Starting phenix.real_space_refine on Thu Dec 26 03:46:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aov_15553/12_2024/8aov_15553.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aov_15553/12_2024/8aov_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_15553/12_2024/8aov_15553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aov_15553/12_2024/8aov_15553.map" model { file = "/net/cci-nas-00/data/ceres_data/8aov_15553/12_2024/8aov_15553.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aov_15553/12_2024/8aov_15553.cif" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: 41.75, per 1000 atoms: 0.97 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: 10.20 Conformation dependent library (CDL) restraints added in 10.3 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: 6.46 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: 21.32 Time building geometry restraints manager: 11.96 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: 0.00 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 472 or resid 601 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 472 or resid 601 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 472 or resid 601 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 472 or resid 601 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 472 or resid 601 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 472 or resid 601 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 472 or resid 601 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 472 or resid 601 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 472 or resid 601 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 472 or resid 601 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 472 or resid 601 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 472 or resid 601 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: 3.590 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: 0.040 Extract box with map and model: 1.480 Check model and map are aligned: 0.290 Set scattering table: 0.370 Process input model: 131.350 Find NCS groups from input model: 2.720 Set up NCS constraints: 0.280 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: 0.020 Load rotamer database and sin/cos tables:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.910 ------------------------------------------------------------------------------- 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 43644 Z= 0.192 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (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 TRP 0.010 0.001 TRP E 258 HIS 0.007 0.001 HIS E 79 PHE 0.018 0.002 PHE S 264 TYR 0.015 0.001 TYR O 382 ARG 0.004 0.000 ARG I 289 *********************** 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 : 5.526 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: 1.3508 time to fit residues: 749.6750 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 : 5.120 ------------------------------------------------------------------------------- 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 445 optimal weight: 3.9990 chunk 400 optimal weight: 0.8980 chunk 222 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 269 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 413 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 251 optimal weight: 6.9990 chunk 308 optimal weight: 7.9990 chunk 479 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 381 ASN ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 203 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 43644 Z= 0.284 Angle : 0.605 9.365 59364 Z= 0.308 Chirality : 0.045 0.173 6732 Planarity : 0.005 0.045 7488 Dihedral : 9.977 171.314 6265 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.39 % Allowed : 17.39 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.11), residues: 5484 helix: 1.31 (0.13), residues: 1944 sheet: 0.44 (0.17), residues: 804 loop : -1.16 (0.11), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 258 HIS 0.005 0.001 HIS E 79 PHE 0.021 0.002 PHE I 183 TYR 0.016 0.002 TYR O 195 ARG 0.005 0.000 ARG Q 252 *********************** 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 504 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 371 time to evaluate : 4.986 Fit side-chains REVERT: A 73 MET cc_start: 0.7241 (OUTLIER) cc_final: 0.6921 (ptm) REVERT: C 73 MET cc_start: 0.6742 (ptp) cc_final: 0.6341 (ptt) REVERT: I 72 MET cc_start: 0.5504 (pmm) cc_final: 0.5209 (ptp) REVERT: I 73 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6192 (ppp) REVERT: I 408 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8376 (mt) REVERT: M 123 MET cc_start: 0.5472 (mmt) cc_final: 0.5212 (mmp) REVERT: M 234 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: O 123 MET cc_start: 0.5387 (mmm) cc_final: 0.4520 (mmp) REVERT: S 234 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8026 (mt-10) outliers start: 133 outliers final: 65 residues processed: 467 average time/residue: 1.3371 time to fit residues: 795.7911 Evaluate side-chains 429 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 359 time to evaluate : 5.261 ------------------------------------------------------------------------------- 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 232 LYS Chi-restraints excluded: chain A residue 246 THR 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 315 CYS 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 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 274 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 81 VAL Chi-restraints excluded: chain M residue 234 GLU Chi-restraints excluded: chain M residue 253 LYS Chi-restraints excluded: chain M residue 345 ILE 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 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 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 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 266 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 399 optimal weight: 3.9990 chunk 326 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 480 optimal weight: 1.9990 chunk 518 optimal weight: 0.6980 chunk 427 optimal weight: 3.9990 chunk 476 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 385 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 165 GLN E 79 HIS G 165 GLN ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 43644 Z= 0.304 Angle : 0.604 8.828 59364 Z= 0.307 Chirality : 0.045 0.171 6732 Planarity : 0.005 0.042 7488 Dihedral : 9.932 172.186 6231 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.52 % Allowed : 17.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.11), residues: 5484 helix: 1.32 (0.12), residues: 1944 sheet: 0.43 (0.17), residues: 804 loop : -1.20 (0.11), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 258 HIS 0.007 0.001 HIS I 79 PHE 0.020 0.002 PHE A 183 TYR 0.017 0.002 TYR O 195 ARG 0.005 0.000 ARG Q 252 *********************** 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 503 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 369 time to evaluate : 4.823 Fit side-chains REVERT: A 72 MET cc_start: 0.6527 (ptp) cc_final: 0.5962 (pmm) REVERT: A 123 MET cc_start: 0.5720 (mmp) cc_final: 0.5411 (mmp) REVERT: A 250 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7482 (mm-30) REVERT: C 73 MET cc_start: 0.6859 (ptp) cc_final: 0.6352 (ptt) REVERT: C 79 HIS cc_start: 0.7974 (t-90) cc_final: 0.7691 (t-90) REVERT: E 225 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6926 (tp) REVERT: G 225 LEU cc_start: 0.6796 (mp) cc_final: 0.6571 (tp) REVERT: G 234 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: I 72 MET cc_start: 0.5382 (pmm) cc_final: 0.5013 (ptp) REVERT: I 73 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6131 (ppp) REVERT: I 408 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8360 (mt) REVERT: M 123 MET cc_start: 0.5432 (mmt) cc_final: 0.5155 (mmp) REVERT: M 234 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: O 123 MET cc_start: 0.5494 (mmm) cc_final: 0.4714 (mmp) REVERT: Q 72 MET cc_start: 0.5651 (ptm) cc_final: 0.5432 (pmm) REVERT: S 234 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8050 (mt-10) REVERT: V 146 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7371 (p0) outliers start: 134 outliers final: 67 residues processed: 472 average time/residue: 1.3411 time to fit residues: 806.6530 Evaluate side-chains 435 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 360 time to evaluate : 4.729 ------------------------------------------------------------------------------- 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 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 274 CYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 225 LEU 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 234 GLU 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 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 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 234 GLU 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 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 0.8980 chunk 361 optimal weight: 10.0000 chunk 249 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 322 optimal weight: 2.9990 chunk 482 optimal weight: 2.9990 chunk 510 optimal weight: 5.9990 chunk 251 optimal weight: 2.9990 chunk 456 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 43644 Z= 0.362 Angle : 0.633 9.954 59364 Z= 0.323 Chirality : 0.046 0.177 6732 Planarity : 0.005 0.041 7488 Dihedral : 10.057 173.244 6230 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.98 % Allowed : 16.58 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.11), residues: 5484 helix: 1.26 (0.12), residues: 1932 sheet: 0.35 (0.17), residues: 804 loop : -1.26 (0.10), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 258 HIS 0.006 0.002 HIS I 79 PHE 0.021 0.003 PHE S 183 TYR 0.018 0.002 TYR O 195 ARG 0.005 0.001 ARG Q 252 *********************** 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 521 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 367 time to evaluate : 4.394 Fit side-chains REVERT: A 72 MET cc_start: 0.6409 (OUTLIER) cc_final: 0.5925 (pmm) REVERT: A 123 MET cc_start: 0.5686 (mmp) cc_final: 0.5349 (mmp) REVERT: A 146 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7410 (p0) REVERT: A 250 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7535 (mm-30) REVERT: C 73 MET cc_start: 0.6811 (ptp) cc_final: 0.6271 (ptp) REVERT: C 146 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7430 (p0) REVERT: G 146 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7394 (p0) REVERT: G 234 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: I 72 MET cc_start: 0.5398 (pmm) cc_final: 0.5059 (ptp) REVERT: I 73 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.6002 (ppp) REVERT: I 146 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7391 (p0) REVERT: I 228 MET cc_start: 0.6700 (OUTLIER) cc_final: 0.6406 (pmm) REVERT: I 408 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8373 (mt) REVERT: K 70 ARG cc_start: 0.6871 (ptt180) cc_final: 0.6498 (ptt90) REVERT: K 228 MET cc_start: 0.6603 (ppp) cc_final: 0.6299 (pp-130) REVERT: M 72 MET cc_start: 0.5949 (OUTLIER) cc_final: 0.5694 (pmm) REVERT: M 123 MET cc_start: 0.5819 (mmt) cc_final: 0.5540 (mmp) REVERT: M 146 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7469 (p0) REVERT: M 234 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: O 123 MET cc_start: 0.5534 (mmm) cc_final: 0.4819 (mmp) REVERT: Q 146 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7664 (p0) REVERT: Q 446 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7723 (mt-10) REVERT: S 146 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7388 (p0) REVERT: S 234 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: V 146 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7472 (p0) REVERT: X 146 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7648 (p0) outliers start: 154 outliers final: 80 residues processed: 483 average time/residue: 1.3623 time to fit residues: 837.0372 Evaluate side-chains 455 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 356 time to evaluate : 4.716 ------------------------------------------------------------------------------- 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 345 ILE 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 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 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 234 GLU Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 55 ILE 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 305 VAL 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 16 LYS 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 234 GLU Chi-restraints excluded: chain M residue 253 LYS 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 44 SER Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 146 ASP 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 Q residue 446 GLU Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 146 ASP 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 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 315 CYS 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 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 386 VAL Chi-restraints excluded: chain X residue 410 VAL Chi-restraints excluded: chain X residue 424 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 0.6980 chunk 289 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 380 optimal weight: 8.9990 chunk 210 optimal weight: 0.8980 chunk 435 optimal weight: 2.9990 chunk 352 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 260 optimal weight: 5.9990 chunk 458 optimal weight: 0.0270 chunk 128 optimal weight: 3.9990 overall best weight: 1.7242 ------------------------------------------------------------------------------- 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** C 165 GLN G 165 GLN ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN M 165 GLN M 429 HIS ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 165 GLN V 165 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 43644 Z= 0.304 Angle : 0.606 10.247 59364 Z= 0.308 Chirality : 0.045 0.167 6732 Planarity : 0.005 0.040 7488 Dihedral : 9.949 173.116 6228 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.67 % Allowed : 16.80 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.11), residues: 5484 helix: 1.35 (0.12), residues: 1932 sheet: 0.35 (0.17), residues: 804 loop : -1.26 (0.10), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 258 HIS 0.005 0.001 HIS I 308 PHE 0.021 0.002 PHE G 183 TYR 0.015 0.002 TYR O 195 ARG 0.006 0.000 ARG I 142 *********************** 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 509 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 369 time to evaluate : 5.002 Fit side-chains REVERT: A 72 MET cc_start: 0.6380 (OUTLIER) cc_final: 0.5939 (pmm) REVERT: A 123 MET cc_start: 0.5748 (mmp) cc_final: 0.5417 (mmp) REVERT: A 146 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7398 (p0) REVERT: C 73 MET cc_start: 0.6734 (ptp) cc_final: 0.6286 (ptp) REVERT: C 229 ARG cc_start: 0.5839 (OUTLIER) cc_final: 0.5538 (tpt90) REVERT: G 146 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7373 (p0) REVERT: G 234 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8107 (mt-10) REVERT: I 72 MET cc_start: 0.5308 (pmm) cc_final: 0.5097 (ptp) REVERT: I 73 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.5990 (ppp) REVERT: I 146 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7405 (p0) REVERT: I 228 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.6463 (pmm) REVERT: I 408 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8364 (mt) REVERT: K 228 MET cc_start: 0.6535 (ppp) cc_final: 0.6236 (pp-130) REVERT: M 72 MET cc_start: 0.5954 (OUTLIER) cc_final: 0.5717 (pmm) REVERT: M 123 MET cc_start: 0.5808 (mmt) cc_final: 0.5521 (mmp) REVERT: M 146 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7444 (p0) REVERT: M 234 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8107 (mt-10) REVERT: O 73 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6215 (ppp) REVERT: O 146 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7476 (p0) REVERT: Q 228 MET cc_start: 0.6578 (ppp) cc_final: 0.6330 (pp-130) REVERT: Q 446 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: S 146 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7465 (p0) REVERT: S 234 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: V 146 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7473 (p0) REVERT: X 146 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7623 (p0) outliers start: 140 outliers final: 78 residues processed: 475 average time/residue: 1.4044 time to fit residues: 842.7157 Evaluate side-chains 453 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 356 time to evaluate : 4.360 ------------------------------------------------------------------------------- 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 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 229 ARG 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 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 196 SER Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 253 LYS Chi-restraints excluded: chain G residue 315 CYS 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 146 ASP Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 305 VAL 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 345 ILE Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain M residue 16 LYS 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 196 SER Chi-restraints excluded: chain M residue 234 GLU 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 73 MET 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 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 Q residue 446 GLU Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 146 ASP 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 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 315 CYS 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 247 LEU 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 Chi-restraints excluded: chain X residue 424 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 1.9990 chunk 459 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 299 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 510 optimal weight: 1.9990 chunk 424 optimal weight: 8.9990 chunk 236 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 268 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 165 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 165 GLN ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 165 GLN X 165 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 43644 Z= 0.240 Angle : 0.575 11.098 59364 Z= 0.291 Chirality : 0.043 0.159 6732 Planarity : 0.004 0.039 7488 Dihedral : 9.819 172.598 6228 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.39 % Allowed : 17.06 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.11), residues: 5484 helix: 1.48 (0.12), residues: 1932 sheet: 0.38 (0.17), residues: 804 loop : -1.24 (0.10), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Q 258 HIS 0.004 0.001 HIS A 308 PHE 0.018 0.002 PHE G 183 TYR 0.014 0.002 TYR I 285 ARG 0.007 0.000 ARG I 142 *********************** 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 492 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 365 time to evaluate : 4.653 Fit side-chains REVERT: A 72 MET cc_start: 0.6345 (OUTLIER) cc_final: 0.6004 (pmm) REVERT: A 250 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7432 (mm-30) REVERT: C 73 MET cc_start: 0.6685 (ptp) cc_final: 0.6215 (ptp) REVERT: C 79 HIS cc_start: 0.8004 (t-90) cc_final: 0.7730 (t-90) REVERT: G 123 MET cc_start: 0.5656 (mmp) cc_final: 0.5380 (mmp) REVERT: I 146 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7344 (p0) REVERT: I 408 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8354 (mt) REVERT: K 228 MET cc_start: 0.6427 (ppp) cc_final: 0.6130 (pp-130) REVERT: M 72 MET cc_start: 0.5976 (OUTLIER) cc_final: 0.5726 (pmm) REVERT: M 123 MET cc_start: 0.5762 (mmt) cc_final: 0.5459 (mmp) REVERT: O 123 MET cc_start: 0.5482 (mmm) cc_final: 0.4700 (mmp) REVERT: O 228 MET cc_start: 0.6944 (pp-130) cc_final: 0.6718 (pp-130) REVERT: Q 446 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: S 234 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8052 (mt-10) REVERT: V 146 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7460 (p0) REVERT: X 446 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7706 (mt-10) outliers start: 127 outliers final: 68 residues processed: 462 average time/residue: 1.4154 time to fit residues: 826.5733 Evaluate side-chains 437 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 360 time to evaluate : 6.008 ------------------------------------------------------------------------------- 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 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 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 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 196 SER Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain G residue 345 ILE 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 274 CYS Chi-restraints excluded: chain I residue 305 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 72 MET Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 196 SER 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 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 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 234 GLU 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 386 VAL Chi-restraints excluded: chain X residue 410 VAL Chi-restraints excluded: chain X residue 446 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 291 optimal weight: 0.3980 chunk 373 optimal weight: 10.0000 chunk 289 optimal weight: 0.0000 chunk 430 optimal weight: 3.9990 chunk 285 optimal weight: 20.0000 chunk 508 optimal weight: 2.9990 chunk 318 optimal weight: 6.9990 chunk 310 optimal weight: 0.9980 chunk 234 optimal weight: 0.0770 overall best weight: 0.8944 ------------------------------------------------------------------------------- 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 ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN M 165 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 165 GLN V 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 43644 Z= 0.207 Angle : 0.563 11.622 59364 Z= 0.284 Chirality : 0.043 0.158 6732 Planarity : 0.004 0.039 7488 Dihedral : 9.678 172.252 6225 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.08 % Allowed : 17.30 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.11), residues: 5484 helix: 1.60 (0.12), residues: 1932 sheet: 0.38 (0.17), residues: 804 loop : -1.21 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 258 HIS 0.003 0.001 HIS C 37 PHE 0.016 0.002 PHE G 183 TYR 0.013 0.002 TYR S 285 ARG 0.007 0.000 ARG C 142 *********************** 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 487 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 374 time to evaluate : 4.853 Fit side-chains REVERT: A 72 MET cc_start: 0.6329 (OUTLIER) cc_final: 0.5989 (pmm) REVERT: A 250 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7408 (mm-30) REVERT: C 73 MET cc_start: 0.6684 (ptp) cc_final: 0.6207 (ptp) REVERT: E 72 MET cc_start: 0.6232 (ptm) cc_final: 0.5577 (pmm) REVERT: E 267 LYS cc_start: 0.8195 (mtmt) cc_final: 0.7977 (mtpp) REVERT: G 123 MET cc_start: 0.5715 (mmp) cc_final: 0.5464 (mmp) REVERT: I 146 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7351 (p0) REVERT: I 408 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8318 (mt) REVERT: I 444 GLN cc_start: 0.8863 (tt0) cc_final: 0.8631 (tt0) REVERT: K 228 MET cc_start: 0.6444 (ppp) cc_final: 0.6139 (pp-130) REVERT: M 72 MET cc_start: 0.5871 (OUTLIER) cc_final: 0.5623 (pmm) REVERT: M 123 MET cc_start: 0.5765 (mmt) cc_final: 0.5446 (mmp) REVERT: O 73 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6183 (ppp) REVERT: O 123 MET cc_start: 0.5510 (mmm) cc_final: 0.4781 (mmp) REVERT: Q 228 MET cc_start: 0.6603 (ppp) cc_final: 0.6308 (pp-130) REVERT: Q 446 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: S 234 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8026 (mt-10) REVERT: V 402 MET cc_start: 0.8466 (mtm) cc_final: 0.8007 (mtm) REVERT: X 446 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7729 (mt-10) outliers start: 113 outliers final: 69 residues processed: 463 average time/residue: 1.4278 time to fit residues: 839.9567 Evaluate side-chains 445 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 367 time to evaluate : 5.143 ------------------------------------------------------------------------------- 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 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 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 196 SER Chi-restraints excluded: chain G residue 253 LYS Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain G residue 345 ILE 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 315 CYS Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 402 MET 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 196 SER 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 73 MET 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 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 234 GLU 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 44 SER Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 81 VAL 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 Chi-restraints excluded: chain X residue 446 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 0.5980 chunk 203 optimal weight: 2.9990 chunk 303 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 323 optimal weight: 0.6980 chunk 346 optimal weight: 5.9990 chunk 251 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 400 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 165 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 165 GLN V 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 43644 Z= 0.224 Angle : 0.569 11.896 59364 Z= 0.288 Chirality : 0.043 0.158 6732 Planarity : 0.004 0.038 7488 Dihedral : 9.681 172.548 6223 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.82 % Allowed : 17.63 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.11), residues: 5484 helix: 1.61 (0.12), residues: 1932 sheet: 0.40 (0.17), residues: 804 loop : -1.21 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 258 HIS 0.007 0.001 HIS C 79 PHE 0.017 0.002 PHE G 183 TYR 0.016 0.002 TYR O 285 ARG 0.006 0.000 ARG I 142 *********************** 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 475 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 374 time to evaluate : 7.226 Fit side-chains REVERT: A 72 MET cc_start: 0.6312 (OUTLIER) cc_final: 0.5978 (pmm) REVERT: A 123 MET cc_start: 0.6047 (mmp) cc_final: 0.5810 (mmp) REVERT: A 250 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7411 (mm-30) REVERT: C 73 MET cc_start: 0.6593 (ptp) cc_final: 0.6178 (ptp) REVERT: E 72 MET cc_start: 0.6237 (ptm) cc_final: 0.5574 (pmm) REVERT: G 123 MET cc_start: 0.5594 (mmp) cc_final: 0.5346 (mmp) REVERT: I 146 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7356 (p0) REVERT: I 228 MET cc_start: 0.6414 (OUTLIER) cc_final: 0.6166 (pmm) REVERT: I 408 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8310 (mt) REVERT: I 444 GLN cc_start: 0.8865 (tt0) cc_final: 0.8618 (tt0) REVERT: K 228 MET cc_start: 0.6557 (ppp) cc_final: 0.6246 (pp-130) REVERT: M 72 MET cc_start: 0.5854 (OUTLIER) cc_final: 0.5551 (pmm) REVERT: M 123 MET cc_start: 0.5768 (mmp) cc_final: 0.5450 (mmp) REVERT: O 123 MET cc_start: 0.5403 (mmm) cc_final: 0.4757 (mmp) REVERT: Q 72 MET cc_start: 0.6182 (ptp) cc_final: 0.5828 (ptm) REVERT: Q 228 MET cc_start: 0.6588 (ppp) cc_final: 0.6314 (pp-130) REVERT: Q 446 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: S 234 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: V 402 MET cc_start: 0.8473 (mtm) cc_final: 0.8020 (mtm) REVERT: X 446 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7735 (mt-10) outliers start: 101 outliers final: 73 residues processed: 451 average time/residue: 1.5288 time to fit residues: 884.5889 Evaluate side-chains 446 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 364 time to evaluate : 4.648 ------------------------------------------------------------------------------- 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 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 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 196 SER Chi-restraints excluded: chain G residue 253 LYS 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 305 VAL Chi-restraints excluded: chain I residue 315 CYS Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 402 MET 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 73 MET Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 196 SER 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 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 234 GLU 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 44 SER Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 81 VAL 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 Chi-restraints excluded: chain X residue 446 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 5.9990 chunk 487 optimal weight: 0.0370 chunk 444 optimal weight: 0.9990 chunk 474 optimal weight: 1.9990 chunk 285 optimal weight: 10.0000 chunk 206 optimal weight: 0.7980 chunk 372 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 428 optimal weight: 1.9990 chunk 448 optimal weight: 10.0000 chunk 472 optimal weight: 0.9990 overall best weight: 0.9664 ------------------------------------------------------------------------------- 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 120 GLN G 165 GLN ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 165 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 165 GLN V 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 43644 Z= 0.213 Angle : 0.563 10.290 59364 Z= 0.284 Chirality : 0.043 0.158 6732 Planarity : 0.004 0.039 7488 Dihedral : 9.639 172.363 6223 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.73 % Allowed : 17.72 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.11), residues: 5484 helix: 1.67 (0.12), residues: 1932 sheet: 0.41 (0.17), residues: 804 loop : -1.21 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 258 HIS 0.007 0.001 HIS C 79 PHE 0.016 0.002 PHE G 183 TYR 0.014 0.002 TYR V 285 ARG 0.006 0.000 ARG C 142 *********************** 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 464 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 367 time to evaluate : 4.824 Fit side-chains REVERT: A 72 MET cc_start: 0.6305 (OUTLIER) cc_final: 0.5970 (pmm) REVERT: A 123 MET cc_start: 0.6034 (mmp) cc_final: 0.5740 (mmp) REVERT: A 234 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: A 250 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7388 (mm-30) REVERT: C 73 MET cc_start: 0.6587 (ptp) cc_final: 0.6173 (ptp) REVERT: E 72 MET cc_start: 0.6216 (ptm) cc_final: 0.5976 (ptm) REVERT: G 123 MET cc_start: 0.5630 (mmp) cc_final: 0.5390 (mmp) REVERT: I 146 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7349 (p0) REVERT: I 228 MET cc_start: 0.6384 (OUTLIER) cc_final: 0.6154 (pmm) REVERT: I 408 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8302 (mt) REVERT: I 444 GLN cc_start: 0.8852 (tt0) cc_final: 0.8609 (tt0) REVERT: K 228 MET cc_start: 0.6567 (ppp) cc_final: 0.6252 (pp-130) REVERT: M 72 MET cc_start: 0.5843 (OUTLIER) cc_final: 0.5533 (pmm) REVERT: M 123 MET cc_start: 0.5689 (mmp) cc_final: 0.5339 (mmp) REVERT: O 123 MET cc_start: 0.5391 (mmm) cc_final: 0.4771 (mmp) REVERT: Q 72 MET cc_start: 0.6203 (ptp) cc_final: 0.5893 (ptm) REVERT: Q 228 MET cc_start: 0.6592 (ppp) cc_final: 0.6314 (pp-130) REVERT: Q 446 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: S 123 MET cc_start: 0.6037 (mmp) cc_final: 0.5796 (mmp) REVERT: S 234 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: V 402 MET cc_start: 0.8466 (mtm) cc_final: 0.8018 (mtm) REVERT: X 446 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7723 (mt-10) outliers start: 97 outliers final: 70 residues processed: 440 average time/residue: 1.4570 time to fit residues: 814.7076 Evaluate side-chains 444 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 364 time to evaluate : 4.984 ------------------------------------------------------------------------------- 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 234 GLU 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 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 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 196 SER Chi-restraints excluded: chain G residue 253 LYS 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 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 73 MET Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 196 SER 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 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 234 GLU 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 44 SER Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 81 VAL 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 Chi-restraints excluded: chain X residue 446 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 3.9990 chunk 501 optimal weight: 0.9980 chunk 306 optimal weight: 3.9990 chunk 237 optimal weight: 0.9990 chunk 348 optimal weight: 0.5980 chunk 526 optimal weight: 0.7980 chunk 484 optimal weight: 7.9990 chunk 418 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 323 optimal weight: 4.9990 chunk 256 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: A 165 GLN ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN G 165 GLN ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 381 ASN M 165 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 165 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 43644 Z= 0.204 Angle : 0.559 12.406 59364 Z= 0.282 Chirality : 0.042 0.158 6732 Planarity : 0.004 0.038 7488 Dihedral : 9.601 172.434 6223 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.52 % Allowed : 17.94 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.11), residues: 5484 helix: 1.70 (0.12), residues: 1932 sheet: 0.41 (0.17), residues: 804 loop : -1.20 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 258 HIS 0.006 0.001 HIS C 79 PHE 0.016 0.002 PHE G 183 TYR 0.015 0.002 TYR Q 285 ARG 0.006 0.000 ARG C 142 ********************** 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: 87 poor density : 365 time to evaluate : 5.264 Fit side-chains REVERT: A 72 MET cc_start: 0.6411 (OUTLIER) cc_final: 0.5998 (pmm) REVERT: A 123 MET cc_start: 0.6116 (mmp) cc_final: 0.5817 (mmp) REVERT: A 234 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: A 250 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7376 (mm-30) REVERT: C 73 MET cc_start: 0.6566 (ptp) cc_final: 0.6144 (ptp) REVERT: E 72 MET cc_start: 0.6262 (ptm) cc_final: 0.6005 (ptm) REVERT: G 123 MET cc_start: 0.5608 (mmp) cc_final: 0.5382 (mmp) REVERT: I 146 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7352 (p0) REVERT: I 228 MET cc_start: 0.6388 (OUTLIER) cc_final: 0.6158 (pmm) REVERT: I 408 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8296 (mt) REVERT: I 444 GLN cc_start: 0.8852 (tt0) cc_final: 0.8609 (tt0) REVERT: K 228 MET cc_start: 0.6573 (ppp) cc_final: 0.6256 (pp-130) REVERT: M 72 MET cc_start: 0.5831 (OUTLIER) cc_final: 0.5521 (pmm) REVERT: M 123 MET cc_start: 0.5718 (mmp) cc_final: 0.5346 (mmp) REVERT: O 123 MET cc_start: 0.5585 (mmm) cc_final: 0.4879 (mmp) REVERT: Q 72 MET cc_start: 0.6172 (ptp) cc_final: 0.5921 (ptm) REVERT: Q 228 MET cc_start: 0.6545 (ppp) cc_final: 0.6263 (pp-130) REVERT: Q 446 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7694 (mt-10) REVERT: S 123 MET cc_start: 0.6034 (mmp) cc_final: 0.5776 (mmp) REVERT: S 234 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: V 402 MET cc_start: 0.8462 (mtm) cc_final: 0.8012 (mtm) REVERT: X 446 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7736 (mt-10) outliers start: 87 outliers final: 72 residues processed: 431 average time/residue: 1.4103 time to fit residues: 770.7493 Evaluate side-chains 445 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 363 time to evaluate : 4.714 ------------------------------------------------------------------------------- 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 234 GLU 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 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 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 196 SER Chi-restraints excluded: chain G residue 253 LYS 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 305 VAL 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 73 MET Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 196 SER 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 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 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 234 GLU Chi-restraints excluded: chain S residue 246 THR Chi-restraints excluded: chain S residue 315 CYS 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 16 LYS 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 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 Chi-restraints excluded: chain X residue 446 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 4.9990 chunk 446 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 386 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 419 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 chunk 430 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 GLN ** I 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 165 GLN V 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.172431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136252 restraints weight = 238178.305| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 4.30 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 43644 Z= 0.440 Angle : 0.674 12.164 59364 Z= 0.344 Chirality : 0.048 0.189 6732 Planarity : 0.005 0.038 7488 Dihedral : 10.013 174.713 6223 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.80 % Allowed : 17.76 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.11), residues: 5484 helix: 1.66 (0.12), residues: 1836 sheet: 0.32 (0.17), residues: 804 loop : -1.35 (0.10), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 258 HIS 0.009 0.002 HIS V 37 PHE 0.026 0.003 PHE S 183 TYR 0.022 0.003 TYR I 285 ARG 0.007 0.001 ARG V 434 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12689.10 seconds wall clock time: 231 minutes 56.97 seconds (13916.97 seconds total)