Starting phenix.real_space_refine on Wed Aug 27 01:51:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w27_43740/08_2025/8w27_43740_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w27_43740/08_2025/8w27_43740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w27_43740/08_2025/8w27_43740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w27_43740/08_2025/8w27_43740.map" model { file = "/net/cci-nas-00/data/ceres_data/8w27_43740/08_2025/8w27_43740_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w27_43740/08_2025/8w27_43740_neut.cif" } resolution = 2.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 20 6.06 5 S 280 5.16 5 C 28680 2.51 5 N 8200 2.21 5 O 8000 1.98 5 F 60 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45240 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "J" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "L" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "M" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "N" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "O" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "P" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "Q" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "R" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "S" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "T" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "U" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2240 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, 'XAV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1632 SG CYS A1081 133.134 95.548 12.343 1.00 86.71 S ATOM 1692 SG CYS A1089 131.428 98.090 10.052 1.00 81.33 S ATOM 1718 SG CYS A1092 129.761 94.690 10.738 1.00 81.08 S ATOM 3872 SG CYS B1081 125.579 42.964 25.800 1.00 62.85 S ATOM 3932 SG CYS B1089 126.551 46.196 23.971 1.00 59.92 S ATOM 3958 SG CYS B1092 122.899 45.389 24.531 1.00 64.17 S ATOM 6112 SG CYS C1081 80.123 17.165 39.668 1.00 59.02 S ATOM 6172 SG CYS C1089 83.088 18.360 37.645 1.00 55.41 S ATOM 6198 SG CYS C1092 80.137 20.718 38.213 1.00 61.16 S ATOM 8352 SG CYS D1081 32.036 37.844 53.155 1.00 63.36 S ATOM 8412 SG CYS D1089 34.757 36.081 51.152 1.00 65.38 S ATOM 8438 SG CYS D1092 34.869 39.886 51.506 1.00 68.22 S ATOM 10592 SG CYS E1081 18.952 88.823 66.935 1.00 64.99 S ATOM 10652 SG CYS E1089 19.176 85.571 64.872 1.00 63.53 S ATOM 10678 SG CYS E1092 22.271 87.816 65.286 1.00 62.83 S ATOM 12832 SG CYS F1081 51.212 130.508 80.484 1.00 65.01 S ATOM 12892 SG CYS F1089 48.808 128.163 78.582 1.00 65.38 S ATOM 12918 SG CYS F1092 52.406 127.147 79.183 1.00 69.58 S ATOM 15072 SG CYS G1081 103.155 130.416 94.128 1.00 78.81 S ATOM 15132 SG CYS G1089 99.942 130.846 92.080 1.00 72.20 S ATOM 15158 SG CYS G1092 101.397 127.335 92.568 1.00 78.24 S ATOM 17312 SG CYS H1081 135.044 88.550 107.838 1.00 97.03 S ATOM 17372 SG CYS H1089 133.723 91.311 105.512 1.00 91.03 S ATOM 17398 SG CYS H1092 131.602 88.145 106.232 1.00 90.23 S ATOM 19552 SG CYS I1081 121.342 37.315 121.352 1.00 95.38 S ATOM 19612 SG CYS I1089 122.640 40.335 119.389 1.00 94.41 S ATOM 19638 SG CYS I1092 118.883 39.917 119.945 1.00 91.49 S ATOM 21792 SG CYS J1081 72.772 17.175 134.918 1.00105.56 S ATOM 21852 SG CYS J1089 76.016 18.169 133.119 1.00102.63 S ATOM 21878 SG CYS J1092 73.229 20.757 133.655 1.00105.22 S ATOM 24032 SG CYS L1081 136.045 81.386 173.906 1.00109.24 S ATOM 24092 SG CYS L1089 135.168 78.374 176.129 1.00107.30 S ATOM 24118 SG CYS L1092 132.624 81.212 175.626 1.00110.06 S ATOM 26272 SG CYS M1081 108.849 127.044 160.493 1.00 93.40 S ATOM 26332 SG CYS M1089 110.981 124.371 162.220 1.00 91.11 S ATOM 26358 SG CYS M1092 107.223 123.864 161.887 1.00 92.51 S ATOM 28512 SG CYS N1081 57.210 133.011 146.791 1.00 87.20 S ATOM 28572 SG CYS N1089 60.553 133.069 148.683 1.00 79.38 S ATOM 28598 SG CYS N1092 58.478 129.848 148.442 1.00 77.06 S ATOM 30752 SG CYS O1081 20.522 95.486 133.007 1.00 78.31 S ATOM 30812 SG CYS O1089 22.297 98.059 135.233 1.00 73.64 S ATOM 30838 SG CYS O1092 23.905 94.603 134.637 1.00 73.21 S ATOM 32992 SG CYS P1081 28.084 43.014 119.408 1.00 56.89 S ATOM 33052 SG CYS P1089 27.088 46.196 121.348 1.00 55.85 S ATOM 33078 SG CYS P1092 30.776 45.336 120.874 1.00 62.62 S ATOM 35232 SG CYS Q1081 73.548 17.236 105.635 1.00 59.09 S ATOM 35292 SG CYS Q1089 70.593 18.368 107.699 1.00 57.09 S ATOM 35318 SG CYS Q1092 73.563 20.726 107.204 1.00 66.49 S ATOM 37472 SG CYS R1081 121.674 37.814 92.139 1.00 69.34 S ATOM 37532 SG CYS R1089 118.913 36.080 94.180 1.00 68.41 S ATOM 37558 SG CYS R1092 118.840 39.886 93.763 1.00 69.00 S ATOM 39712 SG CYS S1081 134.890 88.731 78.472 1.00 71.71 S ATOM 39772 SG CYS S1089 134.527 85.495 80.543 1.00 67.77 S ATOM 39798 SG CYS S1092 131.503 87.798 80.122 1.00 66.28 S ATOM 41952 SG CYS T1081 102.634 130.514 64.864 1.00 75.03 S ATOM 42012 SG CYS T1089 104.932 128.148 66.828 1.00 71.05 S ATOM 42038 SG CYS T1092 101.309 127.203 66.208 1.00 77.19 S ATOM 44192 SG CYS U1081 50.470 130.408 51.231 1.00 90.26 S ATOM 44252 SG CYS U1089 53.690 130.819 53.305 1.00 83.86 S ATOM 44278 SG CYS U1092 52.150 127.346 52.853 1.00 89.92 S Time building chain proxies: 11.35, per 1000 atoms: 0.25 Number of scatterers: 45240 At special positions: 0 Unit cell: (155.288, 155.288, 186.676, 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 20 29.99 S 280 16.00 F 60 9.00 O 8000 8.00 N 8200 7.00 C 28680 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: 4.18 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1202 " pdb="ZN ZN A1202 " - pdb=" ND1 HIS A1084 " pdb="ZN ZN A1202 " - pdb=" SG CYS A1081 " pdb="ZN ZN A1202 " - pdb=" SG CYS A1089 " pdb="ZN ZN A1202 " - pdb=" SG CYS A1092 " pdb=" ZN B1202 " pdb="ZN ZN B1202 " - pdb=" ND1 HIS B1084 " pdb="ZN ZN B1202 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1202 " - pdb=" SG CYS B1089 " pdb="ZN ZN B1202 " - pdb=" SG CYS B1081 " pdb=" ZN C1202 " pdb="ZN ZN C1202 " - pdb=" ND1 HIS C1084 " pdb="ZN ZN C1202 " - pdb=" SG CYS C1081 " pdb="ZN ZN C1202 " - pdb=" SG CYS C1089 " pdb="ZN ZN C1202 " - pdb=" SG CYS C1092 " pdb=" ZN D1202 " pdb="ZN ZN D1202 " - pdb=" ND1 HIS D1084 " pdb="ZN ZN D1202 " - pdb=" SG CYS D1089 " pdb="ZN ZN D1202 " - pdb=" SG CYS D1081 " pdb="ZN ZN D1202 " - pdb=" SG CYS D1092 " pdb=" ZN E1202 " pdb="ZN ZN E1202 " - pdb=" ND1 HIS E1084 " pdb="ZN ZN E1202 " - pdb=" SG CYS E1092 " pdb="ZN ZN E1202 " - pdb=" SG CYS E1081 " pdb="ZN ZN E1202 " - pdb=" SG CYS E1089 " pdb=" ZN F1202 " pdb="ZN ZN F1202 " - pdb=" ND1 HIS F1084 " pdb="ZN ZN F1202 " - pdb=" SG CYS F1092 " pdb="ZN ZN F1202 " - pdb=" SG CYS F1089 " pdb="ZN ZN F1202 " - pdb=" SG CYS F1081 " pdb=" ZN G1202 " pdb="ZN ZN G1202 " - pdb=" ND1 HIS G1084 " pdb="ZN ZN G1202 " - pdb=" SG CYS G1089 " pdb="ZN ZN G1202 " - pdb=" SG CYS G1081 " pdb="ZN ZN G1202 " - pdb=" SG CYS G1092 " pdb=" ZN H1202 " pdb="ZN ZN H1202 " - pdb=" ND1 HIS H1084 " pdb="ZN ZN H1202 " - pdb=" SG CYS H1081 " pdb="ZN ZN H1202 " - pdb=" SG CYS H1089 " pdb="ZN ZN H1202 " - pdb=" SG CYS H1092 " pdb=" ZN I1202 " pdb="ZN ZN I1202 " - pdb=" ND1 HIS I1084 " pdb="ZN ZN I1202 " - pdb=" SG CYS I1089 " pdb="ZN ZN I1202 " - pdb=" SG CYS I1092 " pdb="ZN ZN I1202 " - pdb=" SG CYS I1081 " pdb=" ZN J1202 " pdb="ZN ZN J1202 " - pdb=" ND1 HIS J1084 " pdb="ZN ZN J1202 " - pdb=" SG CYS J1081 " pdb="ZN ZN J1202 " - pdb=" SG CYS J1089 " pdb="ZN ZN J1202 " - pdb=" SG CYS J1092 " pdb=" ZN L1202 " pdb="ZN ZN L1202 " - pdb=" ND1 HIS L1084 " pdb="ZN ZN L1202 " - pdb=" SG CYS L1089 " pdb="ZN ZN L1202 " - pdb=" SG CYS L1081 " pdb="ZN ZN L1202 " - pdb=" SG CYS L1092 " pdb=" ZN M1202 " pdb="ZN ZN M1202 " - pdb=" ND1 HIS M1084 " pdb="ZN ZN M1202 " - pdb=" SG CYS M1092 " pdb="ZN ZN M1202 " - pdb=" SG CYS M1089 " pdb="ZN ZN M1202 " - pdb=" SG CYS M1081 " pdb=" ZN N1202 " pdb="ZN ZN N1202 " - pdb=" ND1 HIS N1084 " pdb="ZN ZN N1202 " - pdb=" SG CYS N1081 " pdb="ZN ZN N1202 " - pdb=" SG CYS N1092 " pdb="ZN ZN N1202 " - pdb=" SG CYS N1089 " pdb=" ZN O1202 " pdb="ZN ZN O1202 " - pdb=" ND1 HIS O1084 " pdb="ZN ZN O1202 " - pdb=" SG CYS O1089 " pdb="ZN ZN O1202 " - pdb=" SG CYS O1081 " pdb="ZN ZN O1202 " - pdb=" SG CYS O1092 " pdb=" ZN P1202 " pdb="ZN ZN P1202 " - pdb=" ND1 HIS P1084 " pdb="ZN ZN P1202 " - pdb=" SG CYS P1092 " pdb="ZN ZN P1202 " - pdb=" SG CYS P1081 " pdb="ZN ZN P1202 " - pdb=" SG CYS P1089 " pdb=" ZN Q1202 " pdb="ZN ZN Q1202 " - pdb=" ND1 HIS Q1084 " pdb="ZN ZN Q1202 " - pdb=" SG CYS Q1089 " pdb="ZN ZN Q1202 " - pdb=" SG CYS Q1081 " pdb="ZN ZN Q1202 " - pdb=" SG CYS Q1092 " pdb=" ZN R1202 " pdb="ZN ZN R1202 " - pdb=" ND1 HIS R1084 " pdb="ZN ZN R1202 " - pdb=" SG CYS R1089 " pdb="ZN ZN R1202 " - pdb=" SG CYS R1081 " pdb="ZN ZN R1202 " - pdb=" SG CYS R1092 " pdb=" ZN S1202 " pdb="ZN ZN S1202 " - pdb=" ND1 HIS S1084 " pdb="ZN ZN S1202 " - pdb=" SG CYS S1092 " pdb="ZN ZN S1202 " - pdb=" SG CYS S1089 " pdb="ZN ZN S1202 " - pdb=" SG CYS S1081 " pdb=" ZN T1202 " pdb="ZN ZN T1202 " - pdb=" ND1 HIS T1084 " pdb="ZN ZN T1202 " - pdb=" SG CYS T1092 " pdb="ZN ZN T1202 " - pdb=" SG CYS T1089 " pdb="ZN ZN T1202 " - pdb=" SG CYS T1081 " pdb=" ZN U1202 " pdb="ZN ZN U1202 " - pdb=" ND1 HIS U1084 " pdb="ZN ZN U1202 " - pdb=" SG CYS U1089 " pdb="ZN ZN U1202 " - pdb=" SG CYS U1081 " pdb="ZN ZN U1202 " - pdb=" SG CYS U1092 " Number of angles added : 60 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10200 Finding SS restraints... Secondary structure from input PDB file: 301 helices and 40 sheets defined 43.9% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 875 through 885 removed outlier: 4.391A pdb=" N THR A 879 " --> pdb=" O ASP A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 889 No H-bonds generated for 'chain 'A' and resid 887 through 889' Processing helix chain 'A' and resid 890 through 897 Processing helix chain 'A' and resid 900 through 905 Processing helix chain 'A' and resid 908 through 915 Processing helix chain 'A' and resid 919 through 935 Processing helix chain 'A' and resid 937 through 940 Processing helix chain 'A' and resid 941 through 947 Processing helix chain 'A' and resid 962 through 975 removed outlier: 3.670A pdb=" N THR A 975 " --> pdb=" O GLU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1019 Processing helix chain 'A' and resid 1035 through 1043 Processing helix chain 'A' and resid 1045 through 1049 Processing helix chain 'A' and resid 1064 through 1070 removed outlier: 3.519A pdb=" N SER A1068 " --> pdb=" O ASN A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1078 Processing helix chain 'A' and resid 1143 through 1145 No H-bonds generated for 'chain 'A' and resid 1143 through 1145' Processing helix chain 'B' and resid 876 through 885 removed outlier: 3.569A pdb=" N LEU B 885 " --> pdb=" O PHE B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 889 removed outlier: 5.487A pdb=" N HIS B 889 " --> pdb=" O GLY B 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 889' Processing helix chain 'B' and resid 890 through 897 Processing helix chain 'B' and resid 900 through 905 Processing helix chain 'B' and resid 908 through 915 Processing helix chain 'B' and resid 919 through 935 Processing helix chain 'B' and resid 937 through 940 Processing helix chain 'B' and resid 941 through 947 Processing helix chain 'B' and resid 962 through 975 removed outlier: 3.591A pdb=" N THR B 975 " --> pdb=" O GLU B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1019 Processing helix chain 'B' and resid 1035 through 1043 Processing helix chain 'B' and resid 1045 through 1049 Processing helix chain 'B' and resid 1064 through 1070 removed outlier: 3.545A pdb=" N SER B1068 " --> pdb=" O ASN B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1078 Processing helix chain 'B' and resid 1143 through 1145 No H-bonds generated for 'chain 'B' and resid 1143 through 1145' Processing helix chain 'C' and resid 876 through 885 Processing helix chain 'C' and resid 887 through 889 No H-bonds generated for 'chain 'C' and resid 887 through 889' Processing helix chain 'C' and resid 890 through 897 Processing helix chain 'C' and resid 900 through 905 Processing helix chain 'C' and resid 908 through 915 Processing helix chain 'C' and resid 919 through 935 Processing helix chain 'C' and resid 937 through 940 Processing helix chain 'C' and resid 941 through 947 Processing helix chain 'C' and resid 962 through 975 removed outlier: 3.604A pdb=" N THR C 975 " --> pdb=" O GLU C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1019 Processing helix chain 'C' and resid 1035 through 1043 Processing helix chain 'C' and resid 1045 through 1049 Processing helix chain 'C' and resid 1064 through 1070 removed outlier: 3.551A pdb=" N SER C1068 " --> pdb=" O ASN C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1078 Processing helix chain 'C' and resid 1143 through 1145 No H-bonds generated for 'chain 'C' and resid 1143 through 1145' Processing helix chain 'D' and resid 876 through 885 Processing helix chain 'D' and resid 887 through 889 No H-bonds generated for 'chain 'D' and resid 887 through 889' Processing helix chain 'D' and resid 890 through 897 Processing helix chain 'D' and resid 900 through 905 Processing helix chain 'D' and resid 908 through 916 Processing helix chain 'D' and resid 919 through 935 Processing helix chain 'D' and resid 937 through 940 Processing helix chain 'D' and resid 941 through 947 Processing helix chain 'D' and resid 962 through 975 removed outlier: 3.581A pdb=" N THR D 975 " --> pdb=" O GLU D 971 " (cutoff:3.500A) Processing helix chain 'D' and resid 1002 through 1020 Processing helix chain 'D' and resid 1035 through 1043 Processing helix chain 'D' and resid 1045 through 1049 Processing helix chain 'D' and resid 1064 through 1070 Processing helix chain 'D' and resid 1074 through 1078 Processing helix chain 'D' and resid 1143 through 1145 No H-bonds generated for 'chain 'D' and resid 1143 through 1145' Processing helix chain 'E' and resid 876 through 885 removed outlier: 3.575A pdb=" N LEU E 885 " --> pdb=" O PHE E 881 " (cutoff:3.500A) Processing helix chain 'E' and resid 887 through 889 No H-bonds generated for 'chain 'E' and resid 887 through 889' Processing helix chain 'E' and resid 890 through 897 Processing helix chain 'E' and resid 900 through 905 Processing helix chain 'E' and resid 908 through 915 Processing helix chain 'E' and resid 919 through 935 Processing helix chain 'E' and resid 937 through 940 Processing helix chain 'E' and resid 941 through 947 Processing helix chain 'E' and resid 962 through 975 removed outlier: 3.638A pdb=" N THR E 975 " --> pdb=" O GLU E 971 " (cutoff:3.500A) Processing helix chain 'E' and resid 1002 through 1020 Processing helix chain 'E' and resid 1035 through 1043 Processing helix chain 'E' and resid 1045 through 1049 Processing helix chain 'E' and resid 1064 through 1070 Processing helix chain 'E' and resid 1074 through 1078 Processing helix chain 'E' and resid 1143 through 1145 No H-bonds generated for 'chain 'E' and resid 1143 through 1145' Processing helix chain 'F' and resid 876 through 885 Processing helix chain 'F' and resid 886 through 889 removed outlier: 5.370A pdb=" N HIS F 889 " --> pdb=" O GLY F 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 886 through 889' Processing helix chain 'F' and resid 890 through 897 Processing helix chain 'F' and resid 900 through 905 Processing helix chain 'F' and resid 908 through 915 Processing helix chain 'F' and resid 919 through 935 Processing helix chain 'F' and resid 937 through 940 Processing helix chain 'F' and resid 941 through 947 Processing helix chain 'F' and resid 962 through 975 removed outlier: 3.566A pdb=" N THR F 975 " --> pdb=" O GLU F 971 " (cutoff:3.500A) Processing helix chain 'F' and resid 1002 through 1020 Processing helix chain 'F' and resid 1035 through 1043 Processing helix chain 'F' and resid 1045 through 1049 Processing helix chain 'F' and resid 1064 through 1070 Processing helix chain 'F' and resid 1074 through 1078 Processing helix chain 'F' and resid 1143 through 1145 No H-bonds generated for 'chain 'F' and resid 1143 through 1145' Processing helix chain 'G' and resid 876 through 885 Processing helix chain 'G' and resid 887 through 889 No H-bonds generated for 'chain 'G' and resid 887 through 889' Processing helix chain 'G' and resid 890 through 897 Processing helix chain 'G' and resid 900 through 905 Processing helix chain 'G' and resid 908 through 915 Processing helix chain 'G' and resid 919 through 935 Processing helix chain 'G' and resid 937 through 940 Processing helix chain 'G' and resid 941 through 947 Processing helix chain 'G' and resid 962 through 975 removed outlier: 3.602A pdb=" N THR G 975 " --> pdb=" O GLU G 971 " (cutoff:3.500A) Processing helix chain 'G' and resid 1002 through 1019 Processing helix chain 'G' and resid 1035 through 1043 Processing helix chain 'G' and resid 1045 through 1049 Processing helix chain 'G' and resid 1064 through 1070 removed outlier: 3.531A pdb=" N SER G1068 " --> pdb=" O ASN G1064 " (cutoff:3.500A) Processing helix chain 'G' and resid 1074 through 1078 Processing helix chain 'G' and resid 1143 through 1145 No H-bonds generated for 'chain 'G' and resid 1143 through 1145' Processing helix chain 'H' and resid 876 through 885 removed outlier: 3.508A pdb=" N LEU H 885 " --> pdb=" O PHE H 881 " (cutoff:3.500A) Processing helix chain 'H' and resid 887 through 889 No H-bonds generated for 'chain 'H' and resid 887 through 889' Processing helix chain 'H' and resid 890 through 897 Processing helix chain 'H' and resid 900 through 905 Processing helix chain 'H' and resid 908 through 916 Processing helix chain 'H' and resid 919 through 935 Processing helix chain 'H' and resid 937 through 940 Processing helix chain 'H' and resid 941 through 947 Processing helix chain 'H' and resid 962 through 975 removed outlier: 3.569A pdb=" N THR H 975 " --> pdb=" O GLU H 971 " (cutoff:3.500A) Processing helix chain 'H' and resid 1002 through 1019 Processing helix chain 'H' and resid 1035 through 1043 Processing helix chain 'H' and resid 1045 through 1049 Processing helix chain 'H' and resid 1064 through 1070 Processing helix chain 'H' and resid 1074 through 1078 Processing helix chain 'H' and resid 1143 through 1145 No H-bonds generated for 'chain 'H' and resid 1143 through 1145' Processing helix chain 'I' and resid 876 through 885 removed outlier: 3.510A pdb=" N LEU I 885 " --> pdb=" O PHE I 881 " (cutoff:3.500A) Processing helix chain 'I' and resid 886 through 889 removed outlier: 5.388A pdb=" N HIS I 889 " --> pdb=" O GLY I 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 886 through 889' Processing helix chain 'I' and resid 890 through 897 Processing helix chain 'I' and resid 900 through 905 Processing helix chain 'I' and resid 908 through 916 Processing helix chain 'I' and resid 919 through 935 Processing helix chain 'I' and resid 937 through 940 Processing helix chain 'I' and resid 941 through 947 removed outlier: 3.553A pdb=" N THR I 945 " --> pdb=" O ASN I 941 " (cutoff:3.500A) Processing helix chain 'I' and resid 962 through 975 removed outlier: 3.616A pdb=" N THR I 975 " --> pdb=" O GLU I 971 " (cutoff:3.500A) Processing helix chain 'I' and resid 1002 through 1019 Processing helix chain 'I' and resid 1035 through 1043 Processing helix chain 'I' and resid 1045 through 1049 Processing helix chain 'I' and resid 1064 through 1070 removed outlier: 3.510A pdb=" N SER I1068 " --> pdb=" O ASN I1064 " (cutoff:3.500A) Processing helix chain 'I' and resid 1074 through 1078 Processing helix chain 'I' and resid 1143 through 1145 No H-bonds generated for 'chain 'I' and resid 1143 through 1145' Processing helix chain 'J' and resid 876 through 885 removed outlier: 3.551A pdb=" N LEU J 885 " --> pdb=" O PHE J 881 " (cutoff:3.500A) Processing helix chain 'J' and resid 886 through 889 removed outlier: 5.727A pdb=" N HIS J 889 " --> pdb=" O GLY J 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 886 through 889' Processing helix chain 'J' and resid 890 through 898 Processing helix chain 'J' and resid 900 through 905 Processing helix chain 'J' and resid 908 through 915 Processing helix chain 'J' and resid 919 through 935 Processing helix chain 'J' and resid 937 through 940 Processing helix chain 'J' and resid 941 through 947 removed outlier: 3.522A pdb=" N THR J 945 " --> pdb=" O ASN J 941 " (cutoff:3.500A) Processing helix chain 'J' and resid 962 through 975 removed outlier: 3.661A pdb=" N THR J 975 " --> pdb=" O GLU J 971 " (cutoff:3.500A) Processing helix chain 'J' and resid 1003 through 1019 Processing helix chain 'J' and resid 1035 through 1043 Processing helix chain 'J' and resid 1045 through 1049 Processing helix chain 'J' and resid 1064 through 1070 removed outlier: 3.523A pdb=" N SER J1068 " --> pdb=" O ASN J1064 " (cutoff:3.500A) Processing helix chain 'J' and resid 1074 through 1078 Processing helix chain 'J' and resid 1143 through 1145 No H-bonds generated for 'chain 'J' and resid 1143 through 1145' Processing helix chain 'L' and resid 876 through 885 Processing helix chain 'L' and resid 887 through 889 No H-bonds generated for 'chain 'L' and resid 887 through 889' Processing helix chain 'L' and resid 890 through 897 Processing helix chain 'L' and resid 900 through 905 Processing helix chain 'L' and resid 908 through 915 Processing helix chain 'L' and resid 919 through 935 Processing helix chain 'L' and resid 937 through 940 Processing helix chain 'L' and resid 941 through 947 removed outlier: 3.572A pdb=" N THR L 945 " --> pdb=" O ASN L 941 " (cutoff:3.500A) Processing helix chain 'L' and resid 962 through 975 removed outlier: 3.601A pdb=" N THR L 975 " --> pdb=" O GLU L 971 " (cutoff:3.500A) Processing helix chain 'L' and resid 1002 through 1019 Processing helix chain 'L' and resid 1035 through 1043 Processing helix chain 'L' and resid 1045 through 1049 Processing helix chain 'L' and resid 1064 through 1070 removed outlier: 3.502A pdb=" N SER L1068 " --> pdb=" O ASN L1064 " (cutoff:3.500A) Processing helix chain 'L' and resid 1074 through 1078 Processing helix chain 'L' and resid 1143 through 1145 No H-bonds generated for 'chain 'L' and resid 1143 through 1145' Processing helix chain 'M' and resid 876 through 885 Processing helix chain 'M' and resid 887 through 889 No H-bonds generated for 'chain 'M' and resid 887 through 889' Processing helix chain 'M' and resid 890 through 897 Processing helix chain 'M' and resid 900 through 905 Processing helix chain 'M' and resid 908 through 915 Processing helix chain 'M' and resid 919 through 935 Processing helix chain 'M' and resid 937 through 940 Processing helix chain 'M' and resid 941 through 947 Processing helix chain 'M' and resid 962 through 975 removed outlier: 3.779A pdb=" N THR M 975 " --> pdb=" O GLU M 971 " (cutoff:3.500A) Processing helix chain 'M' and resid 1002 through 1019 Processing helix chain 'M' and resid 1035 through 1043 Processing helix chain 'M' and resid 1045 through 1049 Processing helix chain 'M' and resid 1064 through 1070 removed outlier: 3.531A pdb=" N SER M1068 " --> pdb=" O ASN M1064 " (cutoff:3.500A) Processing helix chain 'M' and resid 1074 through 1078 Processing helix chain 'M' and resid 1143 through 1145 No H-bonds generated for 'chain 'M' and resid 1143 through 1145' Processing helix chain 'N' and resid 876 through 885 Processing helix chain 'N' and resid 887 through 889 No H-bonds generated for 'chain 'N' and resid 887 through 889' Processing helix chain 'N' and resid 890 through 897 Processing helix chain 'N' and resid 900 through 905 Processing helix chain 'N' and resid 908 through 915 Processing helix chain 'N' and resid 919 through 935 Processing helix chain 'N' and resid 937 through 940 Processing helix chain 'N' and resid 941 through 947 Processing helix chain 'N' and resid 962 through 975 removed outlier: 3.549A pdb=" N THR N 975 " --> pdb=" O GLU N 971 " (cutoff:3.500A) Processing helix chain 'N' and resid 1002 through 1019 removed outlier: 3.502A pdb=" N GLU N1019 " --> pdb=" O GLU N1015 " (cutoff:3.500A) Processing helix chain 'N' and resid 1035 through 1043 Processing helix chain 'N' and resid 1045 through 1049 Processing helix chain 'N' and resid 1064 through 1070 removed outlier: 3.513A pdb=" N SER N1068 " --> pdb=" O ASN N1064 " (cutoff:3.500A) Processing helix chain 'N' and resid 1074 through 1078 Processing helix chain 'N' and resid 1143 through 1145 No H-bonds generated for 'chain 'N' and resid 1143 through 1145' Processing helix chain 'O' and resid 876 through 885 Processing helix chain 'O' and resid 887 through 889 No H-bonds generated for 'chain 'O' and resid 887 through 889' Processing helix chain 'O' and resid 890 through 897 Processing helix chain 'O' and resid 900 through 905 Processing helix chain 'O' and resid 908 through 915 Processing helix chain 'O' and resid 919 through 935 Processing helix chain 'O' and resid 937 through 940 Processing helix chain 'O' and resid 941 through 947 Processing helix chain 'O' and resid 962 through 975 removed outlier: 3.578A pdb=" N THR O 975 " --> pdb=" O GLU O 971 " (cutoff:3.500A) Processing helix chain 'O' and resid 1002 through 1019 Processing helix chain 'O' and resid 1020 through 1023 Processing helix chain 'O' and resid 1035 through 1043 Processing helix chain 'O' and resid 1045 through 1049 Processing helix chain 'O' and resid 1064 through 1070 Processing helix chain 'O' and resid 1074 through 1078 Processing helix chain 'O' and resid 1143 through 1145 No H-bonds generated for 'chain 'O' and resid 1143 through 1145' Processing helix chain 'P' and resid 876 through 885 Processing helix chain 'P' and resid 887 through 889 No H-bonds generated for 'chain 'P' and resid 887 through 889' Processing helix chain 'P' and resid 890 through 897 Processing helix chain 'P' and resid 900 through 905 Processing helix chain 'P' and resid 908 through 915 Processing helix chain 'P' and resid 919 through 935 Processing helix chain 'P' and resid 937 through 940 Processing helix chain 'P' and resid 941 through 947 Processing helix chain 'P' and resid 962 through 975 removed outlier: 3.574A pdb=" N THR P 975 " --> pdb=" O GLU P 971 " (cutoff:3.500A) Processing helix chain 'P' and resid 1002 through 1019 Processing helix chain 'P' and resid 1035 through 1043 Processing helix chain 'P' and resid 1045 through 1049 Processing helix chain 'P' and resid 1064 through 1070 removed outlier: 3.545A pdb=" N SER P1068 " --> pdb=" O ASN P1064 " (cutoff:3.500A) Processing helix chain 'P' and resid 1074 through 1078 Processing helix chain 'P' and resid 1143 through 1145 No H-bonds generated for 'chain 'P' and resid 1143 through 1145' Processing helix chain 'Q' and resid 876 through 885 Processing helix chain 'Q' and resid 887 through 889 No H-bonds generated for 'chain 'Q' and resid 887 through 889' Processing helix chain 'Q' and resid 890 through 897 Processing helix chain 'Q' and resid 900 through 905 Processing helix chain 'Q' and resid 908 through 915 Processing helix chain 'Q' and resid 919 through 935 Processing helix chain 'Q' and resid 937 through 940 Processing helix chain 'Q' and resid 941 through 947 Processing helix chain 'Q' and resid 962 through 975 removed outlier: 3.507A pdb=" N THR Q 975 " --> pdb=" O GLU Q 971 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1002 through 1019 Processing helix chain 'Q' and resid 1035 through 1043 Processing helix chain 'Q' and resid 1045 through 1049 Processing helix chain 'Q' and resid 1064 through 1070 removed outlier: 3.515A pdb=" N SER Q1068 " --> pdb=" O ASN Q1064 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1074 through 1078 Processing helix chain 'Q' and resid 1143 through 1145 No H-bonds generated for 'chain 'Q' and resid 1143 through 1145' Processing helix chain 'R' and resid 876 through 885 Processing helix chain 'R' and resid 887 through 889 No H-bonds generated for 'chain 'R' and resid 887 through 889' Processing helix chain 'R' and resid 890 through 897 Processing helix chain 'R' and resid 900 through 905 Processing helix chain 'R' and resid 908 through 915 Processing helix chain 'R' and resid 919 through 935 Processing helix chain 'R' and resid 937 through 940 Processing helix chain 'R' and resid 941 through 947 Processing helix chain 'R' and resid 962 through 975 removed outlier: 3.560A pdb=" N THR R 975 " --> pdb=" O GLU R 971 " (cutoff:3.500A) Processing helix chain 'R' and resid 1002 through 1019 Processing helix chain 'R' and resid 1035 through 1043 Processing helix chain 'R' and resid 1045 through 1049 Processing helix chain 'R' and resid 1064 through 1070 Processing helix chain 'R' and resid 1074 through 1078 Processing helix chain 'R' and resid 1143 through 1145 No H-bonds generated for 'chain 'R' and resid 1143 through 1145' Processing helix chain 'S' and resid 876 through 885 Processing helix chain 'S' and resid 887 through 889 No H-bonds generated for 'chain 'S' and resid 887 through 889' Processing helix chain 'S' and resid 890 through 897 Processing helix chain 'S' and resid 900 through 905 Processing helix chain 'S' and resid 908 through 916 Processing helix chain 'S' and resid 919 through 935 Processing helix chain 'S' and resid 937 through 940 Processing helix chain 'S' and resid 941 through 947 Processing helix chain 'S' and resid 962 through 975 removed outlier: 3.648A pdb=" N THR S 975 " --> pdb=" O GLU S 971 " (cutoff:3.500A) Processing helix chain 'S' and resid 1002 through 1019 Processing helix chain 'S' and resid 1035 through 1043 Processing helix chain 'S' and resid 1045 through 1049 Processing helix chain 'S' and resid 1064 through 1070 Processing helix chain 'S' and resid 1074 through 1078 Processing helix chain 'S' and resid 1143 through 1145 No H-bonds generated for 'chain 'S' and resid 1143 through 1145' Processing helix chain 'T' and resid 876 through 885 Processing helix chain 'T' and resid 887 through 889 No H-bonds generated for 'chain 'T' and resid 887 through 889' Processing helix chain 'T' and resid 890 through 897 Processing helix chain 'T' and resid 900 through 905 Processing helix chain 'T' and resid 908 through 915 Processing helix chain 'T' and resid 919 through 935 Processing helix chain 'T' and resid 937 through 940 Processing helix chain 'T' and resid 941 through 947 Processing helix chain 'T' and resid 962 through 975 Processing helix chain 'T' and resid 1003 through 1019 removed outlier: 3.577A pdb=" N GLU T1019 " --> pdb=" O GLU T1015 " (cutoff:3.500A) Processing helix chain 'T' and resid 1035 through 1043 Processing helix chain 'T' and resid 1045 through 1049 Processing helix chain 'T' and resid 1064 through 1070 Processing helix chain 'T' and resid 1074 through 1078 Processing helix chain 'T' and resid 1143 through 1145 No H-bonds generated for 'chain 'T' and resid 1143 through 1145' Processing helix chain 'U' and resid 876 through 886 Processing helix chain 'U' and resid 887 through 889 No H-bonds generated for 'chain 'U' and resid 887 through 889' Processing helix chain 'U' and resid 890 through 897 Processing helix chain 'U' and resid 900 through 905 Processing helix chain 'U' and resid 908 through 915 Processing helix chain 'U' and resid 919 through 935 Processing helix chain 'U' and resid 937 through 940 Processing helix chain 'U' and resid 941 through 947 Processing helix chain 'U' and resid 962 through 975 removed outlier: 3.524A pdb=" N THR U 975 " --> pdb=" O GLU U 971 " (cutoff:3.500A) Processing helix chain 'U' and resid 1002 through 1019 Processing helix chain 'U' and resid 1035 through 1043 Processing helix chain 'U' and resid 1045 through 1049 Processing helix chain 'U' and resid 1064 through 1070 removed outlier: 3.531A pdb=" N SER U1068 " --> pdb=" O ASN U1064 " (cutoff:3.500A) Processing helix chain 'U' and resid 1074 through 1078 Processing helix chain 'U' and resid 1143 through 1145 No H-bonds generated for 'chain 'U' and resid 1143 through 1145' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.167A pdb=" N TYR A 992 " --> pdb=" O MET A1158 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N MET A1158 " --> pdb=" O TYR A 992 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ILE A 994 " --> pdb=" O GLN A1156 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLN A1156 " --> pdb=" O ILE A 994 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLU A1150 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ALA A1147 " --> pdb=" O THR A1102 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR A1102 " --> pdb=" O ALA A1147 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG A1100 " --> pdb=" O PRO A1149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1050 through 1053 removed outlier: 3.837A pdb=" N GLY A1058 " --> pdb=" O TYR A1050 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N GLY A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY A1056 " --> pdb=" O GLY A1052 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 954 through 957 removed outlier: 5.180A pdb=" N ILE B 994 " --> pdb=" O GLN B1156 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN B1156 " --> pdb=" O ILE B 994 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N GLU B1150 " --> pdb=" O VAL B1000 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ALA B1147 " --> pdb=" O THR B1102 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR B1102 " --> pdb=" O ALA B1147 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG B1100 " --> pdb=" O PRO B1149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1059 through 1062 removed outlier: 6.005A pdb=" N PHE B1107 " --> pdb=" O THR B1126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 954 through 957 removed outlier: 5.968A pdb=" N TYR C 992 " --> pdb=" O MET C1158 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N MET C1158 " --> pdb=" O TYR C 992 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE C 994 " --> pdb=" O GLN C1156 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLN C1156 " --> pdb=" O ILE C 994 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLU C1150 " --> pdb=" O VAL C1000 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA C1147 " --> pdb=" O THR C1102 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR C1102 " --> pdb=" O ALA C1147 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG C1100 " --> pdb=" O PRO C1149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 1059 through 1061 removed outlier: 5.984A pdb=" N PHE C1107 " --> pdb=" O THR C1126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 954 through 957 removed outlier: 5.217A pdb=" N ILE D 994 " --> pdb=" O GLN D1156 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLN D1156 " --> pdb=" O ILE D 994 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLU D1150 " --> pdb=" O VAL D1000 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ALA D1147 " --> pdb=" O THR D1102 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR D1102 " --> pdb=" O ALA D1147 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ARG D1100 " --> pdb=" O PRO D1149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 1050 through 1053 removed outlier: 3.896A pdb=" N GLY D1058 " --> pdb=" O TYR D1050 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLY D1052 " --> pdb=" O GLY D1056 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY D1056 " --> pdb=" O GLY D1052 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 954 through 957 removed outlier: 5.310A pdb=" N ILE E 994 " --> pdb=" O GLN E1156 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN E1156 " --> pdb=" O ILE E 994 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLU E1150 " --> pdb=" O VAL E1000 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ALA E1147 " --> pdb=" O THR E1102 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N THR E1102 " --> pdb=" O ALA E1147 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG E1100 " --> pdb=" O PRO E1149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 1059 through 1061 removed outlier: 5.871A pdb=" N PHE E1107 " --> pdb=" O THR E1126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 954 through 957 removed outlier: 5.253A pdb=" N ILE F 994 " --> pdb=" O GLN F1156 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN F1156 " --> pdb=" O ILE F 994 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLU F1150 " --> pdb=" O VAL F1000 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ALA F1147 " --> pdb=" O THR F1102 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR F1102 " --> pdb=" O ALA F1147 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG F1100 " --> pdb=" O PRO F1149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 1059 through 1061 removed outlier: 6.043A pdb=" N PHE F1107 " --> pdb=" O THR F1126 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 954 through 957 removed outlier: 6.138A pdb=" N TYR G 992 " --> pdb=" O MET G1158 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N MET G1158 " --> pdb=" O TYR G 992 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE G 994 " --> pdb=" O GLN G1156 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN G1156 " --> pdb=" O ILE G 994 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLU G1150 " --> pdb=" O VAL G1000 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ALA G1147 " --> pdb=" O THR G1102 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR G1102 " --> pdb=" O ALA G1147 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG G1100 " --> pdb=" O PRO G1149 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 1050 through 1053 removed outlier: 3.870A pdb=" N GLY G1058 " --> pdb=" O TYR G1050 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLY G1052 " --> pdb=" O GLY G1056 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLY G1056 " --> pdb=" O GLY G1052 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE G1107 " --> pdb=" O THR G1126 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 954 through 957 removed outlier: 6.045A pdb=" N TYR H 992 " --> pdb=" O MET H1158 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET H1158 " --> pdb=" O TYR H 992 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE H 994 " --> pdb=" O GLN H1156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN H1156 " --> pdb=" O ILE H 994 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLU H1150 " --> pdb=" O VAL H1000 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA H1147 " --> pdb=" O THR H1102 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR H1102 " --> pdb=" O ALA H1147 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG H1100 " --> pdb=" O PRO H1149 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 1059 through 1062 removed outlier: 6.058A pdb=" N PHE H1107 " --> pdb=" O THR H1126 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 954 through 957 removed outlier: 4.769A pdb=" N ARG I 991 " --> pdb=" O MET I1158 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR I1154 " --> pdb=" O LEU I 995 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE I 997 " --> pdb=" O LEU I1152 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU I1152 " --> pdb=" O ILE I 997 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS I 999 " --> pdb=" O GLU I1150 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLU I1150 " --> pdb=" O LYS I 999 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N CYS I1001 " --> pdb=" O TYR I1148 " (cutoff:3.500A) removed outlier: 12.365A pdb=" N TYR I1148 " --> pdb=" O CYS I1001 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE I1098 " --> pdb=" O GLU I1150 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU I1152 " --> pdb=" O LEU I1096 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU I1096 " --> pdb=" O LEU I1152 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR I1154 " --> pdb=" O ARG I1094 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG I1094 " --> pdb=" O THR I1154 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 1059 through 1062 removed outlier: 5.774A pdb=" N PHE I1107 " --> pdb=" O THR I1126 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 953 through 957 removed outlier: 5.716A pdb=" N TYR J 992 " --> pdb=" O MET J1158 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N MET J1158 " --> pdb=" O TYR J 992 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ILE J 994 " --> pdb=" O GLN J1156 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN J1156 " --> pdb=" O ILE J 994 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N GLU J1150 " --> pdb=" O VAL J1000 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N ASN J1002 " --> pdb=" O TYR J1148 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N TYR J1148 " --> pdb=" O ASN J1002 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ALA J1147 " --> pdb=" O THR J1102 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR J1102 " --> pdb=" O ALA J1147 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG J1100 " --> pdb=" O PRO J1149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 1059 through 1062 Processing sheet with id=AC3, first strand: chain 'L' and resid 954 through 957 removed outlier: 5.362A pdb=" N ILE L 994 " --> pdb=" O GLN L1156 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN L1156 " --> pdb=" O ILE L 994 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS L 996 " --> pdb=" O THR L1154 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLU L1150 " --> pdb=" O VAL L1000 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA L1147 " --> pdb=" O THR L1102 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR L1102 " --> pdb=" O ALA L1147 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG L1100 " --> pdb=" O PRO L1149 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 1059 through 1061 Processing sheet with id=AC5, first strand: chain 'M' and resid 954 through 957 removed outlier: 5.242A pdb=" N ILE M 994 " --> pdb=" O GLN M1156 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN M1156 " --> pdb=" O ILE M 994 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS M 996 " --> pdb=" O THR M1154 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLU M1150 " --> pdb=" O VAL M1000 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA M1147 " --> pdb=" O THR M1102 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N THR M1102 " --> pdb=" O ALA M1147 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG M1100 " --> pdb=" O PRO M1149 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 1059 through 1061 removed outlier: 6.066A pdb=" N PHE M1107 " --> pdb=" O THR M1126 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 954 through 957 removed outlier: 5.202A pdb=" N ILE N 994 " --> pdb=" O GLN N1156 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLN N1156 " --> pdb=" O ILE N 994 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLU N1150 " --> pdb=" O VAL N1000 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ALA N1147 " --> pdb=" O THR N1102 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N THR N1102 " --> pdb=" O ALA N1147 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG N1100 " --> pdb=" O PRO N1149 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 1059 through 1061 removed outlier: 6.254A pdb=" N PHE N1107 " --> pdb=" O THR N1126 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 954 through 957 removed outlier: 5.268A pdb=" N ILE O 994 " --> pdb=" O GLN O1156 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLN O1156 " --> pdb=" O ILE O 994 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N GLU O1150 " --> pdb=" O VAL O1000 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ALA O1147 " --> pdb=" O THR O1102 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR O1102 " --> pdb=" O ALA O1147 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG O1100 " --> pdb=" O PRO O1149 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 1059 through 1061 Processing sheet with id=AD2, first strand: chain 'P' and resid 954 through 957 removed outlier: 5.147A pdb=" N ILE P 994 " --> pdb=" O GLN P1156 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN P1156 " --> pdb=" O ILE P 994 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLU P1150 " --> pdb=" O VAL P1000 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA P1147 " --> pdb=" O THR P1102 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR P1102 " --> pdb=" O ALA P1147 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG P1100 " --> pdb=" O PRO P1149 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 1059 through 1061 Processing sheet with id=AD4, first strand: chain 'Q' and resid 954 through 957 removed outlier: 5.189A pdb=" N ILE Q 994 " --> pdb=" O GLN Q1156 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLN Q1156 " --> pdb=" O ILE Q 994 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLU Q1150 " --> pdb=" O VAL Q1000 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA Q1147 " --> pdb=" O THR Q1102 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR Q1102 " --> pdb=" O ALA Q1147 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG Q1100 " --> pdb=" O PRO Q1149 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 1059 through 1061 removed outlier: 6.091A pdb=" N PHE Q1107 " --> pdb=" O THR Q1126 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 954 through 957 removed outlier: 5.234A pdb=" N ILE R 994 " --> pdb=" O GLN R1156 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLN R1156 " --> pdb=" O ILE R 994 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N GLU R1150 " --> pdb=" O VAL R1000 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ALA R1147 " --> pdb=" O THR R1102 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR R1102 " --> pdb=" O ALA R1147 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG R1100 " --> pdb=" O PRO R1149 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 1059 through 1061 Processing sheet with id=AD8, first strand: chain 'S' and resid 954 through 957 removed outlier: 5.281A pdb=" N ILE S 994 " --> pdb=" O GLN S1156 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN S1156 " --> pdb=" O ILE S 994 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLU S1150 " --> pdb=" O VAL S1000 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ALA S1147 " --> pdb=" O THR S1102 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR S1102 " --> pdb=" O ALA S1147 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG S1100 " --> pdb=" O PRO S1149 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 1059 through 1061 removed outlier: 6.021A pdb=" N PHE S1107 " --> pdb=" O THR S1126 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'T' and resid 953 through 957 removed outlier: 5.245A pdb=" N ILE T 994 " --> pdb=" O GLN T1156 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLN T1156 " --> pdb=" O ILE T 994 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLU T1150 " --> pdb=" O VAL T1000 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N ASN T1002 " --> pdb=" O TYR T1148 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N TYR T1148 " --> pdb=" O ASN T1002 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA T1147 " --> pdb=" O THR T1102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR T1102 " --> pdb=" O ALA T1147 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG T1100 " --> pdb=" O PRO T1149 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'T' and resid 1059 through 1061 removed outlier: 6.252A pdb=" N PHE T1107 " --> pdb=" O THR T1126 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'U' and resid 954 through 957 removed outlier: 5.245A pdb=" N ILE U 994 " --> pdb=" O GLN U1156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN U1156 " --> pdb=" O ILE U 994 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLU U1150 " --> pdb=" O VAL U1000 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA U1147 " --> pdb=" O THR U1102 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR U1102 " --> pdb=" O ALA U1147 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG U1100 " --> pdb=" O PRO U1149 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'U' and resid 1059 through 1061 removed outlier: 6.122A pdb=" N PHE U1107 " --> pdb=" O THR U1126 " (cutoff:3.500A) 1944 hydrogen bonds defined for protein. 5298 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.28 Time building geometry restraints manager: 5.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14778 1.33 - 1.46: 8979 1.46 - 1.58: 22103 1.58 - 1.70: 0 1.70 - 1.82: 460 Bond restraints: 46320 Sorted by residual: bond pdb=" CB GLU D1138 " pdb=" CG GLU D1138 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.20e+00 bond pdb=" CG PRO P1119 " pdb=" CD PRO P1119 " ideal model delta sigma weight residual 1.503 1.456 0.047 3.40e-02 8.65e+02 1.91e+00 bond pdb=" C GLU R1019 " pdb=" N ASN R1020 " ideal model delta sigma weight residual 1.333 1.314 0.019 1.42e-02 4.96e+03 1.71e+00 bond pdb=" CB MET C 972 " pdb=" CG MET C 972 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.70e+00 bond pdb=" C GLU Q1019 " pdb=" N ASN Q1020 " ideal model delta sigma weight residual 1.333 1.315 0.019 1.43e-02 4.89e+03 1.68e+00 ... (remaining 46315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 58498 1.08 - 2.15: 3353 2.15 - 3.23: 408 3.23 - 4.30: 152 4.30 - 5.38: 9 Bond angle restraints: 62420 Sorted by residual: angle pdb=" N GLY S1056 " pdb=" CA GLY S1056 " pdb=" C GLY S1056 " ideal model delta sigma weight residual 113.18 118.56 -5.38 2.37e+00 1.78e-01 5.15e+00 angle pdb=" N ALA O1057 " pdb=" CA ALA O1057 " pdb=" C ALA O1057 " ideal model delta sigma weight residual 111.17 114.35 -3.18 1.41e+00 5.03e-01 5.10e+00 angle pdb=" N GLU Q1019 " pdb=" CA GLU Q1019 " pdb=" C GLU Q1019 " ideal model delta sigma weight residual 110.53 107.83 2.70 1.32e+00 5.74e-01 4.18e+00 angle pdb=" N GLU P1019 " pdb=" CA GLU P1019 " pdb=" C GLU P1019 " ideal model delta sigma weight residual 110.53 107.90 2.63 1.29e+00 6.01e-01 4.16e+00 angle pdb=" C GLU T1019 " pdb=" N ASN T1020 " pdb=" CA ASN T1020 " ideal model delta sigma weight residual 122.35 119.38 2.97 1.46e+00 4.69e-01 4.13e+00 ... (remaining 62415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 24866 17.92 - 35.84: 1749 35.84 - 53.76: 381 53.76 - 71.68: 92 71.68 - 89.60: 32 Dihedral angle restraints: 27120 sinusoidal: 10980 harmonic: 16140 Sorted by residual: dihedral pdb=" CA GLU O1018 " pdb=" C GLU O1018 " pdb=" N GLU O1019 " pdb=" CA GLU O1019 " ideal model delta harmonic sigma weight residual 180.00 153.33 26.67 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA GLU P1018 " pdb=" C GLU P1018 " pdb=" N GLU P1019 " pdb=" CA GLU P1019 " ideal model delta harmonic sigma weight residual 180.00 154.43 25.57 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLU S1018 " pdb=" C GLU S1018 " pdb=" N GLU S1019 " pdb=" CA GLU S1019 " ideal model delta harmonic sigma weight residual 180.00 154.44 25.56 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 27117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3101 0.029 - 0.058: 2313 0.058 - 0.087: 658 0.087 - 0.116: 288 0.116 - 0.145: 100 Chirality restraints: 6460 Sorted by residual: chirality pdb=" CA VAL A1000 " pdb=" N VAL A1000 " pdb=" C VAL A1000 " pdb=" CB VAL A1000 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA ILE O1153 " pdb=" N ILE O1153 " pdb=" C ILE O1153 " pdb=" CB ILE O1153 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA ILE U 997 " pdb=" N ILE U 997 " pdb=" C ILE U 997 " pdb=" CB ILE U 997 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 6457 not shown) Planarity restraints: 8080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR S 920 " 0.020 2.00e-02 2.50e+03 1.09e-02 2.35e+00 pdb=" CG TYR S 920 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR S 920 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR S 920 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR S 920 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR S 920 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR S 920 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR S 920 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER P1118 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO P1119 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO P1119 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO P1119 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B1033 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO B1034 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B1034 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B1034 " -0.020 5.00e-02 4.00e+02 ... (remaining 8077 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 162 2.54 - 3.13: 34115 3.13 - 3.72: 69164 3.72 - 4.31: 108529 4.31 - 4.90: 171964 Nonbonded interactions: 383934 Sorted by model distance: nonbonded pdb=" NH1 ARG S1012 " pdb=" OE1 GLU S1015 " model vdw 1.948 3.120 nonbonded pdb=" OG1 THR B 900 " pdb=" OD1 ASP B 902 " model vdw 2.026 3.040 nonbonded pdb=" OG1 THR M 900 " pdb=" OD1 ASP M 902 " model vdw 2.030 3.040 nonbonded pdb=" OG1 THR N 900 " pdb=" OD1 ASP N 902 " model vdw 2.047 3.040 nonbonded pdb=" OG1 THR L 900 " pdb=" OD1 ASP L 902 " model vdw 2.077 3.040 ... (remaining 383929 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 45.000 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 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 : 0.006 0.057 46400 Z= 0.261 Angle : 0.572 5.377 62480 Z= 0.321 Chirality : 0.044 0.145 6460 Planarity : 0.004 0.038 8080 Dihedral : 13.636 89.599 16920 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.76 % Allowed : 6.52 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.11), residues: 5640 helix: 0.33 (0.11), residues: 2040 sheet: -0.07 (0.14), residues: 1220 loop : -0.58 (0.12), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1143 TYR 0.020 0.002 TYR S 920 PHE 0.017 0.002 PHE R 881 TRP 0.015 0.003 TRP F1006 HIS 0.009 0.001 HIS R1041 Details of bonding type rmsd covalent geometry : bond 0.00595 (46320) covalent geometry : angle 0.57142 (62420) hydrogen bonds : bond 0.15390 ( 1944) hydrogen bonds : angle 5.89434 ( 5298) metal coordination : bond 0.01036 ( 80) metal coordination : angle 1.03252 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 916 time to evaluate : 1.700 Fit side-chains revert: symmetry clash REVERT: A 896 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7540 (mtm110) REVERT: A 897 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8200 (mm-30) REVERT: A 913 LYS cc_start: 0.8793 (tmtt) cc_final: 0.8536 (tptt) REVERT: A 1115 MET cc_start: 0.8355 (ptp) cc_final: 0.8113 (ptm) REVERT: B 896 ARG cc_start: 0.8352 (mtp85) cc_final: 0.7623 (mtm110) REVERT: B 943 TYR cc_start: 0.8092 (t80) cc_final: 0.7777 (t80) REVERT: B 959 SER cc_start: 0.8792 (t) cc_final: 0.8588 (m) REVERT: B 1037 ASN cc_start: 0.8183 (t0) cc_final: 0.7808 (m-40) REVERT: C 1042 LYS cc_start: 0.8807 (mmtm) cc_final: 0.8584 (mtmt) REVERT: C 1114 LYS cc_start: 0.8673 (mmmm) cc_final: 0.8404 (mmtm) REVERT: D 896 ARG cc_start: 0.8109 (mtp85) cc_final: 0.7474 (mtm-85) REVERT: D 1114 LYS cc_start: 0.8260 (mmmm) cc_final: 0.7947 (mmtm) REVERT: E 910 LYS cc_start: 0.8508 (ttpp) cc_final: 0.8196 (tttm) REVERT: E 991 ARG cc_start: 0.8211 (ptm160) cc_final: 0.7891 (ptm160) REVERT: F 957 ASP cc_start: 0.8764 (m-30) cc_final: 0.8532 (m-30) REVERT: F 1004 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8239 (mptm) REVERT: F 1014 LYS cc_start: 0.8304 (mttp) cc_final: 0.7943 (tmmt) REVERT: F 1128 ARG cc_start: 0.8206 (mmm-85) cc_final: 0.7970 (mmp80) REVERT: G 932 ARG cc_start: 0.7847 (mtm-85) cc_final: 0.7559 (mtm-85) REVERT: G 971 GLU cc_start: 0.8488 (tp30) cc_final: 0.8133 (tp30) REVERT: G 1004 LYS cc_start: 0.8262 (mtpp) cc_final: 0.8026 (tptp) REVERT: G 1042 LYS cc_start: 0.8543 (mmtm) cc_final: 0.8252 (mppt) REVERT: G 1087 ARG cc_start: 0.7747 (mtt90) cc_final: 0.7424 (mtm-85) REVERT: H 896 ARG cc_start: 0.7851 (mtp85) cc_final: 0.7113 (mtt180) REVERT: H 910 LYS cc_start: 0.8304 (ttpp) cc_final: 0.8051 (tttm) REVERT: H 988 ILE cc_start: 0.8731 (mm) cc_final: 0.8530 (mp) REVERT: H 1004 LYS cc_start: 0.8254 (mtpp) cc_final: 0.7815 (ttpp) REVERT: H 1042 LYS cc_start: 0.8266 (mmtm) cc_final: 0.8041 (mttt) REVERT: H 1054 MET cc_start: 0.8035 (ttp) cc_final: 0.7764 (ttt) REVERT: I 910 LYS cc_start: 0.8263 (ttpp) cc_final: 0.7926 (tttm) REVERT: I 932 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7388 (mtp180) REVERT: I 947 ASN cc_start: 0.8123 (t0) cc_final: 0.7689 (m-40) REVERT: I 990 ASN cc_start: 0.8156 (m-40) cc_final: 0.7719 (p0) REVERT: I 991 ARG cc_start: 0.7488 (ptm160) cc_final: 0.7146 (ptm-80) REVERT: I 1037 ASN cc_start: 0.7358 (t0) cc_final: 0.7115 (m-40) REVERT: I 1042 LYS cc_start: 0.8279 (mmtm) cc_final: 0.8043 (mppt) REVERT: J 1004 LYS cc_start: 0.7601 (mtpp) cc_final: 0.6871 (mtmm) REVERT: J 1020 ASN cc_start: 0.7583 (t0) cc_final: 0.7035 (t0) REVERT: J 1109 GLN cc_start: 0.5945 (tp40) cc_final: 0.5744 (mm-40) REVERT: J 1128 ARG cc_start: 0.8248 (mmm-85) cc_final: 0.8037 (mmm-85) REVERT: L 896 ARG cc_start: 0.7089 (mtt-85) cc_final: 0.6512 (mtt90) REVERT: L 941 ASN cc_start: 0.8177 (m-40) cc_final: 0.7970 (m110) REVERT: L 1004 LYS cc_start: 0.8106 (ttpp) cc_final: 0.7254 (tptp) REVERT: L 1014 LYS cc_start: 0.7199 (mttp) cc_final: 0.6698 (tmmt) REVERT: M 896 ARG cc_start: 0.7857 (mtt-85) cc_final: 0.7167 (mtm110) REVERT: M 910 LYS cc_start: 0.8370 (ttpp) cc_final: 0.7905 (tttm) REVERT: M 911 GLU cc_start: 0.8627 (mp0) cc_final: 0.8222 (mp0) REVERT: M 925 LYS cc_start: 0.8431 (mtpp) cc_final: 0.8192 (mtpt) REVERT: M 969 GLU cc_start: 0.7209 (tt0) cc_final: 0.6860 (tm-30) REVERT: M 991 ARG cc_start: 0.7866 (mtp85) cc_final: 0.7652 (mtp85) REVERT: M 1110 PHE cc_start: 0.8687 (m-80) cc_final: 0.8431 (m-80) REVERT: M 1158 MET cc_start: 0.6456 (mtm) cc_final: 0.6148 (mtp) REVERT: N 896 ARG cc_start: 0.8337 (mtt-85) cc_final: 0.7478 (mtm110) REVERT: N 907 MET cc_start: 0.8859 (mtp) cc_final: 0.8617 (mtp) REVERT: N 991 ARG cc_start: 0.7828 (mtp85) cc_final: 0.7463 (mtp-110) REVERT: N 1004 LYS cc_start: 0.8334 (ttpp) cc_final: 0.7997 (tmmt) REVERT: N 1111 SER cc_start: 0.8589 (m) cc_final: 0.8356 (p) REVERT: N 1158 MET cc_start: 0.6779 (mtm) cc_final: 0.6541 (mtm) REVERT: O 888 GLU cc_start: 0.7909 (mp0) cc_final: 0.7698 (mp0) REVERT: O 896 ARG cc_start: 0.8427 (mtt-85) cc_final: 0.7642 (mtm110) REVERT: O 991 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7570 (ttt90) REVERT: O 1004 LYS cc_start: 0.8436 (ttpp) cc_final: 0.8157 (ttpp) REVERT: P 991 ARG cc_start: 0.7992 (mtp85) cc_final: 0.7749 (mtp-110) REVERT: P 1014 LYS cc_start: 0.8361 (mttp) cc_final: 0.8158 (mtpt) REVERT: P 1114 LYS cc_start: 0.8658 (mmtt) cc_final: 0.8284 (mptt) REVERT: P 1128 ARG cc_start: 0.8075 (mmt90) cc_final: 0.7615 (mmp80) REVERT: Q 932 ARG cc_start: 0.8109 (mtm110) cc_final: 0.7908 (mtp180) REVERT: Q 1114 LYS cc_start: 0.8630 (mmtt) cc_final: 0.8428 (mmtm) REVERT: R 1111 SER cc_start: 0.9073 (m) cc_final: 0.8868 (p) REVERT: S 883 ARG cc_start: 0.8736 (ttm170) cc_final: 0.8506 (ttm110) REVERT: S 910 LYS cc_start: 0.8648 (ttpp) cc_final: 0.8418 (tttm) REVERT: T 910 LYS cc_start: 0.8503 (ttpp) cc_final: 0.8286 (tttm) REVERT: T 1014 LYS cc_start: 0.8105 (mttp) cc_final: 0.7749 (tmmt) REVERT: T 1113 MET cc_start: 0.7892 (ttp) cc_final: 0.7554 (ttp) REVERT: U 943 TYR cc_start: 0.7685 (t80) cc_final: 0.7352 (t80) REVERT: U 991 ARG cc_start: 0.8011 (mtp85) cc_final: 0.7780 (mtp85) REVERT: U 1014 LYS cc_start: 0.8048 (mttp) cc_final: 0.7439 (mmpt) REVERT: U 1107 PHE cc_start: 0.8263 (t80) cc_final: 0.7903 (t80) outliers start: 35 outliers final: 22 residues processed: 949 average time/residue: 0.8179 time to fit residues: 924.9189 Evaluate side-chains 776 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 754 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1126 THR Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain C residue 1066 SER Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain D residue 1126 THR Chi-restraints excluded: chain F residue 1126 THR Chi-restraints excluded: chain H residue 1017 SER Chi-restraints excluded: chain H residue 1106 SER Chi-restraints excluded: chain I residue 1098 PHE Chi-restraints excluded: chain I residue 1106 SER Chi-restraints excluded: chain J residue 1098 PHE Chi-restraints excluded: chain M residue 1036 VAL Chi-restraints excluded: chain N residue 878 ILE Chi-restraints excluded: chain P residue 1036 VAL Chi-restraints excluded: chain P residue 1111 SER Chi-restraints excluded: chain Q residue 1066 SER Chi-restraints excluded: chain R residue 1028 MET Chi-restraints excluded: chain R residue 1099 CYS Chi-restraints excluded: chain S residue 1036 VAL Chi-restraints excluded: chain U residue 1017 SER Chi-restraints excluded: chain U residue 1072 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 394 optimal weight: 3.9990 chunk 430 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 9.9990 chunk 523 optimal weight: 5.9990 chunk 497 optimal weight: 0.0470 chunk 414 optimal weight: 0.9990 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 7.9990 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 947 ASN C 941 ASN E1109 GLN F 990 ASN G 937 GLN H 941 ASN I 889 HIS I 898 GLN I1048 HIS I1095 GLN I1109 GLN J 966 GLN J 973 GLN J1025 ASN J1048 HIS J1069 ASN J1070 GLN ** J1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 947 ASN L1022 ASN M1021 HIS N1109 GLN O1022 ASN Q1022 ASN R 984 HIS S1022 ASN U 941 ASN U 966 GLN U 973 GLN ** U1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.148508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.108658 restraints weight = 38760.669| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.55 r_work: 0.3196 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.234 46400 Z= 0.199 Angle : 0.557 9.668 62480 Z= 0.309 Chirality : 0.045 0.137 6460 Planarity : 0.004 0.050 8080 Dihedral : 5.763 59.431 6427 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.46 % Allowed : 11.09 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.11), residues: 5640 helix: 0.65 (0.11), residues: 2080 sheet: -0.16 (0.14), residues: 1260 loop : -0.21 (0.13), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 896 TYR 0.018 0.002 TYR S 920 PHE 0.017 0.002 PHE R 881 TRP 0.014 0.003 TRP P1006 HIS 0.013 0.001 HIS F1084 Details of bonding type rmsd covalent geometry : bond 0.00437 (46320) covalent geometry : angle 0.54491 (62420) hydrogen bonds : bond 0.06294 ( 1944) hydrogen bonds : angle 4.97225 ( 5298) metal coordination : bond 0.05842 ( 80) metal coordination : angle 3.81329 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 753 time to evaluate : 1.865 Fit side-chains revert: symmetry clash REVERT: A 896 ARG cc_start: 0.8241 (mtp85) cc_final: 0.7634 (mtm110) REVERT: A 897 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8432 (mm-30) REVERT: B 896 ARG cc_start: 0.8454 (mtp85) cc_final: 0.7606 (mtm110) REVERT: B 959 SER cc_start: 0.8743 (t) cc_final: 0.8498 (m) REVERT: B 971 GLU cc_start: 0.7839 (tp30) cc_final: 0.7529 (tp30) REVERT: B 1037 ASN cc_start: 0.8165 (t0) cc_final: 0.7706 (m-40) REVERT: B 1128 ARG cc_start: 0.8014 (mmt-90) cc_final: 0.7671 (mmt-90) REVERT: C 910 LYS cc_start: 0.8593 (ttpt) cc_final: 0.8344 (ttpp) REVERT: C 969 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: C 1042 LYS cc_start: 0.8764 (mmtm) cc_final: 0.8439 (mtmt) REVERT: C 1114 LYS cc_start: 0.8618 (mmmm) cc_final: 0.8352 (mmtm) REVERT: D 896 ARG cc_start: 0.8215 (mtp85) cc_final: 0.7356 (mtm110) REVERT: D 969 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: D 1114 LYS cc_start: 0.8279 (mmmm) cc_final: 0.7811 (mmtm) REVERT: E 910 LYS cc_start: 0.8627 (ttpp) cc_final: 0.8196 (tttm) REVERT: E 931 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7948 (tm-30) REVERT: E 991 ARG cc_start: 0.8137 (ptm160) cc_final: 0.7755 (ptm160) REVERT: F 931 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: F 957 ASP cc_start: 0.8817 (m-30) cc_final: 0.8581 (m-30) REVERT: F 969 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8179 (tt0) REVERT: F 1004 LYS cc_start: 0.8492 (mtpp) cc_final: 0.8123 (mptm) REVERT: F 1014 LYS cc_start: 0.8259 (mttp) cc_final: 0.7789 (tmmt) REVERT: F 1019 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7936 (mt-10) REVERT: F 1128 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.7818 (mmp80) REVERT: G 932 ARG cc_start: 0.7840 (mtm-85) cc_final: 0.7555 (mtm-85) REVERT: G 971 GLU cc_start: 0.8452 (tp30) cc_final: 0.8113 (tp30) REVERT: G 1004 LYS cc_start: 0.8348 (mtpp) cc_final: 0.7986 (tptp) REVERT: G 1042 LYS cc_start: 0.8505 (mmtm) cc_final: 0.8074 (mppt) REVERT: G 1087 ARG cc_start: 0.7812 (mtt90) cc_final: 0.7484 (mtm-85) REVERT: H 888 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: H 896 ARG cc_start: 0.8033 (mtp85) cc_final: 0.7011 (mtm180) REVERT: H 910 LYS cc_start: 0.8311 (ttpp) cc_final: 0.7951 (ttpp) REVERT: H 943 TYR cc_start: 0.7824 (t80) cc_final: 0.7606 (t80) REVERT: H 988 ILE cc_start: 0.8743 (mm) cc_final: 0.8498 (mp) REVERT: H 1004 LYS cc_start: 0.8380 (mtpp) cc_final: 0.7872 (ttpp) REVERT: H 1042 LYS cc_start: 0.8279 (mmtm) cc_final: 0.8051 (mttp) REVERT: H 1054 MET cc_start: 0.8122 (ttp) cc_final: 0.7878 (ttt) REVERT: I 910 LYS cc_start: 0.8309 (ttpp) cc_final: 0.7942 (tttm) REVERT: I 932 ARG cc_start: 0.7768 (mtm-85) cc_final: 0.7468 (mtp180) REVERT: I 947 ASN cc_start: 0.8142 (t0) cc_final: 0.7677 (m-40) REVERT: I 988 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7532 (mm) REVERT: I 990 ASN cc_start: 0.8217 (m-40) cc_final: 0.7664 (p0) REVERT: I 1037 ASN cc_start: 0.7337 (t0) cc_final: 0.7087 (m-40) REVERT: I 1042 LYS cc_start: 0.8341 (mmtm) cc_final: 0.8047 (mppt) REVERT: J 892 ASP cc_start: 0.7445 (p0) cc_final: 0.6812 (p0) REVERT: J 1004 LYS cc_start: 0.7762 (mtpp) cc_final: 0.6942 (mtmm) REVERT: J 1020 ASN cc_start: 0.7432 (t0) cc_final: 0.6838 (t0) REVERT: J 1087 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7541 (mtm-85) REVERT: J 1128 ARG cc_start: 0.8296 (mmm-85) cc_final: 0.7858 (mmm-85) REVERT: L 896 ARG cc_start: 0.7317 (mtt-85) cc_final: 0.6572 (mtm110) REVERT: L 1004 LYS cc_start: 0.8166 (ttpp) cc_final: 0.7267 (tptp) REVERT: L 1014 LYS cc_start: 0.7401 (mttp) cc_final: 0.6785 (tmmt) REVERT: M 896 ARG cc_start: 0.8189 (mtt-85) cc_final: 0.7477 (mtm110) REVERT: M 910 LYS cc_start: 0.8337 (ttpp) cc_final: 0.7810 (tttm) REVERT: M 911 GLU cc_start: 0.8611 (mp0) cc_final: 0.8222 (mp0) REVERT: M 925 LYS cc_start: 0.8475 (mtpp) cc_final: 0.8238 (mtpt) REVERT: M 991 ARG cc_start: 0.7881 (mtp85) cc_final: 0.7653 (mtp85) REVERT: M 1054 MET cc_start: 0.8308 (ttm) cc_final: 0.8093 (ttt) REVERT: M 1063 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7649 (pt0) REVERT: M 1110 PHE cc_start: 0.8557 (m-80) cc_final: 0.8314 (m-80) REVERT: M 1158 MET cc_start: 0.6367 (mtm) cc_final: 0.6064 (mtp) REVERT: N 896 ARG cc_start: 0.8558 (mtt-85) cc_final: 0.7609 (mtm110) REVERT: N 907 MET cc_start: 0.8802 (mtp) cc_final: 0.8585 (mtp) REVERT: N 991 ARG cc_start: 0.7820 (mtp85) cc_final: 0.7406 (mtp-110) REVERT: N 1004 LYS cc_start: 0.8240 (ttpp) cc_final: 0.7956 (tmmt) REVERT: N 1111 SER cc_start: 0.8542 (m) cc_final: 0.8250 (p) REVERT: N 1158 MET cc_start: 0.6670 (mtm) cc_final: 0.6434 (mtm) REVERT: O 888 GLU cc_start: 0.7877 (mp0) cc_final: 0.7625 (mp0) REVERT: O 896 ARG cc_start: 0.8506 (mtt-85) cc_final: 0.7709 (mtm110) REVERT: O 991 ARG cc_start: 0.8006 (mtp85) cc_final: 0.7499 (ttt90) REVERT: O 1004 LYS cc_start: 0.8476 (ttpp) cc_final: 0.8134 (ttpp) REVERT: O 1054 MET cc_start: 0.8637 (ttp) cc_final: 0.8433 (ttp) REVERT: P 1114 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8184 (mptt) REVERT: P 1128 ARG cc_start: 0.8132 (mmt90) cc_final: 0.7620 (mmp80) REVERT: Q 1014 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7832 (mmpt) REVERT: Q 1114 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8353 (mptt) REVERT: R 963 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8198 (pttp) REVERT: R 969 GLU cc_start: 0.8391 (tt0) cc_final: 0.8081 (tm-30) REVERT: R 1111 SER cc_start: 0.8998 (m) cc_final: 0.8737 (p) REVERT: S 883 ARG cc_start: 0.8745 (ttm170) cc_final: 0.8492 (ttm110) REVERT: S 910 LYS cc_start: 0.8654 (ttpp) cc_final: 0.8332 (tttm) REVERT: S 925 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8703 (mttt) REVERT: S 931 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: S 941 ASN cc_start: 0.8024 (m110) cc_final: 0.7667 (m110) REVERT: T 910 LYS cc_start: 0.8505 (ttpp) cc_final: 0.8223 (tttm) REVERT: T 931 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7435 (tp30) REVERT: T 1014 LYS cc_start: 0.8113 (mttp) cc_final: 0.7672 (tmmt) REVERT: T 1037 ASN cc_start: 0.7358 (m110) cc_final: 0.7055 (t0) REVERT: T 1113 MET cc_start: 0.8119 (ttp) cc_final: 0.7730 (ttp) REVERT: U 991 ARG cc_start: 0.8114 (mtp85) cc_final: 0.7871 (mtp85) REVERT: U 1018 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7058 (mt-10) REVERT: U 1107 PHE cc_start: 0.8194 (t80) cc_final: 0.7909 (t80) outliers start: 113 outliers final: 40 residues processed: 803 average time/residue: 0.8642 time to fit residues: 832.4101 Evaluate side-chains 792 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 741 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 972 MET Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1126 THR Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1066 SER Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 990 ASN Chi-restraints excluded: chain D residue 1126 THR Chi-restraints excluded: chain F residue 931 GLU Chi-restraints excluded: chain F residue 969 GLU Chi-restraints excluded: chain G residue 1014 LYS Chi-restraints excluded: chain G residue 1126 THR Chi-restraints excluded: chain H residue 888 GLU Chi-restraints excluded: chain H residue 972 MET Chi-restraints excluded: chain H residue 1017 SER Chi-restraints excluded: chain H residue 1036 VAL Chi-restraints excluded: chain H residue 1126 THR Chi-restraints excluded: chain I residue 988 ILE Chi-restraints excluded: chain I residue 1036 VAL Chi-restraints excluded: chain I residue 1098 PHE Chi-restraints excluded: chain I residue 1115 MET Chi-restraints excluded: chain J residue 1098 PHE Chi-restraints excluded: chain L residue 1036 VAL Chi-restraints excluded: chain M residue 967 SER Chi-restraints excluded: chain M residue 1036 VAL Chi-restraints excluded: chain M residue 1063 GLU Chi-restraints excluded: chain N residue 878 ILE Chi-restraints excluded: chain N residue 931 GLU Chi-restraints excluded: chain N residue 1018 GLU Chi-restraints excluded: chain N residue 1108 LEU Chi-restraints excluded: chain O residue 959 SER Chi-restraints excluded: chain O residue 1017 SER Chi-restraints excluded: chain O residue 1069 ASN Chi-restraints excluded: chain P residue 959 SER Chi-restraints excluded: chain P residue 1036 VAL Chi-restraints excluded: chain P residue 1111 SER Chi-restraints excluded: chain Q residue 947 ASN Chi-restraints excluded: chain Q residue 1014 LYS Chi-restraints excluded: chain Q residue 1066 SER Chi-restraints excluded: chain R residue 963 LYS Chi-restraints excluded: chain R residue 990 ASN Chi-restraints excluded: chain R residue 1028 MET Chi-restraints excluded: chain S residue 925 LYS Chi-restraints excluded: chain S residue 931 GLU Chi-restraints excluded: chain T residue 947 ASN Chi-restraints excluded: chain T residue 1036 VAL Chi-restraints excluded: chain U residue 1042 LYS Chi-restraints excluded: chain U residue 1115 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 222 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 383 optimal weight: 3.9990 chunk 331 optimal weight: 0.9980 chunk 131 optimal weight: 0.5980 chunk 521 optimal weight: 3.9990 chunk 427 optimal weight: 4.9990 chunk 502 optimal weight: 4.9990 chunk 318 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 947 ASN C 941 ASN C 947 ASN D 898 GLN E 947 ASN G 941 ASN ** G1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 937 GLN H 947 ASN H1109 GLN I 880 GLN I 898 GLN I1069 ASN I1095 GLN I1109 GLN J 941 ASN ** J1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 941 ASN L 947 ASN L1064 ASN M1022 ASN N 947 ASN ** P 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 941 ASN U1109 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.148964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.109161 restraints weight = 38716.912| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.55 r_work: 0.3203 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.199 46400 Z= 0.179 Angle : 0.536 10.301 62480 Z= 0.295 Chirality : 0.044 0.136 6460 Planarity : 0.004 0.042 8080 Dihedral : 5.603 58.847 6419 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.70 % Allowed : 11.80 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.11), residues: 5640 helix: 0.75 (0.11), residues: 2080 sheet: -0.16 (0.14), residues: 1260 loop : -0.17 (0.13), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L1128 TYR 0.018 0.002 TYR S 920 PHE 0.017 0.002 PHE D 881 TRP 0.013 0.002 TRP F1006 HIS 0.015 0.001 HIS C1084 Details of bonding type rmsd covalent geometry : bond 0.00393 (46320) covalent geometry : angle 0.52109 (62420) hydrogen bonds : bond 0.05919 ( 1944) hydrogen bonds : angle 4.84420 ( 5298) metal coordination : bond 0.04706 ( 80) metal coordination : angle 4.07386 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 751 time to evaluate : 1.518 Fit side-chains revert: symmetry clash REVERT: A 896 ARG cc_start: 0.8257 (mtp85) cc_final: 0.7653 (mtm110) REVERT: B 896 ARG cc_start: 0.8478 (mtp85) cc_final: 0.7688 (mtm110) REVERT: B 959 SER cc_start: 0.8740 (t) cc_final: 0.8493 (m) REVERT: B 969 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: B 971 GLU cc_start: 0.7801 (tp30) cc_final: 0.7517 (tp30) REVERT: B 1037 ASN cc_start: 0.8157 (t0) cc_final: 0.7688 (m-40) REVERT: B 1128 ARG cc_start: 0.8020 (mmt-90) cc_final: 0.7658 (mmt-90) REVERT: C 969 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: C 996 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7969 (mtmt) REVERT: C 1042 LYS cc_start: 0.8748 (mmtm) cc_final: 0.8426 (mtmt) REVERT: C 1114 LYS cc_start: 0.8650 (mmmm) cc_final: 0.8355 (mmtm) REVERT: D 896 ARG cc_start: 0.8214 (mtp85) cc_final: 0.7327 (mtm110) REVERT: D 969 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: E 910 LYS cc_start: 0.8611 (ttpp) cc_final: 0.8185 (tttm) REVERT: E 931 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7929 (tm-30) REVERT: E 991 ARG cc_start: 0.8140 (ptm160) cc_final: 0.7731 (ptm160) REVERT: F 931 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: F 957 ASP cc_start: 0.8801 (m-30) cc_final: 0.8590 (m-30) REVERT: F 1004 LYS cc_start: 0.8480 (mtpp) cc_final: 0.8117 (mptm) REVERT: F 1014 LYS cc_start: 0.8261 (mttp) cc_final: 0.7768 (tmmt) REVERT: F 1019 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7896 (mt-10) REVERT: G 932 ARG cc_start: 0.7844 (mtm-85) cc_final: 0.7554 (mtm-85) REVERT: G 971 GLU cc_start: 0.8408 (tp30) cc_final: 0.8022 (tp30) REVERT: G 1004 LYS cc_start: 0.8342 (mtpp) cc_final: 0.7994 (tptp) REVERT: G 1042 LYS cc_start: 0.8489 (mmtm) cc_final: 0.8041 (mppt) REVERT: G 1087 ARG cc_start: 0.7786 (mtt90) cc_final: 0.7479 (mtm-85) REVERT: G 1092 CYS cc_start: 0.7659 (m) cc_final: 0.6965 (m) REVERT: H 888 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8080 (tm-30) REVERT: H 896 ARG cc_start: 0.8048 (mtp85) cc_final: 0.7085 (mtm180) REVERT: H 910 LYS cc_start: 0.8310 (ttpp) cc_final: 0.7990 (ttpp) REVERT: H 943 TYR cc_start: 0.7779 (t80) cc_final: 0.7498 (t80) REVERT: H 947 ASN cc_start: 0.7640 (OUTLIER) cc_final: 0.7353 (m110) REVERT: H 988 ILE cc_start: 0.8781 (mm) cc_final: 0.8549 (mp) REVERT: H 1004 LYS cc_start: 0.8384 (mtpp) cc_final: 0.7871 (ttpp) REVERT: H 1042 LYS cc_start: 0.8277 (mmtm) cc_final: 0.7999 (mttt) REVERT: H 1054 MET cc_start: 0.8100 (ttp) cc_final: 0.7869 (ttt) REVERT: H 1113 MET cc_start: 0.8202 (ptm) cc_final: 0.7720 (ptt) REVERT: I 910 LYS cc_start: 0.8337 (ttpp) cc_final: 0.7962 (tttm) REVERT: I 947 ASN cc_start: 0.8094 (t0) cc_final: 0.7666 (m-40) REVERT: I 988 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7546 (mm) REVERT: I 990 ASN cc_start: 0.8211 (m-40) cc_final: 0.7636 (p0) REVERT: I 1037 ASN cc_start: 0.7332 (t0) cc_final: 0.7087 (m-40) REVERT: I 1042 LYS cc_start: 0.8352 (mmtm) cc_final: 0.8067 (mppt) REVERT: J 892 ASP cc_start: 0.7400 (p0) cc_final: 0.6942 (p0) REVERT: J 1004 LYS cc_start: 0.7783 (mtpp) cc_final: 0.6980 (mtmm) REVERT: J 1020 ASN cc_start: 0.7413 (t0) cc_final: 0.6849 (t0) REVERT: J 1087 ARG cc_start: 0.8068 (mtm-85) cc_final: 0.7583 (mtm-85) REVERT: J 1128 ARG cc_start: 0.8297 (mmm-85) cc_final: 0.7827 (mmm-85) REVERT: L 896 ARG cc_start: 0.7384 (mtt-85) cc_final: 0.6689 (mtm180) REVERT: L 1004 LYS cc_start: 0.8147 (ttpp) cc_final: 0.7250 (tptp) REVERT: L 1014 LYS cc_start: 0.7341 (mttp) cc_final: 0.6665 (tmmt) REVERT: L 1018 GLU cc_start: 0.7178 (tp30) cc_final: 0.6946 (tp30) REVERT: M 896 ARG cc_start: 0.8191 (mtt-85) cc_final: 0.7478 (mtm110) REVERT: M 910 LYS cc_start: 0.8351 (ttpp) cc_final: 0.7818 (tttm) REVERT: M 911 GLU cc_start: 0.8622 (mp0) cc_final: 0.8217 (mp0) REVERT: M 925 LYS cc_start: 0.8475 (mtpp) cc_final: 0.8239 (mtpt) REVERT: M 947 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7183 (m-40) REVERT: M 991 ARG cc_start: 0.7866 (mtp85) cc_final: 0.7638 (mtp85) REVERT: M 1018 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: M 1110 PHE cc_start: 0.8560 (m-80) cc_final: 0.8323 (m-80) REVERT: M 1158 MET cc_start: 0.6379 (mtm) cc_final: 0.6068 (mtp) REVERT: N 896 ARG cc_start: 0.8519 (mtt-85) cc_final: 0.7638 (mtm110) REVERT: N 991 ARG cc_start: 0.7815 (mtp85) cc_final: 0.7410 (mtp-110) REVERT: N 1004 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7963 (tmmt) REVERT: N 1111 SER cc_start: 0.8553 (m) cc_final: 0.8265 (p) REVERT: N 1158 MET cc_start: 0.6537 (mtm) cc_final: 0.6251 (mtm) REVERT: O 888 GLU cc_start: 0.7874 (mp0) cc_final: 0.7598 (mp0) REVERT: O 991 ARG cc_start: 0.8009 (mtp85) cc_final: 0.7500 (ttt90) REVERT: O 1004 LYS cc_start: 0.8490 (ttpp) cc_final: 0.8148 (ttpp) REVERT: P 991 ARG cc_start: 0.7873 (mtp-110) cc_final: 0.7579 (mtp-110) REVERT: P 1114 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8163 (mptt) REVERT: P 1128 ARG cc_start: 0.8142 (mmt90) cc_final: 0.7632 (mmp80) REVERT: Q 1014 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7819 (mmpt) REVERT: Q 1114 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8342 (mptt) REVERT: R 896 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7871 (ttt-90) REVERT: R 963 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8179 (pttp) REVERT: R 969 GLU cc_start: 0.8331 (tt0) cc_final: 0.8008 (tm-30) REVERT: R 1111 SER cc_start: 0.8996 (m) cc_final: 0.8740 (p) REVERT: R 1128 ARG cc_start: 0.7692 (mmt90) cc_final: 0.7477 (mmt-90) REVERT: S 883 ARG cc_start: 0.8709 (ttm170) cc_final: 0.8494 (ttm110) REVERT: S 910 LYS cc_start: 0.8653 (ttpp) cc_final: 0.8326 (tttm) REVERT: S 925 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8700 (mttt) REVERT: S 941 ASN cc_start: 0.8046 (m110) cc_final: 0.7725 (m110) REVERT: T 910 LYS cc_start: 0.8548 (ttpp) cc_final: 0.8253 (tttm) REVERT: T 969 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: T 1014 LYS cc_start: 0.8123 (mttp) cc_final: 0.7651 (tmmt) REVERT: T 1037 ASN cc_start: 0.7334 (m110) cc_final: 0.7042 (t0) REVERT: T 1113 MET cc_start: 0.8162 (ttp) cc_final: 0.7756 (ttp) REVERT: U 971 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.6827 (tm-30) REVERT: U 991 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7856 (mtp85) REVERT: U 1014 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7713 (ttmm) REVERT: U 1018 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7045 (mt-10) REVERT: U 1107 PHE cc_start: 0.8241 (t80) cc_final: 0.7930 (t80) REVERT: U 1115 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7692 (ptm) outliers start: 124 outliers final: 55 residues processed: 805 average time/residue: 0.8409 time to fit residues: 814.4420 Evaluate side-chains 812 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 739 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 972 MET Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1126 THR Chi-restraints excluded: chain B residue 910 LYS Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 996 LYS Chi-restraints excluded: chain C residue 1066 SER Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 990 ASN Chi-restraints excluded: chain D residue 1126 THR Chi-restraints excluded: chain F residue 931 GLU Chi-restraints excluded: chain G residue 944 LEU Chi-restraints excluded: chain G residue 1014 LYS Chi-restraints excluded: chain G residue 1126 THR Chi-restraints excluded: chain H residue 888 GLU Chi-restraints excluded: chain H residue 947 ASN Chi-restraints excluded: chain H residue 972 MET Chi-restraints excluded: chain H residue 1017 SER Chi-restraints excluded: chain H residue 1036 VAL Chi-restraints excluded: chain H residue 1126 THR Chi-restraints excluded: chain I residue 988 ILE Chi-restraints excluded: chain I residue 1036 VAL Chi-restraints excluded: chain I residue 1054 MET Chi-restraints excluded: chain I residue 1098 PHE Chi-restraints excluded: chain I residue 1115 MET Chi-restraints excluded: chain J residue 1018 GLU Chi-restraints excluded: chain J residue 1098 PHE Chi-restraints excluded: chain J residue 1102 THR Chi-restraints excluded: chain J residue 1118 SER Chi-restraints excluded: chain L residue 1036 VAL Chi-restraints excluded: chain M residue 882 VAL Chi-restraints excluded: chain M residue 947 ASN Chi-restraints excluded: chain M residue 967 SER Chi-restraints excluded: chain M residue 969 GLU Chi-restraints excluded: chain M residue 1018 GLU Chi-restraints excluded: chain M residue 1036 VAL Chi-restraints excluded: chain M residue 1098 PHE Chi-restraints excluded: chain M residue 1111 SER Chi-restraints excluded: chain N residue 878 ILE Chi-restraints excluded: chain N residue 931 GLU Chi-restraints excluded: chain N residue 990 ASN Chi-restraints excluded: chain N residue 1018 GLU Chi-restraints excluded: chain N residue 1036 VAL Chi-restraints excluded: chain N residue 1099 CYS Chi-restraints excluded: chain N residue 1108 LEU Chi-restraints excluded: chain O residue 959 SER Chi-restraints excluded: chain O residue 1017 SER Chi-restraints excluded: chain O residue 1069 ASN Chi-restraints excluded: chain P residue 1036 VAL Chi-restraints excluded: chain Q residue 947 ASN Chi-restraints excluded: chain Q residue 1014 LYS Chi-restraints excluded: chain R residue 896 ARG Chi-restraints excluded: chain R residue 963 LYS Chi-restraints excluded: chain R residue 990 ASN Chi-restraints excluded: chain R residue 1028 MET Chi-restraints excluded: chain S residue 925 LYS Chi-restraints excluded: chain T residue 947 ASN Chi-restraints excluded: chain T residue 969 GLU Chi-restraints excluded: chain T residue 1036 VAL Chi-restraints excluded: chain T residue 1111 SER Chi-restraints excluded: chain U residue 910 LYS Chi-restraints excluded: chain U residue 971 GLU Chi-restraints excluded: chain U residue 1014 LYS Chi-restraints excluded: chain U residue 1042 LYS Chi-restraints excluded: chain U residue 1072 VAL Chi-restraints excluded: chain U residue 1108 LEU Chi-restraints excluded: chain U residue 1115 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 408 optimal weight: 0.9990 chunk 430 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 547 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 413 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 458 optimal weight: 0.0470 chunk 239 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 947 ASN C 941 ASN E 941 ASN E 947 ASN H 937 GLN H1109 GLN I1069 ASN I1109 GLN J 941 ASN ** J1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 941 ASN O 941 ASN P 947 ASN R 941 ASN U 941 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.148577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.108671 restraints weight = 38769.141| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.56 r_work: 0.3195 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.234 46400 Z= 0.206 Angle : 0.564 11.090 62480 Z= 0.308 Chirality : 0.045 0.147 6460 Planarity : 0.004 0.043 8080 Dihedral : 5.649 58.595 6417 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.11 % Allowed : 11.91 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.11), residues: 5640 helix: 0.70 (0.11), residues: 2080 sheet: -0.18 (0.14), residues: 1260 loop : -0.20 (0.13), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 896 TYR 0.019 0.002 TYR S 920 PHE 0.017 0.002 PHE D 881 TRP 0.014 0.003 TRP P1006 HIS 0.017 0.001 HIS E1084 Details of bonding type rmsd covalent geometry : bond 0.00455 (46320) covalent geometry : angle 0.54593 (62420) hydrogen bonds : bond 0.06129 ( 1944) hydrogen bonds : angle 4.86753 ( 5298) metal coordination : bond 0.06241 ( 80) metal coordination : angle 4.64476 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 735 time to evaluate : 1.671 Fit side-chains revert: symmetry clash REVERT: A 896 ARG cc_start: 0.8332 (mtp85) cc_final: 0.7701 (mtm110) REVERT: A 1115 MET cc_start: 0.8431 (ptp) cc_final: 0.8231 (ptp) REVERT: B 896 ARG cc_start: 0.8506 (mtp85) cc_final: 0.7736 (mtm110) REVERT: B 959 SER cc_start: 0.8756 (t) cc_final: 0.8509 (m) REVERT: B 969 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: B 971 GLU cc_start: 0.7806 (tp30) cc_final: 0.7519 (tp30) REVERT: B 1037 ASN cc_start: 0.8173 (t0) cc_final: 0.7711 (m-40) REVERT: B 1128 ARG cc_start: 0.8031 (mmt-90) cc_final: 0.7657 (mmt-90) REVERT: C 969 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8348 (tt0) REVERT: C 1042 LYS cc_start: 0.8708 (mmtm) cc_final: 0.8411 (mtmt) REVERT: C 1114 LYS cc_start: 0.8658 (mmmm) cc_final: 0.8358 (mmtm) REVERT: D 896 ARG cc_start: 0.8246 (mtp85) cc_final: 0.7427 (mtp180) REVERT: D 969 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: D 1114 LYS cc_start: 0.8346 (mmmt) cc_final: 0.7973 (mmtm) REVERT: E 910 LYS cc_start: 0.8591 (ttpp) cc_final: 0.8187 (tttm) REVERT: E 931 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7940 (tm-30) REVERT: F 931 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: F 1004 LYS cc_start: 0.8486 (mtpp) cc_final: 0.8121 (mptm) REVERT: F 1014 LYS cc_start: 0.8277 (mttp) cc_final: 0.7775 (tmmt) REVERT: G 932 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.7592 (mtm-85) REVERT: G 971 GLU cc_start: 0.8405 (tp30) cc_final: 0.8027 (tp30) REVERT: G 1004 LYS cc_start: 0.8351 (mtpp) cc_final: 0.7997 (tptp) REVERT: G 1042 LYS cc_start: 0.8530 (mmtm) cc_final: 0.8102 (mppt) REVERT: G 1087 ARG cc_start: 0.7833 (mtt90) cc_final: 0.7514 (mtm-85) REVERT: H 888 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8096 (tm-30) REVERT: H 896 ARG cc_start: 0.8032 (mtp85) cc_final: 0.7080 (mtm180) REVERT: H 910 LYS cc_start: 0.8340 (ttpp) cc_final: 0.8014 (ttpp) REVERT: H 943 TYR cc_start: 0.7923 (t80) cc_final: 0.7676 (t80) REVERT: H 988 ILE cc_start: 0.8771 (mm) cc_final: 0.8522 (mp) REVERT: H 1004 LYS cc_start: 0.8419 (mtpp) cc_final: 0.7906 (ttpp) REVERT: H 1042 LYS cc_start: 0.8290 (mmtm) cc_final: 0.8034 (mttp) REVERT: H 1054 MET cc_start: 0.8077 (ttp) cc_final: 0.7860 (ttt) REVERT: I 947 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7653 (m-40) REVERT: I 988 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7554 (mm) REVERT: I 990 ASN cc_start: 0.8223 (m-40) cc_final: 0.7632 (p0) REVERT: I 1037 ASN cc_start: 0.7363 (t0) cc_final: 0.7105 (m-40) REVERT: I 1042 LYS cc_start: 0.8368 (mmtm) cc_final: 0.8084 (mppt) REVERT: J 977 ARG cc_start: 0.6405 (OUTLIER) cc_final: 0.5838 (mmt90) REVERT: J 1004 LYS cc_start: 0.7797 (mtpp) cc_final: 0.6994 (mtmm) REVERT: J 1020 ASN cc_start: 0.7410 (t0) cc_final: 0.6867 (t0) REVERT: J 1087 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7759 (mtm-85) REVERT: J 1128 ARG cc_start: 0.8257 (mmm-85) cc_final: 0.7743 (mmm-85) REVERT: L 896 ARG cc_start: 0.7397 (mtt-85) cc_final: 0.6692 (mtm180) REVERT: L 1004 LYS cc_start: 0.8180 (ttpp) cc_final: 0.7264 (tptp) REVERT: L 1014 LYS cc_start: 0.7442 (mttp) cc_final: 0.6854 (tmmt) REVERT: M 896 ARG cc_start: 0.8196 (mtt-85) cc_final: 0.7488 (mtm110) REVERT: M 910 LYS cc_start: 0.8360 (ttpp) cc_final: 0.7827 (tttm) REVERT: M 911 GLU cc_start: 0.8635 (mp0) cc_final: 0.8222 (mp0) REVERT: M 925 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8249 (mtpt) REVERT: M 947 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7189 (m-40) REVERT: M 991 ARG cc_start: 0.7850 (mtp85) cc_final: 0.7641 (mtp85) REVERT: M 1063 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7548 (pt0) REVERT: M 1158 MET cc_start: 0.6375 (mtm) cc_final: 0.6063 (mtp) REVERT: N 896 ARG cc_start: 0.8533 (mtt-85) cc_final: 0.7650 (mtm110) REVERT: N 991 ARG cc_start: 0.7827 (mtp85) cc_final: 0.7431 (mtp-110) REVERT: N 1004 LYS cc_start: 0.8286 (ttpp) cc_final: 0.8037 (tmmt) REVERT: N 1111 SER cc_start: 0.8564 (m) cc_final: 0.8265 (p) REVERT: N 1158 MET cc_start: 0.6582 (mtm) cc_final: 0.6338 (mtm) REVERT: O 888 GLU cc_start: 0.7910 (mp0) cc_final: 0.7627 (mp0) REVERT: O 991 ARG cc_start: 0.8014 (mtp85) cc_final: 0.7519 (ttt90) REVERT: O 1004 LYS cc_start: 0.8482 (ttpp) cc_final: 0.8133 (ttpp) REVERT: P 991 ARG cc_start: 0.7893 (mtp-110) cc_final: 0.7598 (mtp-110) REVERT: P 1114 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8170 (mptt) REVERT: P 1128 ARG cc_start: 0.8142 (mmt90) cc_final: 0.7655 (mmp80) REVERT: Q 947 ASN cc_start: 0.8156 (OUTLIER) cc_final: 0.7929 (t0) REVERT: Q 1014 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7822 (mmpt) REVERT: Q 1114 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8354 (mptt) REVERT: R 963 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8170 (pttp) REVERT: R 969 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: R 1111 SER cc_start: 0.8998 (m) cc_final: 0.8748 (p) REVERT: R 1128 ARG cc_start: 0.7691 (mmt90) cc_final: 0.7472 (mmt-90) REVERT: S 883 ARG cc_start: 0.8694 (ttm170) cc_final: 0.8491 (ttm110) REVERT: S 910 LYS cc_start: 0.8630 (ttpp) cc_final: 0.8324 (tttm) REVERT: S 925 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8693 (mttt) REVERT: S 941 ASN cc_start: 0.8057 (m110) cc_final: 0.7698 (m110) REVERT: T 910 LYS cc_start: 0.8556 (ttpp) cc_final: 0.8257 (tttm) REVERT: T 969 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: T 1014 LYS cc_start: 0.8150 (mttp) cc_final: 0.7663 (tmmt) REVERT: T 1037 ASN cc_start: 0.7356 (m110) cc_final: 0.7060 (t0) REVERT: T 1113 MET cc_start: 0.8129 (ttp) cc_final: 0.7692 (ttp) REVERT: U 971 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.6823 (tm-30) REVERT: U 991 ARG cc_start: 0.8130 (mtp85) cc_final: 0.7902 (mtp85) REVERT: U 1003 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8583 (tptp) REVERT: U 1014 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7740 (ttmm) REVERT: U 1018 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7063 (mt-10) REVERT: U 1107 PHE cc_start: 0.8261 (t80) cc_final: 0.7988 (t80) REVERT: U 1115 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7760 (ptm) outliers start: 143 outliers final: 63 residues processed: 808 average time/residue: 0.7866 time to fit residues: 764.1670 Evaluate side-chains 823 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 740 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 972 MET Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1126 THR Chi-restraints excluded: chain B residue 910 LYS Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 996 LYS Chi-restraints excluded: chain C residue 1066 SER Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 990 ASN Chi-restraints excluded: chain D residue 1113 MET Chi-restraints excluded: chain D residue 1126 THR Chi-restraints excluded: chain F residue 931 GLU Chi-restraints excluded: chain G residue 944 LEU Chi-restraints excluded: chain G residue 1014 LYS Chi-restraints excluded: chain G residue 1072 VAL Chi-restraints excluded: chain G residue 1108 LEU Chi-restraints excluded: chain G residue 1126 THR Chi-restraints excluded: chain H residue 888 GLU Chi-restraints excluded: chain H residue 972 MET Chi-restraints excluded: chain H residue 996 LYS Chi-restraints excluded: chain H residue 1017 SER Chi-restraints excluded: chain H residue 1036 VAL Chi-restraints excluded: chain H residue 1126 THR Chi-restraints excluded: chain I residue 947 ASN Chi-restraints excluded: chain I residue 988 ILE Chi-restraints excluded: chain I residue 1036 VAL Chi-restraints excluded: chain I residue 1054 MET Chi-restraints excluded: chain I residue 1098 PHE Chi-restraints excluded: chain I residue 1115 MET Chi-restraints excluded: chain J residue 977 ARG Chi-restraints excluded: chain J residue 1018 GLU Chi-restraints excluded: chain J residue 1098 PHE Chi-restraints excluded: chain J residue 1102 THR Chi-restraints excluded: chain J residue 1118 SER Chi-restraints excluded: chain L residue 1036 VAL Chi-restraints excluded: chain M residue 882 VAL Chi-restraints excluded: chain M residue 947 ASN Chi-restraints excluded: chain M residue 967 SER Chi-restraints excluded: chain M residue 969 GLU Chi-restraints excluded: chain M residue 1036 VAL Chi-restraints excluded: chain M residue 1063 GLU Chi-restraints excluded: chain M residue 1098 PHE Chi-restraints excluded: chain M residue 1111 SER Chi-restraints excluded: chain N residue 878 ILE Chi-restraints excluded: chain N residue 931 GLU Chi-restraints excluded: chain N residue 990 ASN Chi-restraints excluded: chain N residue 1018 GLU Chi-restraints excluded: chain N residue 1036 VAL Chi-restraints excluded: chain N residue 1072 VAL Chi-restraints excluded: chain N residue 1099 CYS Chi-restraints excluded: chain N residue 1108 LEU Chi-restraints excluded: chain O residue 959 SER Chi-restraints excluded: chain O residue 1017 SER Chi-restraints excluded: chain O residue 1069 ASN Chi-restraints excluded: chain P residue 1036 VAL Chi-restraints excluded: chain P residue 1111 SER Chi-restraints excluded: chain Q residue 947 ASN Chi-restraints excluded: chain Q residue 1014 LYS Chi-restraints excluded: chain Q residue 1066 SER Chi-restraints excluded: chain R residue 963 LYS Chi-restraints excluded: chain R residue 969 GLU Chi-restraints excluded: chain R residue 990 ASN Chi-restraints excluded: chain R residue 1028 MET Chi-restraints excluded: chain R residue 1108 LEU Chi-restraints excluded: chain S residue 925 LYS Chi-restraints excluded: chain T residue 947 ASN Chi-restraints excluded: chain T residue 969 GLU Chi-restraints excluded: chain T residue 1036 VAL Chi-restraints excluded: chain T residue 1111 SER Chi-restraints excluded: chain U residue 910 LYS Chi-restraints excluded: chain U residue 971 GLU Chi-restraints excluded: chain U residue 1003 LYS Chi-restraints excluded: chain U residue 1014 LYS Chi-restraints excluded: chain U residue 1042 LYS Chi-restraints excluded: chain U residue 1072 VAL Chi-restraints excluded: chain U residue 1108 LEU Chi-restraints excluded: chain U residue 1115 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 128 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 395 optimal weight: 3.9990 chunk 225 optimal weight: 8.9990 chunk 356 optimal weight: 5.9990 chunk 510 optimal weight: 0.6980 chunk 172 optimal weight: 5.9990 chunk 275 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 396 optimal weight: 2.9990 chunk 320 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 947 ASN C 941 ASN E 941 ASN E 947 ASN H 937 GLN H1109 GLN I1069 ASN I1070 GLN I1109 GLN J 941 ASN ** J1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 941 ASN N 947 ASN O 941 ASN P 947 ASN U 941 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.148597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.108766 restraints weight = 38550.812| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.55 r_work: 0.3197 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.227 46400 Z= 0.201 Angle : 0.557 10.550 62480 Z= 0.305 Chirality : 0.045 0.141 6460 Planarity : 0.004 0.042 8080 Dihedral : 5.635 58.083 6417 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.87 % Allowed : 12.22 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.11), residues: 5640 helix: 0.71 (0.11), residues: 2080 sheet: -0.19 (0.14), residues: 1260 loop : -0.21 (0.13), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 896 TYR 0.019 0.002 TYR S 920 PHE 0.017 0.002 PHE D 881 TRP 0.014 0.003 TRP P1006 HIS 0.014 0.001 HIS R1084 Details of bonding type rmsd covalent geometry : bond 0.00445 (46320) covalent geometry : angle 0.54126 (62420) hydrogen bonds : bond 0.06051 ( 1944) hydrogen bonds : angle 4.84796 ( 5298) metal coordination : bond 0.05396 ( 80) metal coordination : angle 4.26061 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 743 time to evaluate : 2.287 Fit side-chains REVERT: A 896 ARG cc_start: 0.8348 (mtp85) cc_final: 0.7686 (mtm110) REVERT: A 1115 MET cc_start: 0.8439 (ptp) cc_final: 0.8209 (ptm) REVERT: B 896 ARG cc_start: 0.8465 (mtp85) cc_final: 0.7690 (mtm110) REVERT: B 959 SER cc_start: 0.8755 (t) cc_final: 0.8507 (m) REVERT: B 969 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: B 971 GLU cc_start: 0.7812 (tp30) cc_final: 0.7523 (tp30) REVERT: B 1037 ASN cc_start: 0.8166 (t0) cc_final: 0.7708 (m-40) REVERT: B 1128 ARG cc_start: 0.8036 (mmt-90) cc_final: 0.7661 (mmt-90) REVERT: C 910 LYS cc_start: 0.8596 (ttpt) cc_final: 0.8354 (ttpp) REVERT: C 969 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8346 (tt0) REVERT: C 1042 LYS cc_start: 0.8726 (mmtm) cc_final: 0.8419 (mtmt) REVERT: C 1114 LYS cc_start: 0.8650 (mmmm) cc_final: 0.8327 (mmtm) REVERT: D 896 ARG cc_start: 0.8233 (mtp85) cc_final: 0.7285 (mtm-85) REVERT: D 969 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: D 1114 LYS cc_start: 0.8347 (mmmt) cc_final: 0.7961 (mmtm) REVERT: E 910 LYS cc_start: 0.8618 (ttpp) cc_final: 0.8207 (tttm) REVERT: E 931 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7934 (tm-30) REVERT: F 888 GLU cc_start: 0.7702 (mp0) cc_final: 0.7425 (pm20) REVERT: F 931 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: F 991 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7986 (ptp-170) REVERT: F 1004 LYS cc_start: 0.8502 (mtpp) cc_final: 0.8132 (mptm) REVERT: F 1014 LYS cc_start: 0.8272 (mttp) cc_final: 0.7771 (tmmt) REVERT: G 932 ARG cc_start: 0.7893 (mtm-85) cc_final: 0.7591 (mtm-85) REVERT: G 971 GLU cc_start: 0.8404 (tp30) cc_final: 0.8013 (tp30) REVERT: G 1004 LYS cc_start: 0.8315 (mtpp) cc_final: 0.7958 (tptp) REVERT: G 1042 LYS cc_start: 0.8532 (mmtm) cc_final: 0.8102 (mppt) REVERT: G 1087 ARG cc_start: 0.7857 (mtt90) cc_final: 0.7556 (mtm-85) REVERT: H 888 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: H 896 ARG cc_start: 0.8063 (mtp85) cc_final: 0.7094 (mtm180) REVERT: H 910 LYS cc_start: 0.8328 (ttpp) cc_final: 0.7964 (ttpp) REVERT: H 988 ILE cc_start: 0.8789 (mm) cc_final: 0.8548 (mp) REVERT: H 1004 LYS cc_start: 0.8430 (mtpp) cc_final: 0.7908 (ttpp) REVERT: H 1042 LYS cc_start: 0.8310 (mmtm) cc_final: 0.8058 (mttp) REVERT: H 1054 MET cc_start: 0.8074 (ttp) cc_final: 0.7867 (ttt) REVERT: H 1113 MET cc_start: 0.8138 (ptm) cc_final: 0.7774 (ptt) REVERT: I 947 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7655 (m-40) REVERT: I 988 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7595 (mm) REVERT: I 990 ASN cc_start: 0.8246 (m-40) cc_final: 0.7628 (p0) REVERT: I 1037 ASN cc_start: 0.7358 (t0) cc_final: 0.7097 (m-40) REVERT: I 1042 LYS cc_start: 0.8379 (mmtm) cc_final: 0.8090 (mppt) REVERT: J 931 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7412 (tp30) REVERT: J 969 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6571 (tm-30) REVERT: J 977 ARG cc_start: 0.6424 (OUTLIER) cc_final: 0.5851 (mmt90) REVERT: J 1004 LYS cc_start: 0.7806 (mtpp) cc_final: 0.7004 (mtmm) REVERT: J 1020 ASN cc_start: 0.7429 (t0) cc_final: 0.6899 (t0) REVERT: J 1087 ARG cc_start: 0.8178 (mtm-85) cc_final: 0.7822 (mtm-85) REVERT: L 896 ARG cc_start: 0.7392 (mtt-85) cc_final: 0.6691 (mtm180) REVERT: L 1004 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7270 (tptp) REVERT: L 1014 LYS cc_start: 0.7452 (mttp) cc_final: 0.6734 (tmmt) REVERT: L 1018 GLU cc_start: 0.7301 (tp30) cc_final: 0.6979 (tp30) REVERT: M 896 ARG cc_start: 0.8219 (mtt-85) cc_final: 0.7502 (mtm110) REVERT: M 910 LYS cc_start: 0.8358 (ttpp) cc_final: 0.7828 (tttm) REVERT: M 911 GLU cc_start: 0.8640 (mp0) cc_final: 0.8228 (mp0) REVERT: M 925 LYS cc_start: 0.8509 (mtpp) cc_final: 0.8267 (mtpt) REVERT: M 947 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7183 (m-40) REVERT: M 1063 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7566 (pt0) REVERT: M 1158 MET cc_start: 0.6409 (mtm) cc_final: 0.6109 (mtp) REVERT: N 896 ARG cc_start: 0.8536 (mtt-85) cc_final: 0.7648 (mtm110) REVERT: N 991 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7452 (mtp-110) REVERT: N 1004 LYS cc_start: 0.8281 (ttpp) cc_final: 0.8033 (tmmt) REVERT: N 1111 SER cc_start: 0.8565 (m) cc_final: 0.8268 (p) REVERT: N 1158 MET cc_start: 0.6521 (mtm) cc_final: 0.6300 (mtm) REVERT: O 888 GLU cc_start: 0.7893 (mp0) cc_final: 0.7604 (mp0) REVERT: O 991 ARG cc_start: 0.8022 (mtp85) cc_final: 0.7547 (ttt90) REVERT: O 1004 LYS cc_start: 0.8498 (ttpp) cc_final: 0.8157 (ttpp) REVERT: O 1054 MET cc_start: 0.8718 (ttp) cc_final: 0.8512 (ttt) REVERT: P 969 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7617 (tt0) REVERT: P 1114 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8168 (mptt) REVERT: P 1128 ARG cc_start: 0.8132 (mmt90) cc_final: 0.7650 (mmp80) REVERT: Q 947 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7934 (t0) REVERT: Q 1014 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7832 (tptp) REVERT: Q 1114 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8346 (mptt) REVERT: R 963 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8170 (pttp) REVERT: R 969 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7983 (tm-30) REVERT: R 1111 SER cc_start: 0.9000 (m) cc_final: 0.8755 (p) REVERT: R 1128 ARG cc_start: 0.7703 (mmt90) cc_final: 0.7488 (mmt-90) REVERT: S 883 ARG cc_start: 0.8693 (ttm170) cc_final: 0.8484 (ttm110) REVERT: S 910 LYS cc_start: 0.8629 (ttpp) cc_final: 0.8310 (tttm) REVERT: S 925 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8697 (mttt) REVERT: S 941 ASN cc_start: 0.8055 (m110) cc_final: 0.7695 (m110) REVERT: T 910 LYS cc_start: 0.8563 (ttpp) cc_final: 0.8263 (tttm) REVERT: T 969 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8040 (tt0) REVERT: T 1014 LYS cc_start: 0.8150 (mttp) cc_final: 0.7655 (tmmt) REVERT: T 1037 ASN cc_start: 0.7392 (m110) cc_final: 0.7091 (t0) REVERT: T 1113 MET cc_start: 0.8097 (ttp) cc_final: 0.7705 (ttp) REVERT: U 947 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.7988 (m110) REVERT: U 971 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.6889 (tm-30) REVERT: U 991 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7898 (mtp85) REVERT: U 1003 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8577 (tptp) REVERT: U 1014 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7746 (ttmm) REVERT: U 1018 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7061 (mt-10) REVERT: U 1107 PHE cc_start: 0.8257 (t80) cc_final: 0.7937 (t80) REVERT: U 1115 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7720 (ptm) outliers start: 132 outliers final: 64 residues processed: 804 average time/residue: 0.6028 time to fit residues: 586.7471 Evaluate side-chains 830 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 741 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 972 MET Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1126 THR Chi-restraints excluded: chain B residue 910 LYS Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 996 LYS Chi-restraints excluded: chain C residue 1066 SER Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 990 ASN Chi-restraints excluded: chain D residue 1113 MET Chi-restraints excluded: chain D residue 1126 THR Chi-restraints excluded: chain F residue 931 GLU Chi-restraints excluded: chain F residue 991 ARG Chi-restraints excluded: chain F residue 1022 ASN Chi-restraints excluded: chain G residue 944 LEU Chi-restraints excluded: chain G residue 1014 LYS Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain G residue 1072 VAL Chi-restraints excluded: chain G residue 1108 LEU Chi-restraints excluded: chain G residue 1126 THR Chi-restraints excluded: chain H residue 888 GLU Chi-restraints excluded: chain H residue 972 MET Chi-restraints excluded: chain H residue 1017 SER Chi-restraints excluded: chain H residue 1036 VAL Chi-restraints excluded: chain H residue 1126 THR Chi-restraints excluded: chain I residue 932 ARG Chi-restraints excluded: chain I residue 947 ASN Chi-restraints excluded: chain I residue 988 ILE Chi-restraints excluded: chain I residue 1036 VAL Chi-restraints excluded: chain I residue 1054 MET Chi-restraints excluded: chain I residue 1098 PHE Chi-restraints excluded: chain I residue 1115 MET Chi-restraints excluded: chain J residue 931 GLU Chi-restraints excluded: chain J residue 969 GLU Chi-restraints excluded: chain J residue 977 ARG Chi-restraints excluded: chain J residue 1098 PHE Chi-restraints excluded: chain J residue 1102 THR Chi-restraints excluded: chain J residue 1118 SER Chi-restraints excluded: chain L residue 878 ILE Chi-restraints excluded: chain L residue 1036 VAL Chi-restraints excluded: chain M residue 882 VAL Chi-restraints excluded: chain M residue 947 ASN Chi-restraints excluded: chain M residue 967 SER Chi-restraints excluded: chain M residue 969 GLU Chi-restraints excluded: chain M residue 1036 VAL Chi-restraints excluded: chain M residue 1063 GLU Chi-restraints excluded: chain M residue 1098 PHE Chi-restraints excluded: chain M residue 1111 SER Chi-restraints excluded: chain N residue 878 ILE Chi-restraints excluded: chain N residue 931 GLU Chi-restraints excluded: chain N residue 990 ASN Chi-restraints excluded: chain N residue 1018 GLU Chi-restraints excluded: chain N residue 1036 VAL Chi-restraints excluded: chain N residue 1099 CYS Chi-restraints excluded: chain N residue 1108 LEU Chi-restraints excluded: chain O residue 959 SER Chi-restraints excluded: chain O residue 1017 SER Chi-restraints excluded: chain O residue 1069 ASN Chi-restraints excluded: chain P residue 969 GLU Chi-restraints excluded: chain P residue 1036 VAL Chi-restraints excluded: chain P residue 1111 SER Chi-restraints excluded: chain Q residue 947 ASN Chi-restraints excluded: chain Q residue 1014 LYS Chi-restraints excluded: chain Q residue 1066 SER Chi-restraints excluded: chain R residue 963 LYS Chi-restraints excluded: chain R residue 969 GLU Chi-restraints excluded: chain R residue 990 ASN Chi-restraints excluded: chain R residue 1018 GLU Chi-restraints excluded: chain R residue 1028 MET Chi-restraints excluded: chain R residue 1108 LEU Chi-restraints excluded: chain S residue 925 LYS Chi-restraints excluded: chain T residue 947 ASN Chi-restraints excluded: chain T residue 969 GLU Chi-restraints excluded: chain T residue 1036 VAL Chi-restraints excluded: chain T residue 1111 SER Chi-restraints excluded: chain U residue 910 LYS Chi-restraints excluded: chain U residue 947 ASN Chi-restraints excluded: chain U residue 971 GLU Chi-restraints excluded: chain U residue 1003 LYS Chi-restraints excluded: chain U residue 1014 LYS Chi-restraints excluded: chain U residue 1072 VAL Chi-restraints excluded: chain U residue 1108 LEU Chi-restraints excluded: chain U residue 1115 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 344 optimal weight: 3.9990 chunk 420 optimal weight: 6.9990 chunk 122 optimal weight: 0.5980 chunk 303 optimal weight: 6.9990 chunk 310 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 407 optimal weight: 5.9990 chunk 144 optimal weight: 0.6980 chunk 532 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 947 ASN B1048 HIS C 889 HIS C 941 ASN E 941 ASN E 947 ASN F1109 GLN H 937 GLN H1109 GLN I1069 ASN I1109 GLN J 889 HIS J 941 ASN ** J1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 941 ASN M 941 ASN N 947 ASN O 941 ASN P 947 ASN R 941 ASN U 941 ASN U1109 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.151624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.112160 restraints weight = 38884.644| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.56 r_work: 0.3243 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.221 46400 Z= 0.108 Angle : 0.462 10.533 62480 Z= 0.253 Chirality : 0.041 0.168 6460 Planarity : 0.003 0.044 8080 Dihedral : 5.188 56.816 6417 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.22 % Allowed : 13.13 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.11), residues: 5640 helix: 1.05 (0.12), residues: 2080 sheet: 0.04 (0.15), residues: 1160 loop : -0.17 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J1128 TYR 0.014 0.001 TYR R 920 PHE 0.015 0.001 PHE D 881 TRP 0.008 0.001 TRP B1006 HIS 0.017 0.001 HIS F1084 Details of bonding type rmsd covalent geometry : bond 0.00207 (46320) covalent geometry : angle 0.44410 (62420) hydrogen bonds : bond 0.04578 ( 1944) hydrogen bonds : angle 4.51912 ( 5298) metal coordination : bond 0.04826 ( 80) metal coordination : angle 4.17147 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 756 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 896 ARG cc_start: 0.8311 (mtp85) cc_final: 0.7687 (mtm110) REVERT: A 1128 ARG cc_start: 0.7241 (mmm160) cc_final: 0.6804 (mmt180) REVERT: B 896 ARG cc_start: 0.8455 (mtp85) cc_final: 0.7684 (mtm110) REVERT: B 959 SER cc_start: 0.8732 (t) cc_final: 0.8496 (m) REVERT: B 969 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: B 971 GLU cc_start: 0.7738 (tp30) cc_final: 0.7406 (tp30) REVERT: B 1037 ASN cc_start: 0.7992 (t0) cc_final: 0.7573 (m-40) REVERT: C 969 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: C 1042 LYS cc_start: 0.8681 (mmtm) cc_final: 0.8388 (mtmt) REVERT: C 1114 LYS cc_start: 0.8648 (mmmm) cc_final: 0.8321 (mmtm) REVERT: D 896 ARG cc_start: 0.8180 (mtp85) cc_final: 0.7287 (mtm-85) REVERT: D 969 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8217 (tm-30) REVERT: D 972 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8391 (tpt) REVERT: D 1114 LYS cc_start: 0.8299 (mmmt) cc_final: 0.7901 (mmtm) REVERT: E 910 LYS cc_start: 0.8556 (ttpp) cc_final: 0.8150 (tttm) REVERT: F 931 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: F 969 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: F 1004 LYS cc_start: 0.8454 (mtpp) cc_final: 0.8106 (mptm) REVERT: F 1014 LYS cc_start: 0.8258 (mttp) cc_final: 0.7769 (tmmt) REVERT: F 1019 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7892 (mt-10) REVERT: G 932 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7494 (mtm-85) REVERT: G 971 GLU cc_start: 0.8397 (tp30) cc_final: 0.8064 (tp30) REVERT: G 1004 LYS cc_start: 0.8283 (mtpp) cc_final: 0.7891 (tptp) REVERT: G 1042 LYS cc_start: 0.8445 (mmtm) cc_final: 0.8000 (mppt) REVERT: G 1087 ARG cc_start: 0.7784 (mtt90) cc_final: 0.7541 (mtm-85) REVERT: H 888 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8054 (tm-30) REVERT: H 896 ARG cc_start: 0.8031 (mtp85) cc_final: 0.7141 (mtm180) REVERT: H 910 LYS cc_start: 0.8283 (ttpp) cc_final: 0.7898 (ttpp) REVERT: H 988 ILE cc_start: 0.8777 (mm) cc_final: 0.8535 (mp) REVERT: H 1004 LYS cc_start: 0.8368 (mtpp) cc_final: 0.7817 (ttpp) REVERT: H 1042 LYS cc_start: 0.8245 (mmtm) cc_final: 0.8006 (mttt) REVERT: H 1054 MET cc_start: 0.7997 (ttp) cc_final: 0.7794 (ttt) REVERT: H 1113 MET cc_start: 0.8050 (ptm) cc_final: 0.7735 (ptt) REVERT: I 947 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7603 (m-40) REVERT: I 988 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7572 (mm) REVERT: I 990 ASN cc_start: 0.8215 (m-40) cc_final: 0.7608 (p0) REVERT: I 993 ASN cc_start: 0.8339 (t0) cc_final: 0.8004 (t0) REVERT: I 1042 LYS cc_start: 0.8316 (mmtm) cc_final: 0.8013 (mppt) REVERT: J 891 MET cc_start: 0.8316 (mmm) cc_final: 0.7992 (tpt) REVERT: J 977 ARG cc_start: 0.6351 (OUTLIER) cc_final: 0.5794 (mmt90) REVERT: J 1020 ASN cc_start: 0.7283 (t0) cc_final: 0.6747 (t0) REVERT: J 1087 ARG cc_start: 0.8129 (mtm-85) cc_final: 0.7660 (mtm-85) REVERT: L 896 ARG cc_start: 0.7327 (mtt-85) cc_final: 0.6579 (mtm110) REVERT: L 1004 LYS cc_start: 0.8087 (ttpp) cc_final: 0.7139 (tptp) REVERT: L 1014 LYS cc_start: 0.7259 (mttp) cc_final: 0.6642 (tmmt) REVERT: L 1018 GLU cc_start: 0.7133 (tp30) cc_final: 0.6837 (tp30) REVERT: L 1036 VAL cc_start: 0.8353 (OUTLIER) cc_final: 0.8042 (p) REVERT: M 896 ARG cc_start: 0.8170 (mtt-85) cc_final: 0.7464 (mtm110) REVERT: M 910 LYS cc_start: 0.8325 (ttpp) cc_final: 0.7768 (tttm) REVERT: M 911 GLU cc_start: 0.8585 (mp0) cc_final: 0.8165 (mp0) REVERT: M 925 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8233 (mtpt) REVERT: M 991 ARG cc_start: 0.7781 (mtp85) cc_final: 0.7264 (mtp-110) REVERT: M 1158 MET cc_start: 0.6373 (mtm) cc_final: 0.6074 (mtp) REVERT: N 991 ARG cc_start: 0.7787 (mtp85) cc_final: 0.7479 (mtp-110) REVERT: N 1003 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8330 (tptp) REVERT: N 1004 LYS cc_start: 0.8085 (ttpp) cc_final: 0.7794 (tmmt) REVERT: N 1111 SER cc_start: 0.8563 (m) cc_final: 0.8310 (p) REVERT: N 1158 MET cc_start: 0.6184 (mtm) cc_final: 0.5965 (mtm) REVERT: O 991 ARG cc_start: 0.8037 (mtp85) cc_final: 0.7549 (ttt90) REVERT: O 1004 LYS cc_start: 0.8394 (ttpp) cc_final: 0.8028 (ttpp) REVERT: P 920 TYR cc_start: 0.8806 (t80) cc_final: 0.8465 (t80) REVERT: P 991 ARG cc_start: 0.7866 (mtp-110) cc_final: 0.7522 (mtp-110) REVERT: P 1114 LYS cc_start: 0.8579 (mmtt) cc_final: 0.8128 (mptt) REVERT: P 1128 ARG cc_start: 0.8170 (mmt90) cc_final: 0.7702 (mmp80) REVERT: Q 1042 LYS cc_start: 0.8596 (mmtm) cc_final: 0.8305 (mtmt) REVERT: Q 1114 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8325 (mptt) REVERT: R 963 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8162 (pttp) REVERT: R 969 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7999 (tm-30) REVERT: S 883 ARG cc_start: 0.8694 (ttm170) cc_final: 0.8474 (ttm110) REVERT: S 910 LYS cc_start: 0.8561 (ttpp) cc_final: 0.8268 (tttm) REVERT: S 1108 LEU cc_start: 0.8221 (mm) cc_final: 0.8016 (tp) REVERT: T 910 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8189 (tttm) REVERT: T 969 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: T 991 ARG cc_start: 0.8186 (mtm180) cc_final: 0.7931 (mtp-110) REVERT: T 1014 LYS cc_start: 0.8112 (mttp) cc_final: 0.7637 (tmmt) REVERT: T 1037 ASN cc_start: 0.7253 (m110) cc_final: 0.6929 (t0) REVERT: T 1113 MET cc_start: 0.7999 (ttp) cc_final: 0.7350 (tpt) REVERT: U 943 TYR cc_start: 0.7945 (t80) cc_final: 0.7546 (t80) REVERT: U 947 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.7939 (m110) REVERT: U 991 ARG cc_start: 0.8105 (mtp85) cc_final: 0.7835 (mtp85) REVERT: U 1018 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7111 (mt-10) REVERT: U 1107 PHE cc_start: 0.8254 (t80) cc_final: 0.7918 (t80) outliers start: 102 outliers final: 34 residues processed: 806 average time/residue: 0.5348 time to fit residues: 525.4773 Evaluate side-chains 788 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 738 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 972 MET Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 1113 MET Chi-restraints excluded: chain D residue 1126 THR Chi-restraints excluded: chain F residue 931 GLU Chi-restraints excluded: chain F residue 969 GLU Chi-restraints excluded: chain G residue 944 LEU Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain G residue 1126 THR Chi-restraints excluded: chain H residue 888 GLU Chi-restraints excluded: chain H residue 972 MET Chi-restraints excluded: chain H residue 1017 SER Chi-restraints excluded: chain H residue 1036 VAL Chi-restraints excluded: chain H residue 1126 THR Chi-restraints excluded: chain I residue 947 ASN Chi-restraints excluded: chain I residue 988 ILE Chi-restraints excluded: chain I residue 1054 MET Chi-restraints excluded: chain I residue 1098 PHE Chi-restraints excluded: chain I residue 1118 SER Chi-restraints excluded: chain J residue 977 ARG Chi-restraints excluded: chain J residue 1098 PHE Chi-restraints excluded: chain J residue 1102 THR Chi-restraints excluded: chain L residue 878 ILE Chi-restraints excluded: chain L residue 1036 VAL Chi-restraints excluded: chain M residue 969 GLU Chi-restraints excluded: chain M residue 1036 VAL Chi-restraints excluded: chain M residue 1098 PHE Chi-restraints excluded: chain M residue 1111 SER Chi-restraints excluded: chain N residue 878 ILE Chi-restraints excluded: chain N residue 931 GLU Chi-restraints excluded: chain N residue 990 ASN Chi-restraints excluded: chain N residue 1003 LYS Chi-restraints excluded: chain N residue 1036 VAL Chi-restraints excluded: chain N residue 1072 VAL Chi-restraints excluded: chain N residue 1099 CYS Chi-restraints excluded: chain O residue 959 SER Chi-restraints excluded: chain O residue 1069 ASN Chi-restraints excluded: chain P residue 1036 VAL Chi-restraints excluded: chain R residue 963 LYS Chi-restraints excluded: chain R residue 969 GLU Chi-restraints excluded: chain R residue 990 ASN Chi-restraints excluded: chain T residue 969 GLU Chi-restraints excluded: chain U residue 947 ASN Chi-restraints excluded: chain U residue 1036 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 511 optimal weight: 0.9990 chunk 218 optimal weight: 9.9990 chunk 504 optimal weight: 8.9990 chunk 318 optimal weight: 0.0030 chunk 157 optimal weight: 0.4980 chunk 120 optimal weight: 2.9990 chunk 493 optimal weight: 7.9990 chunk 413 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 540 optimal weight: 7.9990 chunk 254 optimal weight: 6.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 947 ASN C 941 ASN C 947 ASN D 941 ASN E 941 ASN E 947 ASN H 937 GLN H 941 ASN H1109 GLN I1069 ASN I1109 GLN I1146 GLN J 941 ASN ** J1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 941 ASN O 941 ASN P 947 ASN ** S 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 947 ASN U 941 ASN U1109 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.152514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.113113 restraints weight = 38876.012| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.56 r_work: 0.3259 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.248 46400 Z= 0.105 Angle : 0.451 10.462 62480 Z= 0.245 Chirality : 0.041 0.165 6460 Planarity : 0.003 0.044 8080 Dihedral : 4.928 56.557 6411 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.93 % Allowed : 13.87 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.11), residues: 5640 helix: 1.22 (0.12), residues: 2080 sheet: 0.06 (0.15), residues: 1160 loop : -0.09 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J1128 TYR 0.015 0.001 TYR R 920 PHE 0.015 0.001 PHE D 881 TRP 0.008 0.001 TRP B1006 HIS 0.016 0.001 HIS R1084 Details of bonding type rmsd covalent geometry : bond 0.00196 (46320) covalent geometry : angle 0.43125 (62420) hydrogen bonds : bond 0.04326 ( 1944) hydrogen bonds : angle 4.37215 ( 5298) metal coordination : bond 0.05546 ( 80) metal coordination : angle 4.22907 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 763 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 896 ARG cc_start: 0.8302 (mtp85) cc_final: 0.7671 (mtm110) REVERT: A 1128 ARG cc_start: 0.7171 (mmm160) cc_final: 0.6716 (mmt180) REVERT: B 896 ARG cc_start: 0.8449 (mtp85) cc_final: 0.7662 (mtm110) REVERT: B 959 SER cc_start: 0.8739 (t) cc_final: 0.8505 (m) REVERT: B 971 GLU cc_start: 0.7718 (tp30) cc_final: 0.7420 (tp30) REVERT: B 972 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7358 (tpt) REVERT: B 1037 ASN cc_start: 0.7950 (t0) cc_final: 0.7570 (m-40) REVERT: C 969 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: C 1042 LYS cc_start: 0.8675 (mmtm) cc_final: 0.8389 (mtmt) REVERT: C 1114 LYS cc_start: 0.8641 (mmmm) cc_final: 0.8310 (mmtm) REVERT: D 896 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7401 (mtp180) REVERT: D 969 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8211 (tm-30) REVERT: D 972 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8391 (tpt) REVERT: E 910 LYS cc_start: 0.8544 (ttpp) cc_final: 0.8134 (tttm) REVERT: F 931 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7660 (tm-30) REVERT: F 1004 LYS cc_start: 0.8439 (mtpp) cc_final: 0.8104 (mptm) REVERT: F 1014 LYS cc_start: 0.8205 (mttp) cc_final: 0.7767 (tmmt) REVERT: F 1019 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7890 (mt-10) REVERT: F 1114 LYS cc_start: 0.8640 (mmtp) cc_final: 0.8400 (mptm) REVERT: G 932 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.7467 (mtm-85) REVERT: G 971 GLU cc_start: 0.8384 (tp30) cc_final: 0.8094 (tp30) REVERT: G 1004 LYS cc_start: 0.8282 (mtpp) cc_final: 0.7882 (tptp) REVERT: G 1042 LYS cc_start: 0.8413 (mmtm) cc_final: 0.7979 (mppt) REVERT: G 1087 ARG cc_start: 0.7761 (mtt90) cc_final: 0.7534 (mtm-85) REVERT: H 888 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8070 (tm-30) REVERT: H 896 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7173 (mtm180) REVERT: H 910 LYS cc_start: 0.8272 (ttpp) cc_final: 0.7888 (ttpp) REVERT: H 988 ILE cc_start: 0.8785 (mm) cc_final: 0.8549 (mp) REVERT: H 1004 LYS cc_start: 0.8365 (mtpp) cc_final: 0.7798 (ttpp) REVERT: H 1054 MET cc_start: 0.7976 (ttp) cc_final: 0.7772 (ttt) REVERT: H 1113 MET cc_start: 0.7924 (ptm) cc_final: 0.7665 (ptt) REVERT: I 947 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7621 (m110) REVERT: I 988 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7556 (mm) REVERT: I 990 ASN cc_start: 0.8215 (m-40) cc_final: 0.7984 (m-40) REVERT: I 1145 GLU cc_start: 0.8215 (pm20) cc_final: 0.7968 (pm20) REVERT: J 977 ARG cc_start: 0.6366 (OUTLIER) cc_final: 0.5796 (mmt90) REVERT: J 1020 ASN cc_start: 0.7243 (t0) cc_final: 0.6751 (t0) REVERT: J 1063 GLU cc_start: 0.7993 (pt0) cc_final: 0.7622 (pt0) REVERT: J 1087 ARG cc_start: 0.8135 (mtm-85) cc_final: 0.7671 (mtm-85) REVERT: J 1109 GLN cc_start: 0.6470 (tp40) cc_final: 0.6179 (tp40) REVERT: L 896 ARG cc_start: 0.7329 (mtt-85) cc_final: 0.6687 (mtm110) REVERT: L 1004 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7118 (tptp) REVERT: L 1014 LYS cc_start: 0.7217 (mttp) cc_final: 0.6587 (tmmt) REVERT: L 1018 GLU cc_start: 0.7091 (tp30) cc_final: 0.6854 (tp30) REVERT: M 896 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.7430 (mtm110) REVERT: M 910 LYS cc_start: 0.8295 (ttpp) cc_final: 0.7776 (tttm) REVERT: M 911 GLU cc_start: 0.8606 (mp0) cc_final: 0.8263 (mp0) REVERT: M 925 LYS cc_start: 0.8466 (mtpp) cc_final: 0.8233 (mtpt) REVERT: M 991 ARG cc_start: 0.7759 (mtp85) cc_final: 0.7230 (mtp-110) REVERT: M 1158 MET cc_start: 0.6386 (mtm) cc_final: 0.6067 (mtp) REVERT: N 1004 LYS cc_start: 0.8078 (ttpp) cc_final: 0.7785 (tmmt) REVERT: N 1111 SER cc_start: 0.8550 (m) cc_final: 0.8332 (p) REVERT: N 1158 MET cc_start: 0.6229 (mtm) cc_final: 0.6010 (mtm) REVERT: O 991 ARG cc_start: 0.7974 (mtp85) cc_final: 0.7547 (ttt90) REVERT: O 1004 LYS cc_start: 0.8338 (ttpp) cc_final: 0.7973 (ttpp) REVERT: P 920 TYR cc_start: 0.8810 (t80) cc_final: 0.8507 (t80) REVERT: P 969 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: P 991 ARG cc_start: 0.7858 (mtp-110) cc_final: 0.7492 (mtp-110) REVERT: P 1114 LYS cc_start: 0.8556 (mmtt) cc_final: 0.8104 (mptt) REVERT: P 1128 ARG cc_start: 0.8174 (mmt90) cc_final: 0.7622 (mmt180) REVERT: Q 991 ARG cc_start: 0.8037 (mtm180) cc_final: 0.7821 (mtp85) REVERT: Q 1042 LYS cc_start: 0.8581 (mmtm) cc_final: 0.8312 (mtmt) REVERT: Q 1114 LYS cc_start: 0.8625 (mmtt) cc_final: 0.8343 (mptt) REVERT: Q 1115 MET cc_start: 0.8822 (ptp) cc_final: 0.8537 (ptp) REVERT: R 878 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.7983 (tp) REVERT: R 969 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: R 1014 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8096 (tptp) REVERT: S 910 LYS cc_start: 0.8567 (ttpp) cc_final: 0.8272 (tttm) REVERT: S 1108 LEU cc_start: 0.8144 (mm) cc_final: 0.7939 (tp) REVERT: T 910 LYS cc_start: 0.8470 (ttpp) cc_final: 0.8169 (tttm) REVERT: T 969 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: T 991 ARG cc_start: 0.8161 (mtm180) cc_final: 0.7860 (mtp-110) REVERT: T 1014 LYS cc_start: 0.8082 (mttp) cc_final: 0.7644 (tmmt) REVERT: T 1037 ASN cc_start: 0.7254 (m110) cc_final: 0.6933 (t0) REVERT: T 1113 MET cc_start: 0.8039 (ttp) cc_final: 0.7582 (ttp) REVERT: T 1156 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7628 (mt0) REVERT: U 943 TYR cc_start: 0.7941 (t80) cc_final: 0.7717 (t80) REVERT: U 991 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7792 (mtp85) REVERT: U 1003 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8637 (tptp) REVERT: U 1018 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7024 (mt-10) REVERT: U 1107 PHE cc_start: 0.8210 (t80) cc_final: 0.8004 (t80) outliers start: 89 outliers final: 41 residues processed: 802 average time/residue: 0.4864 time to fit residues: 474.4076 Evaluate side-chains 803 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 746 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 972 MET Chi-restraints excluded: chain B residue 972 MET Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain C residue 947 ASN Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 1113 MET Chi-restraints excluded: chain D residue 1126 THR Chi-restraints excluded: chain F residue 931 GLU Chi-restraints excluded: chain F residue 957 ASP Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain G residue 1126 THR Chi-restraints excluded: chain G residue 1146 GLN Chi-restraints excluded: chain H residue 888 GLU Chi-restraints excluded: chain H residue 972 MET Chi-restraints excluded: chain H residue 1036 VAL Chi-restraints excluded: chain I residue 947 ASN Chi-restraints excluded: chain I residue 988 ILE Chi-restraints excluded: chain I residue 1054 MET Chi-restraints excluded: chain I residue 1098 PHE Chi-restraints excluded: chain J residue 977 ARG Chi-restraints excluded: chain J residue 1098 PHE Chi-restraints excluded: chain J residue 1102 THR Chi-restraints excluded: chain L residue 878 ILE Chi-restraints excluded: chain L residue 1036 VAL Chi-restraints excluded: chain M residue 882 VAL Chi-restraints excluded: chain M residue 969 GLU Chi-restraints excluded: chain M residue 1036 VAL Chi-restraints excluded: chain M residue 1098 PHE Chi-restraints excluded: chain M residue 1111 SER Chi-restraints excluded: chain M residue 1138 GLU Chi-restraints excluded: chain N residue 878 ILE Chi-restraints excluded: chain N residue 931 GLU Chi-restraints excluded: chain N residue 990 ASN Chi-restraints excluded: chain N residue 1099 CYS Chi-restraints excluded: chain O residue 959 SER Chi-restraints excluded: chain O residue 1069 ASN Chi-restraints excluded: chain P residue 969 GLU Chi-restraints excluded: chain P residue 1036 VAL Chi-restraints excluded: chain R residue 878 ILE Chi-restraints excluded: chain R residue 969 GLU Chi-restraints excluded: chain R residue 990 ASN Chi-restraints excluded: chain R residue 1014 LYS Chi-restraints excluded: chain R residue 1099 CYS Chi-restraints excluded: chain R residue 1158 MET Chi-restraints excluded: chain S residue 1113 MET Chi-restraints excluded: chain T residue 882 VAL Chi-restraints excluded: chain T residue 969 GLU Chi-restraints excluded: chain T residue 1036 VAL Chi-restraints excluded: chain T residue 1115 MET Chi-restraints excluded: chain T residue 1156 GLN Chi-restraints excluded: chain U residue 947 ASN Chi-restraints excluded: chain U residue 1003 LYS Chi-restraints excluded: chain U residue 1036 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 276 optimal weight: 0.0570 chunk 406 optimal weight: 0.9990 chunk 365 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 493 optimal weight: 8.9990 chunk 548 optimal weight: 0.8980 chunk 439 optimal weight: 3.9990 chunk 441 optimal weight: 0.8980 chunk 24 optimal weight: 0.0980 chunk 55 optimal weight: 5.9990 chunk 429 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 947 ASN C 941 ASN C 947 ASN E 941 ASN E 947 ASN F 990 ASN H 937 GLN H 941 ASN H1109 GLN I 966 GLN I1109 GLN J 941 ASN J1069 ASN ** J1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 941 ASN O 941 ASN P 947 ASN S 941 ASN S 947 ASN U 941 ASN U1109 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.153813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.114496 restraints weight = 39287.855| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.57 r_work: 0.3278 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.272 46400 Z= 0.099 Angle : 0.452 11.944 62480 Z= 0.239 Chirality : 0.040 0.165 6460 Planarity : 0.003 0.037 8080 Dihedral : 4.760 56.203 6410 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.70 % Allowed : 14.72 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.11), residues: 5640 helix: 1.34 (0.12), residues: 2080 sheet: 0.22 (0.15), residues: 1140 loop : -0.07 (0.13), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J1128 TYR 0.015 0.001 TYR S 920 PHE 0.024 0.001 PHE J1035 TRP 0.007 0.001 TRP F1006 HIS 0.022 0.001 HIS C1084 Details of bonding type rmsd covalent geometry : bond 0.00171 (46320) covalent geometry : angle 0.42181 (62420) hydrogen bonds : bond 0.04000 ( 1944) hydrogen bonds : angle 4.26097 ( 5298) metal coordination : bond 0.06337 ( 80) metal coordination : angle 5.24895 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 763 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 896 ARG cc_start: 0.8297 (mtp85) cc_final: 0.7658 (mtm110) REVERT: A 1128 ARG cc_start: 0.7124 (mmm160) cc_final: 0.6671 (mmt180) REVERT: B 896 ARG cc_start: 0.8463 (mtp85) cc_final: 0.7712 (mtm110) REVERT: B 959 SER cc_start: 0.8714 (t) cc_final: 0.8477 (m) REVERT: B 971 GLU cc_start: 0.7705 (tp30) cc_final: 0.7435 (tp30) REVERT: B 1037 ASN cc_start: 0.7921 (t0) cc_final: 0.7561 (m-40) REVERT: C 1042 LYS cc_start: 0.8659 (mmtm) cc_final: 0.8385 (mtmt) REVERT: C 1114 LYS cc_start: 0.8626 (mmmm) cc_final: 0.8327 (mmtm) REVERT: D 896 ARG cc_start: 0.8129 (mtp85) cc_final: 0.7378 (mtp180) REVERT: D 972 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8463 (tpt) REVERT: E 910 LYS cc_start: 0.8544 (ttpp) cc_final: 0.8128 (tttm) REVERT: F 931 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: F 1004 LYS cc_start: 0.8430 (mtpp) cc_final: 0.8098 (mptm) REVERT: F 1014 LYS cc_start: 0.8197 (mttp) cc_final: 0.7778 (tmmt) REVERT: F 1019 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7885 (mt-10) REVERT: F 1114 LYS cc_start: 0.8689 (mmtp) cc_final: 0.8435 (mptm) REVERT: G 932 ARG cc_start: 0.7743 (mtm-85) cc_final: 0.7459 (mtm-85) REVERT: G 971 GLU cc_start: 0.8442 (tp30) cc_final: 0.8145 (tp30) REVERT: G 1004 LYS cc_start: 0.8304 (mtpp) cc_final: 0.7870 (tptp) REVERT: G 1087 ARG cc_start: 0.7739 (mtt90) cc_final: 0.7532 (mtm-85) REVERT: H 888 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: H 896 ARG cc_start: 0.8033 (mtp85) cc_final: 0.7157 (mtm180) REVERT: H 910 LYS cc_start: 0.8266 (ttpp) cc_final: 0.7880 (ttpp) REVERT: H 988 ILE cc_start: 0.8784 (mm) cc_final: 0.8549 (mp) REVERT: H 1004 LYS cc_start: 0.8361 (mtpp) cc_final: 0.7764 (ttpp) REVERT: H 1113 MET cc_start: 0.7795 (ptm) cc_final: 0.7577 (ptt) REVERT: I 947 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7598 (m110) REVERT: I 972 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7133 (tpt) REVERT: I 988 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7576 (mm) REVERT: I 990 ASN cc_start: 0.8210 (m-40) cc_final: 0.7973 (m-40) REVERT: I 1145 GLU cc_start: 0.8222 (pm20) cc_final: 0.7971 (pm20) REVERT: J 977 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.5804 (mmt90) REVERT: J 1020 ASN cc_start: 0.7221 (t0) cc_final: 0.6729 (t0) REVERT: J 1063 GLU cc_start: 0.7958 (pt0) cc_final: 0.7601 (pt0) REVERT: J 1087 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7664 (mtm-85) REVERT: J 1128 ARG cc_start: 0.8184 (mtp-110) cc_final: 0.7798 (ttm110) REVERT: L 896 ARG cc_start: 0.7294 (mtt-85) cc_final: 0.6641 (mtm110) REVERT: L 1004 LYS cc_start: 0.8037 (ttpp) cc_final: 0.7092 (tptp) REVERT: L 1014 LYS cc_start: 0.7165 (mttp) cc_final: 0.6582 (tmmt) REVERT: L 1018 GLU cc_start: 0.7109 (tp30) cc_final: 0.6852 (tp30) REVERT: L 1036 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8033 (p) REVERT: M 896 ARG cc_start: 0.8097 (mtt-85) cc_final: 0.7431 (mtm110) REVERT: M 910 LYS cc_start: 0.8303 (ttpp) cc_final: 0.7761 (tttm) REVERT: M 911 GLU cc_start: 0.8613 (mp0) cc_final: 0.8260 (mp0) REVERT: M 925 LYS cc_start: 0.8463 (mtpp) cc_final: 0.8231 (mtpt) REVERT: M 1158 MET cc_start: 0.6361 (mtm) cc_final: 0.6033 (mtp) REVERT: N 1004 LYS cc_start: 0.8081 (ttpp) cc_final: 0.7788 (tmmt) REVERT: N 1158 MET cc_start: 0.6256 (mtm) cc_final: 0.6056 (mtm) REVERT: O 991 ARG cc_start: 0.7961 (mtp85) cc_final: 0.7466 (mtp85) REVERT: O 1004 LYS cc_start: 0.8305 (ttpp) cc_final: 0.7909 (ttpp) REVERT: P 920 TYR cc_start: 0.8794 (t80) cc_final: 0.8563 (t80) REVERT: P 969 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: P 991 ARG cc_start: 0.7860 (mtp-110) cc_final: 0.7455 (mtp-110) REVERT: P 1014 LYS cc_start: 0.8144 (mttp) cc_final: 0.7695 (tmmt) REVERT: P 1128 ARG cc_start: 0.8159 (mmt90) cc_final: 0.7624 (mmt180) REVERT: Q 1014 LYS cc_start: 0.7993 (mtmt) cc_final: 0.7699 (tmmt) REVERT: Q 1042 LYS cc_start: 0.8554 (mmtm) cc_final: 0.8311 (mtmt) REVERT: Q 1115 MET cc_start: 0.8763 (ptp) cc_final: 0.8552 (ptp) REVERT: R 878 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.7984 (tp) REVERT: R 969 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7915 (tm-30) REVERT: R 1014 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8116 (tptp) REVERT: S 910 LYS cc_start: 0.8540 (ttpp) cc_final: 0.8244 (tttm) REVERT: T 910 LYS cc_start: 0.8463 (ttpp) cc_final: 0.8161 (tttm) REVERT: T 931 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7396 (tp30) REVERT: T 969 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: T 991 ARG cc_start: 0.8135 (mtm180) cc_final: 0.7803 (mtp-110) REVERT: T 1014 LYS cc_start: 0.7997 (mttp) cc_final: 0.7556 (tmmt) REVERT: T 1037 ASN cc_start: 0.7198 (m110) cc_final: 0.6871 (t0) REVERT: T 1113 MET cc_start: 0.7959 (ttp) cc_final: 0.7307 (ttp) REVERT: T 1156 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7548 (mt0) REVERT: U 943 TYR cc_start: 0.7934 (t80) cc_final: 0.7713 (t80) REVERT: U 991 ARG cc_start: 0.8041 (mtp85) cc_final: 0.7740 (mtp85) REVERT: U 1018 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6995 (mt-10) REVERT: U 1107 PHE cc_start: 0.8221 (t80) cc_final: 0.8012 (t80) outliers start: 78 outliers final: 37 residues processed: 796 average time/residue: 0.4768 time to fit residues: 462.1808 Evaluate side-chains 798 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 747 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 972 MET Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 1113 MET Chi-restraints excluded: chain D residue 1126 THR Chi-restraints excluded: chain F residue 931 GLU Chi-restraints excluded: chain F residue 1022 ASN Chi-restraints excluded: chain F residue 1126 THR Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain G residue 1126 THR Chi-restraints excluded: chain G residue 1146 GLN Chi-restraints excluded: chain H residue 888 GLU Chi-restraints excluded: chain H residue 1036 VAL Chi-restraints excluded: chain I residue 947 ASN Chi-restraints excluded: chain I residue 972 MET Chi-restraints excluded: chain I residue 988 ILE Chi-restraints excluded: chain I residue 1054 MET Chi-restraints excluded: chain I residue 1098 PHE Chi-restraints excluded: chain I residue 1118 SER Chi-restraints excluded: chain J residue 977 ARG Chi-restraints excluded: chain J residue 1098 PHE Chi-restraints excluded: chain J residue 1102 THR Chi-restraints excluded: chain L residue 878 ILE Chi-restraints excluded: chain L residue 1036 VAL Chi-restraints excluded: chain M residue 882 VAL Chi-restraints excluded: chain M residue 969 GLU Chi-restraints excluded: chain M residue 1098 PHE Chi-restraints excluded: chain M residue 1111 SER Chi-restraints excluded: chain M residue 1138 GLU Chi-restraints excluded: chain N residue 931 GLU Chi-restraints excluded: chain N residue 990 ASN Chi-restraints excluded: chain N residue 1099 CYS Chi-restraints excluded: chain O residue 959 SER Chi-restraints excluded: chain O residue 1069 ASN Chi-restraints excluded: chain P residue 969 GLU Chi-restraints excluded: chain P residue 1036 VAL Chi-restraints excluded: chain Q residue 1066 SER Chi-restraints excluded: chain R residue 878 ILE Chi-restraints excluded: chain R residue 969 GLU Chi-restraints excluded: chain R residue 990 ASN Chi-restraints excluded: chain R residue 1014 LYS Chi-restraints excluded: chain R residue 1099 CYS Chi-restraints excluded: chain T residue 882 VAL Chi-restraints excluded: chain T residue 969 GLU Chi-restraints excluded: chain T residue 1036 VAL Chi-restraints excluded: chain T residue 1156 GLN Chi-restraints excluded: chain U residue 947 ASN Chi-restraints excluded: chain U residue 1036 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 140 optimal weight: 10.0000 chunk 180 optimal weight: 0.6980 chunk 378 optimal weight: 0.4980 chunk 167 optimal weight: 0.8980 chunk 556 optimal weight: 0.0870 chunk 250 optimal weight: 6.9990 chunk 268 optimal weight: 0.0270 chunk 533 optimal weight: 5.9990 chunk 468 optimal weight: 5.9990 chunk 81 optimal weight: 0.0870 chunk 222 optimal weight: 6.9990 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 947 ASN B 966 GLN C 941 ASN C1037 ASN E 941 ASN E 947 ASN F 889 HIS F1048 HIS H 937 GLN H 941 ASN H1109 GLN I 966 GLN I1109 GLN J 880 GLN J 941 ASN J1109 GLN ** J1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 941 ASN O 941 ASN P 947 ASN S 941 ASN S 947 ASN S 966 GLN U 941 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.156399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.117476 restraints weight = 39547.545| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.58 r_work: 0.3316 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.296 46400 Z= 0.092 Angle : 0.438 14.072 62480 Z= 0.227 Chirality : 0.040 0.154 6460 Planarity : 0.003 0.036 8080 Dihedral : 4.485 55.295 6407 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.11 % Allowed : 15.57 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.12), residues: 5640 helix: 1.48 (0.12), residues: 2080 sheet: 0.23 (0.14), residues: 1140 loop : -0.03 (0.14), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 896 TYR 0.013 0.001 TYR R 920 PHE 0.015 0.001 PHE D 881 TRP 0.005 0.001 TRP J1006 HIS 0.018 0.001 HIS C1084 Details of bonding type rmsd covalent geometry : bond 0.00148 (46320) covalent geometry : angle 0.39970 (62420) hydrogen bonds : bond 0.03502 ( 1944) hydrogen bonds : angle 4.07347 ( 5298) metal coordination : bond 0.06615 ( 80) metal coordination : angle 5.78795 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 783 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 896 ARG cc_start: 0.8270 (mtp85) cc_final: 0.7754 (ttp-170) REVERT: B 896 ARG cc_start: 0.8434 (mtp85) cc_final: 0.7691 (mtm110) REVERT: B 959 SER cc_start: 0.8702 (t) cc_final: 0.8469 (m) REVERT: B 971 GLU cc_start: 0.7677 (tp30) cc_final: 0.7357 (tp30) REVERT: B 1037 ASN cc_start: 0.7848 (t0) cc_final: 0.7514 (m-40) REVERT: C 910 LYS cc_start: 0.8645 (ttpp) cc_final: 0.8365 (ttpt) REVERT: C 1042 LYS cc_start: 0.8628 (mmtm) cc_final: 0.8368 (mtmt) REVERT: D 896 ARG cc_start: 0.8080 (mtp85) cc_final: 0.7385 (ttp-170) REVERT: D 972 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8175 (tpt) REVERT: E 910 LYS cc_start: 0.8548 (ttpp) cc_final: 0.8118 (tttm) REVERT: E 991 ARG cc_start: 0.8207 (ptm160) cc_final: 0.7731 (ptm160) REVERT: F 1004 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8094 (mptm) REVERT: F 1014 LYS cc_start: 0.8180 (mttp) cc_final: 0.7802 (tmmt) REVERT: F 1019 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7808 (mt-10) REVERT: F 1113 MET cc_start: 0.8124 (ptm) cc_final: 0.7876 (ptt) REVERT: F 1114 LYS cc_start: 0.8632 (mmtp) cc_final: 0.8389 (mptm) REVERT: G 932 ARG cc_start: 0.7705 (mtm-85) cc_final: 0.7444 (mtm-85) REVERT: G 971 GLU cc_start: 0.8417 (tp30) cc_final: 0.8071 (tp30) REVERT: G 1004 LYS cc_start: 0.8305 (mtpp) cc_final: 0.7820 (tptp) REVERT: H 888 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7986 (tm-30) REVERT: H 896 ARG cc_start: 0.7983 (mtp85) cc_final: 0.7088 (mtm180) REVERT: H 910 LYS cc_start: 0.8259 (ttpp) cc_final: 0.7862 (ttpp) REVERT: H 988 ILE cc_start: 0.8769 (mm) cc_final: 0.8536 (mp) REVERT: H 1004 LYS cc_start: 0.8328 (mtpp) cc_final: 0.7751 (ttpp) REVERT: I 947 ASN cc_start: 0.7887 (OUTLIER) cc_final: 0.7549 (m110) REVERT: I 972 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7200 (tpt) REVERT: I 988 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7486 (mm) REVERT: I 990 ASN cc_start: 0.8176 (m-40) cc_final: 0.7957 (m-40) REVERT: I 1090 TYR cc_start: 0.8598 (m-80) cc_final: 0.8387 (m-80) REVERT: I 1145 GLU cc_start: 0.8193 (pm20) cc_final: 0.7956 (pm20) REVERT: J 977 ARG cc_start: 0.6294 (OUTLIER) cc_final: 0.5757 (mmt90) REVERT: J 1020 ASN cc_start: 0.7139 (t0) cc_final: 0.6673 (t0) REVERT: J 1063 GLU cc_start: 0.7916 (pt0) cc_final: 0.7565 (pt0) REVERT: J 1087 ARG cc_start: 0.8093 (mtm-85) cc_final: 0.7635 (mtm-85) REVERT: J 1109 GLN cc_start: 0.5953 (OUTLIER) cc_final: 0.5459 (tp-100) REVERT: J 1113 MET cc_start: 0.6800 (ptm) cc_final: 0.6198 (pmt) REVERT: J 1128 ARG cc_start: 0.8133 (mtp-110) cc_final: 0.7781 (ttm110) REVERT: L 896 ARG cc_start: 0.7251 (mtt-85) cc_final: 0.6606 (mtm110) REVERT: L 963 LYS cc_start: 0.8361 (pttt) cc_final: 0.7640 (tttm) REVERT: L 1004 LYS cc_start: 0.8010 (ttpp) cc_final: 0.7668 (ttmm) REVERT: L 1014 LYS cc_start: 0.7130 (mttp) cc_final: 0.6666 (tmmt) REVERT: L 1036 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8024 (p) REVERT: M 896 ARG cc_start: 0.8029 (mtt-85) cc_final: 0.7380 (mtm110) REVERT: M 910 LYS cc_start: 0.8284 (ttpp) cc_final: 0.7725 (tttm) REVERT: M 911 GLU cc_start: 0.8606 (mp0) cc_final: 0.8224 (mp0) REVERT: M 925 LYS cc_start: 0.8464 (mtpp) cc_final: 0.8249 (mtmt) REVERT: M 991 ARG cc_start: 0.7734 (mtp-110) cc_final: 0.7281 (ptm160) REVERT: M 1158 MET cc_start: 0.6328 (mtm) cc_final: 0.5845 (mtp) REVERT: N 1004 LYS cc_start: 0.8053 (ttpp) cc_final: 0.7761 (tmmt) REVERT: N 1158 MET cc_start: 0.6202 (mtm) cc_final: 0.5978 (mtm) REVERT: O 991 ARG cc_start: 0.7972 (mtp85) cc_final: 0.7544 (ttt90) REVERT: O 1004 LYS cc_start: 0.8230 (ttpp) cc_final: 0.7890 (ttpp) REVERT: P 991 ARG cc_start: 0.7858 (mtp-110) cc_final: 0.7555 (mtp-110) REVERT: P 1014 LYS cc_start: 0.8011 (mttp) cc_final: 0.7660 (tmmt) REVERT: P 1128 ARG cc_start: 0.8114 (mmt90) cc_final: 0.7587 (mmt180) REVERT: Q 1004 LYS cc_start: 0.8521 (tttm) cc_final: 0.8236 (mttt) REVERT: Q 1042 LYS cc_start: 0.8500 (mmtm) cc_final: 0.8282 (mtmt) REVERT: Q 1115 MET cc_start: 0.8809 (ptp) cc_final: 0.8527 (ptp) REVERT: R 1014 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8100 (tptp) REVERT: S 910 LYS cc_start: 0.8532 (ttpp) cc_final: 0.8241 (tttm) REVERT: S 1018 GLU cc_start: 0.7500 (tt0) cc_final: 0.7296 (mt-10) REVERT: T 910 LYS cc_start: 0.8473 (ttpp) cc_final: 0.8144 (tttm) REVERT: T 931 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7363 (tp30) REVERT: T 990 ASN cc_start: 0.8139 (m-40) cc_final: 0.7525 (p0) REVERT: T 991 ARG cc_start: 0.8106 (mtm180) cc_final: 0.7576 (mtp-110) REVERT: T 1014 LYS cc_start: 0.7936 (mttp) cc_final: 0.7469 (tmmt) REVERT: T 1037 ASN cc_start: 0.7183 (m110) cc_final: 0.6834 (t0) REVERT: T 1109 GLN cc_start: 0.7917 (tp40) cc_final: 0.7627 (tt0) REVERT: T 1113 MET cc_start: 0.7793 (ttp) cc_final: 0.7313 (ptm) REVERT: U 943 TYR cc_start: 0.7868 (t80) cc_final: 0.7642 (t80) REVERT: U 991 ARG cc_start: 0.7987 (mtp85) cc_final: 0.7772 (ptm160) REVERT: U 1018 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6829 (mt-10) REVERT: U 1107 PHE cc_start: 0.8251 (t80) cc_final: 0.8040 (t80) REVERT: U 1113 MET cc_start: 0.7382 (ttm) cc_final: 0.6916 (ptp) REVERT: U 1115 MET cc_start: 0.7634 (ptm) cc_final: 0.7269 (ptt) outliers start: 51 outliers final: 25 residues processed: 808 average time/residue: 0.4959 time to fit residues: 486.7602 Evaluate side-chains 797 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 763 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 972 MET Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 1113 MET Chi-restraints excluded: chain D residue 1126 THR Chi-restraints excluded: chain F residue 1126 THR Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain G residue 1126 THR Chi-restraints excluded: chain H residue 888 GLU Chi-restraints excluded: chain I residue 947 ASN Chi-restraints excluded: chain I residue 972 MET Chi-restraints excluded: chain I residue 988 ILE Chi-restraints excluded: chain I residue 1054 MET Chi-restraints excluded: chain I residue 1098 PHE Chi-restraints excluded: chain J residue 977 ARG Chi-restraints excluded: chain J residue 1098 PHE Chi-restraints excluded: chain J residue 1102 THR Chi-restraints excluded: chain J residue 1109 GLN Chi-restraints excluded: chain L residue 878 ILE Chi-restraints excluded: chain L residue 1036 VAL Chi-restraints excluded: chain M residue 882 VAL Chi-restraints excluded: chain M residue 1036 VAL Chi-restraints excluded: chain M residue 1098 PHE Chi-restraints excluded: chain N residue 1099 CYS Chi-restraints excluded: chain O residue 1069 ASN Chi-restraints excluded: chain Q residue 1066 SER Chi-restraints excluded: chain R residue 990 ASN Chi-restraints excluded: chain R residue 1014 LYS Chi-restraints excluded: chain T residue 1036 VAL Chi-restraints excluded: chain U residue 947 ASN Chi-restraints excluded: chain U residue 1036 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 105 optimal weight: 6.9990 chunk 221 optimal weight: 10.0000 chunk 522 optimal weight: 0.8980 chunk 283 optimal weight: 10.0000 chunk 187 optimal weight: 6.9990 chunk 376 optimal weight: 3.9990 chunk 329 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 300 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 947 ASN C 941 ASN E 941 ASN E 947 ASN H 937 GLN H 941 ASN H1109 GLN I1037 ASN I1070 GLN I1109 GLN I1146 GLN J 941 ASN J 947 ASN J 973 GLN J1070 GLN J1109 GLN L 941 ASN N 947 ASN O 941 ASN P 947 ASN S 941 ASN S 947 ASN U 941 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.149492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109470 restraints weight = 38706.334| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.56 r_work: 0.3206 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.415 46400 Z= 0.217 Angle : 0.595 14.159 62480 Z= 0.311 Chirality : 0.045 0.167 6460 Planarity : 0.004 0.040 8080 Dihedral : 5.212 58.052 6406 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.33 % Allowed : 15.52 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.11), residues: 5640 helix: 1.10 (0.12), residues: 2080 sheet: 0.11 (0.15), residues: 1160 loop : -0.11 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 896 TYR 0.023 0.002 TYR S 920 PHE 0.028 0.002 PHE J1035 TRP 0.014 0.003 TRP F1006 HIS 0.025 0.002 HIS Q1084 Details of bonding type rmsd covalent geometry : bond 0.00461 (46320) covalent geometry : angle 0.55180 (62420) hydrogen bonds : bond 0.05920 ( 1944) hydrogen bonds : angle 4.63714 ( 5298) metal coordination : bond 0.09718 ( 80) metal coordination : angle 7.18567 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 742 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 896 ARG cc_start: 0.8321 (mtp85) cc_final: 0.7743 (mtm110) REVERT: A 1128 ARG cc_start: 0.7125 (mmm160) cc_final: 0.6660 (mmt180) REVERT: B 896 ARG cc_start: 0.8411 (mtp85) cc_final: 0.7640 (mtm110) REVERT: B 959 SER cc_start: 0.8750 (t) cc_final: 0.8507 (m) REVERT: B 971 GLU cc_start: 0.7782 (tp30) cc_final: 0.7463 (tp30) REVERT: B 1037 ASN cc_start: 0.8144 (t0) cc_final: 0.7696 (m-40) REVERT: C 991 ARG cc_start: 0.8197 (ptp-110) cc_final: 0.7759 (ptp-170) REVERT: C 1042 LYS cc_start: 0.8714 (mmtm) cc_final: 0.8409 (mtmt) REVERT: C 1114 LYS cc_start: 0.8667 (mmmm) cc_final: 0.8328 (mmtm) REVERT: D 896 ARG cc_start: 0.8224 (mtp85) cc_final: 0.7435 (mtp180) REVERT: D 972 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8220 (tpt) REVERT: E 910 LYS cc_start: 0.8598 (ttpp) cc_final: 0.8175 (tttm) REVERT: F 931 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: F 1004 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8108 (mptm) REVERT: F 1014 LYS cc_start: 0.8269 (mttp) cc_final: 0.7782 (tmmt) REVERT: F 1019 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7972 (mt-10) REVERT: G 913 LYS cc_start: 0.8475 (tmtt) cc_final: 0.8253 (tptp) REVERT: G 931 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: G 932 ARG cc_start: 0.7867 (mtm-85) cc_final: 0.7589 (mtm-85) REVERT: G 971 GLU cc_start: 0.8401 (tp30) cc_final: 0.8083 (tp30) REVERT: G 1004 LYS cc_start: 0.8343 (mtpp) cc_final: 0.7972 (tptp) REVERT: H 888 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: H 896 ARG cc_start: 0.8076 (mtp85) cc_final: 0.7198 (mtm110) REVERT: H 910 LYS cc_start: 0.8309 (ttpp) cc_final: 0.7927 (ttpp) REVERT: H 988 ILE cc_start: 0.8767 (mm) cc_final: 0.8533 (mp) REVERT: H 1004 LYS cc_start: 0.8433 (mtpp) cc_final: 0.7862 (ttpp) REVERT: I 947 ASN cc_start: 0.8017 (OUTLIER) cc_final: 0.7620 (m110) REVERT: I 972 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7182 (tpt) REVERT: I 988 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7621 (mm) REVERT: I 990 ASN cc_start: 0.8185 (m-40) cc_final: 0.7965 (m-40) REVERT: J 977 ARG cc_start: 0.6341 (OUTLIER) cc_final: 0.5738 (mmt90) REVERT: J 1020 ASN cc_start: 0.7388 (t0) cc_final: 0.6928 (t0) REVERT: J 1063 GLU cc_start: 0.7979 (pt0) cc_final: 0.7613 (pt0) REVERT: J 1087 ARG cc_start: 0.8165 (mtm-85) cc_final: 0.7691 (mtm-85) REVERT: J 1109 GLN cc_start: 0.5785 (OUTLIER) cc_final: 0.5351 (tp-100) REVERT: J 1128 ARG cc_start: 0.8178 (mtp-110) cc_final: 0.7845 (ttm110) REVERT: L 896 ARG cc_start: 0.7360 (mtt-85) cc_final: 0.6717 (mtm110) REVERT: L 1004 LYS cc_start: 0.8148 (ttpp) cc_final: 0.7223 (tptp) REVERT: L 1014 LYS cc_start: 0.7272 (mttp) cc_final: 0.6807 (tmmt) REVERT: M 896 ARG cc_start: 0.8154 (mtt-85) cc_final: 0.7451 (mtm110) REVERT: M 910 LYS cc_start: 0.8369 (ttpp) cc_final: 0.7828 (tttm) REVERT: M 911 GLU cc_start: 0.8672 (mp0) cc_final: 0.8251 (mp0) REVERT: M 925 LYS cc_start: 0.8521 (mtpp) cc_final: 0.8287 (mtpt) REVERT: M 1158 MET cc_start: 0.6301 (mtm) cc_final: 0.6076 (mtp) REVERT: N 1004 LYS cc_start: 0.8235 (ttpp) cc_final: 0.7932 (tmmt) REVERT: N 1158 MET cc_start: 0.6598 (mtm) cc_final: 0.6397 (mtm) REVERT: O 991 ARG cc_start: 0.7999 (mtp85) cc_final: 0.7552 (ttt90) REVERT: O 1004 LYS cc_start: 0.8413 (ttpp) cc_final: 0.8028 (ttpp) REVERT: P 991 ARG cc_start: 0.7929 (mtp-110) cc_final: 0.7497 (mtp-110) REVERT: P 1128 ARG cc_start: 0.8225 (mmt90) cc_final: 0.7680 (mmt180) REVERT: Q 966 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8405 (mt0) REVERT: Q 1014 LYS cc_start: 0.8187 (mtmt) cc_final: 0.7944 (tptp) REVERT: Q 1114 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8311 (mptt) REVERT: Q 1115 MET cc_start: 0.8845 (ptp) cc_final: 0.8560 (ptp) REVERT: S 910 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8291 (tttm) REVERT: T 910 LYS cc_start: 0.8532 (ttpp) cc_final: 0.8178 (tttm) REVERT: T 931 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7501 (tp30) REVERT: T 969 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7953 (tt0) REVERT: T 991 ARG cc_start: 0.8150 (mtm180) cc_final: 0.7801 (mtp-110) REVERT: T 1014 LYS cc_start: 0.8173 (mttp) cc_final: 0.7692 (tmmt) REVERT: T 1037 ASN cc_start: 0.7330 (m110) cc_final: 0.7044 (t0) REVERT: T 1113 MET cc_start: 0.7857 (ttp) cc_final: 0.7567 (ptm) REVERT: U 943 TYR cc_start: 0.7933 (t80) cc_final: 0.7706 (t80) REVERT: U 991 ARG cc_start: 0.8045 (mtp85) cc_final: 0.7827 (mtp85) REVERT: U 1018 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7168 (mt-10) REVERT: U 1092 CYS cc_start: 0.7638 (m) cc_final: 0.7107 (m) REVERT: U 1107 PHE cc_start: 0.8247 (t80) cc_final: 0.8028 (t80) outliers start: 61 outliers final: 32 residues processed: 766 average time/residue: 0.4901 time to fit residues: 455.7777 Evaluate side-chains 779 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 736 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 972 MET Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 1113 MET Chi-restraints excluded: chain D residue 1126 THR Chi-restraints excluded: chain F residue 931 GLU Chi-restraints excluded: chain F residue 1126 THR Chi-restraints excluded: chain G residue 931 GLU Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain G residue 1126 THR Chi-restraints excluded: chain H residue 888 GLU Chi-restraints excluded: chain I residue 947 ASN Chi-restraints excluded: chain I residue 972 MET Chi-restraints excluded: chain I residue 988 ILE Chi-restraints excluded: chain I residue 1036 VAL Chi-restraints excluded: chain I residue 1054 MET Chi-restraints excluded: chain I residue 1098 PHE Chi-restraints excluded: chain J residue 977 ARG Chi-restraints excluded: chain J residue 1018 GLU Chi-restraints excluded: chain J residue 1098 PHE Chi-restraints excluded: chain J residue 1102 THR Chi-restraints excluded: chain J residue 1108 LEU Chi-restraints excluded: chain J residue 1109 GLN Chi-restraints excluded: chain L residue 878 ILE Chi-restraints excluded: chain L residue 1036 VAL Chi-restraints excluded: chain M residue 882 VAL Chi-restraints excluded: chain M residue 1036 VAL Chi-restraints excluded: chain N residue 990 ASN Chi-restraints excluded: chain N residue 1099 CYS Chi-restraints excluded: chain O residue 959 SER Chi-restraints excluded: chain O residue 1069 ASN Chi-restraints excluded: chain Q residue 966 GLN Chi-restraints excluded: chain Q residue 1066 SER Chi-restraints excluded: chain R residue 990 ASN Chi-restraints excluded: chain R residue 1014 LYS Chi-restraints excluded: chain R residue 1099 CYS Chi-restraints excluded: chain T residue 969 GLU Chi-restraints excluded: chain T residue 1036 VAL Chi-restraints excluded: chain U residue 947 ASN Chi-restraints excluded: chain U residue 1036 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 442 optimal weight: 1.9990 chunk 246 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 436 optimal weight: 0.7980 chunk 435 optimal weight: 0.9990 chunk 414 optimal weight: 2.9990 chunk 365 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 941 ASN B 947 ASN C 941 ASN E 941 ASN E 947 ASN H 937 GLN H 941 ASN H1109 GLN I 966 GLN I1109 GLN I1146 GLN J 941 ASN J 947 ASN J1070 GLN ** J1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 941 ASN O 941 ASN P 947 ASN R1022 ASN S 941 ASN S 947 ASN U 941 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.153097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.113509 restraints weight = 39363.428| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.57 r_work: 0.3263 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.308 46400 Z= 0.109 Angle : 0.479 13.790 62480 Z= 0.248 Chirality : 0.041 0.184 6460 Planarity : 0.003 0.041 8080 Dihedral : 4.811 56.777 6406 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.83 % Allowed : 15.91 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.11), residues: 5640 helix: 1.28 (0.12), residues: 2080 sheet: 0.12 (0.15), residues: 1160 loop : -0.06 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 896 TYR 0.017 0.001 TYR R 920 PHE 0.022 0.001 PHE J1110 TRP 0.007 0.001 TRP B1006 HIS 0.028 0.001 HIS F1084 Details of bonding type rmsd covalent geometry : bond 0.00190 (46320) covalent geometry : angle 0.43677 (62420) hydrogen bonds : bond 0.04234 ( 1944) hydrogen bonds : angle 4.34306 ( 5298) metal coordination : bond 0.07255 ( 80) metal coordination : angle 6.32185 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19001.86 seconds wall clock time: 322 minutes 11.33 seconds (19331.33 seconds total)