Starting phenix.real_space_refine on Sat Mar 7 11:44:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aov_15553/03_2026/8aov_15553.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aov_15553/03_2026/8aov_15553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8aov_15553/03_2026/8aov_15553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aov_15553/03_2026/8aov_15553.map" model { file = "/net/cci-nas-00/data/ceres_data/8aov_15553/03_2026/8aov_15553.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aov_15553/03_2026/8aov_15553.cif" } resolution = 2.48 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= 0.002 sd= 0.111 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 36 5.49 5 S 348 5.16 5 C 26880 2.51 5 N 7440 2.21 5 O 8184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42900 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "C" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "E" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "G" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "I" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "K" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "M" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "O" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "Q" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "S" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "V" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "X" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "G" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "I" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "K" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "M" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "O" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "Q" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "S" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "V" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "X" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1001 SG CYS A 134 128.478 174.947 63.496 1.00103.91 S ATOM 1053 SG CYS A 141 131.458 173.166 63.285 1.00 76.30 S ATOM 4524 SG CYS C 134 85.473 180.460 63.754 1.00100.14 S ATOM 4576 SG CYS C 141 89.040 180.040 63.330 1.00 77.44 S ATOM 8047 SG CYS E 134 45.794 163.452 63.896 1.00105.72 S ATOM 8099 SG CYS E 141 48.734 164.586 63.380 1.00 86.80 S ATOM 11570 SG CYS G 134 20.083 128.414 63.432 1.00103.43 S ATOM 11622 SG CYS G 141 21.990 131.544 63.252 1.00 72.60 S ATOM 15093 SG CYS I 134 14.523 85.452 63.765 1.00105.75 S ATOM 15145 SG CYS I 141 14.988 89.040 63.332 1.00 74.74 S ATOM 18616 SG CYS K 134 31.986 46.008 63.484 1.00102.75 S ATOM 18668 SG CYS K 141 30.369 48.930 63.256 1.00 88.78 S ATOM 22139 SG CYS M 134 66.609 20.355 63.332 1.00102.10 S ATOM 22191 SG CYS M 141 63.523 21.899 63.295 1.00 77.08 S ATOM 25662 SG CYS O 134 109.571 14.547 63.781 1.00100.18 S ATOM 25714 SG CYS O 141 106.009 15.032 63.296 1.00 71.75 S ATOM 29185 SG CYS Q 134 149.056 31.884 63.563 1.00100.99 S ATOM 29237 SG CYS Q 141 146.073 30.278 63.300 1.00 86.75 S ATOM 32708 SG CYS S 134 175.537 66.363 64.012 1.00113.88 S ATOM 32760 SG CYS S 141 173.213 63.615 63.309 1.00 77.91 S ATOM 36231 SG CYS V 134 180.189 109.369 63.553 1.00 93.65 S ATOM 36283 SG CYS V 141 180.041 105.903 63.304 1.00 76.77 S ATOM 39754 SG CYS X 134 162.941 149.065 63.407 1.00 99.75 S ATOM 39806 SG CYS X 141 164.736 146.107 63.319 1.00 88.17 S Residues with excluded nonbonded symmetry interactions: 71 residue: pdb=" N ALEU A 50 " occ=0.31 ... (14 atoms not shown) pdb=" CD2BLEU A 50 " occ=0.69 residue: pdb=" N AARG A 71 " occ=0.53 ... (20 atoms not shown) pdb=" NH2BARG A 71 " occ=0.47 residue: pdb=" N AARG A 76 " occ=0.35 ... (20 atoms not shown) pdb=" NH2BARG A 76 " occ=0.65 residue: pdb=" N AVAL A 239 " occ=0.53 ... (12 atoms not shown) pdb=" CG2BVAL A 239 " occ=0.47 residue: pdb=" N AASP A 310 " occ=0.51 ... (14 atoms not shown) pdb=" OD2BASP A 310 " occ=0.49 residue: pdb=" N AGLU A 353 " occ=0.45 ... (16 atoms not shown) pdb=" OE2BGLU A 353 " occ=0.55 residue: pdb=" N ALEU C 50 " occ=0.09 ... (14 atoms not shown) pdb=" CD2BLEU C 50 " occ=0.91 residue: pdb=" N AARG C 71 " occ=0.49 ... (20 atoms not shown) pdb=" NH2BARG C 71 " occ=0.51 residue: pdb=" N AARG C 76 " occ=0.54 ... (20 atoms not shown) pdb=" NH2BARG C 76 " occ=0.46 residue: pdb=" N AVAL C 239 " occ=0.62 ... (12 atoms not shown) pdb=" CG2BVAL C 239 " occ=0.38 residue: pdb=" N AASP C 310 " occ=0.45 ... (14 atoms not shown) pdb=" OD2BASP C 310 " occ=0.55 residue: pdb=" N AGLU C 353 " occ=0.55 ... (16 atoms not shown) pdb=" OE2BGLU C 353 " occ=0.45 ... (remaining 59 not shown) Time building chain proxies: 17.40, per 1000 atoms: 0.41 Number of scatterers: 42900 At special positions: 0 Unit cell: (196.1, 196.1, 93.28, 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 348 16.00 P 36 15.00 O 8184 8.00 N 7440 7.00 C 26880 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=0, symmetry=0 Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 141 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 134 " pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 141 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 134 " pdb="ZN ZN C 601 " - pdb=" NE2 HIS C 79 " pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 141 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 134 " pdb="ZN ZN E 601 " - pdb=" NE2 HIS E 79 " pdb=" ZN G 601 " pdb="ZN ZN G 601 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 134 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 141 " pdb=" ZN I 601 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 141 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 134 " pdb="ZN ZN I 601 " - pdb=" NE2 HIS I 79 " pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 141 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 134 " pdb=" ZN M 601 " pdb="ZN ZN M 601 " - pdb=" NE2 HIS M 79 " pdb="ZN ZN M 601 " - pdb=" SG CYS M 134 " pdb="ZN ZN M 601 " - pdb=" SG CYS M 141 " pdb=" ZN O 601 " pdb="ZN ZN O 601 " - pdb=" SG CYS O 141 " pdb="ZN ZN O 601 " - pdb=" SG CYS O 134 " pdb="ZN ZN O 601 " - pdb=" NE2 HIS O 79 " pdb=" ZN Q 601 " pdb="ZN ZN Q 601 " - pdb=" NE2 HIS Q 79 " pdb="ZN ZN Q 601 " - pdb=" SG CYS Q 134 " pdb="ZN ZN Q 601 " - pdb=" SG CYS Q 141 " pdb=" ZN S 601 " pdb="ZN ZN S 601 " - pdb=" SG CYS S 134 " pdb="ZN ZN S 601 " - pdb=" SG CYS S 141 " pdb="ZN ZN S 601 " - pdb=" NE2 HIS S 79 " pdb=" ZN V 601 " pdb="ZN ZN V 601 " - pdb=" SG CYS V 141 " pdb="ZN ZN V 601 " - pdb=" SG CYS V 134 " pdb="ZN ZN V 601 " - pdb=" NE2 HIS V 79 " pdb=" ZN X 601 " pdb="ZN ZN X 601 " - pdb=" NE2 HIS X 79 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 134 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 141 " 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10320 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 60 sheets defined 35.1% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 removed outlier: 4.066A pdb=" N ALA A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 55 Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.505A pdb=" N ARG A 70 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.707A pdb=" N TRP A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 351 through 364 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 404 Processing helix chain 'A' and resid 461 through 471 removed outlier: 3.690A pdb=" N LEU A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 22 removed outlier: 4.043A pdb=" N ALA C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 55 Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.651A pdb=" N ARG C 70 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 252 through 258 removed outlier: 3.731A pdb=" N TRP C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 343 through 348 removed outlier: 3.514A pdb=" N LEU C 346 " --> pdb=" O THR C 343 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR C 348 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 404 Processing helix chain 'C' and resid 461 through 471 removed outlier: 3.655A pdb=" N LEU C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 22 removed outlier: 4.028A pdb=" N ALA E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 55 Processing helix chain 'E' and resid 67 through 72 removed outlier: 3.589A pdb=" N ARG E 70 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET E 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 111 through 125 Processing helix chain 'E' and resid 157 through 167 Processing helix chain 'E' and resid 180 through 185 Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 252 through 258 removed outlier: 3.754A pdb=" N TRP E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 342 Processing helix chain 'E' and resid 344 through 348 removed outlier: 3.713A pdb=" N THR E 348 " --> pdb=" O ILE E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 364 removed outlier: 3.511A pdb=" N GLN E 364 " --> pdb=" O VAL E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 382 No H-bonds generated for 'chain 'E' and resid 380 through 382' Processing helix chain 'E' and resid 383 through 404 Processing helix chain 'E' and resid 461 through 471 removed outlier: 3.653A pdb=" N LEU E 471 " --> pdb=" O ARG E 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 22 removed outlier: 4.065A pdb=" N ALA G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 55 Processing helix chain 'G' and resid 67 through 71 removed outlier: 3.580A pdb=" N ARG G 70 " --> pdb=" O ALA G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 103 Processing helix chain 'G' and resid 111 through 125 Processing helix chain 'G' and resid 157 through 167 Processing helix chain 'G' and resid 180 through 185 Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'G' and resid 252 through 258 removed outlier: 3.679A pdb=" N TRP G 258 " --> pdb=" O LEU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 342 Processing helix chain 'G' and resid 343 through 348 removed outlier: 3.551A pdb=" N THR G 348 " --> pdb=" O ILE G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 364 removed outlier: 3.512A pdb=" N GLN G 364 " --> pdb=" O VAL G 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 382 No H-bonds generated for 'chain 'G' and resid 380 through 382' Processing helix chain 'G' and resid 383 through 404 Processing helix chain 'G' and resid 461 through 471 removed outlier: 3.743A pdb=" N LEU G 471 " --> pdb=" O ARG G 467 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 22 removed outlier: 4.042A pdb=" N ALA I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 55 Processing helix chain 'I' and resid 67 through 71 Processing helix chain 'I' and resid 90 through 102 Processing helix chain 'I' and resid 111 through 125 Processing helix chain 'I' and resid 157 through 167 Processing helix chain 'I' and resid 180 through 185 Processing helix chain 'I' and resid 193 through 195 No H-bonds generated for 'chain 'I' and resid 193 through 195' Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 252 through 258 removed outlier: 3.742A pdb=" N TRP I 258 " --> pdb=" O LEU I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 342 Processing helix chain 'I' and resid 343 through 348 removed outlier: 3.748A pdb=" N THR I 348 " --> pdb=" O ILE I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 363 Processing helix chain 'I' and resid 380 through 382 No H-bonds generated for 'chain 'I' and resid 380 through 382' Processing helix chain 'I' and resid 383 through 404 Processing helix chain 'I' and resid 461 through 471 removed outlier: 3.689A pdb=" N LEU I 471 " --> pdb=" O ARG I 467 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 22 removed outlier: 4.079A pdb=" N ALA K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 55 Processing helix chain 'K' and resid 67 through 71 Processing helix chain 'K' and resid 90 through 103 Processing helix chain 'K' and resid 111 through 125 Processing helix chain 'K' and resid 157 through 167 Processing helix chain 'K' and resid 180 through 185 Processing helix chain 'K' and resid 193 through 195 No H-bonds generated for 'chain 'K' and resid 193 through 195' Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 252 through 258 removed outlier: 3.749A pdb=" N TRP K 258 " --> pdb=" O LEU K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 342 Processing helix chain 'K' and resid 344 through 348 removed outlier: 3.668A pdb=" N THR K 348 " --> pdb=" O ILE K 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 364 Processing helix chain 'K' and resid 380 through 382 No H-bonds generated for 'chain 'K' and resid 380 through 382' Processing helix chain 'K' and resid 383 through 404 Processing helix chain 'K' and resid 461 through 471 removed outlier: 3.639A pdb=" N LEU K 471 " --> pdb=" O ARG K 467 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 22 removed outlier: 4.070A pdb=" N ALA M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 55 Processing helix chain 'M' and resid 67 through 71 Processing helix chain 'M' and resid 90 through 103 Processing helix chain 'M' and resid 111 through 125 Processing helix chain 'M' and resid 157 through 167 Processing helix chain 'M' and resid 180 through 185 Processing helix chain 'M' and resid 193 through 195 No H-bonds generated for 'chain 'M' and resid 193 through 195' Processing helix chain 'M' and resid 203 through 205 No H-bonds generated for 'chain 'M' and resid 203 through 205' Processing helix chain 'M' and resid 252 through 258 removed outlier: 3.673A pdb=" N TRP M 258 " --> pdb=" O LEU M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 342 Processing helix chain 'M' and resid 343 through 348 removed outlier: 3.537A pdb=" N THR M 348 " --> pdb=" O ILE M 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 364 Processing helix chain 'M' and resid 380 through 382 No H-bonds generated for 'chain 'M' and resid 380 through 382' Processing helix chain 'M' and resid 383 through 404 Processing helix chain 'M' and resid 461 through 471 removed outlier: 3.542A pdb=" N LEU M 471 " --> pdb=" O ARG M 467 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 22 removed outlier: 4.036A pdb=" N ALA O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 55 Processing helix chain 'O' and resid 67 through 71 removed outlier: 3.513A pdb=" N ARG O 70 " --> pdb=" O ALA O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 103 Processing helix chain 'O' and resid 111 through 125 Processing helix chain 'O' and resid 157 through 167 Processing helix chain 'O' and resid 180 through 185 Processing helix chain 'O' and resid 193 through 195 No H-bonds generated for 'chain 'O' and resid 193 through 195' Processing helix chain 'O' and resid 203 through 205 No H-bonds generated for 'chain 'O' and resid 203 through 205' Processing helix chain 'O' and resid 252 through 258 removed outlier: 3.685A pdb=" N TRP O 258 " --> pdb=" O LEU O 254 " (cutoff:3.500A) Processing helix chain 'O' and resid 335 through 342 Processing helix chain 'O' and resid 343 through 348 removed outlier: 3.767A pdb=" N THR O 348 " --> pdb=" O ILE O 345 " (cutoff:3.500A) Processing helix chain 'O' and resid 351 through 364 removed outlier: 3.501A pdb=" N GLN O 364 " --> pdb=" O VAL O 360 " (cutoff:3.500A) Processing helix chain 'O' and resid 380 through 382 No H-bonds generated for 'chain 'O' and resid 380 through 382' Processing helix chain 'O' and resid 383 through 404 Processing helix chain 'O' and resid 461 through 471 removed outlier: 3.659A pdb=" N LEU O 471 " --> pdb=" O ARG O 467 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 22 removed outlier: 4.059A pdb=" N ALA Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 55 Processing helix chain 'Q' and resid 67 through 72 removed outlier: 3.579A pdb=" N ARG Q 70 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N MET Q 72 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 103 Processing helix chain 'Q' and resid 111 through 125 Processing helix chain 'Q' and resid 157 through 167 Processing helix chain 'Q' and resid 180 through 185 Processing helix chain 'Q' and resid 193 through 195 No H-bonds generated for 'chain 'Q' and resid 193 through 195' Processing helix chain 'Q' and resid 203 through 205 No H-bonds generated for 'chain 'Q' and resid 203 through 205' Processing helix chain 'Q' and resid 252 through 258 removed outlier: 3.801A pdb=" N TRP Q 258 " --> pdb=" O LEU Q 254 " (cutoff:3.500A) Processing helix chain 'Q' and resid 335 through 342 Processing helix chain 'Q' and resid 344 through 348 removed outlier: 3.731A pdb=" N THR Q 348 " --> pdb=" O ILE Q 345 " (cutoff:3.500A) Processing helix chain 'Q' and resid 351 through 364 removed outlier: 3.513A pdb=" N GLN Q 364 " --> pdb=" O VAL Q 360 " (cutoff:3.500A) Processing helix chain 'Q' and resid 380 through 382 No H-bonds generated for 'chain 'Q' and resid 380 through 382' Processing helix chain 'Q' and resid 383 through 404 Processing helix chain 'Q' and resid 461 through 471 removed outlier: 3.534A pdb=" N LEU Q 471 " --> pdb=" O ARG Q 467 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 22 removed outlier: 4.040A pdb=" N ALA S 17 " --> pdb=" O ALA S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 55 Processing helix chain 'S' and resid 67 through 72 removed outlier: 3.523A pdb=" N ARG S 70 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N MET S 72 " --> pdb=" O ALA S 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 90 through 102 Processing helix chain 'S' and resid 111 through 125 Processing helix chain 'S' and resid 157 through 167 Processing helix chain 'S' and resid 180 through 185 Processing helix chain 'S' and resid 193 through 195 No H-bonds generated for 'chain 'S' and resid 193 through 195' Processing helix chain 'S' and resid 203 through 205 No H-bonds generated for 'chain 'S' and resid 203 through 205' Processing helix chain 'S' and resid 252 through 258 removed outlier: 3.705A pdb=" N TRP S 258 " --> pdb=" O LEU S 254 " (cutoff:3.500A) Processing helix chain 'S' and resid 335 through 342 Processing helix chain 'S' and resid 343 through 348 removed outlier: 3.505A pdb=" N LEU S 346 " --> pdb=" O THR S 343 " (cutoff:3.500A) Processing helix chain 'S' and resid 351 through 364 Processing helix chain 'S' and resid 380 through 382 No H-bonds generated for 'chain 'S' and resid 380 through 382' Processing helix chain 'S' and resid 383 through 404 Processing helix chain 'S' and resid 461 through 471 removed outlier: 3.734A pdb=" N LEU S 471 " --> pdb=" O ARG S 467 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 22 removed outlier: 4.045A pdb=" N ALA V 17 " --> pdb=" O ALA V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 37 through 55 Processing helix chain 'V' and resid 67 through 71 removed outlier: 3.535A pdb=" N ARG V 70 " --> pdb=" O ALA V 67 " (cutoff:3.500A) Processing helix chain 'V' and resid 90 through 102 Processing helix chain 'V' and resid 111 through 125 Processing helix chain 'V' and resid 157 through 167 Processing helix chain 'V' and resid 180 through 185 Processing helix chain 'V' and resid 193 through 195 No H-bonds generated for 'chain 'V' and resid 193 through 195' Processing helix chain 'V' and resid 203 through 205 No H-bonds generated for 'chain 'V' and resid 203 through 205' Processing helix chain 'V' and resid 252 through 258 removed outlier: 3.762A pdb=" N TRP V 258 " --> pdb=" O LEU V 254 " (cutoff:3.500A) Processing helix chain 'V' and resid 335 through 342 Processing helix chain 'V' and resid 343 through 348 removed outlier: 3.733A pdb=" N THR V 348 " --> pdb=" O ILE V 345 " (cutoff:3.500A) Processing helix chain 'V' and resid 351 through 364 Processing helix chain 'V' and resid 380 through 382 No H-bonds generated for 'chain 'V' and resid 380 through 382' Processing helix chain 'V' and resid 383 through 404 Processing helix chain 'V' and resid 461 through 471 removed outlier: 3.708A pdb=" N LEU V 471 " --> pdb=" O ARG V 467 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 22 removed outlier: 4.022A pdb=" N ALA X 17 " --> pdb=" O ALA X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 55 Processing helix chain 'X' and resid 67 through 71 Processing helix chain 'X' and resid 90 through 102 Processing helix chain 'X' and resid 111 through 125 Processing helix chain 'X' and resid 157 through 167 Processing helix chain 'X' and resid 180 through 185 Processing helix chain 'X' and resid 193 through 195 No H-bonds generated for 'chain 'X' and resid 193 through 195' Processing helix chain 'X' and resid 203 through 205 No H-bonds generated for 'chain 'X' and resid 203 through 205' Processing helix chain 'X' and resid 252 through 258 removed outlier: 3.769A pdb=" N TRP X 258 " --> pdb=" O LEU X 254 " (cutoff:3.500A) Processing helix chain 'X' and resid 335 through 342 Processing helix chain 'X' and resid 343 through 348 removed outlier: 3.526A pdb=" N LEU X 346 " --> pdb=" O THR X 343 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR X 348 " --> pdb=" O ILE X 345 " (cutoff:3.500A) Processing helix chain 'X' and resid 351 through 364 removed outlier: 3.524A pdb=" N GLN X 364 " --> pdb=" O VAL X 360 " (cutoff:3.500A) Processing helix chain 'X' and resid 380 through 382 No H-bonds generated for 'chain 'X' and resid 380 through 382' Processing helix chain 'X' and resid 383 through 404 Processing helix chain 'X' and resid 461 through 471 removed outlier: 3.635A pdb=" N LEU X 471 " --> pdb=" O ARG X 467 " (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 77 through 81 removed outlier: 4.492A pdb=" N GLN A 151 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER A 281 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL A 287 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N PHE A 447 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS A 265 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 251 removed outlier: 6.778A pdb=" N ALA A 189 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N TYR A 333 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ALA A 191 " --> pdb=" O TYR A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 226 Processing sheet with id=AA5, first strand: chain 'A' and resid 303 through 308 removed outlier: 3.961A pdb=" N THR A 437 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 81 removed outlier: 4.432A pdb=" N GLN C 151 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER C 281 " --> pdb=" O TYR C 285 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL C 287 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N PHE C 447 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N HIS C 265 " --> pdb=" O PHE C 447 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 246 through 251 removed outlier: 6.760A pdb=" N ALA C 189 " --> pdb=" O CYS C 331 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N TYR C 333 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ALA C 191 " --> pdb=" O TYR C 333 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 225 through 226 Processing sheet with id=AB2, first strand: chain 'C' and resid 303 through 308 removed outlier: 3.924A pdb=" N THR C 437 " --> pdb=" O HIS C 308 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AB4, first strand: chain 'E' and resid 133 through 134 removed outlier: 7.148A pdb=" N CYS E 134 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N CYS E 80 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLN E 151 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR E 285 " --> pdb=" O SER E 281 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER E 281 " --> pdb=" O TYR E 285 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL E 287 " --> pdb=" O VAL E 279 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N PHE E 447 " --> pdb=" O VAL E 263 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N HIS E 265 " --> pdb=" O PHE E 447 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 246 through 251 removed outlier: 6.839A pdb=" N ALA E 189 " --> pdb=" O CYS E 331 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N TYR E 333 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ALA E 191 " --> pdb=" O TYR E 333 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 225 through 226 Processing sheet with id=AB7, first strand: chain 'E' and resid 303 through 308 removed outlier: 3.919A pdb=" N THR E 437 " --> pdb=" O HIS E 308 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'G' and resid 77 through 79 removed outlier: 4.487A pdb=" N GLN G 151 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR G 285 " --> pdb=" O SER G 281 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER G 281 " --> pdb=" O TYR G 285 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL G 287 " --> pdb=" O VAL G 279 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N PHE G 447 " --> pdb=" O VAL G 263 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N HIS G 265 " --> pdb=" O PHE G 447 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 246 through 251 removed outlier: 6.796A pdb=" N ALA G 189 " --> pdb=" O CYS G 331 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N TYR G 333 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ALA G 191 " --> pdb=" O TYR G 333 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 225 through 226 Processing sheet with id=AC3, first strand: chain 'G' and resid 303 through 308 removed outlier: 3.925A pdb=" N THR G 437 " --> pdb=" O HIS G 308 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AC5, first strand: chain 'I' and resid 77 through 79 removed outlier: 4.483A pdb=" N GLN I 151 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR I 285 " --> pdb=" O SER I 281 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER I 281 " --> pdb=" O TYR I 285 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL I 287 " --> pdb=" O VAL I 279 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N PHE I 447 " --> pdb=" O VAL I 263 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N HIS I 265 " --> pdb=" O PHE I 447 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 246 through 251 removed outlier: 6.801A pdb=" N ALA I 189 " --> pdb=" O CYS I 331 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N TYR I 333 " --> pdb=" O ALA I 189 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA I 191 " --> pdb=" O TYR I 333 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 225 through 226 Processing sheet with id=AC8, first strand: chain 'I' and resid 303 through 308 removed outlier: 3.942A pdb=" N THR I 437 " --> pdb=" O HIS I 308 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AD1, first strand: chain 'K' and resid 78 through 79 removed outlier: 6.159A pdb=" N ILE K 61 " --> pdb=" O HIS K 79 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLN K 151 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR K 285 " --> pdb=" O SER K 281 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER K 281 " --> pdb=" O TYR K 285 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL K 287 " --> pdb=" O VAL K 279 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N PHE K 447 " --> pdb=" O VAL K 263 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N HIS K 265 " --> pdb=" O PHE K 447 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 246 through 251 removed outlier: 6.818A pdb=" N ALA K 189 " --> pdb=" O CYS K 331 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N TYR K 333 " --> pdb=" O ALA K 189 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ALA K 191 " --> pdb=" O TYR K 333 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 225 through 226 Processing sheet with id=AD4, first strand: chain 'K' and resid 303 through 308 removed outlier: 3.909A pdb=" N THR K 437 " --> pdb=" O HIS K 308 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AD6, first strand: chain 'M' and resid 77 through 81 removed outlier: 4.582A pdb=" N GLN M 151 " --> pdb=" O ILE M 64 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TYR M 285 " --> pdb=" O SER M 281 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER M 281 " --> pdb=" O TYR M 285 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL M 287 " --> pdb=" O VAL M 279 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N PHE M 447 " --> pdb=" O VAL M 263 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N HIS M 265 " --> pdb=" O PHE M 447 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 246 through 251 removed outlier: 6.794A pdb=" N ALA M 189 " --> pdb=" O CYS M 331 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N TYR M 333 " --> pdb=" O ALA M 189 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ALA M 191 " --> pdb=" O TYR M 333 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 225 through 226 Processing sheet with id=AD9, first strand: chain 'M' and resid 303 through 308 removed outlier: 3.958A pdb=" N THR M 437 " --> pdb=" O HIS M 308 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'O' and resid 77 through 81 removed outlier: 4.413A pdb=" N GLN O 151 " --> pdb=" O ILE O 64 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR O 285 " --> pdb=" O SER O 281 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER O 281 " --> pdb=" O TYR O 285 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL O 287 " --> pdb=" O VAL O 279 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N PHE O 447 " --> pdb=" O VAL O 263 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N HIS O 265 " --> pdb=" O PHE O 447 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 246 through 251 removed outlier: 6.746A pdb=" N ALA O 189 " --> pdb=" O CYS O 331 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N TYR O 333 " --> pdb=" O ALA O 189 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ALA O 191 " --> pdb=" O TYR O 333 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 225 through 226 Processing sheet with id=AE5, first strand: chain 'O' and resid 303 through 308 removed outlier: 3.910A pdb=" N THR O 437 " --> pdb=" O HIS O 308 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 4 through 6 Processing sheet with id=AE7, first strand: chain 'Q' and resid 77 through 81 removed outlier: 4.419A pdb=" N GLN Q 151 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR Q 285 " --> pdb=" O SER Q 281 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER Q 281 " --> pdb=" O TYR Q 285 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL Q 287 " --> pdb=" O VAL Q 279 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N PHE Q 447 " --> pdb=" O VAL Q 263 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N HIS Q 265 " --> pdb=" O PHE Q 447 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 246 through 251 removed outlier: 6.829A pdb=" N ALA Q 189 " --> pdb=" O CYS Q 331 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N TYR Q 333 " --> pdb=" O ALA Q 189 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ALA Q 191 " --> pdb=" O TYR Q 333 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 225 through 226 Processing sheet with id=AF1, first strand: chain 'Q' and resid 303 through 308 removed outlier: 3.923A pdb=" N THR Q 437 " --> pdb=" O HIS Q 308 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 4 through 6 Processing sheet with id=AF3, first strand: chain 'S' and resid 77 through 81 removed outlier: 4.555A pdb=" N GLN S 151 " --> pdb=" O ILE S 64 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TYR S 285 " --> pdb=" O SER S 281 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER S 281 " --> pdb=" O TYR S 285 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL S 287 " --> pdb=" O VAL S 279 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N PHE S 447 " --> pdb=" O VAL S 263 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N HIS S 265 " --> pdb=" O PHE S 447 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 246 through 251 removed outlier: 6.792A pdb=" N ALA S 189 " --> pdb=" O CYS S 331 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N TYR S 333 " --> pdb=" O ALA S 189 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ALA S 191 " --> pdb=" O TYR S 333 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 225 through 226 Processing sheet with id=AF6, first strand: chain 'S' and resid 303 through 308 removed outlier: 3.976A pdb=" N THR S 437 " --> pdb=" O HIS S 308 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 4 through 6 removed outlier: 6.549A pdb=" N VAL V 4 " --> pdb=" O GLU V 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'V' and resid 77 through 81 removed outlier: 4.474A pdb=" N GLN V 151 " --> pdb=" O ILE V 64 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TYR V 285 " --> pdb=" O SER V 281 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER V 281 " --> pdb=" O TYR V 285 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL V 287 " --> pdb=" O VAL V 279 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N PHE V 447 " --> pdb=" O VAL V 263 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS V 265 " --> pdb=" O PHE V 447 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 246 through 251 removed outlier: 6.790A pdb=" N ALA V 189 " --> pdb=" O CYS V 331 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N TYR V 333 " --> pdb=" O ALA V 189 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ALA V 191 " --> pdb=" O TYR V 333 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 225 through 226 Processing sheet with id=AG2, first strand: chain 'V' and resid 303 through 308 removed outlier: 3.927A pdb=" N THR V 437 " --> pdb=" O HIS V 308 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 4 through 6 Processing sheet with id=AG4, first strand: chain 'X' and resid 77 through 81 removed outlier: 4.378A pdb=" N GLN X 151 " --> pdb=" O ILE X 64 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TYR X 285 " --> pdb=" O SER X 281 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER X 281 " --> pdb=" O TYR X 285 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL X 287 " --> pdb=" O VAL X 279 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N PHE X 447 " --> pdb=" O VAL X 263 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N HIS X 265 " --> pdb=" O PHE X 447 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 246 through 251 removed outlier: 6.839A pdb=" N ALA X 189 " --> pdb=" O CYS X 331 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N TYR X 333 " --> pdb=" O ALA X 189 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ALA X 191 " --> pdb=" O TYR X 333 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 303 through 308 removed outlier: 3.926A pdb=" N THR X 437 " --> pdb=" O HIS X 308 " (cutoff:3.500A) 2007 hydrogen bonds defined for protein. 5607 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.14 Time building geometry restraints manager: 4.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 13826 1.35 - 1.47: 10173 1.47 - 1.59: 19081 1.59 - 1.71: 60 1.71 - 1.83: 504 Bond restraints: 43644 Sorted by residual: bond pdb=" C ASP I 89 " pdb=" N PRO I 90 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.20e-02 6.94e+03 3.79e+00 bond pdb=" CB MET K 73 " pdb=" CG MET K 73 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.24e+00 bond pdb=" CA MET C 73 " pdb=" CB MET C 73 " ideal model delta sigma weight residual 1.527 1.543 -0.016 1.15e-02 7.56e+03 1.92e+00 bond pdb=" CA MET K 73 " pdb=" CB MET K 73 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.15e-02 7.56e+03 1.80e+00 bond pdb=" CA ASP C 89 " pdb=" C ASP C 89 " ideal model delta sigma weight residual 1.525 1.553 -0.028 2.10e-02 2.27e+03 1.78e+00 ... (remaining 43639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 58996 2.55 - 5.10: 293 5.10 - 7.66: 70 7.66 - 10.21: 3 10.21 - 12.76: 2 Bond angle restraints: 59364 Sorted by residual: angle pdb=" CB MET K 123 " pdb=" CG MET K 123 " pdb=" SD MET K 123 " ideal model delta sigma weight residual 112.70 125.46 -12.76 3.00e+00 1.11e-01 1.81e+01 angle pdb=" CB MET K 73 " pdb=" CG MET K 73 " pdb=" SD MET K 73 " ideal model delta sigma weight residual 112.70 124.54 -11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" N ASP C 89 " pdb=" CA ASP C 89 " pdb=" C ASP C 89 " ideal model delta sigma weight residual 111.00 119.55 -8.55 2.80e+00 1.28e-01 9.33e+00 angle pdb=" CA LYS C 231 " pdb=" CB LYS C 231 " pdb=" CG LYS C 231 " ideal model delta sigma weight residual 114.10 120.17 -6.07 2.00e+00 2.50e-01 9.21e+00 angle pdb=" CB MET Q 123 " pdb=" CG MET Q 123 " pdb=" SD MET Q 123 " ideal model delta sigma weight residual 112.70 120.81 -8.11 3.00e+00 1.11e-01 7.30e+00 ... (remaining 59359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.90: 25582 33.90 - 67.81: 805 67.81 - 101.71: 37 101.71 - 135.62: 0 135.62 - 169.52: 12 Dihedral angle restraints: 26436 sinusoidal: 10428 harmonic: 16008 Sorted by residual: dihedral pdb=" C8 GTP I 602 " pdb=" C1' GTP I 602 " pdb=" N9 GTP I 602 " pdb=" O4' GTP I 602 " ideal model delta sinusoidal sigma weight residual 104.59 -85.88 -169.52 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C8 GTP X 602 " pdb=" C1' GTP X 602 " pdb=" N9 GTP X 602 " pdb=" O4' GTP X 602 " ideal model delta sinusoidal sigma weight residual 104.59 -86.71 -168.70 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C8 GTP Q 602 " pdb=" C1' GTP Q 602 " pdb=" N9 GTP Q 602 " pdb=" O4' GTP Q 602 " ideal model delta sinusoidal sigma weight residual 104.59 -86.88 -168.53 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 26433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 4636 0.036 - 0.073: 1422 0.073 - 0.109: 514 0.109 - 0.145: 158 0.145 - 0.181: 2 Chirality restraints: 6732 Sorted by residual: chirality pdb=" CA ASP C 89 " pdb=" N ASP C 89 " pdb=" C ASP C 89 " pdb=" CB ASP C 89 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CB ILE G 440 " pdb=" CA ILE G 440 " pdb=" CG1 ILE G 440 " pdb=" CG2 ILE G 440 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CB ILE V 440 " pdb=" CA ILE V 440 " pdb=" CG1 ILE V 440 " pdb=" CG2 ILE V 440 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 6729 not shown) Planarity restraints: 7488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP O 56 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO O 57 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO O 57 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO O 57 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP V 56 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO V 57 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO V 57 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO V 57 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU I 234 " 0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO I 235 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO I 235 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO I 235 " 0.029 5.00e-02 4.00e+02 ... (remaining 7485 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 502 2.61 - 3.19: 36442 3.19 - 3.76: 74251 3.76 - 4.33: 104543 4.33 - 4.90: 167978 Nonbonded interactions: 383716 Sorted by model distance: nonbonded pdb=" OE1 GLU X 129 " pdb="ZN ZN X 601 " model vdw 2.044 2.230 nonbonded pdb=" OE1 GLU G 129 " pdb="ZN ZN G 601 " model vdw 2.057 2.230 nonbonded pdb=" OE1 GLU K 129 " pdb="ZN ZN K 601 " model vdw 2.093 2.230 nonbonded pdb=" OD2 ASP S 63 " pdb=" OG SER S 66 " model vdw 2.111 3.040 nonbonded pdb=" OD2 ASP O 63 " pdb=" OG SER O 66 " model vdw 2.113 3.040 ... (remaining 383711 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' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 602)) selection = (chain 'C' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 602)) selection = (chain 'E' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 602)) selection = (chain 'G' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 602)) selection = (chain 'I' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 602)) selection = (chain 'K' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 602)) selection = (chain 'M' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 602)) selection = (chain 'O' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 602)) selection = (chain 'Q' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 602)) selection = (chain 'S' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 602)) selection = (chain 'V' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 602)) selection = (chain 'X' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 602)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 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: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 57.670 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.140 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:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 : 0.003 0.045 43680 Z= 0.135 Angle : 0.568 12.760 59364 Z= 0.291 Chirality : 0.042 0.181 6732 Planarity : 0.005 0.055 7488 Dihedral : 16.267 169.524 16116 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.01 % Allowed : 19.49 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.11), residues: 5484 helix: 0.72 (0.12), residues: 1968 sheet: 0.32 (0.17), residues: 804 loop : -1.12 (0.11), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 289 TYR 0.015 0.001 TYR O 382 PHE 0.018 0.002 PHE S 264 TRP 0.010 0.001 TRP E 258 HIS 0.007 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00290 (43644) covalent geometry : angle 0.56788 (59364) hydrogen bonds : bond 0.11805 ( 2007) hydrogen bonds : angle 5.67881 ( 5607) metal coordination : bond 0.00453 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 367 time to evaluate : 1.601 Fit side-chains REVERT: A 72 MET cc_start: 0.5806 (pmm) cc_final: 0.5583 (ptp) REVERT: A 73 MET cc_start: 0.7292 (ppp) cc_final: 0.6931 (ptm) REVERT: C 73 MET cc_start: 0.6371 (ptp) cc_final: 0.5843 (ptp) REVERT: I 408 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8206 (mt) REVERT: S 357 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8323 (mttp) REVERT: X 72 MET cc_start: 0.6274 (pmm) cc_final: 0.5698 (ptm) REVERT: X 73 MET cc_start: 0.6721 (ptt) cc_final: 0.6441 (ptp) outliers start: 73 outliers final: 63 residues processed: 434 average time/residue: 0.6518 time to fit residues: 359.7704 Evaluate side-chains 421 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 356 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 74 SER Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain O residue 44 SER Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 305 VAL Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 262 SER Chi-restraints excluded: chain S residue 274 CYS Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 330 VAL Chi-restraints excluded: chain S residue 357 LYS Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 274 CYS Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 410 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 394 optimal weight: 0.9990 chunk 430 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 0.8980 chunk 523 optimal weight: 0.9980 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 1.9990 chunk 488 optimal weight: 2.9990 chunk 366 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS E 79 HIS ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 429 HIS ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.167863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.128575 restraints weight = 237819.350| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 4.51 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.0588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.397 43680 Z= 0.161 Angle : 0.572 9.484 59364 Z= 0.290 Chirality : 0.043 0.171 6732 Planarity : 0.004 0.045 7488 Dihedral : 9.810 170.057 6265 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.06 % Allowed : 17.52 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.11), residues: 5484 helix: 1.44 (0.13), residues: 1944 sheet: 0.43 (0.17), residues: 804 loop : -1.14 (0.11), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 289 TYR 0.013 0.001 TYR O 195 PHE 0.018 0.002 PHE I 183 TRP 0.010 0.001 TRP E 258 HIS 0.004 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00326 (43644) covalent geometry : angle 0.57220 (59364) hydrogen bonds : bond 0.03594 ( 2007) hydrogen bonds : angle 4.34986 ( 5607) metal coordination : bond 0.06620 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 377 time to evaluate : 1.599 Fit side-chains REVERT: A 73 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6756 (ptm) REVERT: C 73 MET cc_start: 0.6346 (ptp) cc_final: 0.6089 (ptt) REVERT: I 72 MET cc_start: 0.5416 (pmm) cc_final: 0.5183 (ptp) REVERT: I 408 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8098 (mt) REVERT: M 234 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: O 123 MET cc_start: 0.5860 (mmm) cc_final: 0.5078 (mmp) REVERT: S 234 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7678 (mt-10) outliers start: 120 outliers final: 57 residues processed: 464 average time/residue: 0.6383 time to fit residues: 377.2507 Evaluate side-chains 423 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 362 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 402 MET Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 234 GLU Chi-restraints excluded: chain M residue 253 LYS Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 274 CYS Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 402 MET Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain S residue 246 THR Chi-restraints excluded: chain S residue 274 CYS Chi-restraints excluded: chain V residue 58 ASP Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 384 ILE Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 274 CYS Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 410 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 357 optimal weight: 0.7980 chunk 235 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 512 optimal weight: 8.9990 chunk 497 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 401 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 468 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 351 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN G 165 GLN I 203 GLN I 444 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.166105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124077 restraints weight = 233993.049| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 5.61 r_work: 0.2814 rms_B_bonded: 5.51 restraints_weight: 2.0000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 43680 Z= 0.225 Angle : 0.617 8.534 59364 Z= 0.314 Chirality : 0.045 0.169 6732 Planarity : 0.005 0.043 7488 Dihedral : 9.928 172.391 6228 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.48 % Allowed : 17.13 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.11), residues: 5484 helix: 1.27 (0.12), residues: 1956 sheet: 0.41 (0.17), residues: 804 loop : -1.18 (0.11), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 252 TYR 0.019 0.002 TYR O 195 PHE 0.021 0.003 PHE A 183 TRP 0.012 0.002 TRP K 258 HIS 0.006 0.002 HIS C 79 Details of bonding type rmsd covalent geometry : bond 0.00507 (43644) covalent geometry : angle 0.61701 (59364) hydrogen bonds : bond 0.03936 ( 2007) hydrogen bonds : angle 4.35347 ( 5607) metal coordination : bond 0.00523 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 367 time to evaluate : 1.628 Fit side-chains REVERT: A 72 MET cc_start: 0.6711 (ptp) cc_final: 0.5999 (pmm) REVERT: A 123 MET cc_start: 0.5155 (mmp) cc_final: 0.4897 (mmp) REVERT: A 146 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7685 (p0) REVERT: A 250 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7817 (mm-30) REVERT: C 73 MET cc_start: 0.6720 (ptp) cc_final: 0.6159 (ptt) REVERT: C 146 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.7792 (p0) REVERT: I 72 MET cc_start: 0.5605 (pmm) cc_final: 0.5149 (ptp) REVERT: I 73 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6276 (ppp) REVERT: I 408 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8327 (mt) REVERT: M 123 MET cc_start: 0.5132 (mmp) cc_final: 0.4864 (mmp) REVERT: O 123 MET cc_start: 0.4687 (mmm) cc_final: 0.4059 (mmp) REVERT: Q 72 MET cc_start: 0.5631 (ptm) cc_final: 0.5366 (pmm) REVERT: V 146 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7773 (p0) REVERT: X 267 LYS cc_start: 0.8344 (mtpt) cc_final: 0.8074 (mtpp) outliers start: 132 outliers final: 67 residues processed: 467 average time/residue: 0.5946 time to fit residues: 353.7576 Evaluate side-chains 429 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 356 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 253 LYS Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 274 CYS Chi-restraints excluded: chain O residue 315 CYS Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain Q residue 44 SER Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 386 VAL Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 232 LYS Chi-restraints excluded: chain S residue 246 THR Chi-restraints excluded: chain S residue 402 MET Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 58 ASP Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 146 ASP Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 247 LEU Chi-restraints excluded: chain X residue 274 CYS Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 410 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 20 optimal weight: 1.9990 chunk 442 optimal weight: 1.9990 chunk 330 optimal weight: 0.6980 chunk 341 optimal weight: 2.9990 chunk 513 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 443 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 467 optimal weight: 0.9980 chunk 400 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN G 381 ASN I 381 ASN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.167632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127598 restraints weight = 230093.964| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 5.47 r_work: 0.2868 rms_B_bonded: 5.38 restraints_weight: 2.0000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 43680 Z= 0.139 Angle : 0.556 10.171 59364 Z= 0.281 Chirality : 0.043 0.159 6732 Planarity : 0.004 0.040 7488 Dihedral : 9.697 171.090 6227 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.39 % Allowed : 16.97 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.11), residues: 5484 helix: 1.55 (0.13), residues: 1932 sheet: 0.43 (0.17), residues: 804 loop : -1.17 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 289 TYR 0.012 0.001 TYR O 195 PHE 0.016 0.002 PHE G 183 TRP 0.010 0.001 TRP C 258 HIS 0.004 0.001 HIS C 79 Details of bonding type rmsd covalent geometry : bond 0.00308 (43644) covalent geometry : angle 0.55567 (59364) hydrogen bonds : bond 0.03223 ( 2007) hydrogen bonds : angle 4.22867 ( 5607) metal coordination : bond 0.00324 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 378 time to evaluate : 1.603 Fit side-chains REVERT: A 72 MET cc_start: 0.6505 (OUTLIER) cc_final: 0.6043 (pmm) REVERT: A 123 MET cc_start: 0.5463 (mmp) cc_final: 0.5169 (mmp) REVERT: A 250 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7637 (mm-30) REVERT: C 73 MET cc_start: 0.6608 (ptp) cc_final: 0.6154 (ptt) REVERT: I 72 MET cc_start: 0.5550 (pmm) cc_final: 0.5148 (ptp) REVERT: I 73 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6152 (ppp) REVERT: I 228 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.6415 (pmm) REVERT: I 408 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8319 (mt) REVERT: K 72 MET cc_start: 0.6039 (pmm) cc_final: 0.5829 (ptp) REVERT: K 228 MET cc_start: 0.6694 (ppp) cc_final: 0.6356 (pp-130) REVERT: M 123 MET cc_start: 0.5328 (mmp) cc_final: 0.4956 (mmp) REVERT: O 123 MET cc_start: 0.4803 (mmm) cc_final: 0.4172 (mmp) REVERT: Q 72 MET cc_start: 0.5621 (ptm) cc_final: 0.4878 (ttp) REVERT: Q 151 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8586 (tt0) REVERT: Q 446 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8191 (mt-10) REVERT: V 402 MET cc_start: 0.8765 (mtm) cc_final: 0.8375 (mtm) outliers start: 127 outliers final: 63 residues processed: 475 average time/residue: 0.6488 time to fit residues: 392.4365 Evaluate side-chains 426 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 356 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 315 CYS Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 253 LYS Chi-restraints excluded: chain M residue 315 CYS Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 274 CYS Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 151 GLN Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 446 GLU Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 246 THR Chi-restraints excluded: chain S residue 402 MET Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 58 ASP Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 274 CYS Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 386 VAL Chi-restraints excluded: chain X residue 410 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 379 optimal weight: 2.9990 chunk 365 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 293 optimal weight: 0.5980 chunk 161 optimal weight: 5.9990 chunk 414 optimal weight: 2.9990 chunk 410 optimal weight: 0.3980 chunk 273 optimal weight: 0.0980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN M 165 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 444 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.167619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.127657 restraints weight = 246463.419| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 5.59 r_work: 0.2866 rms_B_bonded: 5.39 restraints_weight: 2.0000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 43680 Z= 0.145 Angle : 0.557 10.391 59364 Z= 0.281 Chirality : 0.043 0.159 6732 Planarity : 0.004 0.039 7488 Dihedral : 9.663 171.340 6226 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.11 % Allowed : 17.19 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.11), residues: 5484 helix: 1.59 (0.13), residues: 1932 sheet: 0.39 (0.17), residues: 804 loop : -1.18 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 252 TYR 0.013 0.002 TYR O 195 PHE 0.016 0.002 PHE G 183 TRP 0.010 0.001 TRP E 258 HIS 0.003 0.001 HIS C 79 Details of bonding type rmsd covalent geometry : bond 0.00323 (43644) covalent geometry : angle 0.55735 (59364) hydrogen bonds : bond 0.03199 ( 2007) hydrogen bonds : angle 4.19668 ( 5607) metal coordination : bond 0.00261 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 371 time to evaluate : 1.622 Fit side-chains REVERT: A 72 MET cc_start: 0.6555 (OUTLIER) cc_final: 0.6015 (pmm) REVERT: A 123 MET cc_start: 0.5416 (mmp) cc_final: 0.5124 (mmp) REVERT: A 250 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7659 (mm-30) REVERT: C 73 MET cc_start: 0.6607 (ptp) cc_final: 0.6115 (ptp) REVERT: C 146 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7686 (p0) REVERT: I 72 MET cc_start: 0.5513 (pmm) cc_final: 0.5102 (ptp) REVERT: I 73 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6209 (ppp) REVERT: I 146 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7759 (p0) REVERT: I 228 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.6414 (pmm) REVERT: I 402 MET cc_start: 0.8758 (mtm) cc_final: 0.8453 (mtm) REVERT: I 408 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8323 (mt) REVERT: K 228 MET cc_start: 0.6706 (ppp) cc_final: 0.6356 (pp-130) REVERT: M 72 MET cc_start: 0.6181 (OUTLIER) cc_final: 0.5801 (pmm) REVERT: M 123 MET cc_start: 0.5327 (mmp) cc_final: 0.4963 (mmp) REVERT: O 123 MET cc_start: 0.4818 (mmm) cc_final: 0.4200 (mmp) REVERT: Q 72 MET cc_start: 0.5604 (ptm) cc_final: 0.4870 (ttp) REVERT: Q 151 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8677 (tt0) REVERT: Q 446 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8223 (mt-10) REVERT: V 73 MET cc_start: 0.6896 (ptm) cc_final: 0.6648 (ptt) REVERT: V 402 MET cc_start: 0.8769 (mtm) cc_final: 0.8361 (mtm) outliers start: 114 outliers final: 69 residues processed: 460 average time/residue: 0.6699 time to fit residues: 390.5913 Evaluate side-chains 438 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 359 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 146 ASP Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 315 CYS Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain M residue 72 MET Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 253 LYS Chi-restraints excluded: chain M residue 315 CYS Chi-restraints excluded: chain M residue 402 MET Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 274 CYS Chi-restraints excluded: chain O residue 315 CYS Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 151 GLN Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 446 GLU Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 246 THR Chi-restraints excluded: chain S residue 402 MET Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 58 ASP Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 274 CYS Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain X residue 44 SER Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 274 CYS Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 386 VAL Chi-restraints excluded: chain X residue 410 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 80 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 367 optimal weight: 0.8980 chunk 435 optimal weight: 0.8980 chunk 410 optimal weight: 3.9990 chunk 491 optimal weight: 4.9990 chunk 349 optimal weight: 0.6980 chunk 157 optimal weight: 0.3980 chunk 465 optimal weight: 0.5980 chunk 108 optimal weight: 0.1980 chunk 336 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN M 165 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.170513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128051 restraints weight = 235619.340| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 5.57 r_work: 0.2902 rms_B_bonded: 5.43 restraints_weight: 2.0000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 43680 Z= 0.110 Angle : 0.528 11.322 59364 Z= 0.265 Chirality : 0.042 0.156 6732 Planarity : 0.004 0.039 7488 Dihedral : 9.478 170.350 6225 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.00 % Allowed : 17.21 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.11), residues: 5484 helix: 1.77 (0.13), residues: 1932 sheet: 0.42 (0.17), residues: 804 loop : -1.16 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 289 TYR 0.010 0.001 TYR Q 150 PHE 0.013 0.001 PHE S 264 TRP 0.009 0.001 TRP E 258 HIS 0.004 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00242 (43644) covalent geometry : angle 0.52792 (59364) hydrogen bonds : bond 0.02807 ( 2007) hydrogen bonds : angle 4.12253 ( 5607) metal coordination : bond 0.00155 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 375 time to evaluate : 1.639 Fit side-chains REVERT: A 72 MET cc_start: 0.6521 (OUTLIER) cc_final: 0.5994 (pmm) REVERT: A 123 MET cc_start: 0.5426 (mmp) cc_final: 0.5132 (mmp) REVERT: A 250 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7548 (mm-30) REVERT: C 73 MET cc_start: 0.6538 (ptp) cc_final: 0.6024 (ptp) REVERT: C 444 GLN cc_start: 0.9079 (tt0) cc_final: 0.8763 (tt0) REVERT: E 72 MET cc_start: 0.6144 (ptm) cc_final: 0.5928 (ptm) REVERT: G 123 MET cc_start: 0.5135 (mmp) cc_final: 0.4833 (mmp) REVERT: I 72 MET cc_start: 0.5529 (pmm) cc_final: 0.5219 (ptp) REVERT: I 73 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6890 (ptt) REVERT: I 402 MET cc_start: 0.8707 (mtm) cc_final: 0.8366 (mtm) REVERT: I 408 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8312 (mt) REVERT: M 72 MET cc_start: 0.6128 (OUTLIER) cc_final: 0.5766 (pmm) REVERT: M 123 MET cc_start: 0.5336 (mmp) cc_final: 0.5017 (mmp) REVERT: O 123 MET cc_start: 0.4826 (mmm) cc_final: 0.4339 (mmp) REVERT: Q 72 MET cc_start: 0.5794 (ptm) cc_final: 0.4929 (ttp) REVERT: Q 151 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8652 (tt0) REVERT: Q 446 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: S 423 PHE cc_start: 0.8045 (p90) cc_final: 0.7820 (p90) REVERT: V 402 MET cc_start: 0.8713 (mtm) cc_final: 0.8304 (mtm) outliers start: 109 outliers final: 63 residues processed: 460 average time/residue: 0.6502 time to fit residues: 378.8917 Evaluate side-chains 436 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 366 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 315 CYS Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain M residue 72 MET Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 315 CYS Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 274 CYS Chi-restraints excluded: chain O residue 315 CYS Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 151 GLN Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 446 GLU Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 246 THR Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 58 ASP Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 274 CYS Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 274 CYS Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 386 VAL Chi-restraints excluded: chain X residue 410 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 471 optimal weight: 1.9990 chunk 418 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 363 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 274 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 473 optimal weight: 2.9990 chunk 292 optimal weight: 8.9990 chunk 129 optimal weight: 0.4980 chunk 489 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 203 GLN ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN M 165 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 165 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.166415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.124497 restraints weight = 228411.950| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 5.55 r_work: 0.2822 rms_B_bonded: 5.48 restraints_weight: 2.0000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 43680 Z= 0.217 Angle : 0.608 11.896 59364 Z= 0.309 Chirality : 0.045 0.159 6732 Planarity : 0.005 0.036 7488 Dihedral : 9.792 172.859 6225 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.06 % Allowed : 17.04 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.11), residues: 5484 helix: 1.52 (0.12), residues: 1932 sheet: 0.43 (0.17), residues: 804 loop : -1.18 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 252 TYR 0.018 0.002 TYR O 285 PHE 0.021 0.002 PHE S 183 TRP 0.011 0.002 TRP K 258 HIS 0.007 0.002 HIS O 37 Details of bonding type rmsd covalent geometry : bond 0.00490 (43644) covalent geometry : angle 0.60800 (59364) hydrogen bonds : bond 0.03654 ( 2007) hydrogen bonds : angle 4.26939 ( 5607) metal coordination : bond 0.00432 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 367 time to evaluate : 1.637 Fit side-chains REVERT: A 72 MET cc_start: 0.6509 (OUTLIER) cc_final: 0.5988 (pmm) REVERT: A 123 MET cc_start: 0.5283 (mmp) cc_final: 0.4975 (mmp) REVERT: A 146 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7672 (p0) REVERT: A 234 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8703 (mt-10) REVERT: A 250 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7794 (mm-30) REVERT: C 73 MET cc_start: 0.6466 (ptp) cc_final: 0.6017 (ptp) REVERT: G 123 MET cc_start: 0.5243 (mmp) cc_final: 0.4904 (mmp) REVERT: G 146 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7689 (p0) REVERT: G 225 LEU cc_start: 0.6578 (mp) cc_final: 0.6360 (tp) REVERT: I 72 MET cc_start: 0.5535 (pmm) cc_final: 0.5207 (ptp) REVERT: I 73 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6000 (ppp) REVERT: I 146 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7786 (p0) REVERT: I 402 MET cc_start: 0.8775 (mtm) cc_final: 0.8487 (mtm) REVERT: I 408 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8306 (mt) REVERT: K 28 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8242 (mt-10) REVERT: K 70 ARG cc_start: 0.7127 (ptt180) cc_final: 0.6722 (ptt90) REVERT: K 228 MET cc_start: 0.6863 (ppp) cc_final: 0.6547 (pp-130) REVERT: M 72 MET cc_start: 0.6166 (OUTLIER) cc_final: 0.5812 (pmm) REVERT: M 123 MET cc_start: 0.5282 (mmp) cc_final: 0.4974 (mmp) REVERT: M 146 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7789 (p0) REVERT: O 72 MET cc_start: 0.5844 (pmm) cc_final: 0.5632 (ptp) REVERT: O 146 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.7836 (p0) REVERT: Q 72 MET cc_start: 0.5632 (ptm) cc_final: 0.4897 (ttp) REVERT: Q 151 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8753 (tt0) REVERT: Q 446 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8270 (mt-10) REVERT: S 345 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8411 (tp) REVERT: S 357 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8636 (mttp) REVERT: V 72 MET cc_start: 0.5802 (pmm) cc_final: 0.5568 (ptp) REVERT: V 402 MET cc_start: 0.8783 (mtm) cc_final: 0.8401 (mtm) REVERT: X 146 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7805 (p0) outliers start: 112 outliers final: 71 residues processed: 454 average time/residue: 0.6381 time to fit residues: 366.4085 Evaluate side-chains 447 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 361 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain G residue 402 MET Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 146 ASP Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 315 CYS Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain M residue 72 MET Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 315 CYS Chi-restraints excluded: chain M residue 402 MET Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 274 CYS Chi-restraints excluded: chain O residue 315 CYS Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain O residue 402 MET Chi-restraints excluded: chain Q residue 44 SER Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 151 GLN Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 446 GLU Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 246 THR Chi-restraints excluded: chain S residue 345 ILE Chi-restraints excluded: chain S residue 357 LYS Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 58 ASP Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 274 CYS Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain X residue 44 SER Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 74 SER Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 146 ASP Chi-restraints excluded: chain X residue 274 CYS Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 315 CYS Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 386 VAL Chi-restraints excluded: chain X residue 410 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 196 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 71 optimal weight: 0.0270 chunk 201 optimal weight: 3.9990 chunk 471 optimal weight: 5.9990 chunk 292 optimal weight: 5.9990 chunk 181 optimal weight: 0.8980 chunk 322 optimal weight: 0.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN I 165 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.167274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.125438 restraints weight = 239134.653| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 5.67 r_work: 0.2823 rms_B_bonded: 5.60 restraints_weight: 2.0000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 43680 Z= 0.175 Angle : 0.579 11.860 59364 Z= 0.293 Chirality : 0.044 0.158 6732 Planarity : 0.004 0.037 7488 Dihedral : 9.735 172.552 6224 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.73 % Allowed : 17.43 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.11), residues: 5484 helix: 1.55 (0.12), residues: 1932 sheet: 0.43 (0.17), residues: 804 loop : -1.21 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 142 TYR 0.017 0.002 TYR Q 285 PHE 0.019 0.002 PHE G 183 TRP 0.010 0.002 TRP K 258 HIS 0.004 0.001 HIS O 37 Details of bonding type rmsd covalent geometry : bond 0.00393 (43644) covalent geometry : angle 0.57866 (59364) hydrogen bonds : bond 0.03388 ( 2007) hydrogen bonds : angle 4.23994 ( 5607) metal coordination : bond 0.00339 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 362 time to evaluate : 1.271 Fit side-chains REVERT: A 72 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.5956 (pmm) REVERT: A 123 MET cc_start: 0.5313 (mmp) cc_final: 0.4967 (mmp) REVERT: A 234 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8694 (mt-10) REVERT: A 250 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7727 (mm-30) REVERT: C 73 MET cc_start: 0.6465 (ptp) cc_final: 0.6017 (ptp) REVERT: G 123 MET cc_start: 0.5285 (mmp) cc_final: 0.4974 (mmp) REVERT: G 146 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7661 (p0) REVERT: I 73 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6182 (ppp) REVERT: I 146 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7756 (p0) REVERT: I 402 MET cc_start: 0.8748 (mtm) cc_final: 0.8399 (mtm) REVERT: I 408 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8321 (mt) REVERT: K 28 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8227 (mt-10) REVERT: K 72 MET cc_start: 0.6150 (pmm) cc_final: 0.5895 (ptp) REVERT: K 228 MET cc_start: 0.6868 (ppp) cc_final: 0.6563 (pp-130) REVERT: M 72 MET cc_start: 0.6192 (OUTLIER) cc_final: 0.5818 (pmm) REVERT: O 72 MET cc_start: 0.5784 (pmm) cc_final: 0.5561 (ptp) REVERT: O 123 MET cc_start: 0.4551 (mmp) cc_final: 0.4119 (mmp) REVERT: Q 72 MET cc_start: 0.5800 (ptm) cc_final: 0.4937 (ttp) REVERT: Q 151 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8760 (tt0) REVERT: Q 446 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8252 (mt-10) REVERT: V 72 MET cc_start: 0.5788 (pmm) cc_final: 0.5585 (ptp) REVERT: V 146 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7735 (p0) REVERT: V 402 MET cc_start: 0.8751 (mtm) cc_final: 0.8376 (mtm) outliers start: 97 outliers final: 72 residues processed: 435 average time/residue: 0.6417 time to fit residues: 352.7449 Evaluate side-chains 440 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 358 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain G residue 402 MET Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 146 ASP Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 315 CYS Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain M residue 72 MET Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 315 CYS Chi-restraints excluded: chain M residue 402 MET Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 274 CYS Chi-restraints excluded: chain O residue 315 CYS Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain O residue 402 MET Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 151 GLN Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 446 GLU Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 246 THR Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 58 ASP Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 146 ASP Chi-restraints excluded: chain V residue 274 CYS Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain X residue 44 SER Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 74 SER Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 274 CYS Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 315 CYS Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 386 VAL Chi-restraints excluded: chain X residue 410 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 276 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 chunk 82 optimal weight: 7.9990 chunk 212 optimal weight: 0.9990 chunk 377 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 300 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 317 optimal weight: 9.9990 chunk 489 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.167142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.125265 restraints weight = 231619.779| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 5.59 r_work: 0.2835 rms_B_bonded: 5.51 restraints_weight: 2.0000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 43680 Z= 0.171 Angle : 0.578 12.151 59364 Z= 0.293 Chirality : 0.043 0.158 6732 Planarity : 0.004 0.037 7488 Dihedral : 9.720 172.645 6224 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.78 % Allowed : 17.48 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.11), residues: 5484 helix: 1.57 (0.12), residues: 1932 sheet: 0.43 (0.17), residues: 804 loop : -1.21 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 142 TYR 0.018 0.002 TYR O 285 PHE 0.018 0.002 PHE G 183 TRP 0.010 0.002 TRP C 258 HIS 0.004 0.001 HIS O 37 Details of bonding type rmsd covalent geometry : bond 0.00383 (43644) covalent geometry : angle 0.57812 (59364) hydrogen bonds : bond 0.03361 ( 2007) hydrogen bonds : angle 4.23097 ( 5607) metal coordination : bond 0.00348 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 366 time to evaluate : 1.596 Fit side-chains REVERT: A 72 MET cc_start: 0.6471 (OUTLIER) cc_final: 0.6049 (pmm) REVERT: A 123 MET cc_start: 0.5345 (mmp) cc_final: 0.4997 (mmp) REVERT: A 234 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8686 (mt-10) REVERT: A 250 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7709 (mm-30) REVERT: C 73 MET cc_start: 0.6493 (ptp) cc_final: 0.6047 (ptp) REVERT: E 72 MET cc_start: 0.6278 (ptm) cc_final: 0.5576 (pmm) REVERT: G 123 MET cc_start: 0.5189 (mmp) cc_final: 0.4872 (mmp) REVERT: G 146 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7629 (p0) REVERT: G 345 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8482 (tp) REVERT: I 72 MET cc_start: 0.6083 (ptp) cc_final: 0.5796 (pmm) REVERT: I 146 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7743 (p0) REVERT: I 228 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6431 (pmm) REVERT: I 402 MET cc_start: 0.8720 (mtm) cc_final: 0.8434 (mtm) REVERT: I 408 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8322 (mt) REVERT: K 28 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8217 (mt-10) REVERT: K 70 ARG cc_start: 0.7110 (ptt180) cc_final: 0.6652 (ptt90) REVERT: K 228 MET cc_start: 0.6864 (ppp) cc_final: 0.6555 (pp-130) REVERT: M 72 MET cc_start: 0.6175 (OUTLIER) cc_final: 0.5800 (pmm) REVERT: M 345 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8473 (tp) REVERT: O 72 MET cc_start: 0.5771 (pmm) cc_final: 0.5564 (ptp) REVERT: O 89 ASP cc_start: 0.4327 (t0) cc_final: 0.4091 (t0) REVERT: Q 72 MET cc_start: 0.5726 (ptm) cc_final: 0.4892 (ttp) REVERT: Q 151 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8764 (tt0) REVERT: Q 446 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8236 (mt-10) REVERT: S 123 MET cc_start: 0.5474 (mmp) cc_final: 0.5268 (mmp) REVERT: V 72 MET cc_start: 0.5746 (pmm) cc_final: 0.5531 (ptp) REVERT: V 146 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.7732 (p0) REVERT: V 402 MET cc_start: 0.8747 (mtm) cc_final: 0.8370 (mtm) REVERT: X 146 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7787 (p0) outliers start: 99 outliers final: 71 residues processed: 442 average time/residue: 0.6303 time to fit residues: 352.2083 Evaluate side-chains 443 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 359 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 402 MET Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 146 ASP Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 315 CYS Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain M residue 72 MET Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 315 CYS Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain M residue 402 MET Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 274 CYS Chi-restraints excluded: chain O residue 315 CYS Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain O residue 402 MET Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 151 GLN Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 446 GLU Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 246 THR Chi-restraints excluded: chain S residue 402 MET Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 58 ASP Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 146 ASP Chi-restraints excluded: chain V residue 274 CYS Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain X residue 44 SER Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 146 ASP Chi-restraints excluded: chain X residue 274 CYS Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 315 CYS Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 386 VAL Chi-restraints excluded: chain X residue 410 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 191 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 273 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 208 optimal weight: 0.6980 chunk 257 optimal weight: 0.8980 chunk 398 optimal weight: 0.6980 chunk 157 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.169414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.126993 restraints weight = 237693.759| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 5.64 r_work: 0.2884 rms_B_bonded: 5.32 restraints_weight: 2.0000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 43680 Z= 0.124 Angle : 0.546 12.478 59364 Z= 0.275 Chirality : 0.042 0.157 6732 Planarity : 0.004 0.038 7488 Dihedral : 9.550 171.675 6224 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.47 % Allowed : 17.85 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.11), residues: 5484 helix: 1.76 (0.13), residues: 1932 sheet: 0.45 (0.17), residues: 804 loop : -1.19 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 142 TYR 0.013 0.001 TYR Q 285 PHE 0.016 0.002 PHE G 183 TRP 0.009 0.001 TRP E 258 HIS 0.003 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00275 (43644) covalent geometry : angle 0.54598 (59364) hydrogen bonds : bond 0.02949 ( 2007) hydrogen bonds : angle 4.15251 ( 5607) metal coordination : bond 0.00200 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 367 time to evaluate : 1.772 Fit side-chains REVERT: A 72 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.6117 (pmm) REVERT: A 123 MET cc_start: 0.5475 (mmp) cc_final: 0.5135 (mmp) REVERT: A 234 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8686 (mt-10) REVERT: A 250 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7626 (mm-30) REVERT: C 73 MET cc_start: 0.6490 (ptp) cc_final: 0.6037 (ptp) REVERT: E 72 MET cc_start: 0.6348 (ptm) cc_final: 0.6079 (ptm) REVERT: G 123 MET cc_start: 0.5342 (mmp) cc_final: 0.4989 (mmp) REVERT: G 345 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8472 (tp) REVERT: I 72 MET cc_start: 0.5944 (ptp) cc_final: 0.5712 (pmm) REVERT: I 228 MET cc_start: 0.6702 (OUTLIER) cc_final: 0.6394 (pmm) REVERT: I 402 MET cc_start: 0.8677 (mtm) cc_final: 0.8346 (mtm) REVERT: I 408 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8308 (mt) REVERT: K 228 MET cc_start: 0.6655 (ppp) cc_final: 0.6373 (pp-130) REVERT: M 72 MET cc_start: 0.6202 (OUTLIER) cc_final: 0.5843 (pmm) REVERT: M 123 MET cc_start: 0.5808 (mmp) cc_final: 0.5593 (mmp) REVERT: O 123 MET cc_start: 0.5308 (mmp) cc_final: 0.4857 (mmm) REVERT: Q 72 MET cc_start: 0.5707 (ptm) cc_final: 0.4876 (ttp) REVERT: Q 151 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8684 (tt0) REVERT: Q 232 LYS cc_start: 0.8053 (pttp) cc_final: 0.7720 (ptmt) REVERT: Q 446 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8157 (mt-10) REVERT: S 123 MET cc_start: 0.5708 (mmp) cc_final: 0.5429 (mmp) REVERT: V 146 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7694 (p0) REVERT: V 402 MET cc_start: 0.8690 (mtm) cc_final: 0.8290 (mtm) outliers start: 85 outliers final: 66 residues processed: 433 average time/residue: 0.6321 time to fit residues: 348.0503 Evaluate side-chains 436 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 361 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 402 MET Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 315 CYS Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain M residue 72 MET Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 315 CYS Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 274 CYS Chi-restraints excluded: chain O residue 315 CYS Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain Q residue 44 SER Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 151 GLN Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain Q residue 446 GLU Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 246 THR Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 58 ASP Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 146 ASP Chi-restraints excluded: chain V residue 274 CYS Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 274 CYS Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 315 CYS Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 410 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 481 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 499 optimal weight: 0.7980 chunk 232 optimal weight: 8.9990 chunk 199 optimal weight: 0.7980 chunk 208 optimal weight: 2.9990 chunk 344 optimal weight: 0.9980 chunk 249 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 296 optimal weight: 0.6980 chunk 485 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.176226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.140023 restraints weight = 248351.775| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 4.42 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 43680 Z= 0.121 Angle : 0.542 9.680 59364 Z= 0.273 Chirality : 0.042 0.157 6732 Planarity : 0.004 0.038 7488 Dihedral : 9.498 171.627 6224 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.38 % Allowed : 17.96 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.11), residues: 5484 helix: 1.81 (0.13), residues: 1932 sheet: 0.47 (0.17), residues: 804 loop : -1.18 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 142 TYR 0.013 0.001 TYR Q 285 PHE 0.015 0.001 PHE G 183 TRP 0.009 0.001 TRP E 421 HIS 0.003 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00270 (43644) covalent geometry : angle 0.54205 (59364) hydrogen bonds : bond 0.02898 ( 2007) hydrogen bonds : angle 4.12380 ( 5607) metal coordination : bond 0.00180 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14294.79 seconds wall clock time: 246 minutes 1.42 seconds (14761.42 seconds total)