_start: 0.7281 (tt0) cc_final: 0.6992 (tt0) REVERT: J 393 LYS cc_start: 0.8549 (mttp) cc_final: 0.8302 (mttp) REVERT: J 397 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7814 (mm-30) REVERT: J 400 LYS cc_start: 0.8251 (tppt) cc_final: 0.7359 (tppt) REVERT: J 403 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: J 404 ASP cc_start: 0.7918 (m-30) cc_final: 0.7624 (m-30) REVERT: J 406 LYS cc_start: 0.8754 (mmtp) cc_final: 0.8554 (mmtp) REVERT: K 28 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7430 (mm-30) REVERT: K 76 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7935 (mtt90) REVERT: K 115 LYS cc_start: 0.8788 (mptp) cc_final: 0.8202 (mptp) REVERT: K 171 ARG cc_start: 0.7301 (mtm-85) cc_final: 0.6920 (mtm-85) REVERT: K 238 ARG cc_start: 0.7750 (ttm110) cc_final: 0.7389 (mtm110) REVERT: K 274 CYS cc_start: 0.8136 (m) cc_final: 0.7477 (m) REVERT: K 289 ARG cc_start: 0.7715 (ttp80) cc_final: 0.7409 (mtp-110) REVERT: K 313 LEU cc_start: 0.8328 (mt) cc_final: 0.7973 (mm) REVERT: K 340 ASP cc_start: 0.7785 (t0) cc_final: 0.7404 (t0) REVERT: K 341 GLN cc_start: 0.8265 (tt0) cc_final: 0.8029 (tt0) REVERT: L 20 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7680 (mtm-85) REVERT: L 43 PHE cc_start: 0.8897 (t80) cc_final: 0.8140 (t80) REVERT: L 51 ILE cc_start: 0.8595 (mm) cc_final: 0.8335 (mm) REVERT: L 63 ASP cc_start: 0.7527 (t0) cc_final: 0.6797 (t0) REVERT: L 71 ARG cc_start: 0.7883 (mtm-85) cc_final: 0.7416 (ptp-110) REVERT: L 92 ARG cc_start: 0.7809 (mmp80) cc_final: 0.7269 (mmp80) REVERT: L 106 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8136 (mtmm) REVERT: L 115 LYS cc_start: 0.8838 (mptp) cc_final: 0.8162 (mptp) REVERT: L 168 LYS cc_start: 0.8881 (mtmt) cc_final: 0.8436 (mtpp) REVERT: L 171 ARG cc_start: 0.7117 (mtm-85) cc_final: 0.6701 (mtm-85) REVERT: L 179 ASP cc_start: 0.8081 (t0) cc_final: 0.7779 (t0) REVERT: L 184 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.8057 (tpp) REVERT: L 195 TYR cc_start: 0.8472 (m-80) cc_final: 0.8204 (m-80) REVERT: L 202 GLU cc_start: 0.8094 (tp30) cc_final: 0.7600 (tp30) REVERT: L 232 LYS cc_start: 0.8328 (ptmt) cc_final: 0.7877 (ptmt) REVERT: L 238 ARG cc_start: 0.7679 (ttm110) cc_final: 0.7400 (mtm110) REVERT: L 258 TRP cc_start: 0.8623 (m100) cc_final: 0.7592 (m100) REVERT: L 266 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8469 (mt) REVERT: L 283 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: L 285 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7154 (t80) REVERT: L 400 LYS cc_start: 0.8080 (tppt) cc_final: 0.7872 (tppt) REVERT: L 402 MET cc_start: 0.7409 (tpp) cc_final: 0.7038 (tpp) REVERT: L 403 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: L 405 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: L 427 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7333 (mmtt) REVERT: L 429 HIS cc_start: 0.8480 (OUTLIER) cc_final: 0.8052 (m-70) outliers start: 242 outliers final: 179 residues processed: 1938 average time/residue: 0.2836 time to fit residues: 851.0440 Evaluate side-chains 2039 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 1825 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 396 LYS Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 53 GLN Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 292 MET Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 238 ARG Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 275 ARG Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 411 ARG Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 292 MET Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 342 MET Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 398 CYS Chi-restraints excluded: chain H residue 403 GLU Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 429 HIS Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 314 MET Chi-restraints excluded: chain I residue 319 ASP Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 76 ARG Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 236 CYS Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 283 GLU Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain J residue 301 THR Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 403 GLU Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 283 GLU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain K residue 349 GLU Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 398 CYS Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain K residue 408 LEU Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain L residue 120 GLN Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 152 ASP Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain L residue 194 SER Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 283 GLU Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain L residue 348 THR Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 405 GLU Chi-restraints excluded: chain L residue 427 LYS Chi-restraints excluded: chain L residue 429 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 440 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 238 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 262 optimal weight: 0.7980 chunk 300 optimal weight: 5.9990 chunk 331 optimal weight: 0.5980 chunk 82 optimal weight: 20.0000 chunk 103 optimal weight: 0.4980 chunk 173 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.133835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117502 restraints weight = 64340.496| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.82 r_work: 0.3416 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 42540 Z= 0.128 Angle : 0.685 14.307 57612 Z= 0.328 Chirality : 0.043 0.144 6564 Planarity : 0.005 0.128 7248 Dihedral : 13.573 178.343 6348 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 5.57 % Allowed : 32.88 % Favored : 61.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.97 % Twisted General : 0.02 % 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: -0.98 (0.11), residues: 5148 helix: 1.42 (0.13), residues: 1692 sheet: -0.86 (0.15), residues: 1056 loop : -2.15 (0.11), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 30 TYR 0.024 0.002 TYR G 5 PHE 0.033 0.002 PHE B 264 TRP 0.018 0.002 TRP C 258 HIS 0.004 0.001 HIS G 429 Details of bonding type rmsd covalent geometry : bond 0.00306 (42480) covalent geometry : angle 0.68522 (57612) hydrogen bonds : bond 0.02762 ( 1577) hydrogen bonds : angle 4.38741 ( 4476) metal coordination : bond 0.00461 ( 36) Misc. bond : bond 0.00034 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2096 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 1850 time to evaluate : 1.581 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: 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: 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 41 ARG cc_start: 0.7906 (tpp-160) cc_final: 0.7354 (tpp-160) REVERT: A 43 PHE cc_start: 0.8794 (t80) cc_final: 0.8420 (t80) REVERT: A 76 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7841 (mtt90) REVERT: A 88 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6161 (tm-30) REVERT: A 92 ARG cc_start: 0.7604 (mmp80) cc_final: 0.7081 (mmp80) REVERT: A 133 PHE cc_start: 0.7915 (t80) cc_final: 0.7601 (t80) REVERT: A 135 LEU cc_start: 0.8587 (mt) cc_final: 0.8261 (mm) REVERT: A 163 TYR cc_start: 0.8515 (t80) cc_final: 0.8227 (t80) REVERT: A 171 ARG cc_start: 0.7208 (mtm-85) cc_final: 0.6971 (mtm-85) REVERT: A 188 MET cc_start: 0.8396 (mmt) cc_final: 0.7942 (mmt) REVERT: A 214 SER cc_start: 0.8479 (t) cc_final: 0.7904 (p) REVERT: A 242 SER cc_start: 0.8195 (t) cc_final: 0.7662 (p) REVERT: A 243 VAL cc_start: 0.8031 (t) cc_final: 0.7743 (t) REVERT: A 248 TYR cc_start: 0.8070 (m-10) cc_final: 0.7746 (m-10) REVERT: A 278 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8635 (p) REVERT: A 285 TYR cc_start: 0.8352 (OUTLIER) cc_final: 0.6920 (t80) REVERT: A 363 ASN cc_start: 0.8472 (t0) cc_final: 0.8142 (t0) REVERT: A 399 ARG cc_start: 0.7983 (tpp80) cc_final: 0.7198 (tpp80) REVERT: A 403 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7062 (mt-10) REVERT: A 427 LYS cc_start: 0.8074 (tptt) cc_final: 0.7492 (tttt) REVERT: B 24 MET cc_start: 0.8483 (pmm) cc_final: 0.8234 (pmm) REVERT: B 86 SER cc_start: 0.7125 (p) cc_final: 0.6761 (p) REVERT: B 111 ASN cc_start: 0.8653 (t0) cc_final: 0.8090 (t0) REVERT: B 115 LYS cc_start: 0.8777 (mptp) cc_final: 0.8013 (mptp) REVERT: B 140 SER cc_start: 0.8246 (p) cc_final: 0.7982 (p) REVERT: B 171 ARG cc_start: 0.7393 (mtm-85) cc_final: 0.7162 (mtm-85) REVERT: B 184 MET cc_start: 0.8502 (mmm) cc_final: 0.7970 (mmm) REVERT: B 236 CYS cc_start: 0.8116 (p) cc_final: 0.7852 (p) REVERT: B 245 SER cc_start: 0.8547 (p) cc_final: 0.8262 (t) REVERT: B 313 LEU cc_start: 0.8306 (mt) cc_final: 0.7963 (mm) REVERT: B 340 ASP cc_start: 0.7751 (t0) cc_final: 0.7339 (t0) REVERT: B 396 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7831 (mmtm) REVERT: B 400 LYS cc_start: 0.8370 (tppt) cc_final: 0.7930 (mppt) REVERT: B 405 GLU cc_start: 0.7737 (tp30) cc_final: 0.7393 (mp0) REVERT: B 436 ASP cc_start: 0.8333 (t0) cc_final: 0.7429 (t0) REVERT: C 24 MET cc_start: 0.8645 (pmm) cc_final: 0.8045 (pmm) REVERT: C 111 ASN cc_start: 0.8607 (t0) cc_final: 0.8278 (t0) REVERT: C 115 LYS cc_start: 0.8737 (mptp) cc_final: 0.8107 (mptp) REVERT: C 135 LEU cc_start: 0.8504 (mt) cc_final: 0.8080 (mm) REVERT: C 179 ASP cc_start: 0.7991 (t0) cc_final: 0.7726 (t0) REVERT: C 184 MET cc_start: 0.8613 (mmm) cc_final: 0.8208 (mmm) REVERT: C 195 TYR cc_start: 0.8401 (m-80) cc_final: 0.8179 (m-80) REVERT: C 203 GLN cc_start: 0.8728 (mt0) cc_final: 0.8460 (mt0) REVERT: C 256 LYS cc_start: 0.8477 (ttpt) cc_final: 0.8161 (ttmt) REVERT: C 285 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.7287 (t80) REVERT: C 358 LEU cc_start: 0.8880 (tp) cc_final: 0.8628 (tp) REVERT: C 403 GLU cc_start: 0.7778 (mp0) cc_final: 0.7314 (mp0) REVERT: C 427 LYS cc_start: 0.7888 (mmmm) cc_final: 0.7455 (mmmm) REVERT: C 436 ASP cc_start: 0.8220 (t0) cc_final: 0.7558 (t0) REVERT: D 28 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7379 (mm-30) REVERT: D 63 ASP cc_start: 0.7425 (t0) cc_final: 0.7196 (t0) REVERT: D 76 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8050 (mtt90) REVERT: D 88 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6824 (tm-30) REVERT: D 92 ARG cc_start: 0.7997 (mtp85) cc_final: 0.7272 (mtp85) REVERT: D 115 LYS cc_start: 0.8824 (mptp) cc_final: 0.8287 (mptp) REVERT: D 163 TYR cc_start: 0.8565 (t80) cc_final: 0.8235 (t80) REVERT: D 165 GLN cc_start: 0.8019 (mt0) cc_final: 0.7752 (mt0) REVERT: D 171 ARG cc_start: 0.7319 (mtm-85) cc_final: 0.6857 (mtm-85) REVERT: D 179 ASP cc_start: 0.8132 (t0) cc_final: 0.7644 (t0) REVERT: D 197 THR cc_start: 0.8298 (p) cc_final: 0.7978 (t) REVERT: D 243 VAL cc_start: 0.8347 (m) cc_final: 0.8020 (p) REVERT: D 274 CYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7702 (m) REVERT: D 285 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7476 (t80) REVERT: D 293 SER cc_start: 0.8136 (m) cc_final: 0.7543 (p) REVERT: D 340 ASP cc_start: 0.7635 (m-30) cc_final: 0.7153 (t0) REVERT: D 362 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8376 (tt) REVERT: D 380 LYS cc_start: 0.8504 (mmmm) cc_final: 0.8087 (mmtp) REVERT: D 426 GLN cc_start: 0.7203 (mt0) cc_final: 0.6959 (mt0) REVERT: D 448 ASP cc_start: 0.7635 (t0) cc_final: 0.7335 (t0) REVERT: E 16 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8208 (mmmt) REVERT: E 24 MET cc_start: 0.8564 (pmm) cc_final: 0.8326 (pmm) REVERT: E 53 GLN cc_start: 0.8348 (tp40) cc_final: 0.7761 (tt0) REVERT: E 111 ASN cc_start: 0.8677 (t0) cc_final: 0.8252 (t0) REVERT: E 115 LYS cc_start: 0.8818 (mptp) cc_final: 0.8151 (mptp) REVERT: E 144 ARG cc_start: 0.8195 (ttm110) cc_final: 0.7648 (ttm110) REVERT: E 150 TYR cc_start: 0.8467 (m-80) cc_final: 0.8148 (m-80) REVERT: E 168 LYS cc_start: 0.8863 (mtmt) cc_final: 0.8205 (mtpt) REVERT: E 180 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7852 (m) REVERT: E 184 MET cc_start: 0.8201 (mmm) cc_final: 0.7728 (mmm) REVERT: E 197 THR cc_start: 0.8383 (p) cc_final: 0.7959 (t) REVERT: E 236 CYS cc_start: 0.8264 (p) cc_final: 0.7950 (p) REVERT: E 275 ARG cc_start: 0.7912 (ttt180) cc_final: 0.7636 (ptt180) REVERT: E 289 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7579 (mtp-110) REVERT: E 313 LEU cc_start: 0.8354 (mt) cc_final: 0.7958 (mm) REVERT: E 436 ASP cc_start: 0.8424 (t0) cc_final: 0.7649 (t70) REVERT: E 447 PHE cc_start: 0.8363 (m-80) cc_final: 0.7976 (m-10) REVERT: F 30 ARG cc_start: 0.7247 (ptp-170) cc_final: 0.6783 (ttm110) REVERT: F 54 GLU cc_start: 0.8376 (tp30) cc_final: 0.8055 (tp30) REVERT: F 115 LYS cc_start: 0.8748 (mptp) cc_final: 0.8157 (mptp) REVERT: F 135 LEU cc_start: 0.8421 (mt) cc_final: 0.8160 (mm) REVERT: F 184 MET cc_start: 0.8521 (tpp) cc_final: 0.8168 (tpp) REVERT: F 188 MET cc_start: 0.8254 (mmt) cc_final: 0.7954 (mmt) REVERT: F 232 LYS cc_start: 0.8157 (ptmt) cc_final: 0.7759 (ptmt) REVERT: F 240 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7865 (mt) REVERT: F 325 ARG cc_start: 0.7624 (ptp-110) cc_final: 0.7263 (ttm110) REVERT: F 340 ASP cc_start: 0.7691 (t0) cc_final: 0.7427 (t0) REVERT: F 345 ILE cc_start: 0.8982 (mm) cc_final: 0.8775 (mm) REVERT: F 396 LYS cc_start: 0.8237 (mmtm) cc_final: 0.7825 (mmmm) REVERT: F 406 LYS cc_start: 0.8738 (mmtp) cc_final: 0.8366 (mmtt) REVERT: F 441 GLN cc_start: 0.7671 (mt0) cc_final: 0.7428 (mt0) REVERT: G 20 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.7719 (mtm-85) REVERT: G 41 ARG cc_start: 0.7936 (tpp-160) cc_final: 0.7340 (tpp-160) REVERT: G 43 PHE cc_start: 0.8839 (t80) cc_final: 0.8380 (t80) REVERT: G 71 ARG cc_start: 0.7999 (mtm-85) cc_final: 0.7692 (mtm-85) REVERT: G 76 ARG cc_start: 0.8230 (mtt90) cc_final: 0.7910 (mtt90) REVERT: G 92 ARG cc_start: 0.7716 (mmp80) cc_final: 0.7274 (mmp80) REVERT: G 106 LYS cc_start: 0.8158 (mtmm) cc_final: 0.7913 (mtmm) REVERT: G 111 ASN cc_start: 0.8690 (t0) cc_final: 0.8087 (t0) REVERT: G 115 LYS cc_start: 0.8814 (mptp) cc_final: 0.8135 (mptp) REVERT: G 151 GLN cc_start: 0.8354 (tp40) cc_final: 0.8125 (tp40) REVERT: G 163 TYR cc_start: 0.8574 (t80) cc_final: 0.8138 (t80) REVERT: G 171 ARG cc_start: 0.7589 (mtm-85) cc_final: 0.7381 (mtm-85) REVERT: G 179 ASP cc_start: 0.8230 (t0) cc_final: 0.7799 (t70) REVERT: G 188 MET cc_start: 0.8317 (tpp) cc_final: 0.7956 (mmt) REVERT: G 234 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7476 (mm-30) REVERT: G 274 CYS cc_start: 0.8114 (m) cc_final: 0.7750 (m) REVERT: G 275 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7612 (ptt180) REVERT: G 285 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.6904 (t80) REVERT: G 293 SER cc_start: 0.8142 (m) cc_final: 0.7496 (p) REVERT: G 324 GLU cc_start: 0.7022 (tt0) cc_final: 0.6644 (tt0) REVERT: G 363 ASN cc_start: 0.8249 (t0) cc_final: 0.7813 (t0) REVERT: G 380 LYS cc_start: 0.8352 (mmmm) cc_final: 0.8149 (mmtp) REVERT: G 399 ARG cc_start: 0.7788 (tpp80) cc_final: 0.6977 (tpp80) REVERT: G 400 LYS cc_start: 0.8268 (tppt) cc_final: 0.7800 (tppt) REVERT: G 403 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: G 406 LYS cc_start: 0.8850 (mmmm) cc_final: 0.8543 (mmtp) REVERT: G 430 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8301 (p) REVERT: H 28 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7314 (mm-30) REVERT: H 56 ASP cc_start: 0.7733 (t70) cc_final: 0.7439 (t70) REVERT: H 76 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7575 (mtt90) REVERT: H 88 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6630 (tm-30) REVERT: H 111 ASN cc_start: 0.8690 (t0) cc_final: 0.8159 (t0) REVERT: H 115 LYS cc_start: 0.8835 (mptp) cc_final: 0.8170 (mptp) REVERT: H 150 TYR cc_start: 0.8548 (m-80) cc_final: 0.8225 (m-80) REVERT: H 171 ARG cc_start: 0.7194 (mtm-85) cc_final: 0.6828 (mtm-85) REVERT: H 258 TRP cc_start: 0.8510 (m100) cc_final: 0.8276 (m100) REVERT: H 275 ARG cc_start: 0.7838 (ttt180) cc_final: 0.7429 (ptt180) REVERT: H 303 TYR cc_start: 0.8577 (m-80) cc_final: 0.8354 (m-80) REVERT: H 362 LEU cc_start: 0.8594 (mm) cc_final: 0.8375 (tt) REVERT: H 399 ARG cc_start: 0.7727 (tpp80) cc_final: 0.7294 (tpp-160) REVERT: H 400 LYS cc_start: 0.8138 (tppt) cc_final: 0.7737 (tppt) REVERT: H 436 ASP cc_start: 0.8410 (t0) cc_final: 0.8039 (t70) REVERT: H 447 PHE cc_start: 0.8474 (m-80) cc_final: 0.8072 (m-80) REVERT: I 16 LYS cc_start: 0.8473 (mppt) cc_final: 0.8190 (mtpt) REVERT: I 22 TYR cc_start: 0.8424 (m-80) cc_final: 0.8099 (m-80) REVERT: I 72 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7693 (tmm) REVERT: I 106 LYS cc_start: 0.8251 (mtmm) cc_final: 0.7849 (mtmm) REVERT: I 111 ASN cc_start: 0.8545 (t0) cc_final: 0.8205 (t0) REVERT: I 115 LYS cc_start: 0.8760 (mptp) cc_final: 0.8093 (mptp) REVERT: I 184 MET cc_start: 0.8570 (tpp) cc_final: 0.8147 (tpp) REVERT: I 289 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7480 (mtp-110) REVERT: I 357 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8429 (ttmt) REVERT: I 400 LYS cc_start: 0.8226 (tppt) cc_final: 0.7536 (ttpt) REVERT: I 404 ASP cc_start: 0.8129 (m-30) cc_final: 0.7865 (m-30) REVERT: I 405 GLU cc_start: 0.7866 (mp0) cc_final: 0.7393 (mp0) REVERT: I 436 ASP cc_start: 0.8363 (t0) cc_final: 0.7982 (t0) REVERT: I 441 GLN cc_start: 0.7668 (mt0) cc_final: 0.7384 (mt0) REVERT: I 446 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7393 (mm-30) REVERT: J 20 ARG cc_start: 0.8116 (mtp-110) cc_final: 0.7881 (mtp-110) REVERT: J 28 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7328 (mm-30) REVERT: J 43 PHE cc_start: 0.8790 (t80) cc_final: 0.8491 (t80) REVERT: J 76 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8110 (mtt90) REVERT: J 92 ARG cc_start: 0.7697 (mmp80) cc_final: 0.7193 (mmp80) REVERT: J 99 LYS cc_start: 0.8945 (mmmm) cc_final: 0.8660 (mmmm) REVERT: J 115 LYS cc_start: 0.8771 (mptp) cc_final: 0.8167 (mptp) REVERT: J 140 SER cc_start: 0.8175 (p) cc_final: 0.7925 (p) REVERT: J 163 TYR cc_start: 0.8536 (t80) cc_final: 0.8280 (t80) REVERT: J 171 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.7072 (mtm-85) REVERT: J 183 PHE cc_start: 0.8523 (m-80) cc_final: 0.8166 (m-80) REVERT: J 195 TYR cc_start: 0.8441 (m-80) cc_final: 0.8125 (m-80) REVERT: J 274 CYS cc_start: 0.8105 (m) cc_final: 0.7804 (m) REVERT: J 275 ARG cc_start: 0.7747 (ttt180) cc_final: 0.7398 (ptt180) REVERT: J 278 THR cc_start: 0.8860 (m) cc_final: 0.8543 (p) REVERT: J 283 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: J 285 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.6660 (t80) REVERT: J 313 LEU cc_start: 0.8272 (mt) cc_final: 0.7917 (mp) REVERT: J 324 GLU cc_start: 0.7324 (tt0) cc_final: 0.7015 (tt0) REVERT: J 357 LYS cc_start: 0.8626 (ttmm) cc_final: 0.8405 (ttmt) REVERT: J 393 LYS cc_start: 0.8545 (mttp) cc_final: 0.8276 (mttp) REVERT: J 397 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7842 (mm-30) REVERT: J 400 LYS cc_start: 0.8232 (tppt) cc_final: 0.7333 (tppt) REVERT: J 403 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: J 404 ASP cc_start: 0.7947 (m-30) cc_final: 0.7617 (m-30) REVERT: K 28 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7413 (mm-30) REVERT: K 76 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7926 (mtt90) REVERT: K 115 LYS cc_start: 0.8797 (mptp) cc_final: 0.8216 (mptp) REVERT: K 171 ARG cc_start: 0.7248 (mtm-85) cc_final: 0.6866 (mtm-85) REVERT: K 238 ARG cc_start: 0.7778 (ttm110) cc_final: 0.7399 (mtm110) REVERT: K 264 PHE cc_start: 0.8202 (p90) cc_final: 0.7891 (p90) REVERT: K 274 CYS cc_start: 0.8071 (m) cc_final: 0.7564 (m) REVERT: K 289 ARG cc_start: 0.7733 (ttp80) cc_final: 0.7411 (mtp-110) REVERT: K 313 LEU cc_start: 0.8324 (mt) cc_final: 0.7968 (mm) REVERT: K 340 ASP cc_start: 0.7788 (t0) cc_final: 0.7398 (t0) REVERT: K 341 GLN cc_start: 0.8280 (tt0) cc_final: 0.7979 (tt0) REVERT: K 436 ASP cc_start: 0.8415 (t0) cc_final: 0.7841 (t0) REVERT: L 20 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7672 (mtm-85) REVERT: L 43 PHE cc_start: 0.8882 (t80) cc_final: 0.8082 (t80) REVERT: L 51 ILE cc_start: 0.8622 (mm) cc_final: 0.8375 (mm) REVERT: L 92 ARG cc_start: 0.7844 (mmp80) cc_final: 0.7287 (mmp80) REVERT: L 106 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8202 (mtmm) REVERT: L 115 LYS cc_start: 0.8839 (mptp) cc_final: 0.8149 (mptp) REVERT: L 168 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8427 (mtpp) REVERT: L 171 ARG cc_start: 0.7138 (mtm-85) cc_final: 0.6656 (mtm-85) REVERT: L 184 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.8063 (tpp) REVERT: L 195 TYR cc_start: 0.8471 (m-80) cc_final: 0.8177 (m-80) REVERT: L 202 GLU cc_start: 0.8109 (tp30) cc_final: 0.7653 (tp30) REVERT: L 232 LYS cc_start: 0.8347 (ptmt) cc_final: 0.7893 (ptmt) REVERT: L 238 ARG cc_start: 0.7698 (ttm110) cc_final: 0.7403 (mtm110) REVERT: L 258 TRP cc_start: 0.8624 (m100) cc_final: 0.7567 (m100) REVERT: L 266 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8447 (mt) REVERT: L 283 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: L 285 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.7161 (t80) REVERT: L 400 LYS cc_start: 0.8036 (tppt) cc_final: 0.7794 (tppt) REVERT: L 403 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: L 427 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7339 (mmtt) REVERT: L 429 HIS cc_start: 0.8477 (OUTLIER) cc_final: 0.8173 (m-70) outliers start: 246 outliers final: 185 residues processed: 1939 average time/residue: 0.2906 time to fit residues: 870.2829 Evaluate side-chains 2053 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 1835 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 396 LYS Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 238 ARG Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 275 ARG Chi-restraints excluded: chain G residue 283 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 396 LYS Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 411 ARG Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain H residue 19 GLN Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 342 MET Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 396 LYS Chi-restraints excluded: chain H residue 398 CYS Chi-restraints excluded: chain H residue 403 GLU Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 429 HIS Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 314 MET Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain I residue 425 LYS Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 76 ARG Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 236 CYS Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 283 GLU Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain J residue 301 THR Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 403 GLU Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 283 GLU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 398 CYS Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain K residue 408 LEU Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain L residue 120 GLN Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 152 ASP Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain L residue 194 SER Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 283 GLU Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain L residue 348 THR Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 427 LYS Chi-restraints excluded: chain L residue 429 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 507 optimal weight: 0.9990 chunk 269 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 428 optimal weight: 0.2980 chunk 440 optimal weight: 3.9990 chunk 364 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 278 optimal weight: 0.9990 chunk 469 optimal weight: 0.6980 chunk 361 optimal weight: 0.6980 chunk 254 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.133991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.117492 restraints weight = 64400.857| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.82 r_work: 0.3416 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 42540 Z= 0.132 Angle : 0.698 14.336 57612 Z= 0.335 Chirality : 0.044 0.342 6564 Planarity : 0.005 0.085 7248 Dihedral : 13.542 179.374 6348 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 5.25 % Allowed : 33.51 % Favored : 61.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.97 % 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: -0.95 (0.11), residues: 5148 helix: 1.47 (0.14), residues: 1692 sheet: -1.05 (0.14), residues: 1260 loop : -2.10 (0.11), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 30 TYR 0.032 0.002 TYR G 5 PHE 0.030 0.002 PHE B 264 TRP 0.017 0.002 TRP C 258 HIS 0.006 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00314 (42480) covalent geometry : angle 0.69770 (57612) hydrogen bonds : bond 0.02772 ( 1577) hydrogen bonds : angle 4.36033 ( 4476) metal coordination : bond 0.00467 ( 36) Misc. bond : bond 0.00036 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2056 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 1824 time to evaluate : 1.497 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: 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: 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 41 ARG cc_start: 0.7912 (tpp-160) cc_final: 0.7375 (tpp-160) REVERT: A 43 PHE cc_start: 0.8800 (t80) cc_final: 0.8449 (t80) REVERT: A 71 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7775 (mtm110) REVERT: A 76 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7868 (mtt90) REVERT: A 88 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6153 (tm-30) REVERT: A 92 ARG cc_start: 0.7610 (mmp80) cc_final: 0.7113 (mmp80) REVERT: A 133 PHE cc_start: 0.7972 (t80) cc_final: 0.7639 (t80) REVERT: A 135 LEU cc_start: 0.8594 (mt) cc_final: 0.8266 (mm) REVERT: A 137 THR cc_start: 0.8246 (m) cc_final: 0.7856 (t) REVERT: A 163 TYR cc_start: 0.8534 (t80) cc_final: 0.8277 (t80) REVERT: A 171 ARG cc_start: 0.7201 (mtm-85) cc_final: 0.6947 (mtm-85) REVERT: A 188 MET cc_start: 0.8431 (mmt) cc_final: 0.7964 (mmt) REVERT: A 214 SER cc_start: 0.8497 (t) cc_final: 0.7920 (p) REVERT: A 242 SER cc_start: 0.8222 (t) cc_final: 0.7676 (p) REVERT: A 243 VAL cc_start: 0.8060 (t) cc_final: 0.7772 (t) REVERT: A 248 TYR cc_start: 0.8047 (m-10) cc_final: 0.7744 (m-10) REVERT: A 266 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8489 (mt) REVERT: A 278 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8599 (p) REVERT: A 285 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.6971 (t80) REVERT: A 363 ASN cc_start: 0.8405 (t0) cc_final: 0.8141 (t0) REVERT: A 399 ARG cc_start: 0.7972 (tpp80) cc_final: 0.7183 (tpp80) REVERT: A 403 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7066 (mt-10) REVERT: A 427 LYS cc_start: 0.8053 (tptt) cc_final: 0.7537 (tttt) REVERT: B 24 MET cc_start: 0.8441 (pmm) cc_final: 0.8206 (pmm) REVERT: B 41 ARG cc_start: 0.7906 (tpp-160) cc_final: 0.7380 (tpp-160) REVERT: B 63 ASP cc_start: 0.6978 (t0) cc_final: 0.6569 (t0) REVERT: B 71 ARG cc_start: 0.8219 (mtm-85) cc_final: 0.7997 (mtm-85) REVERT: B 86 SER cc_start: 0.7149 (p) cc_final: 0.6782 (p) REVERT: B 111 ASN cc_start: 0.8642 (t0) cc_final: 0.8086 (t0) REVERT: B 115 LYS cc_start: 0.8787 (mptp) cc_final: 0.8026 (mptp) REVERT: B 140 SER cc_start: 0.8253 (p) cc_final: 0.7984 (p) REVERT: B 171 ARG cc_start: 0.7395 (mtm-85) cc_final: 0.7106 (mtm-85) REVERT: B 184 MET cc_start: 0.8516 (mmm) cc_final: 0.7982 (mmm) REVERT: B 236 CYS cc_start: 0.8152 (p) cc_final: 0.7877 (p) REVERT: B 245 SER cc_start: 0.8577 (p) cc_final: 0.8298 (t) REVERT: B 274 CYS cc_start: 0.8138 (m) cc_final: 0.7859 (m) REVERT: B 313 LEU cc_start: 0.8299 (mt) cc_final: 0.7963 (mm) REVERT: B 340 ASP cc_start: 0.7743 (t0) cc_final: 0.7338 (t0) REVERT: B 400 LYS cc_start: 0.8338 (tppt) cc_final: 0.7819 (mppt) REVERT: B 405 GLU cc_start: 0.7743 (tp30) cc_final: 0.7367 (mp0) REVERT: B 436 ASP cc_start: 0.8320 (t0) cc_final: 0.7755 (t70) REVERT: C 24 MET cc_start: 0.8634 (pmm) cc_final: 0.8048 (pmm) REVERT: C 111 ASN cc_start: 0.8614 (t0) cc_final: 0.8229 (t0) REVERT: C 115 LYS cc_start: 0.8733 (mptp) cc_final: 0.8077 (mptp) REVERT: C 135 LEU cc_start: 0.8506 (mt) cc_final: 0.8080 (mm) REVERT: C 195 TYR cc_start: 0.8404 (m-80) cc_final: 0.8182 (m-80) REVERT: C 203 GLN cc_start: 0.8707 (mt0) cc_final: 0.8429 (mt0) REVERT: C 256 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8138 (ttmt) REVERT: C 258 TRP cc_start: 0.8370 (m100) cc_final: 0.7107 (m100) REVERT: C 285 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.7173 (t80) REVERT: C 358 LEU cc_start: 0.8865 (tp) cc_final: 0.8622 (tp) REVERT: C 403 GLU cc_start: 0.7775 (mp0) cc_final: 0.7306 (mp0) REVERT: C 427 LYS cc_start: 0.7885 (mmmm) cc_final: 0.7471 (mmmm) REVERT: C 436 ASP cc_start: 0.8207 (t0) cc_final: 0.7564 (t0) REVERT: D 28 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7357 (mm-30) REVERT: D 43 PHE cc_start: 0.8724 (t80) cc_final: 0.8511 (t80) REVERT: D 76 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8140 (mtp85) REVERT: D 88 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: D 92 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7303 (mtp85) REVERT: D 115 LYS cc_start: 0.8823 (mptp) cc_final: 0.8284 (mptp) REVERT: D 163 TYR cc_start: 0.8563 (t80) cc_final: 0.8234 (t80) REVERT: D 165 GLN cc_start: 0.8025 (mt0) cc_final: 0.7752 (mt0) REVERT: D 171 ARG cc_start: 0.7285 (mtm-85) cc_final: 0.6839 (mtm-85) REVERT: D 179 ASP cc_start: 0.8153 (t0) cc_final: 0.7718 (t70) REVERT: D 184 MET cc_start: 0.8152 (mmm) cc_final: 0.7932 (tpp) REVERT: D 197 THR cc_start: 0.8258 (p) cc_final: 0.7942 (t) REVERT: D 240 LEU cc_start: 0.8048 (mt) cc_final: 0.7768 (mp) REVERT: D 243 VAL cc_start: 0.8370 (m) cc_final: 0.8033 (p) REVERT: D 274 CYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7856 (m) REVERT: D 285 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.7421 (t80) REVERT: D 293 SER cc_start: 0.8129 (m) cc_final: 0.7546 (p) REVERT: D 340 ASP cc_start: 0.7592 (m-30) cc_final: 0.7116 (t0) REVERT: D 362 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8364 (tt) REVERT: D 380 LYS cc_start: 0.8493 (mmmm) cc_final: 0.8070 (mmtp) REVERT: D 426 GLN cc_start: 0.7100 (mt0) cc_final: 0.6809 (mt0) REVERT: D 448 ASP cc_start: 0.7612 (t0) cc_final: 0.7345 (t0) REVERT: E 16 LYS cc_start: 0.8510 (mmtt) cc_final: 0.8210 (mmmt) REVERT: E 53 GLN cc_start: 0.8347 (tp40) cc_final: 0.7753 (tt0) REVERT: E 111 ASN cc_start: 0.8659 (t0) cc_final: 0.8234 (t0) REVERT: E 115 LYS cc_start: 0.8816 (mptp) cc_final: 0.8148 (mptp) REVERT: E 144 ARG cc_start: 0.8163 (ttm110) cc_final: 0.7617 (ttm110) REVERT: E 150 TYR cc_start: 0.8448 (m-80) cc_final: 0.8145 (m-80) REVERT: E 168 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8203 (mtpt) REVERT: E 180 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7834 (m) REVERT: E 184 MET cc_start: 0.8168 (mmm) cc_final: 0.7692 (mmm) REVERT: E 197 THR cc_start: 0.8388 (p) cc_final: 0.7952 (t) REVERT: E 236 CYS cc_start: 0.8298 (p) cc_final: 0.8022 (p) REVERT: E 275 ARG cc_start: 0.7925 (ttt180) cc_final: 0.7653 (ptt180) REVERT: E 289 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7565 (mtp-110) REVERT: E 313 LEU cc_start: 0.8354 (mt) cc_final: 0.7963 (mm) REVERT: E 436 ASP cc_start: 0.8397 (t0) cc_final: 0.7655 (t70) REVERT: E 447 PHE cc_start: 0.8389 (m-80) cc_final: 0.7972 (m-10) REVERT: F 30 ARG cc_start: 0.7198 (ptp-170) cc_final: 0.6734 (ttm110) REVERT: F 54 GLU cc_start: 0.8427 (tp30) cc_final: 0.8137 (tp30) REVERT: F 111 ASN cc_start: 0.8688 (t0) cc_final: 0.8129 (t0) REVERT: F 115 LYS cc_start: 0.8742 (mptp) cc_final: 0.8039 (mptp) REVERT: F 135 LEU cc_start: 0.8424 (mt) cc_final: 0.8185 (mm) REVERT: F 184 MET cc_start: 0.8557 (tpp) cc_final: 0.8212 (tpp) REVERT: F 188 MET cc_start: 0.8249 (mmt) cc_final: 0.7942 (mmt) REVERT: F 201 ASP cc_start: 0.8009 (t0) cc_final: 0.7783 (t0) REVERT: F 232 LYS cc_start: 0.8192 (ptmt) cc_final: 0.7792 (ptmt) REVERT: F 240 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7889 (mt) REVERT: F 340 ASP cc_start: 0.7689 (t0) cc_final: 0.7433 (t0) REVERT: F 396 LYS cc_start: 0.8271 (mmtm) cc_final: 0.7843 (mmmm) REVERT: F 441 GLN cc_start: 0.7692 (mt0) cc_final: 0.7445 (mt0) REVERT: G 20 ARG cc_start: 0.7957 (ttm-80) cc_final: 0.7674 (mtm-85) REVERT: G 41 ARG cc_start: 0.7905 (tpp-160) cc_final: 0.7329 (tpp-160) REVERT: G 43 PHE cc_start: 0.8837 (t80) cc_final: 0.8383 (t80) REVERT: G 71 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7674 (mtm-85) REVERT: G 76 ARG cc_start: 0.8217 (mtt90) cc_final: 0.7901 (mtt90) REVERT: G 92 ARG cc_start: 0.7737 (mmp80) cc_final: 0.7370 (mmp80) REVERT: G 106 LYS cc_start: 0.8131 (mtmm) cc_final: 0.7892 (mtmm) REVERT: G 111 ASN cc_start: 0.8677 (t0) cc_final: 0.8069 (t0) REVERT: G 115 LYS cc_start: 0.8807 (mptp) cc_final: 0.8138 (mptp) REVERT: G 140 SER cc_start: 0.8370 (p) cc_final: 0.8122 (p) REVERT: G 151 GLN cc_start: 0.8351 (tp40) cc_final: 0.8129 (tp40) REVERT: G 163 TYR cc_start: 0.8522 (t80) cc_final: 0.8110 (t80) REVERT: G 171 ARG cc_start: 0.7521 (mtm-85) cc_final: 0.7271 (mtm-85) REVERT: G 179 ASP cc_start: 0.8218 (t0) cc_final: 0.7777 (t70) REVERT: G 188 MET cc_start: 0.8298 (tpp) cc_final: 0.7971 (mmt) REVERT: G 234 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7460 (mm-30) REVERT: G 274 CYS cc_start: 0.8117 (m) cc_final: 0.7794 (m) REVERT: G 275 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7614 (ptt180) REVERT: G 283 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: G 285 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.6953 (t80) REVERT: G 293 SER cc_start: 0.8141 (m) cc_final: 0.7492 (p) REVERT: G 324 GLU cc_start: 0.7052 (tt0) cc_final: 0.6696 (tt0) REVERT: G 331 CYS cc_start: 0.8049 (p) cc_final: 0.7836 (p) REVERT: G 363 ASN cc_start: 0.8253 (t0) cc_final: 0.7903 (t0) REVERT: G 399 ARG cc_start: 0.7808 (tpp80) cc_final: 0.6925 (tpp80) REVERT: G 400 LYS cc_start: 0.8269 (tppt) cc_final: 0.7772 (tppt) REVERT: G 403 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: G 406 LYS cc_start: 0.8846 (mmmm) cc_final: 0.8544 (mmtp) REVERT: G 430 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8329 (p) REVERT: H 28 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7259 (mm-30) REVERT: H 56 ASP cc_start: 0.7736 (t70) cc_final: 0.7437 (t70) REVERT: H 76 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7514 (mtt90) REVERT: H 88 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6665 (tm-30) REVERT: H 111 ASN cc_start: 0.8694 (t0) cc_final: 0.8155 (t0) REVERT: H 115 LYS cc_start: 0.8831 (mptp) cc_final: 0.8173 (mptp) REVERT: H 171 ARG cc_start: 0.7196 (mtm-85) cc_final: 0.6681 (mtm-85) REVERT: H 258 TRP cc_start: 0.8510 (m100) cc_final: 0.8250 (m100) REVERT: H 264 PHE cc_start: 0.8171 (p90) cc_final: 0.7864 (p90) REVERT: H 275 ARG cc_start: 0.7821 (ttt180) cc_final: 0.7430 (ptt180) REVERT: H 362 LEU cc_start: 0.8568 (mm) cc_final: 0.8361 (tt) REVERT: H 399 ARG cc_start: 0.7713 (tpp80) cc_final: 0.7498 (tpp80) REVERT: H 400 LYS cc_start: 0.8162 (tppt) cc_final: 0.7741 (tppt) REVERT: H 434 ARG cc_start: 0.8538 (mpp80) cc_final: 0.7949 (tpp80) REVERT: H 436 ASP cc_start: 0.8387 (t0) cc_final: 0.8002 (t70) REVERT: H 447 PHE cc_start: 0.8472 (m-80) cc_final: 0.8096 (m-80) REVERT: I 16 LYS cc_start: 0.8477 (mppt) cc_final: 0.8193 (mtpt) REVERT: I 22 TYR cc_start: 0.8404 (m-80) cc_final: 0.8116 (m-80) REVERT: I 72 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7737 (tmm) REVERT: I 106 LYS cc_start: 0.8252 (mtmm) cc_final: 0.7884 (mtmm) REVERT: I 111 ASN cc_start: 0.8530 (t0) cc_final: 0.8181 (t0) REVERT: I 115 LYS cc_start: 0.8774 (mptp) cc_final: 0.8064 (mptp) REVERT: I 171 ARG cc_start: 0.7056 (mtm-85) cc_final: 0.6793 (mtm-85) REVERT: I 184 MET cc_start: 0.8575 (tpp) cc_final: 0.8150 (tpp) REVERT: I 346 LEU cc_start: 0.8666 (tp) cc_final: 0.8381 (tt) REVERT: I 357 LYS cc_start: 0.8697 (ttmm) cc_final: 0.8423 (ttmt) REVERT: I 400 LYS cc_start: 0.8224 (tppt) cc_final: 0.7521 (ttpt) REVERT: I 404 ASP cc_start: 0.8151 (m-30) cc_final: 0.7883 (m-30) REVERT: I 405 GLU cc_start: 0.7871 (mp0) cc_final: 0.7437 (mp0) REVERT: I 436 ASP cc_start: 0.8351 (t0) cc_final: 0.7881 (t70) REVERT: I 446 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7324 (mm-30) REVERT: J 20 ARG cc_start: 0.8111 (mtp-110) cc_final: 0.7872 (mtp-110) REVERT: J 43 PHE cc_start: 0.8789 (t80) cc_final: 0.8502 (t80) REVERT: J 76 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8105 (mtt90) REVERT: J 92 ARG cc_start: 0.7674 (mmp80) cc_final: 0.7162 (mmp80) REVERT: J 115 LYS cc_start: 0.8781 (mptp) cc_final: 0.8178 (mptp) REVERT: J 140 SER cc_start: 0.8147 (p) cc_final: 0.7891 (p) REVERT: J 163 TYR cc_start: 0.8527 (t80) cc_final: 0.8258 (t80) REVERT: J 171 ARG cc_start: 0.7637 (mtm-85) cc_final: 0.7056 (mtm-85) REVERT: J 183 PHE cc_start: 0.8542 (m-80) cc_final: 0.8173 (m-80) REVERT: J 195 TYR cc_start: 0.8420 (m-80) cc_final: 0.8110 (m-80) REVERT: J 240 LEU cc_start: 0.8142 (mm) cc_final: 0.7856 (mp) REVERT: J 274 CYS cc_start: 0.8046 (m) cc_final: 0.7129 (m) REVERT: J 275 ARG cc_start: 0.7755 (ttt180) cc_final: 0.7371 (ptt180) REVERT: J 278 THR cc_start: 0.8840 (m) cc_final: 0.8539 (p) REVERT: J 283 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: J 285 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.6629 (t80) REVERT: J 292 MET cc_start: 0.7797 (mmt) cc_final: 0.7562 (mmt) REVERT: J 313 LEU cc_start: 0.8271 (mt) cc_final: 0.7916 (mp) REVERT: J 324 GLU cc_start: 0.7263 (tt0) cc_final: 0.6963 (tt0) REVERT: J 357 LYS cc_start: 0.8571 (ttmm) cc_final: 0.8359 (ttmt) REVERT: J 397 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7828 (mm-30) REVERT: J 403 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: J 404 ASP cc_start: 0.7967 (m-30) cc_final: 0.7717 (m-30) REVERT: K 28 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7323 (mm-30) REVERT: K 76 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7946 (mtt90) REVERT: K 115 LYS cc_start: 0.8783 (mptp) cc_final: 0.8199 (mptp) REVERT: K 171 ARG cc_start: 0.7223 (mtm-85) cc_final: 0.6863 (mtm-85) REVERT: K 238 ARG cc_start: 0.7775 (ttm110) cc_final: 0.7409 (mtm110) REVERT: K 264 PHE cc_start: 0.8174 (p90) cc_final: 0.7866 (p90) REVERT: K 274 CYS cc_start: 0.8119 (m) cc_final: 0.7678 (m) REVERT: K 289 ARG cc_start: 0.7728 (ttp80) cc_final: 0.7423 (mtp-110) REVERT: K 313 LEU cc_start: 0.8312 (mt) cc_final: 0.7966 (mm) REVERT: K 340 ASP cc_start: 0.7780 (t0) cc_final: 0.7384 (t0) REVERT: K 341 GLN cc_start: 0.8293 (tt0) cc_final: 0.7998 (tt0) REVERT: K 434 ARG cc_start: 0.8608 (mpp80) cc_final: 0.7286 (tpp80) REVERT: K 436 ASP cc_start: 0.8400 (t0) cc_final: 0.8125 (t0) REVERT: L 20 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7680 (mtm-85) REVERT: L 43 PHE cc_start: 0.8909 (t80) cc_final: 0.8117 (t80) REVERT: L 51 ILE cc_start: 0.8644 (mm) cc_final: 0.8410 (mm) REVERT: L 63 ASP cc_start: 0.7762 (t0) cc_final: 0.7200 (t0) REVERT: L 92 ARG cc_start: 0.7844 (mmp80) cc_final: 0.7283 (mmp80) REVERT: L 106 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8212 (mtmm) REVERT: L 115 LYS cc_start: 0.8828 (mptp) cc_final: 0.8124 (mptp) REVERT: L 168 LYS cc_start: 0.8854 (mtmt) cc_final: 0.8408 (mtpp) REVERT: L 184 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.8041 (tpp) REVERT: L 195 TYR cc_start: 0.8463 (m-80) cc_final: 0.8165 (m-80) REVERT: L 202 GLU cc_start: 0.8107 (tp30) cc_final: 0.7631 (tp30) REVERT: L 232 LYS cc_start: 0.8359 (ptmt) cc_final: 0.7930 (ptmt) REVERT: L 238 ARG cc_start: 0.7693 (ttm110) cc_final: 0.7428 (mtm110) REVERT: L 258 TRP cc_start: 0.8603 (m100) cc_final: 0.7544 (m100) REVERT: L 266 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8440 (mt) REVERT: L 283 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: L 285 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.7144 (t80) REVERT: L 400 LYS cc_start: 0.7981 (tppt) cc_final: 0.7686 (tppt) REVERT: L 403 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: L 427 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7372 (mmtt) REVERT: L 429 HIS cc_start: 0.8471 (OUTLIER) cc_final: 0.8039 (m-70) REVERT: L 436 ASP cc_start: 0.8289 (t0) cc_final: 0.7929 (t0) REVERT: L 446 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7263 (mm-30) outliers start: 232 outliers final: 181 residues processed: 1916 average time/residue: 0.2823 time to fit residues: 837.3041 Evaluate side-chains 2023 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 1808 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 238 ARG Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 275 ARG Chi-restraints excluded: chain G residue 283 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 396 LYS Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 411 ARG Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain H residue 19 GLN Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 342 MET Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 398 CYS Chi-restraints excluded: chain H residue 403 GLU Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 429 HIS Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 314 MET Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 425 LYS Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 76 ARG Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 236 CYS Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 283 GLU Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain J residue 301 THR Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 403 GLU Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 283 GLU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 398 CYS Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain K residue 408 LEU Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain L residue 120 GLN Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain L residue 194 SER Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 283 GLU Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain L residue 346 LEU Chi-restraints excluded: chain L residue 348 THR Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 427 LYS Chi-restraints excluded: chain L residue 429 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 8 optimal weight: 0.9980 chunk 264 optimal weight: 6.9990 chunk 189 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 477 optimal weight: 0.9990 chunk 430 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 480 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 452 optimal weight: 0.2980 chunk 21 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117507 restraints weight = 64551.769| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.79 r_work: 0.3419 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 42540 Z= 0.135 Angle : 0.702 14.371 57612 Z= 0.337 Chirality : 0.044 0.153 6564 Planarity : 0.005 0.090 7248 Dihedral : 13.500 177.982 6348 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.98 % Allowed : 34.17 % Favored : 60.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.97 % 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: -0.93 (0.11), residues: 5148 helix: 1.48 (0.14), residues: 1692 sheet: -0.83 (0.15), residues: 1056 loop : -2.14 (0.11), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 30 TYR 0.022 0.001 TYR K 174 PHE 0.030 0.002 PHE B 264 TRP 0.023 0.002 TRP F 258 HIS 0.003 0.001 HIS J 308 Details of bonding type rmsd covalent geometry : bond 0.00321 (42480) covalent geometry : angle 0.70250 (57612) hydrogen bonds : bond 0.02785 ( 1577) hydrogen bonds : angle 4.36697 ( 4476) metal coordination : bond 0.00470 ( 36) Misc. bond : bond 0.00038 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13667.48 seconds wall clock time: 234 minutes 15.63 seconds (14055.63 seconds total)